Critique: Exploring "Explore Evolution"

In 2007, a new “intelligent design” book entitled Explore Evolution (“EE”) appeared on the market.

Explore Evolution is explicitly marketed to public school teachers. For example, at a 2008 Biola University symposium for science teachers a pitch was made for adopting Explore Evolution. The quote below comes from the symposium's website:

A US Supreme Court decision allows teachers to teach biology in a way that incorporates “a variety of scientific theories…with the clear secular intent of enhancing the effectiveness of science instruction.” The new supplemental textbook Explore Evolution, when coordinated with other materials, empowers teachers and students to better fulfill these public educational goals.

Biola Science Teacher Symposium 2008 (accessed August 8, 2008.)

But students who read Explore Evolution will come away with a flat-out wrong understanding of evolution.

Explore EvolutionExplore Evolution

This book uses the creationist “evidence against evolution” and “teach the controversy” strategies to misrepresent scientific consensus and distort the conclusions of legitimate scientific research. Explore Evolution offers anonymous “critics” in place of substantive analysis.

Explore Evolution promotes “intelligent design” creationism. Four of the book’s five co-authors are closely tied to the “intelligent design” creationism movement. Lead author Stephen C. Meyer is a Discovery Institute (DI) vice president and program director of the DI’s Center for Science and Culture. Paul A. Nelson is a fellow of the DI. In 2005 in the Kitzmiller trial, Scott Minnich testified in favor of teaching “intelligent design” in public schools.

Beneath all its distortions, all its misrepresentations of modern evolutionary science, Explore Evolution uses familiar and long-refuted creationist anti-evolution arguments. Students who are required to read this book in a science classroom will be confused by its flagrant inaccuracies, and will be put at a disadvantage in standardized tests which require an understanding of modern biology.

NCSE and a team of consulting scientists have prepared this detailed chapter-by-chapter, page-by-page analysis of the book’s errors, failings, and distortions.

Each link below corresponds to a chapter in Explore Evolution. Each chapter expands into a list of specific problems in Explore Evolution.

Preface

Explore Evolution systematically misrepresents scientific facts and the scientific process. Its effect is to proselytize fringe ideas outside of science and to confuse students about evolution. Many of the errors that lace Explore Evolution are introduced in the preface.

p. v: “…the theory of evolution remains the focus of intense public controversy … [and there are] real (and more interesting) scientific controversies about evolution.”

Evolution is not scientifically controversial. To claim otherwise is simply wrong and, worse, unfair to students. Evolution is the fundamental, unifying principle of the life sciences, including medical and agricultural research, and recent advances in genomics and developmental biology.

Explore Evolution misleadingly equates the social controversy over evolution with past and present controversies over string theory, plate tectonics, and global warming. This serves only to confuse students. String theory is currently scientifically controversial, just as plate tectonics was controversial until the 1960s, and global warming was scientifically controversial until the late 1990s. There has not been a scientific controversy about whether life evolved since the 19th century. Social controversies are independent of scientific assessments--and are subjects best taught in social studies, rather than science classes.

p. v: “…scientists question key aspects of [contemporary Darwinian theory].”

These alleged “key aspects” are issues that are not scientifically controversial, yet for decades, creationists have claimed that they are. Biologists have reached a strong consensus about the validity of universal common descent, the power of natural selection, and the importance of studying fossils, embryology, biogeography, and homologous structures. Ongoing disputes about the details of evolution do not support the implication of Explore Evolution that there is scientific doubt of the underlying validity of evolution itself. This classic creationist strategy is simply false.

p. v: “The approach we are using in this book is called ‘inquiry-based’ education.”

The approach toward learning actually used in Explore Evolution is old-fashioned, and directly at odds with the inquiry-based approaches developed by leading science educators. Inquiry-based education provides students with appropriate background information and encourages them to formulate testable hypotheses. Explore Evolution does not do this.

p. vi: “[U.S. and U.K. national policies] call for teaching students about competing views of controversial scientific issues.”

Neither government treats evolution as scientifically controversial, nor do they recommend that students should be taught that they are. The “policy” statements from Congress and the United Kingdom cited in Explore Evolution are misrepresented and misquoted. The phrase “Where topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of views that exist” occurs nowhere in the No Child Left Behind education act, but in an addendum called a conference committee report. The NCLB does not even mention evolution, much less suggest how it should be taught. The sentence, from what is informally called the “Santorum Amendment to NCLB” is regularly used by creationists who justify their attacks on evolution by claiming it is policy or law. It is neither. Although creationists attempted to get wording inserted into NCLB that would weaken the teaching of evolution, they failed. But constant repetition of the Santorum Amendment language has led to belief in what has become an urban legend: that teachers have been directed by Congress to teach that evolution is a scientifically controversial topic.

The quote allegedly from the British national standards (“Pupils should be taught how scientific controversies can arise from different ways of interpreting empirical evidence [for example, Darwin's theory of evolution]”), is also false and misleading. It is not found in the National Curriculum, which was revised in 2006. It does occur in the decade-old 1999 National Curriculum for England, but it is not part of current British national policy. Where you will find the quotation in abundance is on creationist websites, where, as in Explore Evolution, it is cited to claim governmental imprimatur for teaching that evolution is scientifically controversial.

p. vii: “The main thing you need to know is that ‘the critics’ are not … the same from chapter to chapter.”

To further the misinformation that scientists seriously are debating whether evolution occurred, the authors suggest that a scientist might be cited in the “Case For” (pro-evolution) section in one chapter and in the “Case Against” section in another. A reader ought to know a good deal more about the “critics” cited throughout the book than that they might change from chapter to chapter. In fact, most of the critics cited are creationists, who have been repeatedly shown to misrepresent the facts and concepts of evolution and other sciences. We will illustrate this claim in the remainder of our analysis of Explore Evolution

Major flaws

Scientific controversy vs. social controversy: Explore Evolution consistently muddles the idea of controversy within the scientific community with societal disagreement about the political and moral implications of a scientific idea. Evolution is scientifically well-established and accepted by every major scientific society. The only controversy surrounding it comes from particular religious groups who object to evolution for reasons well outside of science.

Educational policy: Despite claims in Explore Evolution, neither the British nor American governments treat evolution as scientifically controversial, nor do they encourage social controversies to be taught in science classes.

Educational terminology: Inquiry-based learning is a new pedagogical system that holds great promise for the improvement of science education. Explore Evolution does not employ this pedagogical approach. Explore Evolution discourages inquiry and independent exploration of topics, especially evolution. Instead, Explore Evolution harangues students, confusing them with irrelevant and often erroneous information, and encourages them to give up on answering what questions it raises.

Scientific controversy vs. social controversy

In the first few pages, Explore Evolution misidentifies social controversy as scientific dispute, misdefines basic terminology, misrepresents scientists, and misunderstands pedagogical principles. The book’s religious agenda is misleadingly obscured. Papers and government policies are presented out of context and thus likely to be misunderstood. These errors are smoothly woven together like a conjurer’s words, misdirecting the reader from the mundane mechanics going on up the authors’ sleeves.

These errors are not random; they are all essential to sustain the premise of the book which is that under the guise of “critical thinking”, students should be encouraged to embrace creationist criticisms of evolution as valid science, and thus reject evolution in favor of intelligent design or some other form of creationism. That premise justifies the authors’ presentation of supposed “critics” of evolution, the identities and agendas of whom are masked. Under the guise of “presenting all sides”, the authors instead present information rejected by the scientific mainstream, obscuring from students the fact that ongoing research into evolution is scientifically uncontroversial. Current research and scientific debate focuses not on whether evolution happens and can explain the diversity of life, but which evolutionary mechanisms have dominated. Students reading Explore Evolution will not understand this key fact, and will be ill-prepared for more advanced science classes.

"Controversy" over evolution

Summary of problems:

Evolution is as well-established as a scientific theory can be. While scientists continue to investigate the importance of different mechanisms involved in evolution, the scientific community agrees that the descent with modification of living things -- the big idea of biological evolution -- accounts for the diversity of life on earth today. To claim or imply otherwise is simply wrong, and miseducates students about a critically important scientific idea.

Full discussion:

…the theory of evolution remains the focus of intense public controversy.
Explore Evolution , p. v
Indeed, the public debate over evolution waxes and wanes and takes various forums, and often is conducted with considerable heat. However, a few sentences later, the book refers to alleged “real (and more interesting) scientific controversies about evolution” (p. v, emphasis added). This implies the existence of a scientific controversy which does not exist.

In reality, evolutionary theory, the common ancestry of living things, is the core, fundamental, unifying construct of the life sciences. In the biomedical sciences, it has been a highly productive and powerful explanatory framework for research over the past five decades. In the last 10 years, the explosion of data in genomics and new insights in developmental biology have given evolutionary theory an even higher prominence and greater importance than it enjoyed before. It is for these reasons that the National Academy of Sciences recently wrote:

Biological evolution is the central organizing principle of modern biology.

The study of biological evolution has transformed our understanding of life on this planet. Evolution provides a scientific explanation for why there are so many different kinds of organisms on Earth and how all organisms on this planet are part of an evolutionary lineage. It demonstrates why some organisms that look quite different are in fact related, while other organisms that may look similar are only distantly related. It accounts for the appearance of humans on Earth and reveals our species’ biological connections with other living things. It details how different groups of humans are related to each other and how we acquired many of our traits. It enables the development of effective new ways to protect ourselves against constantly evolving bacteria and viruses.
National Academy of Sciences and Institute of Medicine of the National Academies (2008) Science, Evolution, and Creationism. Washington, DC:The National Academies Press

Evolution, climate change, plate tectonics, and string theory

Summary of problems:

Explore Evolution equates alleged controversy about evolution with controversies over plate tectonics, climate change, and string theory. This elevates social and political controversies to the same level as scientific controversy. Whether evolution takes place and explains the diversity of life is no longer scientifically controversial; the remaining controversy derives from political and cultural concerns.

String theory is currently scientifically controversial, just as plate tectonics was controversial until the 1960s, and global warming was scientifically controversial until the late 1990s. Evolution was last scientifically controversial in the 19th century and that controversy ended by the 1870s. By that date, essentially all practicing scientists accepted that natural causes could account for the formation of new species and that all living things share a common ancestry.

Full discussion:

Explore Evolution describes these supposed controversies in this passage from the Preface:
Controversies in science are nothing new. As recently as the early 1960s, for example, most geologists accepted the “geosynclinal theory” as the explanation of how mountain ranges form. After a significant period of controversy, most scientists came to accept the theory of plate tectonics because it provided a better explanation for a larger number of scientific observations. Yet without understanding the arguments that led to the acceptance of plate tectonics, it is very difficult to understand the theory itself or its current standing in the scientific community.

Today we continue to have important unresolved scientific controversies in many branches of science. In climatology, for example, scientists disagree over what global warming is, whether it is a natural phenomenon or a man-made problem, how big a problem it presents, and what (if anything) should be done about it. In theoretical physics, scientists disagree over the meaning and importance of string theory.
Explore Evolution, p. vi

This passage conflates scientific controversies with social controversies, an error that runs throughout Explore Evolution. In general, theories are scientifically controversial until they can provide testable and well-tested explanations for phenomena. By that standard, string theory is currently controversial, but global warming and plate tectonics are not scientifically controversial today. Despite the cessation of scientific controversy over evolution or global warming, both concepts continue to generate social controversy over their implications for policy or for personally-held religious views.

String theory provides a powerful theoretical model for unifying our understanding of various physical forces. On the other hand, it has yet to yield testable predictions that can be measured on current equipment in a way that distinguishes them from results generated using the existing 'standard' theory (see Smolin [2006], The Trouble with Physics, for an excellent review of these problems). It is therefore unknown whether the novel aspects of string theory are correct. String theory may be right; it may be a dead end; science simply does not know yet. Improvements in our scientific instruments may someday allow physicists to validate or disprove string theory. At that time, some or most of the controversy over its validity will die down and physicists will shift to debates over details of string theory rather than to debates over its scientific status per se. Pangaea and Fossil Distribution: from United States Geological SurveyPangaea and Fossil Distribution: from United States Geological Survey

This scientific process for examining ideas was used for the now-accepted explanations plate tectonics, evolution, and global warming. When Alfred Wegener proposed that the seeming lock and key fit of the coastlines of South America and Africa could be explained by moving continents, he backed his proposal with significant paleontological evidence, but could not explain the mechanisms involved in continental movement. Later research showed evidence of new crust forming as molten rock rose from deep sea rifts, including one midway between the African and South American coasts. Geologists developed a model in which plates are pushed together and pulled apart, creating new crust and destroying old crust, and found that it explained not only the evidence Wegener provided, but other questions about the formation of mountain ranges and the occurrences of volcanoes and large earthquakes.

Once Wegener’s idea had a testable model and a literal mountain of supporting evidence, it was rapidly accepted by geologists and ceased to be controversial. It should be noted that, contrary to Explore Evolution’s claim, students have no trouble understanding plate tectonics without first learning about discredited ideas that preceded it.

In fact, a similar process took place in the 19th and early 20th centuries as scientists addressed Darwin and Wallace’s evolutionary ideas. The idea of common ancestry of living things was rather quickly accepted in the scientific community; Darwin's choice for the most important mechanism of evolution, natural selection, was slower to be accepted. A major problem was the lack of a mechanism for new variation to be replenished each generation after natural selection had whittled out the survivors, a problem that could be solved only with a clearer understanding of how characteristics were passed down from generation to generation. Critics rightly objected to the model of inheritance Darwin proposed in the Origin of Species, which involved simply averaging parental characteristics. Of course, none of Darwin's contemporaries understood how heredity worked either: it wasn't until the rediscovery of Mendelian genetics in the early 20th century that an accurate basis for inheritance became available.

Mendelian genetics resolved a key scientific controversy that surrounded natural selection, much as sea-floor spreading resolved a key scientific controversy about continental drift. As scientists integrated their new understanding of genetics with the existing evolutionary ideas, they produced a more comprehensive picture of evolutionary biology, often referred to as the Modern Synthesis. But during the debate about the validity of natural selection and the development of the Modern Synthesis, scientists were not seriously questioning whether evolution occurred or whether universal common descent was the most reasonable inference from the data. Those scientific questions had been resolved decades earlier.

More recently, climate scientists went through a similar transition regarding global climate change. The idea that adding carbon dioxide to the atmosphere might cause global warming was first proposed in 1896 by Svante Arrhenius. Until modern supercomputers, it was impossible to fully model the global climate or to predict the consequences of human interactions with the atmosphere. Without modern satellites and high-altitude measurements, it was impossible to test those models. When weather stations demonstrated a global trend of rising temperatures in the 1980s and 1990s, some scientists attributed that change to the rise in atmospheric carbon dioxide measured globally, while others felt that the models available at the time were not accurate enough, and that the natural variability of the climate was too large relative to measured temperature changes to require anything but a natural explanation. In 1990, scientists with the non-partisan Intergovernmental Panel on Climate Change (IPCC) agreed that “there is a natural greenhouse effect,” that “emissions resulting from human activities are substantially increasing the atmospheric concentrations of the greenhouse gases.” At the time, they concluded that “global mean surface air temperature has increased by 0.3 to 0.6° C over the last 100 years. The size of this warming is broadly consistent with predictions of climate models, but it is also of the same magnitude as natural climate variability. Thus the observed increase could be largely due to this natural variability; alternatively this variability and other human factors could have offset a still larger human-induced greenhouse warming. The unequivocal detection of the enhanced greenhouse effect is not likely for a decade or more.”

However, by 1995, the IPCC report found that “The balance of evidence suggests a discernible human influence on global climate,” observing that “[s]ince the 1990 IPCC Report, considerable progress has been made in attempts to distinguish between natural and anthropogenic influences on climate.” In 2001, the IPCC's Third Assessment Report found “There is new and stronger evidence that most of the warming observed over the last 50 years is attributable to human activities,” and concluded that “most of the observed warming over the last 50 years is likely to have been due to the increase in greenhouse gas concentrations.” In IPCC reports, “likely” means that the scientists assess the likelihood of the statement being true at between 66-90% chance, while the 1995 statement about the “balance of evidence” refers to a chance slightly higher than 50%. When the IPCC released its Fourth Assessment Report in 2007, the team of climate scientists concluded that “[w]arming of the climate system is unequivocal,” and that “[m]ost of the observed increase in globally averaged temperatures since the mid-20th century is very likely due to the observed increase in anthropogenic greenhouse gas concentrations." “Very likely” means better than 90% chance.

Between the third and fourth reports, a researcher on the sociology of science demonstrated the growth of a scientific consensus behind anthropogenic climate change. Dr. Naomi Oreskes published a paper in the December 3, 2004 issue of Science surveying publications about climate change between 1993 and 2003. Oreskes classified those papers as either accepting the 2001 consensus that “most of the observed warming over the last 50 years is likely to have been due to the increase in greenhouse gas concentrations," rejecting that statement, or taking no position on it. Of 928 papers identified in scientific databases which contained the phrase “global climate change,” 75% supported the IPCC consensus, 25% did not discuss it, and none explicitly rejected it. While such papers may exist, it is clear that there was not a vociferous debate between scientists in the field over whether humans are causing global warming. That consensus can also be demonstrated by statements from major scientific bodies, including the National Academies of Science, the American Meteorological Society, the American Geophysical Union, and the American Association for the Advancement of Science, all essentially restating the IPCC assessment.

This is not to say that debate in any of these fields has ended. Just as geologists continue to make new discoveries about plate tectonics, and to debate those discoveries with intensity, evolutionary biologists continue to debate the relative influence of the various forces driving evolution, and climate scientists continue to disagree about the precise implications of current human activities for the future of Earth's climate. The era of controversy ends when the scientific community comes to accept that a particular theory is testable and offers superior explanations for known phenomena.

The era of controversy ended for evolution decades ago, and Explore Evolution's claims to the contrary are disingenuous. The current controversy surrounding evolution is not a scientific controversy. The comparison to global warming is instructive. Global warming is scientifically uncontroversial, but the question of whether society ought to make some effort to avert it, and what should be done in that event, are subject to intense disagreement. Thus, global warming is scientifically uncontroversial, but generates controversy because of its policy implications. Similarly, evolution is not scientifically controversial, but does generate social controversy because of people's disagreements about its philosophical, religious and metaphysical implications. Those controversies cannot be resolved based on empirical scientific evidence alone.

"Key aspects" of evolution

Summary of problems:

Explore Evolution asserts that "this book will help you understand … why many scientists find [contemporary Darwinian theory] persuasive, and why other scientists question key aspects of it" (p. v). The supposedly "key aspects" or "key claims" which Explore Evolution targets are issues that are not scientifically controversial, yet are persistent targets of creationist attack. Biologists have reached a strong consensus about the validity of universal common descent, the power of natural selection, and the importance of studying fossils, embryology, biogeography, homologous structures, etc. There is ongoing research and disagreements concerning the details in all these areas. However, Explore Evolution implies that any controversy or disagreements within evolutionary biology casts doubt on the underlying validity of the theory of evolution. This is a classic creationist falsehood.

Full discussion:

The preface states

We hope this book will help you understand what contemporary Darwinian theory is, why many scientists find it persuasive, and why other scientists question key aspects of it.
Explore Evolution, preface

If we assume that this statement is referring to scientists in fields with some relevance to evolutionary theory (e.g. biologists, geologists, anthropologists etc.), this statement cannot be supported. Nearly every relevant national and international scientific organization has taken a position in favor of the basics of evolutionary theory, and in opposition to creationism and intelligent design. This February 2006 statement from the American Association for the Advancement of Science, the largest general scientific society in the world (serving 262 affiliated scientific societies and academies, with over 10 million members), is only one example of many.

Evolution is one of the most robust and widely accepted principles of modern science. It is the foundation for research in a wide array of scientific fields and, accordingly, a core element in science education. The AAAS Board of Directors is deeply concerned, therefore, about legislation and policies recently introduced in a number of states and localities that would undermine the teaching of evolution and deprive students of the education they need to be informed and productive citizens in an increasingly technological, global community. Although their language and strategy differ, all of these proposals, if passed, would weaken science education. The AAAS Board of Directors strongly opposes these attacks on the integrity of science and science education. They threaten not just the teaching of evolution, but students' understanding of the biological, physical, and geological sciences.

Some bills seek to discredit evolution by emphasizing so-called "flaws" in the theory of evolution or "disagreements" within the scientific community. Others insist that teachers have absolute freedom within their classrooms and cannot be disciplined for teaching non-scientific "alternatives" to evolution. A number of bills require that students be taught to "critically analyze" evolution or to understand "the controversy." But there is no significant controversy within the scientific community about the validity of the theory of evolution. The current controversy surrounding the teaching of evolution is not a scientific one.

In contrast, the Discovery Institute lists only 700 scientists on their Dissent from Darwin statement. No scientific societies have signed on to that statement. Many of the signers do not have degrees or research interests in relevant scientific disciplines. Not surprisingly, the Dissent from Darwin list has many names of engineers and computer scientists, whose everyday work does not bring them in contact with modern evolutionary theory. This number of dissenters, even if they were all working in a relevant scientific field, is certainly small when compared to the hundreds of thousands of scientists affiliated with the scientific societies which have passed statements or resolutions supporting modern evolutionary theory. It is even small compared to the number of graduate students in science and engineering disciplines. According to the National Science Foundation, institutions of higher education in the USA alone produce over 20,000 doctoral graduates in science and engineering annually.

So while it is certainly true that "some scientists" question evolution, hardly any working scientists in the relevant disciplines find it to be controversial, and no relevant scientific society finds it to be controversial. The perception left by this statement in Explore Evolution is completely wrong.

It would fair to say that there are debates and controversies within evolutionary biology over questions such as the relative importance of natural selection and neutral mutations to evolutionary change, the role of symbiosis, or the nature of large-scale patterns of evolutionary change. These questions, though, are not the discussed in Explore Evolution. The supposedly "key aspects" of the theory which Explore Evolutionclaims to present "both sides" of are, in fact, simply repetitions of long-discredited creationist claims, as will be shown throughout this critique.

References

Ronald Numbers, The Creationists, pp.__

Bowler, The Non-Darwinian Revolution, pp.__

Matzke and Gross in Scott and Branch, NIOC.

S. Sarkar, Doubting Darwin? Creationist Designs on Evolution, Blackwell, 2007, pp. 163-166

Educational policy and terminology

In order to attract the attention of textbook-purchasing teachers and administrators, Explore Evolution claims it is utilizing the most up-to-date science pedagogy. "Inquiry-based" education is indeed an approach encouraged in most states' science education standards, and teachers should be encouraged to find ways for students to apply the scientific method in the process of learning science. An inquiry-based approach is one in which students, under the guidance of the teacher, actively construct an understanding of a scientific explanation. It involves active learning, rather than passive absorption of facts, and often utilizes hands-on exercises to help students learn to think like a scientist.

Unlike the claim made in Explore Evolution,inquiry-based education does not require students to evaluate "arguments scientists have had and are having, about current theories in light of the evidence." The purpose of a middle school or high school science classroom is to provide students with a sound understanding of the basics of a scientific discipline upon which (ideally) they can build a further understanding. It is not to encourage beginning learners to debate cutting-edge scientific research which they have inadequate background to evaluate. The supposed goals of inquiry-learning as presented in Explore Evolution bear little kinship to how this approach is understood by educators.

Similarly, Explore Evolution is incorrect that inquiry-learning assumes that "students gain a better understanding of a subject if they are taught about the arguments that scientists have in the process of formulating their theories." Students certainly can profit from looking at the history of the development of evolutionary biology, but this is not what the authors of Explore Evolution are proposing. Instead, they want students to investigate alleged arguments among scientists over the "truth" of evolution, an argument that takes place only in the creationist literature, not in the university science classrooms or professional scientific journals.

According to the authors, students will become better critical thinkers after undertaking the "critical analysis of evolution" presented in Explore Evolution. And yet students are never given the opportunity to develop and test their own hypotheses, and are rarely if ever given the information they would need to undertake such an exercise. On the contrary, the inaccurate information presented in Explore Evolution, would handicap any student actually trying to construct an understanding of evolution. Thus in this book, "critical analysis of evolution" is translated to "criticize evolution". Needless to say, this is far cry from true inquiry-based education.

The authors are partly correct when they contend that inquiry-learning makes science more interesting and enjoyable, and controversy may indeed pique student interest in a subject. But how much more appropriate it would be to use an actual scientific controversy within evolution, rather than a nonexistent one: evolutionary biologists are not debating whether evolution occurred, only the details.

Santorum Amendment and UK National Curriculum

Summary of problems:

Neither the United States Congress nor the UK's National Curriculum treat evolution as scientifically controversial nor do they recommend teaching about social controversies. The "policy" statements found in this section of Explore Evolution are misrepresented and misquoted. For example, the so-called "Santorum amendment", was actually removed from No Child Left Behind legislation before it was passed, yet EE quotes it, pretending it has the weight of policy or law. Even if it were the law of the land - which it is not - it only speaks to a political issue, not a scientific controversy. The authors of EE are once again attempting to blur the important distinction between public controversy and scientific controversy.

Full discussion:

Explore Evolution states,
United States federal education policy calls for teaching students about competing views of controversial scientific issues. As the U.S. Congress has stated, "[W]here topics are taught that may generate controversy (such as biological evolution), the curriculum should help students to understand the full range of views that exist." [footnote in original: This statement occurs in the authoritative conference report language of the No Child Left Behind federal education act.] In the United Kingdom, the National Curriculum for Key Stage 4 Science now recommends that, "Pupils should be taught how scientific controversies can arise from different ways of interpreting empirical evidence (for example, Darwin's theory of evolution)."
EE, p. ii

The Congressional "language" was in an amendment that was briefly inserted into the No Child Left Behind bill by a creationist Senator, Rick Santorum, but removed by the committee which unified the versions of the bill passed by the House and Senate. The passage EE cites was never approved by Congress, and was explicitly removed from the bill with the approval of both Houses. It cannot be construed as federal policy, let alone as a statement by Congress, and is not at all "authoritative". For more, see NCSE's discussion of the topic (PDF) for more background and analysis.

The treatment of the U.K.'s "National Curriculum" is equally contorted. The OCR (Oxford Cambridge and RSA Examinations board - the group responsible for evaluating students' comprehension of issues in the curriculum) explains that they do not regard evolution as a scientific controversy today, only at the time Darwin published:

At OCR, we believe candidates need to understand the social and historical context to scientific ideas both pre and post Darwin. In our Gateway Science specification, candidates are asked to discuss why the opponents of Darwinism thought the way they did and how scientific controversies can arise from different ways of interpreting empirical evidence. Creationism and "intelligent design" are not regarded by OCR as scientific theories. They are beliefs that do not lie within scientific understanding.

The authors of EE lifted some of the wording out of this statement regarding "social and historical context to ideas", deleted the reference to the past in "why the opponents of Darwinism thought the way they did", and added words to make their snippet grammatical. They put quotes around their patchwork and try passing it off as a recommendation found in the U.K.'s "National Curriculum".

The British Minister of Education, who supervises OCR, later explained that "The national curriculum programme of study for science at key stage 4 covers evolution. It sets out that pupils should be taught 'that the fossil record is evidence for evolution' and also 'how variation and selection may lead to evolution or extinction'." Clearly, the British standards contradict the statement in Explore Evolution that there are competing scientific views on evolution's validity and, in fact, affirm the importance of evolution in modern biology.

These two examples of egregious "quote mining" should dispel any notion that Explore Evolution embraces ethical scholarship.

Inquiry-based learning

Summary of problems:

The approach toward learning actually used in EE is directly at odds with the inquiry-based approaches developed by leading science educators. EE gives students incomplete and/or misleading information and provides canned questions and answers, rather than providing students with appropriate background information and allowing them to formulate testable hypotheses.

Full discussion:

In the inquiry-based approaches which are gaining acceptance in science education, the student is provided with appropriate background data, and then encouraged to generate a testable hypothesis, test it, and decide if the hypothesis should be accepted or rejected. These approaches reinforce the student's knowledge of the power and the limitations of the scientific method, and allow the student to arrive at a novel (to them) answer via their own efforts. Such "Eureka moments" can strongly reinforce the facts and concepts that are deemed pedagogically important by the instructors, and can even lead to insights that are unrelated to the immediate facts and observations. The power of this approach rests entirely on the notion that the student understands the background, poses the hypothesis, tests the hypothesis, and makes his/her own conclusions. The role of the instructor is very different in this model. As noted on the Duke University Center for Inquiry-based Learning site: "When using inquiry, teachers must bite their tongues. Too many hints, too many questions, and too many answers take all the learning out of the process. And all the fun, too."

Unfortunately, this description is completely at odds with the approach used in Explore Evolution. In every instance, students are led through exercises where the authors provide the questions. In every instance, the student is given incomplete or even misleading information in the sections labeled "Case For", and then this incomplete or misleading information is rebutted by the authors (not by the student) in the "Reply" sections. Even in the "Further Debate" sections, there is no attempt to add critical information (e.g. citations of recent publications), which might allow the student to generate hypotheses and test those hypotheses. There is no opportunity for the Eureka moment; the students are merely led down the path that the authors desire them to tread. So the claim that this book is "inquiry-based" fails on at least two counts. First, the information needed to promote genuine inquiry is never given; the authors set up strawman arguments rather than provide the necessary complete information. Secondly, the students do not generate their own questions, do not test their own hypotheses, and never get a chance to experience the joy of discovery that has been found to be critical in any truly inquiry-based endeavor.

The approach taken in this book is old-fashioned in terms of pedagogy, and radically different from the innovative and effective inquiry-based approaches developed in recent years. EE's method most closely resembles legal argumentation. The jurors (the students) are subjected to two presentations of opposite sides in a dichotomy, and asked to make up their minds. Jurors are not allowed to ask questions in a courtroom, and students are not allowed to ask questions in this book. Furthermore, just as might be the case in a courtroom, the jurors do not have access to all of the facts.

The phrase "inquiry-based learning" is exploited to promote the view that students should "debate Darwinism" in order to learn it. This is simply the Discovery Institute's latest strategy for insinuating and reinforcing doubts about the evolutionary sciences.

"Our goal in using this approach is to expose you to the discoveries, evidence, and arguments that are shaping the current debates over the modern version of Darwin's theory, and to encourage you to think deeply and critically about them."

No good teacher or scientist is against scientific debate or critical thinking. The authors of EE, however, use this ideal as a guise for promoting misleading, incorrect, and incomplete information about evolution. Unfortunately, anti-evolutionists have time and time again called for "critical thinking" or "critical analysis" of evolution, as a way to encourage students to criticize evolution and doubt its validity.

This statement is skillfully written to sound like good pedagogy. In reality, it deceptively uses the phrase "debates over the modern version of Darwin's theory" to insinuate doubt about the validity of evolution.

It is quite telling that Dave Springer, one of the administrators of Uncommon Descent, the blog of ID-proponent William Demsbki, recently wrote this on one of the threads there.

Why is it that chance worshipping (sic) biologists are continually surprised at what they discover but design advocates aren’t surprised at all?
DaveScot (Dave Springer, blog administrator) Uncommon Descent Discovery Institute website, August 15, 2007.

This question clarifies a distinction between the authors/publishers of EE and the scientific enterprise. The surprise of discovery is one of the best things about science. The smugness implicit in "I knew it all along", captured in this comment and fostered by the DI in this book, disdains surprises, and is the antithesis of inquiry-based learning. Scientists doing research actually do make unexpected discoveries; they are the lifeblood of real science. Surprises, discovery, and the joy of discovery are the incentives in inquiry-based learning. Explore Evolution is neither scientific nor inquiry-based. Instead, it reveals its revelation-based roots of neo-creationism, in stark contrast to the inquiry-based roots of modern science and modern science education.

Introduction

The Introduction is laden with errors about biology, evolution, and what science is and how it is practiced. Beginning with the definitions of evolution, Explore Evolution misstates theoretical and factual components of evolutionary biology, omits other key evolutionary mechanisms, and misrepresents professional scientists. As is common in creationist literature, to present a veneer of scientific respectability for the views presented, Explore Evolution cites for student reference technical research requiring scientific and mathematical background that high school students simply will not have. It also misrepresents the nature of science in many ways, contending (among other errors) that evolutionary sciences are qualitatively different in their scientific approach. The book further distorts students' understanding of science by pretending that the classroom is where scientific debates ought to be resolved.

p. 3: "[I]n the historical sciences, neither side can directly verify its claims."

Philosophers of science dispute Explore Evolution’s claimed distinction between two kinds of science, and do not hold historical claims to be any less testable than others. But marginalizing evolution as an allegedly different kind of science allows the authors to cast doubt on its validity &mdash an approach commonly encountered in creationist sources.

p. 5: "The best explanation will be the one that explains more of the evidence than any other."

This is an incomplete and misleading view of science. To be scientifically useful, a hypothesis must be more than explanatory or verifiable, it must make predictions which lead us to new observations. In addition, Explore Evolution omits the means by which scientists actually evaluate scientific explanations. The focus on good science as explaining "more of the evidence" is commonly promoted in the intelligent design (ID) literature, where emphasis is on the "weaknesses" of evolution &mdash i.e., what evolution allegedly does not explain. From the perspective of an ID supporter, the lack of an evolutionary explanation for a phenomenon is evidence for God's involvement.

p. 8: "…three major uses of 'evolution.'"

Antievolutionists have a problem. It would be absurd to deny the phenomenon of natural selection, which is well-supported by much evidence, and they don't. Similarly, observations demonstrate that populations of organisms can change from generation to generation, and over many generations. Natural selection and change over time, then, have to be acknowledged as real entities &mdash yet such ideas are part of modern evolutionary biology. The solution: separate these "acceptable" ideas from the component of evolution they find most troublesome: the idea that living things share common ancestry (rather than having been specially created in their present form). The authors thus carve up evolution into three artificial components: "change over time", "universal common descent", and "the creative ower of natural selection", in order to single out the idea of common descent, even though all three ideas are related.

Alas, even here, they create a caricature, referring to "universal common descent" (i.e., a single organism at the base of the tree of life). The validity of common ancestry does not stand or fall on whether there is a single organism to which all living things can be traced. Whether all mammals share a common ancestor, for example, does not depend on whether mammals and all other organisms descended with modification from a single common ancestor. But claiming that this universal ancestor is essential allows the authors later in the book to cite some scientists who propose a more complex root of the tree as providing "evidence against evolution". The goal here, as always in this book, is to cast doubt about the validity of evolution. The unstated but obvious alternative, of course, is special creation.

p. 8: "Some people use the term evolution to refer to a cause or mechanism of change. When evolution is used in this way, it usually refers to the mechanism of natural selection."

The authors would do students a service by correcting rather than reinforcing the errors of "some people" (unidentified, but not likely to be scientists). The statement is simply wrong. A mechanism is not the same as the phenomenon that it affects. Evolution is the inference of common ancestry of living things, whereas natural selection is a powerful mechanism that produces adaptation, and therefore contributes to differences as seen in the tree of life. But even if "some people" use evolution to refer to natural selection as a mechanism of change, this is a greatly reduced and inadequate understanding of how evolution is brought about. Students cannot "explore evolution" without discussing mechanisms like neutral drift, gene flow, mutation, and recombination. Explore Evolution never presents a full range of mechanisms, a lapse which blocks inquiry and exploration.

p. 8: "…all modern life forms emerged and developed from the first one-celled organism."

The tree of life as envisioned by many evolutionary biologists.The tree of life as envisioned by many evolutionary biologists: W. Ford Doolittle (2000) Scientific American, 282:90-95.

Again, the number of organisms at the base of the tree of life is not critical to the concept of common ancestry. Scientists cited by Explore Evolution are not questioning the idea of common ancestry, but propose that there was a period when early life swapped genes so frequently as to form a common ancestral population of cells, from which all modern lineages split. Thus it would be impossible to recreate the exact common ancestor of all living things (other scientists disagree). In any event, there is evidence that much gene swapping took place early in the history of life (see illustration at the left) making the base of the tree of life spaghetti-like. This is irrelevant to whether and when humans and chimpanzees shared a common ancestor, or what the common ancestor of plants and animals looked like.

p. 9: "[Scientists disagree whether] natural selection [can] produce fundamentally new organisms."

Indeed, evolutionary biologists debate the strength of natural selection in producing new structures and body plans &mdash but the debates are over whether natural selection alone or combined with other mechanisms produces such changes. No one is debating whether such changes occur, but Explore Evolution wishes to leave the student with the belief that 1) natural selection is the be-all and end-all of evolutionary mechanisms, and 2) without natural selection as a mechanism, common ancestry fails as a theory. The book ignores the many additional mechanisms and processes affecting evolution, to the detriment of the students' understanding.

Neo-Creationist OrchardNeo-Creationist Orchard: Proceedings of the Second International Conference on Creationism, Vol. 2. pp. 345-360.

p. 10: "According to these scientists, the history of life should not be presented as a single tree, but as a series of parallel lines representing an orchard of distinct trees."

"These scientists" are found only on the pages of creationist journals. Creationists have long proposed that God specially created the "kinds", which then adapted and branched "within the kind". Although Explore Evolution does not use biblical terminology, the trees in the orchard (see illustration, left) are created "kinds", as described in the Bible. Mainstream science knows nothing of this orchard; standard science proposes a single tree of life of related organisms, and sees no evidence for separate entities.

Major Flaws:

Nature of Science: High school biology classes form the foundation of a student's understanding of how science works, not just of how the living world works. Explore Evolution badly misrepresents the way science is practiced.

Evolution: It is unacceptable that Explore Evolution misdefines evolution, and unacceptable that basic evolutionary mechanisms are ignored entirely. This mishandling of the central concept that the book claims to explore should disqualify it from use in any classroom.

Nature of Science

The Introduction to Explore Evolution packs a tremendous number of fundamental errors into a remarkably brief chapter. These errors bear not only on the science of evolution, nor even biology in general, but on the nature of science itself. The introduction fundamentally skews a student's understanding of what science is and how it is practiced. The definitions of evolution it provides are badly flawed and misleading, and misrepresent the state of scientific views on evolutionary biology with the clear goal of propping up a bogus creationist model of biology.

This chapter begins by introducing several basic errors about the nature of science. The first of these errors is a flawed distinction between historical sciences and experimental science, as if the scientific method were applied differently in different fields. The apparent goal of that distinction is to cast doubt on scientific knowledge regarding historical phenomena like the age of the earth and the diversification of life. This error is profound, as it misinforms students about the fundamentals of how science is practiced in every field. A similar error occurs when the authors misdefine how scientists determine "the best explanation." Since explaining a phenomenon after the fact is easy, merely explaining more evidence is not enough. Scientists judge explanations by their ability to make testable predictions, predictions which would disconfirm the theory if they were found to be wrong. Unlike the authors of this book, philosophers of science regard this testability as central to science, and regard approaches based only on verification and post hoc explanation as non-scientific.

"Historical science" vs. "experimental science"

Summary of problems:

Explore Evolution relies on an ill-defined distinction between "experimental science" and "historical sciences," and asserts that claims about the latter cannot be directly verified. While the terms Explore Evolution uses are indeed applied by philosophers of science, those philosophers use the terms quite differently. Both approaches to scientific questions are valid, a given scientific field can draw on both approaches, and neither approach is less scientifically powerful. Explore Evolution is wrong to state that these different approaches require "different methods," and even more wrong to state that "in the historical sciences, neither side can directly verify its claims about past events" (p. 3).

Full discussion:

Philosophers of science draw a distinction between research directed towards identifying laws and research which seeks to determine how particular historical events occurred. They do not claim, however, that the line between these sorts of science can be drawn neatly, and certainly do not agree that historical claims are any less empirically verifiable than other sorts of claims. Philosopher of science Elliott Sober explains:

This division between nomothetic ("nomos" is Greek for law) and historical sciences does not mean that each science is exclusively one or the other. The particle physicist might find that the collisions of interest often occur on the surface of the sun; if so, a detailed study of that particular object might help to infer the general law. Symmetrically, the astronomer interested in obtaining an accurate description of the star might use various laws to help make the inference.

Although the particle physicist and the astronomer may attend to both general laws and historical particulars, we can separate their two enterprises by distinguishing means from ends. The astronomer's problem is a historical one because the goal is to infer the properties of a particular object; the astronomer uses laws only as a means. Particle physics, on the other hand, is a nomothetic discipline because the goal is to infer general laws; descriptions of particular objects are only relevant as a means.

The same division exists within evolutionary biology. When a systematist infers that human beings are more closely related to chimps than they are to gorillas, this phylogenetic proposition describes a family tree that connects three species. The proposition is logically of the same type as the proposition that says that Alice is more closely related to Berry than she is to Carl. … Reconstructing genealogical relationships is the goal of a historical science.
Sober (2000) Philosophy of Biology 2nd ed., Westview Press: Boulder, CO. pp. 14-15

Sober continues by observing that the sort of mathematical modeling undertaken by some evolutionary biologists is not historical in this sense, but seeks after the sort of general "if-then" statements which include scientific laws. Evolutionary biology thus is both a nomothetic science and an historical science. Furthermore:

Although inferring laws and reconstructing history are distinct scientific goals, they often are fruitfully pursued together. Theoreticians hope their models are not vacuous; they want them to apply to the real world of living organisms. Likewise, naturalists who describe the present and past of particular species often do so with an eye to providing data that have a wider theoretical significance. Nomothetic and historical disciplines in evolutionary biology have much to learn from each other.
Sober (2000), p. 18

As an example, Sober points to ongoing research into the origins of sexual reproduction. Biologists pursuing historical scientific programs have identified a number of species which do and do not reproduce sexually, and have reconstructed the evolutionary relationships between these species. Other researchers have developed generalized models which show that sexual reproduction ought to evolve under certain circumstances, and that asexual reproduction is more advantageous under other conditions. If both groups worked independently, they might consider the problem solved. By working together, the theoreticians can see which model of the origins of sex is most applicable to any given lineage, testing the model and yielding both historical and theoretical insights. Through such collaborations, researchers have found that the precise conditions and predictions of existing models for the evolution of sex do not match the actual circumstances observed, indicating that theoretical work remains to be done, and that further research in the field is necessary.

Sober concludes "[o]nly by combining laws and history can one say why sex did evolve" (p. 18, emphasis original). This contrasts sharply with the claim in Explore Evolution that "in the historical sciences, neither side can directly verify its claims about past events" (p. 3). Explore Evolution here seeks to sow doubt about certain scientific results, and as a consequence, presents an inaccurate description of the scientific process. Both acts are irresponsible for a textbook, but the latter will have consequences on the students' successes in all their scientific endeavors.

See also Carol E. Cleland (2001) "Historical science, experimental science, and the scientific method" Geology, 29(11):987-990 for a discussion of why "the claim that historical science is methodologically inferior to experimental science cannot be sustained."

Explore Evolution follows a long history of creationist misrepresentation on this point. Creationists have long attempted to undercut the validity of evolutionary theory by claiming that it is not genuine science and therefore need not be taken seriously. Evolution has been called "just a theory" as opposed to fact, "speculative" as opposed to demonstrated, and "historical" as opposed to "experimental."

For example, in the creationist book The Mysteries of Life's Origin (1984), Charles Thaxton, et al. contrast supposedly reliable operations (experimental) science with the "speculative" science of origins. Similarly, in Origin Science: A proposal for the creation-evolution controversy, Norman Geisler and Kerby Anderson attempt to resolve that social controversy by distinguishing "empirical" or "operational" science (equivalent to Explore Evolution's "experimental science") from "forensic" or "origins" science (equivalent to "historical science" in Explore Evolution:

It is the proposal of this book that a science which deals with origin events does not fall within the category of empirical science, which deals with observed regularities in the present. Rather, it is more like a forensic science, which concentrates on the unobserved singularities in the past. … A science about the past does not observe the past singularity but must depend on the principle of uniformity (analogy), as historical geology and archaeology do. That is, since these kinds of sciences deal with unobserved past events (whether regular or singular), those events can be "known" only in terms of like events in the present. …

The great events of origin were singularities. The origin of the universe is not recurring. Nor is the origin of life, or the origin of major new forms of life. These are past singularities over which creationists and evolutionists debate. Evolutionists posit a secondary natural cause for them, creationists argue for a supernatural primary cause.
Geisler, Norman L. and J. Kerby Anderson (1987) Origin science: A proposal for the creation-evolution controversy. Grand Rapids, MI: Baker Book House, 198 p.

The problem with these attempts to divide science neatly into two piles is that, as Sober observes, a given science, and even a given scientist, can switch between approaches in the quest to address a single question. Geologists can plumb the oldest rocks on earth for evidence of the first life, but they can also go to the lab and recreate the conditions of early earth to test predictions of hypothesis about events billions of years ago. And those results from a modern laboratory will send researchers back to the field to test predictions about historical events generated in the laboratory.

Similarly, physicists at the Large Hadron Collider in Switzerland are testing theories about the origin of the universe:

The LHC will recreate, on a microscale, conditions that existed during the first billionth of a second of the Big Bang.

At the earliest moments of the Big Bang, the Universe consisted of a searingly hot soup of fundamental particles - quarks, leptons and the force carriers. As the Universe cooled to 1000 billion degrees, the quarks and gluons (carriers of the strong force) combined into composite particles like protons and neutrons. The LHC will collide lead nuclei so that they release their constituent quarks in a fleeting 'Little Bang'. This will take us back to the time before these particles formed, re-creating the conditions early in the evolution of the universe, when quarks and gluons were free to mix without combining. The debris detected will provide important information about this very early state of matter.
Science and Technology Facilities Council (2008) "The Big Questions" page on "The Large Hadron Collider" website. Accessed September 18, 2008.

Which category of science does this belong to? Clearly, it is both historical science and experimental science. Other such historical claims can be evaluated using modern experiments. Another example of this approach can be found in the episode of Mythbusters in which claims about the destruction of the Hindenburg are tested using modern models of the combustible zeppelin. If a television show can accurately navigate these philosophical waters, it is entirely appropriate to expect a textbook to handle them responsibly as well.

Evaluating the quality of a scientific explanation

Summary of problems:

Scientific explanations are judged by their ability to make accurate predictions of new data. Explore Evolution obscures this point by stating that "The best explanation will be the one that explains more of the evidence than any other" (p. 5). This claim sneakily twists the student's understanding of how we evaluate scientific explanations. Doing that is necessary to get the subsequent erroneous claims through the door. It also cracks the door for a discussion of the supernatural in science classes, since the suspension of natural law can explain absolutely anything (making it useless as a scientific prediction).

Full discussion:

To be scientifically useful, an explanation ought to do more than merely explain existing observations. A good hypothesis may begin as an inference drawn from known facts, but it also must make some predictions which lead us to new observations. If the observations are not what we predicted, we can reject that hypothesis, but we do not regard it as proven if the observation is as predicted. That predictive power is part of what allows us to evaluate the quality of a scientific explanation.

The evidence in Explore Evolution would not allow us to distinguish between multiple hypotheses about who washed the car in their chosen example, nor is it impossible that some mischievous gremlin planted all of that evidence merely to make it seem as if someone washed the car.

Indeed, that latter hypothesis could explain any set of evidence we might possibly gather. It does not, however, predict the details of any new observation at all. That doesn't mean it's wrong, but it does make it a worse explanation than a hypothesis which makes testable predictions. This would be true even if it explained existing observations which existing theories did not explain, of the existing theories had a track record of producing correct predictions.

Philosopher Elliott Sober uses gremlins to make a related point:

You and I are sitting in a cabin one night, and we hear rumbling in the attic. We consider what could have produced the noise. I suggest that the explanation is that there are gremlins in the attic and that they are bowling. You dismiss this explanation as implausible. … I hope you see that, … If there actually were gremlins bowling up there, we would expect to hear noise. But the mere fact that we hear the noise does not make it very probably that there are gremlins bowling.
Elliott Sober (2000) Philosophy of Biology, 2nd ed., Westview Press:Boulder, CO. p. 32

Sober's point is that the gremlin hypothesis may be likely, but it is not plausible in part because it is not likely that there are gremlins in the attic to begin with. Thus, an explanation which seems to explain more evidence can be a worse hypothesis if it fails to make novel predictions, or if it requires us to invoke unlikely phenomena, such as the existence of gremlins.

Explore Evolution offers few hypothesis about biology, preferring to attack existing explanations. But where it does offer alternatives, they tend to exhibit the same flaws as the two "gremlin" hypotheses offered above. For instance, EE suggests that there may be multiple trees of life arranged in an "orchard". The gremlin(s) which tend that orchard could undoubtedly have planted it in any way, and they could have been planted in a manner which produces a pattern of modern diversity indistinguishable from what we would find if there were a single tree of life (which is to say, indistinguishable from what we actually find). A hypothesis involving multiple trees of life requires us to understand multiple origins of life, and a hypothesis involving an orchard of trees (rather than a forest) requires that we hypothesize something capable of planting and tending all of those trees. The orchard hypothesis and the single tree hypothesis might both explain all the extant data, but to hypothesize an orchard raises more questions than it resolves, while making no novel, testable predictions in its own right. This makes it a worse explanation, and these flaws would persist even if it could account for observations that existing hypotheses cannot explain.

Again, the misrepresentation of basic issues in the nature of science invalidate the book, even if the misrepresentations were not clearly intended to open the door to nonscientific ideas in the science class.

References

Cleland, Carol E. "Historical science, experimental science, and the scientific method", Geology 11:987-90, 2001.

Cleland, Carol E., "Methodological and Epistemic Differences between Historical and Experimental Science," Philosophy of Science 69,474-96, 2002.

Miller, K.B. "The similarity of theory testing in the historical and 'hard' sciences." Perspectives on Science and Christian Faithe 54:119-122, 2002.

For more information

Peter Lipton (2005) "Testing Hypotheses: Prediction and Prejudice" Science 307(5707):219-221.

Lipton explains some reasons why we should prefer predictions to post hoc explanations.

Evolution

Misdefining science is a critical component of the modern creationist strategy, and a necessary precondition for their attacks on evolution. While its definition of science would sweep phenomena like astrology into science classes, EE sticks to the usual creationist focus on evolution. Though acknowledging that "the process of teaching requires a precise, unambiguous use of language," EE introduces three definitions for the term "evolution" which range from the erroneous to the irrelevant. One definition introduces a false distinction between microevolution and macroevolution (the seed of later confusing treatment of basic concepts). The next definition wrongly treats common descent as if it were independent of the mechanisms that produce evolutionary change, and the third definition simply ignores major evolutionary mechanisms, mechanisms central to major research programs in evolutionary biology. In arguing that these definitions are truly distinct, EE obscures a critical component evolutionary biology: the way that evolutionary mechanisms produce biological novelty, and the way that understanding evolutionary mechanisms today produces testable predictions about the past. Far from being totally disparate concepts, the three definitions of evolution offered by EE are three aspects of the same concept.

The author's incomplete description of evolutionary mechanisms extends throughout the rest of the chapter, and of the book. The authors treat natural selection and evolution as if the words were synonyms, ignoring important evolutionary mechanisms like neutral drift, recombination and population processes like gene flow. Treating limits on natural selection as if they represent problems for evolution is not accurate, and serves no valid pedagogical or scientific purpose. In order to make this invalid point, EE's authors misrepresent, misquote and miscite professional scientists.

The pattern of misrepresenting scientists' views repeats in the next section, and indeed throughout the book. A misrepresentation of current thinking about universal common descent is set against a dolled up creationist model of life's history and diversity ripped from the Proceedings of the Second International Conference on Creationism. They claim that this view of life is backed by real scientists, and justify that claim with citations to scientists who actually reject these ideas vociferously. Along the way, the authors make errors in basic biology (e.g., treating evolution as a process occurring within an individual, rather than within a population), and reduce ongoing scientific dialog about the nature of the very earliest life to a petty creationist caricature. The research they cite is part of ongoing studies that draw on molecular biology, biochemistry, ecology and evolution, and students in a high school biology class have nowhere near the background needed to understand that research, let alone serve as judges in that discussion. Scientific questions are not resolved in the high school classroom, but in the laboratory and through learned dialog. Yet again, the presentation in Explore Evolution misrepresents not only the details of science, but the nature of science itself.

Meanings of "evolution"

Summary of problems:

As used in standard biology textbooks, "evolution" has several connotations, but they all derive from a single concept. Explore Evolution obscures the relationship between these concepts by treating them as three definitions which can be taken in isolation from one another. These definitions are not actually different ideas, just different consequences of the same idea. Attempting to divide these topics and act as though students can choose which to accept a la carte is a common creationist fallacy.

Full discussion:

In describing what we now refer to as "evolution," Darwin usually used the phrase "descent with modification," using the word "evolve" only once in the The Origin of Species:

It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone on cycling on according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.
Charles Darwin (1859) On the Origin of Species, 1st ed., John Murray, London (facsimile edition, Harvard University Press), p. 490

In this concluding paragraph to the book, Darwin lays out the connections between the senses of "evolution" which Explore Evolution attempts to keep separate. Traits vary between individuals, and some of those differences can be passed from parent to child. Some of those heritable differences leave the offspring at a greater advantage than others. That process of natural selection can cause one population to become increasingly different, branching off from the ancestral population. Where heritable variation exists, this branching pattern of descent is inevitable, and it is possible to trace the evidence of that common descent back through history. Thus, the existence of change over time (first definition in EE) is part and parcel with the power of evolution to produce novelty (third definition in EE), and that change over time will inevitably produce a pattern of common descent (second definition in EE).

Why do we talk about universal common descent in particular? The most basic reason is that the idea of a single origin of life is the simplest explanation for the diversity of life that we see in the world today. A scientist who wants to challenge universal common descent cannot simply say that there may be something, somewhere, which doesn't share an ancestor with the rest of life on earth (as EE's "critics" do). That scientist would have to present evidence that a particular group of organisms does not share an ancestor with the rest of life, and show how that hypothesis is better than the hypothesis of universal common descent. Explore Evolution does not propose to replace a successful hypothesis with a better hypothesis, it merely emphasizes areas of uncertainty, but doesn't provide students with the knowledge or tools to gather new knowledge or improve our existing knowledge. Thus, the textbook fails both to accurately represent how science is practiced, but also a failure to live up to its claim of being "inquiry-based."

Evolutionary mechanisms

Summary of problems:

Explore Evolution describes only two evolutionary mechanisms, yet standard biology texts describe many more. The discussion of evolutionary mechanisms completely omits any reference to genetic drift, endosymbiosis, gene flow, genetic recombination. This despite the fact that prominent biologists have argued that genetic drift and symbiosis may actually be more important to the history of life than natural selection or mutation, the only mechanisms mentioned anywhere in Explore Evolution.

Full discussion:

Biologists recognize many evolutionary mechanisms, including not only natural selection and mutation, but the effects of chance fluctuations in gene frequency (genetic drift), the effects of genetic rearrangements on a chromosome (recombination), the effects of migration of genetic variants into and out of a population (gene flow) and the effects of wholesale incorporation of genetic material by one species from another species (endosymbiosis). There is an ongoing debate within evolutionary biology over whether genetic drift is more influential than natural selection on the course of evolution. Other biologists have suggested that endosymbiosis may be even more important, and continue to test that hypothesis. If Explore Evolution really intended to present ongoing scientific controversies regarding evolution, those debates over evolutionary mechanisms would have a prominent place. And yet, in discussing "the creative power of natural selection," EE states:

Some people use the term evolution to refer to a cause or mechanism of change. When evolution is used in this way, it usually refers to the mechanism of natural selection (acting on random variations and mutations). This third use of evolution affirms that the natural selection/mutation mechanism is capable of creating new living forms, and has thus produced the major changes we see in the history of life (as represented by Darwin's Tree of Life.)
EE, p. 8

It's certainly true that scientists refer to evolution in this broad mechanistic sense, but no biologist restricts that discussion to mutation and natural selection. Biologist Michael Lynch recently pointed out that the mistake Explore Evolution makes is a common one:

Evolutionary biology is treated unlike any science by both academics and the general public. For the average person, evolution is equivalent to natural selection, and because the concept of selection is easy to grasp, a reasonable understanding of comparative biology is often taken to be a license for evolutionary speculation. It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise in the popular literature. … There is, of course, a substantial difference between the popular literature and the knowledge base that has grown from a century of evolutionary research, but this distinction is often missed by nonevolutionary biologists [including the authors of EE].

[E]volution is a population-genetic process governed by four fundamental forces. Darwin articulated one of those forces, the process of natural selection, for which an elaborate theory in terms of genotype frequencies now exists. The remaining three evolutionary forces are nonadaptive in the sense that they are not a function of the fitness properties of individuals: mutation is the ultimate source of variation on which natural selection acts, recombination assorts variation within and among chromosomes, and genetic drift ensures that gene frequencies will deviate a bit from generation to generation independent of other forces.

[A]ll four major forces play a substantial role in genomic evolution. It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement.
Michael Lynch (2007) "The frailty of adaptive hypotheses for the origins of organismal complexity," Proceedings of the National Academy of Sciences 104(S1):8597-8604

Explore Evolution provides a perfect example of the errors Lynch describes. Genetic drift and recombination do not occur in the index to the book, nor the glossary, nor does the EE passage quoted above even acknowledge the existence of evolutionary processes other than natural selection acting on mutations. Evolutionary biology textbooks typically devote at least a full chapter to discussing the role of genetic drift (e.g., chapter 7 in Ridley's Evolution, chapter 11 in Futuyma's Evolutionary Biology), and introductory textbooks address the topic as well (e.g., p. 400 in Miller and Levine's Biology, pp. 450-451 in Campbell and Reece's Biology, 6th ed., and pp. 393-399 in Raven and Johnson's Biology, 5th ed.). There is no way to "explore evolution" accurately without including a discussion of all the major evolutionary processes. The inaccurate and biased presentation of even such basic knowledge demonstrates how EE would misinform and miseducate students.

It should not come as a surprise to learn that the caricature of evolution as "natural selection (acting on random variations and mutations)" is a common creationist trope, and the discussion of the definitions of evolution in EE is basically identical to that in a seminal work of ID creationism, Phillip Johnson's Darwin on Trial (with one interesting omission):

"Evolution" in the Darwinist usage implies a completely naturalistic metaphysical system, in which matter evolved to its present state of organized complexity without any participation by a Creator. But "evolution" also refers to much more modest concepts, such as microevolution and biological relationship.
Phillip E. Johnson (1991) Darwin on Trial, Regnery Gateway, Washington, DC, p. 151

Explore Evolution employs the same argument, but lets innuendo replace Johnson's forthright advocacy of "a Creator." This is in keeping with EE's habit of parroting creationist criticisms of evolution and attempting to cloak the religious nature of those objections through omission and obfuscation.

Universal Common Descent

Summary of problems:

Scientists continue to research the origins of life, and to investigate the possibility that early lineages of life shared genes so freely that very early living things cannot be separated into multiple discrete lineages. The extent of that sharing is a subject of active research and scientific debate. Explore Evolution misrepresents that ongoing research as if it were between advocates of a single tree of life and supporters of a "neocreationist orchard."

Full discussion:

The nature of the Last Universal Common Ancestor is a topic of ongoing research today, and a book which intended to explore current scientific controversies within evolution would have to address that topic. A growing body of evidence suggests that there was so much sharing of genetic material among the single-celled organisms at the base of the tree of life that the different strands cannot be separated. Some scientists go so far as to treat the entire community of organisms alive at the time as essentially a single superorganism which shuffled genes freely between components. They treat that community of cells as the Last Universal Common Ancestor (LUCA). As particular genes became more tightly entwined with the functioning of other genes, the sharing decreased and lineages began to diverge.

Other scientists hold that gene transfer between organisms is not an obstacle to tracing the lineages of modern life, and insist that the branching trees of life can be traced all the way back to the earliest cell.

Explore Evolution ignores this ongoing and fascinating scientific controversy. To the extent they acknowledge its existence, it is only to misrepresent the views of participants in that debate. This statement, for example, betrays a profound lack of understanding of evolution and could hardly be more inaccurate or misleading about basic biology:

Darwin envisioned this 'Tree of Life' beginning as a simple one-celled organism that gradually developed and changed over many generations into new and more complex living forms.
EE, p.6

A central point of the Origin of Species is that evolutionary change takes place in populations of organisms, not in individuals. To elide this point, or fail to make it clear, is obviously an egregious error in a book supposed to be about evolution.

Furthermore, even in 1859 Darwin allowed for the possibility of more than one type of early organism. At the end of The Origin of Species, for example, Darwin wrote:

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one;

Since then, the evolution of the earliest cells has been and continues to be a dynamic area of research.

Neo-creationist orchard: From Kurt Wise (1990) "Baraminology: A Young-Earth Creation Biosystematic Method," in Robert E. Walsh (ed.) Proceedings of the Second International Conference on Creationism, Vol. 2. Creation Science Fellowship, Inc.: Pittsburgh, PA. p. 345-360.Neo-creationist orchard: From Kurt Wise (1990) "Baraminology: A Young-Earth Creation Biosystematic Method," in Robert E. Walsh (ed.) Proceedings of the Second International Conference on Creationism, Vol. 2. Creation Science Fellowship, Inc.: Pittsburgh, PA. p. 345-360.Furthermore, Explore Evolution badly misrepresents the state of science when it states "Other scientists doubt that all organisms have descended from one — and only one — common ancestor" (p. 9). While some scientists dispute the strict monophyly of the early history of life, but only because they think that genes from other branches of the tree of life moved between lineages, not because they dispute that life can be traced to a common ancestor. Researchers in the field do not "say that the evidence does indeed show some branching groups of organisms, but not between the larger groups" (pp. 9-10, emphasis original), and scientists absolutely reject the notion that "the history of life should … be represented … as a series of parallel lines representing an orchard of distinct trees" (p. 10). In fact, that way of talking about life's history was originated by creationists, as shown in the figure at right. In describing his "orchard" view of life, young earth creationist Kurt Wise explains:
Some modern creationists are suggesting a metaphor of their own — a metaphor which is planted between the Evolutionary Tree and the Creationist Lawn. The new metaphor may be described as the "Neo-creationist Orchard" (see figure 1C [reproduced here]). In this metaphor, life is specially created (as fruit trees are specially planted) and polyphyletic (i.e. each tree has a separate trunk and root system). There are also discontinuities between the major groups (trees are spaced so that branches do not overlap and could not and never did anastomose [grow together]) and there are constraints to change (a given tree is limited to a particular size and branching style according to its type). In these ways, the Neo-creationist Orchard is similar to the Creationist Lawn [Figure 1A]. They differ, though, in that the Neo-creationist Orchard allows change, including speciation, within each created group (each tree branches off of the main stem). Permitting this type of change (variously called by creationists 'diversification', 'variation', 'horizontal evolution', and 'microevolution') in different amounts in different groups allows the creation model to accomodate microevolutionary evidences (e.g. changing allelic rations, genetic recombination, speciation, etc.).
Kurt Wise (1990) "Baraminology: A Young-Earth Creation Biosystematic Method," in Robert E. Walsh (ed.) Proceedings of the Second International Conference on Creationism, Vol. 2. Creation Science Fellowship, Inc.: Pittsburgh, PA. p. 345

In this passage, Kurt Wise introduces his explicitly creationist concepts in the exact terms that Explore Evolution uses. Dr. Wise, is undoubtedly one of the "critics" EE refers to, but he is never cited in EE. Not surprisingly, the book doesn't mention that the young earth creationist group Answers in Genesis states that the same figure shows "the true creationist 'orchard' model."

"Creation model": Explore Evolution co-author Paul Nelson's preferred "creation model," copied from a German creationist textbook.    Paul Nelson (2001) "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, Ma. pp. 685."Creation model": Explore Evolution co-author Paul Nelson's preferred "creation model," copied from a German creationist textbook.

Paul Nelson (2001) "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, MA pp. 685.

Nor does the book point out that one author, Paul Nelson, previously presented the "polyphyletic" model shown at left, writing that "creationists defend the dynamic pattern of figure 32.2," rather than the models like the lawn illustrated by part a) of Wise's figure (Paul Nelson, 2001. "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, Ma. pp. 684-685). Elsewhere, Nelson and a co-author defended their young earth creationist views by arguing that "The overall geometry of the history of life … depict[s] … a forest of trees, each with its own independent root" (Paul Nelson and John Mark Reynolds, 1999, "Young Earth Creationism" in Three Views on Creation and Evolution, J. P. Moreland and John Mark Reynolds, eds. Zondervan Publishing: Grand Rapids, MI. p. 45).

This vision of multiple trees of life, totally independent of one another is a creationist concept, and bears no relationship with any position being advanced in the scientific literature. There are challenges to the idea that diversity of life followed a strict branching pattern from the earliest days, but as shown in the figure at the right, this view rests heavily on exactly the sort of mixing (or "anastomosis") that Nelson and Wise reject. The figure EE uses to illustrate its proposed alternative view of life also does not include the complex exchanges of genetic information proposed by the authors Explore Evolution cites as critics.

A modern view of the tree of life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5.  Note that distances are not necessarily to scale in this image.  This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor.  They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.A modern view of the tree of life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5. Note that distances are not necessarily to scale in this image. This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor. They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.

The scientists cited as supporting this "orchard" view of life actually advocate a tree very different from the one illustrated by Explore Evolution (figure i:4). As the figure to the right shows, the group of scientists challenging traditional views of the tree of life are not proposing the sort of orchard that EE illustrates. Where EE and its creationist antecedents' embrace "discontinuities between major groups," the objection raised by the scientists EE cites actually object that there aren't enough connections between the branches of the tree of life.

These authors do not dispute that we can talk about a single common ancestor, merely that we should talk about it in a different sense. Doolittle explains:

As Woese [an author cited as a critic of monophyly by EE] has written, "The ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn become the three primary lines of descent [eubacteria, archaea and eukaryotes]." In other words, early cells, each having relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains remain recognizable because much (though by no means all) of the gene transfer that occurs these days goes on within domains.
W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-95

This is a nuanced view, one that high school students are ill-equipped to understand until they have a fuller grasp on the basic concepts of biology. As Doolittle observes, even "some biologists find these notions confusing." It is hardly reasonable to expect students who are still learning what the genome is to appreciate a debate about the ways that gene swapping between ancient bacteria would have produced the sort of communal superorganism Woese and Doolittle describe. It would pedagogically inappropriate for Explore Evolution to thrust students into the midst of that debate without any background or support. Indeed, many biology teachers would be ill-prepared to lead such a discussion. This does not excuse the failure of EE to accurately describe the nature of that scientific debate.

Woese and Doolittle do not advocate an orchard, they simply thing that the trunk of the tree of life cannot be separated into distinct strands. They are not opponents of evolution, and Explore Evolution does the authors they cite no favors when they misrepresent the underlying science. That loose treatment of the underlying science also would do students and teachers no favors. A truly inquiry-based text might be able to wring some useful educational lessons from the debate going on over the base of the tree of life, but it is doubtful that high school students would benefit from that highly technical discussion, and they could not use Explore Evolution to understand even the basic nature of that ongoing research.

"Fundamentally new" organisms

Summary of problems:

Evolutionary theory predicts relatively smooth and incremental transitions, not the sudden emergence of new traits or species. Even so, Explore Evolution discusses "whether natural selection can produce fundamentally new forms of life, or major innovations in the anatomical structure of animals" without ever explaining how students ought to distinguish "fundamentally new forms" of life from merely "new" forms, nor how "major innovations" can be distinguished from more mundane "innovations." The assumption that any trait would spring forth, fully formed, without precedent, is not a prediction of evolution, nor are these concepts in general use by biologists.

Full discussion:

As noted above, real textbooks about evolution distinguish several evolutionary mechanisms, including natural selection and mutation, but also genetic drift and gene flow, as mechanisms for evolutionary change. In particular, mutation is a change in the DNA of a cell in a single organism, and if it happens in a cell which goes on to produce an egg or sperm cell, it can be passed on to all the descendants of that individual. This makes mutation "the origin of genetic variation" (Futuyma, 1998, Evolutionary Biology, 3rd ed., ch. 7). When Explore Evolution speculates about "whether natural selection can produce fundamentally new forms of life, or major innovations" in anatomy (p. 9), it wrongly omits the generative power of mutation, as well as other evolutionary mechanisms, several of which may be more important to the course of evolution than natural selection.

The discussion of whether evolution is "creative or conservative" (section heading, p. 9) in Explore Evolution is profoundly confusing because it fails to distinguish between different evolutionary processes, and between the levels at which they operate. For instance, the discussion about whether natural selection itself is "creative" ignores the role of other mechanisms in generating variation, and the difference between novelty at a genetic level, at a genomic level, or at a population level. Also, EE's focus on whether natural selection can produce "fundamentally new forms of life" fails to describe over what time scale it might be operating, nor what processes scientists hypothesize in addition to (not instead of) natural selection.

More worrisome in the educational setting, the authors of Explore Evolution misrepresent several of the authors that they quote regarding the "creative" power of natural selection. They write:

Zoologist Ernst Mayr writes that natural selection is a "positive, constructive force," and adds "one can go even further and call natural selection a creative force."
EE, p. 9

As the footnote points out, these two quotations come from different sources; Mayr did not "add" one phrase to the other. Neither does the first quotation refer to Mayr's own views on whether natural selection was a "creative" force, he was pointing out that Charles Darwin "considered selection not a purely negative force that eliminates the unfit, but a positive, constructive force that accumulates the beneficial" (Ernst Mayr, 1964, "Introduction" to On the Origin of Species by Charles Darwin: A Facsimile of the First Edition, Harvard University Press: Cambridge, MA. p. xvii). The latter quotation comes from a passage that addresses exactly the misconceptions EE promotes, and is worth quoting at length.

An understanding of the working of natural selection is the key to the Darwinian theory of evolution. I know of no other scientific theory that has been as misunderstood and misrepresented as greatly as the theory of natural selection. First of all, it is usually represented as strictly negative, as a force that eliminates, a force that kills and destroys. Yet Darwin, by his choice of the name "selection," clearly emphasized the positive aspects of this force. Indeed, we now know that one can go even further and call natural selection a creative force. Second, natural selection is not an all-or-none phenomenon. The typologist, the follower of Plato, seems to think that alternatives are always either good or bad, black or white, worthy of preservation or doomed to rejection. This viewpoint is represented in two statements by well-known contemporary philosophers, chosen at random from the recent literature: "Natural selection requires life and death utility before it can come into play"; and "Unsuccessful types will be weeded out by the survival of the fittest but it cannot produce successful types."

Actually, types in the sense of these statements do not exist; only variable populations exist. No one will ever understand natural selection until he realizes that it is a statistical phenomenon. In order to appreciate this fully, one must think in terms of populations rather than in terms of types [or EE's "forms" -ed.].
&hellip
A further consideration will help to make the role of natural selection even clearer. Not the "naked gene" but the total phenotype is exposed to selection. A gene occurring in a population will contribute toward very many phenotypes. In some cases these phenotypes will be successful, in others they will not. The success of the phenotypes will depend on the fitness of the particular gene, within the framework of the gene pool of this population. And this again will be an essentially statistical phenomenon.

Let us also remember that recombination, not mutation as such, is the primary source of the phenotypic variation encountered by natural selection. The usual argument of the anti-Darwinian is: "How can an organism rely on the opportune occurrence of a favorable mutation whenever one is needed, considering that most mutations are deleterious? Surely all organisms would be doomed to extinction of in times of need they had to rely on such rare events?" Those who ask such questions confuse genetic variability and phenotypic variability. To be sure, mutation is ultimately the source of all genetic variation. But natural selection operates not at the level of the gene but at the level of the phenotype. Further, the main source of phenotypic variation is recombination rather than mutation, and this source of variation is ever present. With every individual differing genetically from every other one, every phenotypic character is variable, showing deviations of varying intensities and directions around the mean. Under normal conditions, selection will favor the mean (stabilizing selection), but if a deviation in any direction should be required by a newly arising selective force, the material is instantaneously available to respond to this force (directive selection).

Natural selection in this modern nontypological interpretation is an exceedingly sensitive instrument. The phenotype in nearly every case is actually a compromise between a number of conflicting selective forces.
Ernst Mayr (1962) "Accident or Design: The Paradox of Evolution," in The Evolution of Living Organisms, (proceedings of the Darwin Centenary Symposium of the Royal Society of Victoria), and reprinted in Mayr (1976) Evolution and the Diversity of Life: Selected Essays, Harvard University Press:Cambridge, MA, ch. 4, pp. 36-38

Given that it is the combinations of genes which produces the final organism, recombination of genes during cell replication and sexual reproduction plays a critical role in generating variation within the population. Natural selection acts on combinations of genes as much as it operates on the individual genes themselves, and the sum total of the selection on particular genes and particular combinations of genes can and does produce biological novelties. It is fair to say that this process of selecting genes and gene combinations makes natural selection "an editor" (EE, p. 9, emphasis original). Editing can be creative work; EE would have benefited from a particularly creative editor, and good authors often regard their editors as collaborators whose creativity is necessary for the final product.

Explore Evolution hedges a bit on this point, arguing that it is not enough for something to be new, it must be "fundamentally new." By this they seem to mean a "major innovation[] in the anatomical structure of animals" (or plants, fungi and other living things, presumably). Unfortunately, it is not clear what makes an innovation "major," any more than it is clear when a novelty is "fundamentally new," rather than simply new. More importantly, it is not clear how quickly novelties must appear in a population in order to qualify as "major innovations" or "fundamentally new." The accumulation of small novelties over many generations is the hallmark of evolutionary change. The sudden appearance of new structures without any intermediates is not an evolutionary prediction, and no examples of such a change exist to require evolutionary explanations.

There are indeed many innovations which cannot be explained by natural selection alone. The mitochondria and chloroplasts are a perfect example, discussed in more detail in our critique of the chapter on Natural Selection. Endosymbiosis, a sort of cooption at the cellular level, is comparable to the role of recombination within the genome and gene flow in populations, and the authors of Explore Evolution would have done well to have expanded their exploration to include the full range of evolutionary processes. It would have benefited their own writing, and helped any students unfortunate enough to have this book inflicted upon them.

References

Antonis Rokas, Sean B. Carroll, (2006) "Bushes in the Tree of Life," PLOS Biology 4(11): e352 doi:10.1371/journal.pbio.0040352.

Timothy D. Colmer, Timothy J. Flowers, and Rana Munns. (2006) "Use of wild relatives to improve salt tolerance in wheat," Journal of Experimental Botany 57: 1059-1078

Fossil Succession

Overview

This chapter promotes the view that different lineages of living things have independent histories and do not share common ancestry. This idea attacks the core tenet of evolutionary theory--that all living things are genealogically related. The refusal to accept common ancestry is the sine qua non (indispensable idea) of creationism in all of its various guises.

To try to undermine confidence in common ancestry, this chapter trots out some hackneyed creationist claims:

  1. transitional fossils are rare.
  2. the major animal phyla appeared abruptly in the Cambrian explosion.

The chapter also misuses the work of scientists who study the tempo and mode of evolution by implying that criticisms of gradual change in evolution undercuts common ancestry.

This chapter also engages in a truly atrocious brand of pedagogy. Rather than teaching students what we do know about fossils, it focuses on what we do not currently know. The dangers of this approach can be seen when we examine the actual history of fossil discoveries, and the steadily shrinking lacunae (gaps) in the fossil record. A student who is made to learn about unfilled gaps in 9th grade is likely to carry a memory of that lesson for the rest of his or her life, long after paleontologists have found fossils which clarify the situation.

Scientific inquiry thrives by identifying gaps in our knowledge, proposing a hypothesis which explains the underlying situation, and then testing that hypothesis with experiments. Fossil hunters do the same, combining their knowledge of geology with evolutionary history to narrow down their search for particular fossils. This approach has revealed details of the evolution of humans, of whales, and of life itself which were unimagined when the authors of this critique were in high school. Had our teachers taught us that science could never fill in the gaps, we might be as incurious as the authors of Explore Evolution seem to be.

Transitional Fossils

Although creationists frequently claim that there are no transitional fossils, the paleontological record tells a very different story.

Transitional Fossils Are Not Rare

Are Transitional fossils are extremely rare?

Summary of problems with claim:

Fossils with transitional morphology are not rare. Fossils illustrating the gradual origin of humans, horses, rhinos, whales, seacows, mammals, birds, tetrapods, and various major Cambrian "phyla" have been discovered and are well-known to scientists. Explore Evolution's claims to the contrary are just a rehash of older creationist arguments on this point, relying on out-of-context quotes, confusion over terminology and classification, and ignoring inconvenient evidence.
"Though a possible whale-to-mammal transitional sequence has recently been unearthed, critics maintain that transitional sequences are rare, at best. For this reason, critics argue that Darwin's theory has failed an important test.
Explore Evolution, p. 27
Scientists have long thought that amphibians were a transitioinal form between aquatic and land-dwelling life forms. Why? Because amphibians can live in both the water and on land. Yet, the fossil record has revealed at least two problems with this idea... land-dwelling amphibians, themselves, appear suddenly in the fossil record.
Explore Evolution, p. 27
Darwin himself was well aware of the problems that the fossil record posed for his theory. … Where were the multitudes of transitional forms connecting different groups, as predicted (and expected) by his theory?
Explore Evolution, p. 30
Some critics say neo-Darwinism is not consistent with fossil data. Other critics say that punctuated equilibrium is consistent with fossil evidence, but lacks and adequate mechanism. Critics of both views argue that there are still far fewer transitional forms in the fossil record than we would expect, even if new forms of life did arise quickly.
Explore Evolution, p. 33

Full discussion:

First, a note on terminology. The phrase "neo-Darwinism" is not widely used by scientists, and may reflect a desire by creationists to dismiss Darwin's ideas merely as another "-ism," rather than a robust scientific theory. A PubMed search of over 18 million scientific articles found 131 variations on "neo-Darwinism," compared to 226,476 uses of "evolution."

Explore Evolution compounds many errors in attempting to claim that fossils representing evolutionary transitions are rare. The first error is its reliance on concepts like 'missing links' and 'transitional forms'. These terms are outdated and founded in incorrect and archaic ways of categorizing life. Until relatively recently, the classification system used to group living things did not aim to represent true evolutionary relationships, and some groups contained only some descendants of a common ancestor, excluding others. For example, birds were not traditionally placed within the reptiles while the 'Sarcopterygii' (lungfish, coelocanths, etc.) classically excludes tetrapods. When we try to connect these poorly defined groups with the grade school evolutionary view that, "fish gave rise to amphibians, which gave rise to reptiles, which gave rise to…," the problems with the underlying classification system confuse the matter. Some so-called 'fish' were more closely related to amphibians than to other so-called 'fish' – and some so-called 'reptiles' were more closely related to non-reptiles (e.g., birds) than they were to other 'reptiles'. Drawing upon discontinuities produced by our misclassification, people sought to find 'transitions' or 'links' between wrongly grouped 'fish' and 'amphibians' or 'reptiles' and 'birds' – historically, and quite literally creating the concept of 'missing link' or 'transitional form.'

Fortunately, evolutionary biologists have been doing away with such artificial groups for some time now. We no longer accept that birds evolved from reptiles and that birds are not reptiles themselves - since the term Reptilia now includes birds. Viewing life's history and classification in this more realistic (i.e., evolutionary) context – where we name groups based on a common ancestor plus all of it's descendants – we come to realize that quite literally, all critters have 'transitional' features. In other words, all living things possess a combination of ancestral and derived traits. The shared derived traits (discussed further in the response to chapter 4) inform us of close relationships, while ancestral traits include ancient features retained from an early evolutionary heritage. For example, salmon – which most people wouldn't have any trouble classifying – retain paired appendages and jaws – ancestral traits shared with species like sharks – but also have derived traits like bone that forms from a cartilaginous precursor – a trait which sharks do not have, but which tetrapods do. This sort of bone is a derived feature linking salmon as closer relatives of tetrapods than sharks are, even though salmon still have fins and other 'fishy' traits that sharks share.

Does this mean salmon are transitional forms or 'links' between sharks and tetrapods? Were salmon our ancestors? Of course not. The issue is that upon properly classifying life into groups sharing a common ancestor, we see that all of life is characterized by these ancestral and derived traits. Just as salmon did not give rise to tetrapods, frogs are not links between salmon and reptiles. These traits inform us of common ancestry among groups, not a sequential movement of an entire group into another group (e.g., amphibians to reptiles).

As to the actual rarity of fossils illustrating evolutionary transitions, Explore Evolution makes additional errors. First, fossils in general are rare, relative to the actual diversity of life which once existed. The chances of a given species fossilizing are slight. Thus, the fossils referred to as transitional are not necessarily the direct ancestors of modern taxa, but may represent failed branches off of the stem which led to modern forms. Depending where they branched off, they possess some, but not all, of the traits we associate with modern groups, which provides evidence of the form the transition took, even if we lack fossils of the directly ancestral species. Knowing the age of these fossils, we can have substantial certainty about the latest date at which various evolutionary novelties must have originated. Explore Evolution fails to explain what paleontologists actually use fossils to illustrate, sowing confusion among students where it ought to bring clarity.

Given the general rarity of fossils, fossils showing evolutionary transitions are not at all rare. This can be illustrated with a range of examples, of which the record of hominid fossils is especially striking. The skulls shown below display a clear, smooth transition from the early ancestors of modern humans to the modern form of the human skull. A wag might suggest that there is a gap between each of those fossils, and demand a transitional fossil to fill each such gap. Because this evolutionary sequence is relatively recent, there are enough fossils that we can only show the full transition with graphs like the one below. Fossil hominid skulls:  Labeled with specimen name, species, age, and cranial capacity in milliliters (cranial capacity is the volume of the space inside the skull, and correlates closely with brain size). Images © 2000  Smithsonian Institution, modified from: TalkOrigins Common Ancestry FAQFossil hominid skulls: Labeled with specimen name, species, age, and cranial capacity in milliliters (cranial capacity is the volume of the space inside the skull, and correlates closely with brain size). Images © 2000 Smithsonian Institution, modified from: TalkOrigins Common Ancestry FAQ

That graph illustrates one particular aspect of human evolution, the growth of the brain over the last 3.5 million years of human evolution. At no point could anyone credibly point to a discontinuity between our australopithecine ancestors and modern humans which is not filled by some ancestral fossil form.

Ages and cranial capacity data: C. De Miguel and M. Henneberg (2001). "Variation in hominid brain size: How much is due to method?"  Homo 52(1), pp. 3-58.    Cranial capacity of modern humans: McHenry et al. (1994). "Tempo and mode in human evolution." Proceedings of the National Academy of Sciences, 91:6780-6.  Graphic by Nick Matzke, National Center for Science Education.  May be freely reproduced for nonprofit educational purposes.Ages and cranial capacity data: C. De Miguel and M. Henneberg (2001). "Variation in hominid brain size: How much is due to method?" Homo 52(1), pp. 3-58. Cranial capacity of modern humans: McHenry et al. (1994). "Tempo and mode in human evolution." Proceedings of the National Academy of Sciences, 91:6780-6. Graphic by Nick Matzke, National Center for Science Education. May be freely reproduced for nonprofit educational purposes. As we look at events further back in time, the chances of a fossil surviving decrease, so forms of life from the more distant past tend to show larger gaps - greater morphological variation - between fossils. Nonetheless, new fossils are constantly being found which shrink the gaps between ancient species, such that cases once presented by creationists as insurmountable problems for evolution are now textbook examples of fossil transitions. Indeed, of the two sources Explore Evolution cites to support the claim that "Paleontologists have identified many gaps that remain to be filled in the fossil record" (p. 20), only one actually addresses the quality of the fossil record, and it is from 1981. Even that paper does not support the claim that such gaps reflect an absence of transitional forms. Everett C. Olson wrote:
The problem of the existence of linkages and phylogenies at the species and generic levels has been much reduced during the last one hundred and twenty years. How this reduction supports or denies Darwin's concepts of phyletic gradualism is still a matter of interpretation of the evidence. At familial and higher levels, the establishment of linkages between categories has been much less successful, and decreasingly so at each successive higher level. Under the very best circumstances, however, morphological and stratigraphically graded transitions between classes and subclasses have been found.
Everett C. Olson (1980) "The Problem of Missing Links: Today and Yesterday," The Quarterly Review of Biology 56(4):405-442.

Even twenty-seven years ago, the record of species-level transitions was considered quite good, and at higher taxonomic levels, the situation was improving and quite strong in situations where preservation of fossils had been favorable. Since that time, the state of transitional fossils has only improved. Explore Evolution uses a 1982 reference in an attempt to discredit these recent fossil discoveries (without actually mentioning what those discoveries are). Staying up to date with research in science is critical for students and for textbook authors, and Explore Evolution's reliance on an outdated, non-applicable, 25 year old reference is unacceptable.

Tiktaalik roseae: a transitional fossil. Image from WikiCommons.Tiktaalik roseae: a transitional fossil. Image from WikiCommons.

A recent example from the news is the discovery of the fossil species Tiktaalik roseae.

Tiktaalik is a transitional form in the evolution of vertebrates on four legs. Ahlberg and Clack (2006) describe the importance of the discovery:

It demonstrates the predictive capacity of palaeontology. The Nunavut field project had the express aim of finding an intermediate between Panderichthys and tetrapods, by searching in sediments from the most probable environment (rivers) and time (early Late Devonian). Second, Tiktaalik adds enormously to our understanding of the fish–tetrapod transition because of its position on the tree and the combination of characters it displays.
Per Erik Ahlberg and Jennifer A. Clack (2006) "Palaeontology: A firm step from water to land," Nature 440:747-749
Tiktaalik roseae was predicted before it was discovered. As Neil Shubin describes in his 2008 book Your Inner Fish:
My colleague Jenny Clack at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. WIth their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins, conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals.
Neil Shubin, 2008. Your Inner Fish. Pantheon Books, New York, 0375424472. P. 10.
Tiktaalik roseae: Its wrist configuration allowed it to "do a pushup." Image from WikiCommons.Tiktaalik roseae: Its wrist configuration allowed it to "do a pushup." Image from WikiCommons.    

And when Shubin started investigating sedimentary rocks laid down in shallow water about 375 million years old, he found Tiktaalik roseae.

     

Subsequent investigation confirmed that Tiktaalik roseae's transitional morphology.

[Tiktaalik roseae shows] a marked reorganization of the cranial endoskeleton ... [with] morphology intermediate between the condition observed in more primitive fish and that observed in tetrapods.
Downs, J.P., Daescher, E.B., Jenkins, F.A., and Shubin, N.H., 2008. "The cranial endoskeleton of Tiktaalik roseae." Nature, vol. 455, no. 16, 16 Oct 2008, pp. 925-929.
Origin of Tetrapods: Fossil and modern species illustrate the morphological transition from fishes to tetrapods. Five of the most completely fossils from the time of the transition are known are the osteolepiform Eusthenopteron; the transitional forms Panderichthys and Tiktaalik; and the primitive tetrapods Acanthostega and Ichthyostega. In addition to the clear evidence of the transition from fish fins to vertebrate legs, these fossils show the loss of the gill cover and other morphological shifts associated with the move from the water to the land.  Image courtesy of Brian Swartz.Origin of Tetrapods: Fossil and modern species illustrate the morphological transition from fishes to tetrapods. Five of the most completely fossils from the time of the transition are known are the osteolepiform Eusthenopteron; the transitional forms Panderichthys and Tiktaalik; and the primitive tetrapods Acanthostega and Ichthyostega. In addition to the clear evidence of the transition from fish fins to vertebrate legs, these fossils show the loss of the gill cover and other morphological shifts associated with the move from the water to the land.

Image courtesy of Brian Swartz.

Based on known fossils, scientists could estimate what time period the transitional form had to have existed in. Based on the known locations of fossil beds, they could select a bed known to be from the right time and to have possessed the right environment 375 million years ago to contain a transitional form. They knew what sorts of fossils to look for at that site by considering the known fossils from before and after the era in question. And after selecting that site, they found exactly the fossils they sought, a transitional form which allowed a detailed examination of the evolution of critical structures in the transition from aquatic fish to terrestrial tetrapods.

This process is exactly how science works, and a textbook interested in encouraging students to explore the way evolutionary biology is practiced would do well to help students see how paleontologists actually deal with gaps in our knowledge of the fossil record.

The approach Explore Evolution takes does not present any such understanding of the inquiry-based process of science. Gaps in our current knowledge are treated as insurmountable barriers. If scientists truly took that approach, we would never have achieved the sorts of advances seen in paleontology over the last 20 years, let alone the last 150.

Some scientists say the absence of transitional forms should dramatically change the story we tell about life's history. They point out that when we study the fossil we have actually found, the evidence does not lead us to connect the major lines of descent through a single, branching tree.
Explore Evolution, p. 35

It would be very interesting to know who "some scientists" actually are. The "they" Explore Evolution discusses have not published in the peer-reviewed literature, because there is in fact substantial agreement that all the major phyla lines do indeed come from a single, branching tree.

Look through any college-level biology textbook (Campbell, p. 470-71; Raven, p. 654-55; Starr, p. 318-321), and you will see diagrams showing only the single, branching tree model. A multiple-tree view is not shown simply because the evidence for it is so weak, and the evidence for a single-tree so strong, that the multiple-tree model can be discarded in the same way a flat earth model can be discarded from a geography textbook.

This straw man logic—set up a false claim, knock it down easily, declare victory—is itself a lesson on how not to teach logic and rhetoric to children.

Some advocates of punctuated equilibrium do acknowledge that the absence of transitions between major groups of organisms is an unsolved problem for evolutionary theory as whole.
Explore Evolution, p. 35

These unnamed, uncited "advocates" strike again. While certainly paleontologists would enjoy having more "transitional" fossils—whatever that vague terms actually means—there are many examples of fossils that bridge the gap between species. Thus, the phrase "absence of transitions" is wrong to imply that there are no transitions.

Do animal forms change or stay the same?

The fossil record provides many examples of living organisms that have remained stable in their form and structure over many millions of years--sometimes over hundreds of millions of years.
Explore Evolution, p. 25


Summary of problems with claim: This is not evidence against evolution.

Full discussion: Explore Evolution brings this up to suggest:

  • Something is wrong with the model of evolution if organisms do not change.
  • Something may be wrong with the geologic timeline, if organisms show no change over such a long time period.
Coelacanth: a "living fossil." Image from WikiCommons. Coelacanth: a "living fossil." Image from WikiCommons.

The long-lived, unchanged existence of an organism in the fossil only poses a problem to evolution is one makes the (false) assumption that change occurs at a steady background pace. In fact, a better analogy is Newton's First Law: "Objects at rest stay at rest unless acted upon." If an organism lives in a stable environment and is able to reproduce in sufficient numbers to pass on its genes, then there is no impetus to change.

Other examples of long-lived, relatively unchanged species include sharks, the coelacanth, the oppossum, crocodiles, and the horseshoe crab.

Darwin on Transitional Fossils

Darwin himself was well aware of the problems that the fossil record posed for his theory...Where were the multitudes of transitional forms connecting different groups, as predicted (and expected) by his theory?
Explore Evolution, p. 30

What Darwin actually wrote:

Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record. Charles Darwin (1859), The Origin of Species, p. 280.

Darwin's statement acknowledges an incomplete fossil record rather than a problem with his theory.

The Sequence of Transitional Fossils

Do transitional fossils appear in sequence as they should? problem

Summary of problems with claim:

Paleontologists employ methods to test whether their results are better than would be expected by chance. Evolutionary biologists draw data from multiple lines of evidence, and each of those lines of evidence reveals the same pattern — the same branching tree of life.

Full discussion:

Explore Evolution asserts:

Given the millions of different fossil forms in the fossil record, critics argue that we would expect to find, if only by pure chance, at least a few fossil forms that could be arranged in plausible evolutionary sequences. To understand what they mean, imagine that a representative of every organism that has ever lived on earth was randomly pasted to an enormous wall representing the geologic column. Most of the fossils would bear no relationship to the other fossils stuck closest to them on the wall. Nevertheless, by chance a few of them might end up next to forms that do have some resemblance. These forms might then appear to be related as ancestors and descendants, even if they were not. Is it possible that the mammal-like reptile sequence is a statistical anomaly rather than a legitimate sequence of ancestors and descendants.
Explore Evolution, p. 27
Paleontologist at Work: Image from WikiCommonsPaleontologist at Work: Image from WikiCommons

Paleontology doesn't work in a vacuum. In other words, paleontology is only one branch (or subset) of evolutionary biology. Paleontological contributions consist of morphology and stratigraphic sequence data, data that is then integrated with morphological data from living critters, their DNA (and other molecules), as well as developmental data that all work together to support common descent.

In other words, as DNA changes, that affects the proteins produced, the developmental trajectory, and the subsequent morphology of traits in individuals and lineages through time. All of these fields – molecular biology, developmental biology, and comparative anatomy – are intertwined at the heart of evolutionary theory. These fields each work from independent data sets, yet still return to converge on similar answers. For example, molecular sequence data tells us that humans and rats share more DNA in common than either do with a bird; that birds, humans, and rats are more genetically similar than any are to salamanders; and that salamanders, birds, rats, and humans share more DNA with each other than any do with salmon. In turn, developmental and morphological features are shared uniquely with this same pattern of similarity and dissimilarity. For example, humans and rats have placentas (as embryos) and hair as adults while birds do not. Birds, rats, and humans possess a chorion and allantois (extra-embryonic membranes – modified in mammals, though still present) during development, and a fully developed atlas/axis (vertebral arches) that allow up/down and side-to-side movement of the head – features which salamanders do not have. Finally, salamanders, birds, humans, and rats all share unique modes of digit development and adult hips that are fused to the vertebral column – features lacking in salmon. Thus, evolutionary biologists do not solely rely on fossils to understand evolutionary relationships; instead, fossils fall into a much larger picture of other data that returns to corroborate our understanding of history.

The statistical argument presented by Explore Evolution not only fails from a strict paleontological perspective – since paleontologists test for randomness in their data sets – but moreover, paleontologists work within the bracket of extant diversity, and data from living critters also contributes to our understanding of relationships and ancestral/derived traits.

A recent paper addressing this evidence explained:

It is clear that the fossil record cannot be read literally (Darwin 1859). There are many gaps, and many organisms, and indeed whole groups of poorly preservable organisms that have never been preserved and are doubtless lost for ever (Raup 1972). Some have even gone so far as to suggest that the fossil record is almost entirely an artifact of the rock record, with appearances and disappearances of fossil taxa controlled by the occurrence of suitable rock units for their preservation (Peters and Foote 2001, 2002), or the matching rock and fossil records controlled by a third common cause (Peters 2005). However, the widespread congruence between the order of fossils in the rocks and the order of nodes in cladograms (Norell and Novacek 1992; Benton et al. 2000) indicates that the order of appearance of lineages within the fossil record is not a random pattern.
Michael J. Benton and Philip C. J. Donoghue (2007) "Paleontological Evidence to Date the Tree of Life,"Molecular Biology and Evolution, 24(1): 26-53

The Norell and Novacek (1992) citation is the same source Explore Evolution cites to justify the claim that the fossil record is statistically problematic. How can this conflict exist? The problem comes from two sources. First, that the authors of Explore Evolution do not understand (and count on their audience not understanding) how fossils are actually used. As Benton and Donoghue observe, "Fossils can provide good 'minimum' age estimates for branches in the tree, but 'maximum' constraints on those ages are poorer." In order to find a fossil possessing a transitional feature, it is necessary for that feature to have evolved, for the population in which it evolved to diversify, and for some descendant of the first individual with that trait to have died, been fossilized, and that a paleontologist have discovered that fossil. More intense sampling will never move the oldest date of a feature closer to the present, but will move that earliest occurrence back further, approaching the time of its first occurrence.

A second error derives from the authors' fundamental misunderstanding of evolutionary processes. Lineages with traits characteristic of a transitional form may persist long after another lineage has evolved novel traits, and which lineage will have the oldest fossil will depend on where and how fossils from each group formed, and where paleontologists have looked for those fossils. Complaints that such fossils are not in sequence are equivalent to claiming that my grandmother could not be ancestor because she and I lived at the same time. The figure illustrating mammalian evolution in the section below demonstrates how the overlapping histories of different lineages could produce fossils which appear to be out of order if the branching evolutionary process were not clear.

This explains why Norrell and Novacek, after observing that the fossil record of primates is spotty because the sequence of the earliest representatives (as of 1992) of two groups is not as predicted (because the fossil record is limited or absent for those groups), nonetheless state, "Despite these discrepancies, there is a noteworthy correspondence between the fossil record and the independently constructed phylogeny for many vertebrate groups. Statistically significant correlations were found in 18 of 24 cases examined" (Mark A. Norrell and Michael J. Novacek (1992) "The fossil record and evolution: comparing cladistic and paleontological evidence for vertebrate history," Science 255(5052):1690-1693). It is worth noting that new fossil discoveries and improved phylogenetic reconstructions in the 15 years since they wrote that paper, have resulted in a much improved fit between hypothesis and the hominid fossil record. This illustrates the danger in basing an argument on what we don't know, the core of the argument of Explore Evolution.

Whale Evolution

Ambulocetus: a transitional whale. Image from WikiCommonsAmbulocetus: a transitional whale. Image from WikiCommons Summary of problems with claim: In reality, all paleontology experts agree that Pakicetus, Ambulocetus, and other famous "whales with legs" fossils are classic cases of fossils with transitional morphology. The people who disagree are Discovery Institute fellows and other creationists.

Full discussion: This is another example of the authors of Explore Evolution exploiting the vagueness of the phrase "some scientists." Here, they make it appear as if a creationist position (no fossils illustrating the transition between walking mammals and whales) has significant scientific support.

Recently, some scientists think they have discovered a transitional fossil sequence connecting land dwelling mammals to whales.
Explore Evolution, p. 20

The authors neglect to mention that the terrestrial forebears of whales were correctly hypothesized in the 1800's. In the 1980's, a compelling fossil sequence for whale evolution was put forth and since then, the fossil sequence has grown to dozens of intermediates. Anyone familiar with scientific literature on this topic knows that the fossils of "whales with legs" are famous throughout evolutionary biology, are the subject of dozens of papers in top journals like Science, used in many textbooks, and have been covered by numerous science journalists. There is no scientific opposition to the idea that these fossils show transitional morphology.

For a review of the walking-mammal to whale transition, see:

It is interesting to compare the treatment of whale fossils in Explore Evolution with the treatment of whale fossils in its creationist ancestors. Creationist Duane Gish wrote:

The marine mammals abruptly appear in the fossil record as whales, dolphins, sea-cows, etc. … There simply are no transitional forms in the fossil record between the marine mammals and their supposed land mammal ancestors.
Duane Gish (1992)

Evolution: The Challenge of the Fossil Record. Creation-Life Publishers: El Cajon, CA. p. 79

In Evolution: A Theory in Crisis Michael Denton spends several pages commenting on what he believed to be the unfortunate necessity of having:

…to postulate a large number of entirely extinct hypothetical species starting from a small, relatively unspecialized land mammal … and leading successively through an otter-like state, seal-like stage, sirenian-like stage and finally to a putative organism which could serve as the ancestor of the modern whales. Even from the hypothetical whale ancestor stage we need to postulate many hypothetical primitive whales to bridge the not inconsiderable gaps which separate the modern filter feeders (baleen whales) and the toothed whales.
Denton (1985) Evolution: A Theory in Crisis

Adler & Adler Publishers:Chevy Chase, MD. p. 174

In his next book, published in 1998 (after the fossils described above where discovered), whale fossils were no longer a subject of discussion. Likewise, the authors of Explore Evolution, rather than celebrating the growth of scientific knowledge, stir up confusion around it. Needless to say, this approach is neither inquiry-based nor scientific, and sows confusion where a textbook should educate and inspire.

The Sizes of Transitional Fossils

Explore Evolution claims that because transitional fossils come in different sizes, they aren't really transitional

Summary of problems with claim: The point of presenting fossils at the same size is to illustrate the appearance of novel anatomical structures. Size is a feature that changes with age, diet and changes relatively easily in response to evolutionary pressures. The shift from three bones on each side of the lower jaw to a single dentary bone is far rarer and more informative about evolutionary history.

Full discussion: Explore Evolution takes umbrage at a diagram from T.S. Kemp's 2005 book The Origin and Evolution of Mammals. Page 21 of Explore Evolution shows a series of skulls (Figure 1:6), each the same size, and then compares this on page 29 (Figure 1:8) to the same skulls at relative sizes, where some are much larger than others.

Scaling for Clarity: A shovel, a mole paw, a human hand, and a mole cricket forelimb. Scaling for Clarity: A shovel, a mole paw, a human hand, and a mole cricket forelimb. Altering the scale is done for clarity, not deception, as the authors well know. Explore Evolution does the very same scaling in its Figures 2:1 and 2:4, on pages 41 and 43, where the arm of a bat, a porpoise, a horse, and a human (2:1) and cricket and a mole (2:4) are all drawn at similar scales.

In Figure 1:8 the miniscule size of Thrinaxodon or Probainognathus makes it impossible to identify bones and structures. In Figure 1:6, critical features which distinguish mammals from their amniote ancestors (structures like the opening in the bones behind the eyes and the locations of bones in the lower jaw) can be seen quite clearly. Mammals range in size from a few grams (e.g., the Bumblebee Bat) to several tons (e.g., a Blue Whale), but nevertheless, all of them have a single bone (the dentary) that makes up their lower jaw, hair, mammary glands, and numerous other features that diagnoses them as "mammals." Indeed, the range of sizes seen in domestic dogs is greater than the range shown in figure 1:8 (see the discussion of dog size and morphology in the critique of chapter 7), and that size range does not interfere with our understanding of the "close genealogical relationship" (Explore Evolution, p. 29) between dogs. The illustration in figure 1:6 (from Kemp's The Origin and Evolution of Mammals) is meant to illustrate the transition of a particular set of structures, and not (as Explore Evolution suggests) to make a point about the size of the organisms. Explore Evolution’s point about size is ultimately a semantic and silly argument which misrepresents (or misunderstands) what scientists look for in assessing fossil transitions. Size is not regarded as a factor which signifies "close genealogical relationship," while the arrangement of post-orbital and jaw bones is significant.

Proper scaling in figures is a great pedagogical tool that helps students and researchers in their comparative anatomy - and at least in professional publications, scale bars are commonly included so viewers and critics can ascertain specimen size. Explore Evolution’s figure 1.8 hides information, obscuring evidence of the evolution of evolutionarily significant features like postdentary bones whose modification is coupled to the origin of the mammalian middle ear.

In evaluating the evolution of modern mammals from the amniote ancestors of reptiles and mammals, there are several important traits that scientists examine. Mammalogy, by Vaughan, et al. (2000) lists 25 major features, selected from a much longer list of traits distinguishing mammals. The traits that do not fossilize from that list include skin glands (mammary glands, sweat glands, sebaceous glands), hair, specialized muscles in the skin, the epiglottis, details of the soft anatomy of the lung and diaphragm, brain structures, facial muscles, red blood cells lacking nuclei, and the anatomy of the heart. We will discuss some of them in more detail in the critique of chapter 12.

Skeletal characteristics are easier to identify in fossils. These include a change in the bones of the jaw with a shift of three bones out of the structure of the jaw and their reuse in the ear, a trait paleontologists regard as the dividing line between mammals and their non-mammalian ancestors. Vaughan, et al. explain "By this definition, Mammalia does not include the extinct near-mammals, the Mammaliaformes" (p. 11). Paleontologists debate which fossils represent the earliest mammals because of differing criteria, and the increasingly fine differences between the fossils make it harder to draw a clear line. Vaughan, et al. explain:

…when mammals first appeared in the Triassic period, they represented no radical structural departure from the therapsid plan but had attained a level of development … that is interpreted by most vertebrate paleontologists as a key indication that the animals had crossed the non-mammalian-mammalian boundary. … Many of the mammalian characters discussed in this chapter resulted from evolutionary trends clearly characteristic of therapsids.
Terry A. Vaughan, James M. Ryan and Nicholas J. Czaplewski (2000) Mammalogy 4th ed., Saunders College Publishing: Orlando, FL. p. 10 of 565.


The "mammal-like reptiles" that Explore Evolution refers to are these therapsids, as well as other members of the Clade Synapsida. As mentioned above, scientists do not refer to the group as "mammal-like reptiles." The University of California Museum of Paleontology explains "This term is now discouraged because although many had characteristics in common with mammals, none of them were actually reptiles." Reptiles are a lineage which shares a common ancestor with mammals and other synapsids, not a group ancestral to mammals. Understanding that relationship can help clarify much of the confusion that laces the treatment of transitions in Explore Evolution.

The ancestors of modern reptiles, mammals and birds are known as amniotes. That name refers to a feature of the eggs of all those groups, one of several shared, derived characteristics which suggests that those groups share a common ancestor. A common challenge in talking about the transitional forms between mammals and reptiles is attempting to imagine a form intermediate to modern reptiles and modern mammals. In evolutionary terms, a transitional form is a common ancestor of two groups, one which shares traits with earlier forms and possesses a few of the traits which uniquely identify later lineages. We have such fossils illustrating the transition of early amniotes to the several lineages which led to modern mammals and to reptiles.

Early Amniotes: Despite their morphological similarities, critical differences show that these fossils represent the first branches between the lineages that would go on to produce diverse modern groups.  From fig. 10.11 of Robert L. Carroll (1988) Vertebrate Paleontology and Evolution W. H. Freeman and Co.: New York. 698 p.Early Amniotes: Despite their morphological similarities, critical differences show that these fossils represent the first branches between the lineages that would go on to produce diverse modern groups. From fig. 10.11 of Robert L. Carroll (1988) Vertebrate Paleontology and Evolution W. H. Freeman and Co.: New York. 698 p. The first skull in the figure at the right shows the basic anatomy of the ancestral condition of the amniote lineage. Of particular importance, there is no hole in the skull behind the eye socket. The lower jaw in all of these fossil species consists of three bones, one of which is on the inside of the jaw, not visible in the illustration.

That first skull dates to roughly 315 million years ago, and represents one of the earliest known amniotes. Fossils of this and other early amniotes are found in the fossilized stumps of a species of tree which grew in floodplains. These early amniotes took refuge in the hollow stumps of those trees, and without the discovery of those stumps, our knowledge of the base of the amniote tree of life would be much poorer. Those sorts of historical contingencies are common in paleontology, and help explain the unevenness of the fossil record.

The next skull dates from around 300 million years ago, and belongs to an ancestor of mammals. The main difference between it and the first species is that there is a gap between two bones behind the eye socket. This gap may have allowed greater freedom for jaw muscles, or may have carried neither adaptive benefit nor harm. The size of that gap varies between fossils, as does the size of that gap, but its existence marks descendants of a common ancestor. Complaints about the size of the skull miss a critical point about the shared derived characters that united that lineage, named the synapsids (to which all mammals belong). Another major branch of the amniotes evolved two holes in the skull, as shown in the third part of the figure. This group, the diapsids, includes birds and most reptiles. The fourth skull represents a derived lineage of diapsids, in which one of the gaps expanded, secondarily producing a skull with a single hole but which shares other traits with diapsids that demonstrate its common ancestry.

By examining the traits that these skulls share, it is possible to trace the origin of several separate lineages as they originated. The many similarities between these skulls demonstrate their close relatedness, and suggest that they all would have looked more similar to a large iguana or salamander than to any living mammal or bird. Nonetheless, certain novel traits in the skulls indicate that they represent very different lineages, the ancestors of modern groups that differ widely.

The evolution of early mammals, mentioned briefly, then criticized trivially in Explore Evolution helps demonstrate other important aspects of the scientific evaluation of fossils. As mentioned previously, the major feature that distinguishes the earliest mammals from their ancestors is the presence of a single bone in the lower jaw, rather than the four bones seen in amniotes and in amniotes other than mammals. PICTURE 2 Mammal Jaw Evolution: The transition from a four-boned lower jaw to the mammalian jaw with a single element.  Skull illustrations from Kardong (2002), as reproduced by Theobald (2004).  The jawbones on the left illustrate the the inside of the mouth; the illustrations on the right show the outside of the jaw. The quadrate (the incus or anvil of the mammalian ear) is in turquoise, the articular (malleus or hammer in the mammalian ear) is in yellow, and the angular (tympanic annulus in the mammalian ear) is in pink. Teeth are not shown, and skulls are scaled to constant size for clarity. Q = quadrate, Ar = articular, An = angular, I = incus (anvil), Ma = malleus (hammer), Ty = tympanic annulus, D = dentary.     Skull figures reproduced from Kardong, K. V. (2002) Vertebrates: Comparative Anatomy, Function, Evolution. 3 ed. New York: McGraw Hill, fig. 1.4.3.  The bubble plot of mammalian evolution is based on figure 17.1 in Carroll (1988), and shows the diversification of major groups and the separation of distinct lineages through time.Mammal Jaw Evolution: The transition from a four-boned lower jaw to the mammalian jaw with a single element. Skull illustrations from Kardong (2002), as reproduced by Theobald (2004). The jawbones on the left illustrate the the inside of the mouth; the illustrations on the right show the outside of the jaw. The quadrate (the incus or anvil of the mammalian ear) is in turquoise, the articular (malleus or hammer in the mammalian ear) is in yellow, and the angular (tympanic annulus in the mammalian ear) is in pink. Teeth are not shown, and skulls are scaled to constant size for clarity. Q = quadrate, Ar = articular, An = angular, I = incus (anvil), Ma = malleus (hammer), Ty = tympanic annulus, D = dentary. Skull figures reproduced from Kardong, K. V. (2002) Vertebrates: Comparative Anatomy, Function, Evolution. 3 ed. New York: McGraw Hill, fig. 1.4.3. The bubble plot of mammalian evolution is based on figure 17.1 in Carroll (1988), and shows the diversification of major groups and the separation of distinct lineages through time. As the figure above shows, the transition in the jaw bones can be traced through fossils. Figure 1:6 in Explore Evolution shows additional transitional fossils, and there are even more species which fill in the gaps between those species. The figure above highlights the bones that transitioned into the ear in different colors, making it easier to see how the relative sizes and locations of those bones changed over a hundred million years, allowing them to serve a greater role in transmitting sound, while the jaw hinge shifted from one of those bones (the articulate) to the dentary. In pelycosaurs, the first major lineage of synapsids, the four bones of the lower jaw are firmly joined together. One bone, the articulate, has structures which may have helped transmit sound, but it is unclear how effectively that would have worked.

The pelycosaurs differentiated into several major lineages, and a branch from one of those lineages further diversified into the therapsids. In therapsids, the sutures joining the post-dentary bones became looser, allowing the bones to vibrate in response to sound, and making them less useful as structural components of the jaw. While the major hinge in the jaw remained on the articulate in the therapsids, members of a group of therapsids known as cynodonts developed a second hinge on the dentary bone. This transition was probably driven partly by the increasing strength of jaw musculature, and the growing role of the postdentary bones in the ears. The formation of the second joint can be found in later cynodonts, and the older joint is much reduced in early mammals like Morganucodon, disappearing entirely in modern mammals. The jaws of embryonic marsupials go through similar transitions, indicating that the ancestral developmental processes are still at work in the formation of the jaw.

The shift in the jaw hinge and the change in size, shape, and location of earbones/jawbones is powerful evidence linking modern mammals with therapsids, pelycosaurs and the ancestors of all amniotes. Other transitions in the shape of the teeth and other details of the skeleton confirm this pattern, revealing the nested hierarchy of traits that is predicted by evolution and common descent.

Explore Evolution invites to consider this and other transitions, but without actually presenting any actual evidence for them to consider. Indeed, it is not clear whether the authors of Explore Evolution themselves understand this transition, since their main objection to calling these fossils "transitional" seems to be that the fossils are of different sizes. They ignore the actual morphological transitions that scientists study, instead focusing on size differences which carry little evolutionary significance. Far from establishing any problem with the fossil record of the transition from amniotes to mammals (not, as Explore Evolution puts it, from reptiles to mammals), the discussion in Explore Evolution yet again demonstrates the authors' own problems.

The Cambrian Radiation

Halkieria evangelista: from the Lower Cambrian. Image from WikiCommonsHalkieria evangelista: from the Lower Cambrian. Image from WikiCommons For the vast majority of Earth's history, there existed only single-celled organisms. During the Cryogenian Period, 850-630 Ma (millions of years ago), the Earth experienced a series of deep glaciations, sometimes referred to as "Snowball Earth." As the ice waned, Ediacaran organisms made their first appearance. Ediacarans were large, strange, and probably sessile creatures of unknown affinity who lived between 630-542 Ma.

At 542.0 ± 1 Ma, life on Earth radically changed, with the appearance of Trichophycus pedum, a mud burrower with complex movement. The first appearance of Trichophycus pedum marks the beginning of the Cambrian Period (542-488 Ma). From 542 Ma, and especially during the middle Cambrian, animal diversity rapidly increased. This is referred to as the Cambrian Explosion or the Cambrian Radiation.

Sudden Appearance?

Did animal phyla suddenly appear in the Cambrian Explosion?

Paleontologists have discovered that new animal forms almost always appear abruptly--not gradually--in the fossil record, without any obvious connections to the animals that came before.
Explore Evolution, p. 22


About 530 million years ago, more than half of the major animal groups (called phyla) appear suddenly in the fossil record.
Explore Evolution, p. 22


Anomalacaris: a fearsome predator of the Cambrian. Image from WikiCommonsAnomalacaris: a fearsome predator of the Cambrian. Image from WikiCommons

Summary of problems with claim: The events of the Cambrian explosion are subject of ongoing debate and research. Some scientists argue that the fossils we see in the Cambrian represent the ancestors of modern phyla before those different groups had fully separated, and that the phyla truly emerged over a longer period of time. There are also questions about the preservation of fossils before the Cambrian, and it is possible that the explosion of fossils during the Cambrian represents a shift toward predator-resistant (and readily fossilized) exo-skeletons, rather than a shift in the actual diversity of life.

Full discussion: To suggest that, during the Cambrian explosion, "more than half of the major animal groups (called phyla) appear suddenly in the fossil record" (Explore Evolution, p. 22) stretches the true state of affairs. A number of fossils discovered from that period of time possess traits characteristic of modern phyla. Other species found at that time cannot be clearly classified in any modern phyla at all. Fossils from the period following the Cambrian, an era known as the Ordovician, more clearly show the distinct groups possessing the traits associated with many modern phyla. Fossil deposits before the Cambrian are rarer, making it difficult to be sure how sudden any appearances were.

Modes of Life as Function of Time: Figure 8 from Richard K. Bambach, Andrew M. Bush, Douglas H. Erwin (2007) "Autecology and The Filling of Ecospace: Key Metazoan Radiations" <cite>Palaeontology</cite> 50(1):1–22.     "Change through time in realized ecospace. Top line represents all recorded modes of life, middle line represents modes of life of skeletal fauna only; bottom line records mean number of modes of life for single assemblages. For the Recent, the open circle represents those recent taxa with readily preserved hard parts, and the open circle containing an asterisk represents those taxa with a diverse fossil record."Modes of Life as Function of Time: Figure 8 from Richard K. Bambach, Andrew M. Bush, Douglas H. Erwin (2007) "Autecology and The Filling of Ecospace: Key Metazoan Radiations" Palaeontology 50(1):1–22. "Change through time in realized ecospace. Top line represents all recorded modes of life, middle line represents modes of life of skeletal fauna only; bottom line records mean number of modes of life for single assemblages. For the Recent, the open circle represents those recent taxa with readily preserved hard parts, and the open circle containing an asterisk represents those taxa with a diverse fossil record."

Ecologically, the Cambrian fossils represent a smooth extension of the rate of diversification before and after. An analysis of the lifestyles of the Cambrian fossils, Ediacaran (pre-Cambrian) fossils, and fossils from eras after the Cambrian shows a steady increase in ecological complexity, not an explosion of diversity. The nature of that expansion is informative, though.

Cambrian fossils include the first predators capable of hunting and capturing prey (rather than passive filter-feeders). This behavioral development had adaptive consequences for concurrent species, and some evidence supports the contention that the Cambrian fossils seem more diverse simply because hard bodyparts — evolved as protection against predators — preserved better than the soft bodies that preceded the Cambrian. For these and other reasons, the record of pre-Cambrian fossils is not necessarily adequate for a full evaluation of the predecessors of Cambrian fauna.

New fossil finds, and improved understanding of the biological basis for the changing body forms we find in the Cambrian, have led to revisions of the claim that so many phyla emerged in the Cambrian explosion. Fossilized remains found in Australia appear to represent a group of pre-Cambrian chordates, representatives of the phylum to which humans belong. More detailed analysis of Cambrian fossils has also shown some species to be significant branches off of the tree which led to modern species within the same phylum (Derek E. G. Briggs and Richard A. Fortey, 2005, "Wonderful strife: systematics, stem groups, and the phylogenetic signal of the Cambrian radiation," Paleobiology 31:94-112), a finding which indicates that the origin of the phylum itself lies earlier.

Study of the Cambrian fossils has also revealed that some of the examples of divergent Cambrian phyla may have been premature. Some fossils possess features indicating that they evolved from a time before certain existing phyla emerged. Because they possess certain traits in common with existing phyla, certain authors assign them to one phylum or the other, but such assignments are debatable, and new knowledge about the relationships between the modern groups has caused some such assignments to be reevaluated. Thus, the range of time over which modern phyla are seen to emerge tends to get wider as we improve our understanding of both modern and fossilized life.

Finally, our improving understanding of developmental biology is allowing scientists to better understand why the Ediacaran, Cambrian and Ordovician saw so many new body forms enter the fossil record, and why so many features of modern living things emerged during those geologic periods. A major theme of emerging from the field of developmental biology is the discovery that the process of forming the body from a fertilized egg cell is controlled by a group of genes which regulate the way that body segments form (whether the segments of an insect's exoskeleton, or the segments visible in the muscles of a fish fillet and the human spinal column). These genes, including the Hox genes mentioned elsewhere in Explore Evolution are shared by nearly all multicellular organisms, from sea sponges to humans. Those genes appear to have duplicated, diverged and played an expanded role in structuring development during the same period when the major body forms begin appearing in the fossil record (Jordi Garcia-Fernàndez, 2005, "The genesis and evolution of homeobox gene clusters" Nature Reviews Genetics 6, 881-892). Paleontologists and developmental biologists have begun working together on the hypothesis that the diversification of these genes drove the changes in body forms during that period (see, for instance, Robert Carroll, 2000, "Towards a new evolutionary synthesis," Trends in Ecology and Evolutionary Biology 15(1):27-32, or Sean Carroll's popular treatment Endless Forms Most Beautiful, ch. 6). Once critical developmental pathways became established, it may have become harder to produce major new body forms, and that may explain why those basic forms seem to appear and stabilize relatively rapidly during that period.

Evolutionary developmental biology is an active area of research, a field of study only opened in the last 10-20 years, which has the potential to radically reshape how we think about the processes driving diversity, and the framework within which we interpret fossils from the Cambrian and from earlier eras. Students should not be taught simply that fossil forms suddenly appear, they need to be taught the developmental biology, and provided with a conceptual framework so that they can appreciate the ways that life 500 million years ago differed from life as they know it. That would provide students with a map which would guide their exploration of evolution. The approach taken by Explore Evolution simply discourages students from pursuing ideas in this cutting edge field.


Advocates of the artifact hypothesis say that the Cambrian explosion is not real; it is only the result--or an "artifact"--of having too small a sample of fossils to work with.
Explore Evolution, p. 30


No paleontologists say this about the Cambrian explosion. Explore Evolution does not cite references for this claim, but any casual examination of the peer-reviewed literature about the Cambrian explosion will fail to turn up a single instance of a paleontologist claiming the Cambrian explosion was "not real."

Many paleontologists now estimate the Cambrian explosion took place over a period of 10 million years or less... If Earth's whole history were a timeline the length of an American football field, the Cambrian explosion time would take up just 4 inches of the football field's total length.
Explore Evolution, p. 22

We need better math in creationist textbooks:
American football field = 100 yards
1 yard = 3 feet
football field = 300 feet
1 foot = 12 inches
football field = 3600 inches
4 inches/3600 inches = 0.0011 = 0.11%

age of the Earth = 4.54 billion years = 4,540 million years
length of Cambrian Explosion according to
Explore Evolution = ~10 million years
10 million / 4540 million = 0.0022 = 0.22%

0.11% does not equal 0.22%. Q.E.D.

The Cambrian Radiation in the Geologic Record

The Precambrian/Cambrian boundary appears relatively abruptly when examined from the perspective of large, shelled fossils. However, because a geologic process taking many millions of years may leave behind only a few inches of rock, when geologists say "suddenly" it has a different meaning than the common usage. Trilobite Fragments: from the Cambrian Andrews Mountain Member of the Campito Formation, White-Inyo Mtns., California. Photo by Steven Newton.Trilobite Fragments: from the Cambrian Andrews Mountain Formation, White-Inyo Mtns., California. Photo by Steven Newton.

Precambrian rocks are usually free of bioturbation, which is the destruction of fine layering by animals burrowing into soft sediment. In rock forming today, sediments are usually bioturbated. The absence of bioturbation indicates something is unusual—for example, anoxic conditions, where there is not enough oxygen dissolved in water to sustain life. Today such conditions are rare.

Just prior to the Cambrian/Precambrian boundary, worldwide massive carbonate deposits (limestone, dolomite) heralded the end of "Snowball Earth," a 220 million year period of deep glaciation now called the Cryogenic Period (850-630 Ma). Above these carbonate deposits geologists start to find the signs of complex life: burrowing, bioturbation, shells. Fragments of shelled animals are much more common than whole fossils of the animals themselves.

Peter Ward of the University of Washington beautifully describes the boundary this way:

I kicked an empty pop can with my thick field boots as I walked along the country road near Addy, surrounded by the roadside sandstones, vestiges of that long-ago world. I was walking stratigraphically upward in these sediments; they lie at an angle, tilted about 30 degrees from their original horizontal. As I walked northward along the road I was thus going up through time, into ever higher and thus younger beds of these sandstones. With each step I passed upward through thousands of years of time; with my quarter-mile hike along the road I had traversed several millions of years among these buff-colored sandstones. I was somewhat disappointed. I was training to become a paleontologist and disdained geological phenomena not associated with fossils…

"I had been lulled by the walk and the endless slabs of sandstone showing nothing but featureless bedding planes. The small slab now in my hands thus elicited no immediate response. I stared with unseeing eyes at the small oblong shell and tossed the rock before the message from my eyes finally burned through into my brain. The small rock followed a beautiful ballistic arc down the talus slope as I realized that I had just seen an unmistakable announcement of life…

"I picked up another piece and saw more shells, amid even more wondrous fossils. I saw the heads of large trilobites, looking something like large crabs yet very different, fossils with segments and strange crescent-shaped eyes unlike anything now living. I was surrounded by fossils, sitting atop a teaming graveyard, a joyous assemblage announcing that after 3 billion years skeletonized life had arrived. I was sitting on the base of the Cambrian System, the start of the Paleozoic era, the beginning of the Phanerozoic, the time of life.

Peter Ward, 1991. On Methuselah's Trail: Living Fossils and the Great Extinctions, p. 27


An important caveat here is that the base the Cambrian, at 542 Ma, is not the beginning of life at all. Nor will the Cambrian Radiation occur for another ~7 Ma, at 535 Ma. So what the geologist sees in outcrops—the appearance of large, shelled organisms—is not the complete story.

Creationist Statistics

Statistical Sampling 101 …Suppose you find a big box of marbles. You reach in and grab six marbles at random. When you remove the marbles, you discover that each marble is either red, green, or blue…This sample is so small that is may not be representative of all the colors in the box…However, you keep going until you've pulled about 1,000 marbles out of the box. You look at them all, and still find only red, green, and blue ones. There are still some marbles left in the box. What colors would you guess they are?
Explore Evolution, p. 31


What Explore Evolution is really saying here is this: We do not see abundant trace fossils because there were no animals to make them. Therefore Cambrian animals had no ancestors, but were suddenly "created." This is wrong in that it fails to consider the type of animal that existed at that time. Marbles: from  Wikicommons Marbles: from Wikicommons

But in an additional sense, this example shows why every scientist must have a working knowledge of statistics. Yes, the likelihood is that the next marble produced in this scenario would be red, green, or blue. But if among the thousands of marbles, you had planted a white marble, then even though this white marble was present, it would be very unlikely to be found. That's not the same thing as saying it could not be there. In fact, not until every single marble was removed could you say with any assurance that this hypothetical box contained only red, green, or blue. There might have been 1 white, 2 black, 3 purple, and so on. But the very small numbers of these odd colors make it very unlikely that would they be found in a random draw.

There's an old joke that goes like this:

A businessman, a philosopher, and a scientist are on a train traveling through the countryside. They see a solitary black sheep grazing in a field.

The businessman says, "Sheep are black."

The philosopher says, "At least one sheep is black."

The scientist says, "At least one side of one sheep is black."

Soft-bodied fossils

Explore Evolution claims that the ancestors of the Cambrian phyla could not have been soft-bodied

Summary of problems with claim: This claim is based solely on an quotation from a Discovery Institute Fellow, a toxicologist whose credentials are misrepresented to claim he is a "marine paleobiologist." This claim is a variant of the "gaps in the fossil record" argument, a gap that is being steadily filled by scientists.

Full discussion: This is yet another argument based on a creationist antecedent, "Complex life forms appear suddenly in the Cambrian explosion, with no ancestral fossils." This argument first appeared in Henry Morris's book Scientific Creationism in 1985 (pp 80-81). The authors of Explore Evolution then recast the argument, and cite an interesting source.

This point has been further emphasized by a recent Precambrian fossil find near Chengjiang, China. Scientists there recently discovered incredibly preserved microscopic fossils of sponge embryos. (Sponges are obviously soft-bodied. Their embryos are small and soft-bodied, too—other than their tiny spicules.) Paul Chien, a marine paleobiologist at the University of San Francisco argues that this discovery poses a grave difficulty for the artifact hypothesis. If the Precambrian rocks can preserve microscopic soft-bodied organisms, why don't they contain the ancestors to the Cambrian animals? (footnote 28)
Explore Evolution, p. 31

Who is Paul Chien? What are his credentials? What peer-reviewed evidence is cited in footnote 28?

The USF webpage lists Chien's research interests thusly

Prof. Chien is interested in the physiology and ecology of inter-tidal organisms. His research has involved the transport of amino acids and metal ions across cell membranes and the detoxification mechanisms of metal ions.

He is also a "senior fellow" of the Center for Science and Culture, a part of the Discovery Institute, where his credentials are listed somewhat differently.

Paul Chien is a Professor in the Department of Biology at the University of San Francisco and he was elected Chairman of his department twice. He received his Ph.D. in Biology from the University of California at Irvine's Department of Developmental & Cell Biology. He has held such positions as Postdoctoral Fellow in the Department of Environmental Engineering at the California Institute of Technology, Pasadena (CIT); Instructor of Biology at The Chinese University of Hong Kong; and a consultant to both the Kerckhoff Marine Laboratory of the CIT, and the Scanning Electron Microscopy & Micro X-ray Analyst in the Biology Department of Santa Clara University, California. Dr. Chien's work has been published in over fifty technical journals and he has spoken internationally, and on numerous occasions, from Brazil to mainland China-where he has also been involved in cooperative research programs. Dr. Chien edited and translated Phillip Johnson's book Darwin on Trial into Chinese as well as Jonathan Wells' Icons of Evolution.

A search of Web of Science (July 2007) reveals that he is the author of 15 peer-reviewed articles, but none in the area of "marine paleobiology". The most recent article is dated 1998, and is not in any relevant field of biology at all; the title is "Relocation of civilization centers in ancient China: Environmental factors". The most recent biology-related article is from 1995; all of the articles seem to be focused on heavy metal toxicity and antidotes in marine animals, particularly worms (e.g. Uptake, Binding and Clearance of Divalent Cadmium in Gycera dibranchiata (Annelida-Polychaeta); MA Rice and PK Chien; Marine Biology 53 (1): 33-39 1979). He is also apparently a creationist, judging from his statements in a 1997 interview in The Real Issue, which is a publication of the Christian Leadership Ministries, whose Statement of Faith includes the belief in the inerrancy of the Bible.

But when I read Genesis chapter one, the fifth day seems to read very much like the fossil record we see now because it talks about all the creatures teeming in the oceans. Now, to me that sounds like the Cambrian explosion in a very short period of time, [the animals] are all there.

Why, then, is Paul K. Chien described by the authors as a "marine paleobiologist"? He appears to be a toxicologist, whose last peer-reviewed paper appeared in 1998. Those articles in "over fifty technical journals", cited by the Discovery Institute, somehow never made it into the Web of Science. Finally, in the interview cited above, when the interviewer asks him directly if he should be described as a paleontologist, he replies "Not really; that's not my purpose." We can only speculate as to the "purpose" of the authors who do describe him as a "paleobiologist".

What about the references cited in footnote 28? There are two of them. One is a paper (not peer-reviewed) by Chien et al., presented at the North American Paleontological Convention at Berkeley in 2001, entitled "SEM observation of Precambrian sponge embryos from southern China, revealing ultrastructures including yolk granules, secretion granules, cytoskeleton and nuclei". This paper, unsurprisingly, is not indexed in the Web of Science.

The other citation from footnote 28 is Hagadorn, et al., Science, 314:291-294, 2006, "Cellular and subscellular structure of neoproterozoic animal embryos". That paper has already been cited 10 times (Web of Science search performed in July 2007). None of the papers citing Hagadorn et al., cite Chien's 2001 contribution. The Hagadorn paper does not cite Chien either. All of these observations contribute to the perception that Chien's credentials in this area are nil, and that his non-peer-reviewed paper of 2001 has had no impact on this field. His concern about the lack of Precambrian fossils of ancestors to the Cambrian fauna should thus also be viewed with a more critical eye than was used by the authors of this textbook.

But is this question, despite its lack of academic credentials, a valid concern? Why don't we find these missing fossils? More importantly, is a gap in the fossil record a good reason to cast doubt on evolutionary theory and common descent? Probably not. This gap in the fossil record, like all gaps identified by the creationists, is being filled. For some of this more recent information, see the references cited below.

References

"Darwin's dilemma: the realities of the Cambrian 'explosion'", Morris SC, Philosophical Transactions of the Royal Society B-Biological Sciences 361(1470): 1069-1083 2006

"Fossilized embryos are widespread but the record is temporally and taxonomically biased.", Donoghue PCJ et al. Evolution and Development 8(2):232-238, 2006

Cal Academy of Sciences display

Did a 1990s Cal Academy of Sciences display on Cambrian phyla showed the phyla connected without common ancestors?

…A fossil exhibit on display at the California Academy of Sciences in the 1990s. It showed fossils arranged in the familiar branching-tree pattern… the phyla lines are parallel, illustrating that each phylum remains distinct--separate from the other phyla--during the entire time it appears in the fossil record.
Explore Evolution, p. 34

Summary of problems with claim: If description of exhibit is accurate, this display does not undermine evolution. Even if a hypothetical exhibit were inaccurate, one mistaken exhibit is not evidence against evolution any more than a misspelling on a picture caption changes the spelling of the word.

Full discussion:

Attempts by NCSE to verify this with the California Academy of Sciences have proven fruitless; this was so long ago that the information is unverifiable.

But if we accept their premise and assume that the diagram is a faithful representation of the CAS exhibit, then several things are wrong with Explore Evolution's claims:

1. Explore Evolution Misunderstands the Definition of Phyla

Phyla are ways of classifying body plans of animals. We are part of Phylum Chordata, for example, meaning that we have a spinal cord. So are birds, fish, snakes, and so on. Phylum Cnidaria is the home of animals without a spinal cord and with stinging cells; jellies and corals and anemones are all cnidarians.

2. Phyla Remain Distinct

Phyla are not expected to change within the fossil record; they are expected to evolve in parallel, separate branches. While Phylum Chordata plays many variations on the theme of spinal cords, no one would expect a chordate to evolve into Phylum Cnidaria. A jelly might evolve into another type of jelly, but not into a bird. Nor will the chordate bird evolve into a cnidarian.

Explore Evolution assumes that such transformations should occur, yet this evolutionary route has never been claimed by scientists.

Polyphyletic vs. Monophyletic

One major issue for creationists is whether organisms are best described by polyphyletism or monophyletism. While science views organisms as having a common ancestor, creationism posits multiple creations into biblical "kinds," which are also termed "baramins."

Do scientists support polyphyletism?

Do many scientists think that the fossil record supports a polyphyletic view of the history of life?

Summary of problems with claim: There is no evidence to support this assertion; moreover, Explore Evolution misunderstands the terminology.

Full discussion:

Diagram 1:12 shows three models of evolution.

In the first, we see a diagram labeled "the neo-Darwinist picture." This diagram shows smooth transitions between branches.

In the second, this diagram is labeled "punctuated equilibrium," and shows a similar structure to the first diagram, with the exception of the branches being sharp and angular. The idea with this diagram is that transitions occur more rapidly than in the first diagram.

The third diagram is labeled "a polyphyletic view," and shows five separate trees all beginning at the same time. Curiously, the transitions between branches seem to be a mixture of the first and second diagrams.

A Orchard?: Explore Evolution's inaccurate diagram of polyphyletic relationshipsA Orchard?: Explore Evolution's inaccurate diagram of polyphyletic relationships

The writers of Explore Evolution do not understand the term polyphyletic.

In the sense that they mean it, a polyphyletic model involves several different trees of life, each starting separately (Explore Evolution, p. 10). This is not what scientists mean when they use the term polyphyletic.

From Campbell (p. 471):

A taxon is said to be monophyletic is a single ancestor gave rise to all species in that taxon and to no species placed in any other taxon. A taxon is polyphyletic if its members are derived from two or more ancestral forms not common to all members. A paraphyletic taxon excludes species that share a common ancestor that gave rise to the species included in the taxon.
Campbell, Biology, 4th edition, 1996

Therefore, in this diagram, A = monophyletic, B = paraphyletic , and C = polyphyletic

Trees of Life:: Monophyletic (A), paraphyletic (B), and polyphyletic (C) relationshipsTrees of Life:: Monophyletic (A), paraphyletic (B), and polyphyletic (C) relationships

This is a completely different sense than the way Explore Evolution uses these terms. Note that in the case of C, polyphyletic, the splitting branches still originate from a single common ancestor.

On page 19 of Explore Evolution, three cartoons show Charles Darwin drawing a "Tree of Life."

Explore Evolution asks:

His famous tree analogy was Darwin’s way of interpreting (or making sense of) the fossil data. But what sense did he make of it?
Explore Evolution, p. 19

Explore Evolution answers its own question, saying that Darwin thought "younger fossil forms arose from older ones," and

Every creature on Earth must ultimately be linked to a single common ancestor in the distant past: the root or trunk of the Tree Life.
Explore Evolution, p. 19
Haeckel's Tree of Life: Image from WikiCommons Haeckel's Tree of Life: Image from WikiCommons

Although he discussed the concept, Darwin did not actually make any Tree of Life diagram in Origin of Species. Showing Darwin, even in cartoon form, drawing such a tree is a distortion of Darwin's writings.

Ernst Haeckel drew the earliest phylogenetic trees. The modern term for phylogenetic trees is cladograms. Cladograms are a very useful way to represent the phylogenetic tree of life and to show the common descent of animals.

Explore Evolution asserts:

In the overwhelming majority of cases, Common Descent does not match the evidence of the fossil record.
Explore Evolution, p. 27

This is an absurd claim, completely at odds with the scholarship of 150 years of paleontological research. Explore Evolution does not have a citation to back up this claim because no such reference exists outside creationist works.

Evidence for Single Origin of Life

Sidebar: Evidence for a single origin of life

There is significant scientific evidence that life originated from a single source. Two major lines of evidence involve RNA and the shape of amino acids.

Left-Right Chirality:  Image from WikiCommons [http://commons.wikimedia.org/wiki/Image:Chirality_with_hands.jpg]Left-Right Chirality: Image from WikiCommons [http://commons.wikimedia.org/wiki/Image:Chirality_with_hands.jpg]

1. RNA Evidence

All cells use ribosomes and transfer RNA (tRNA) to synthesize proteins from chains of amino acids. This process is very similar in all living organisms. This strongly argues for a single origin.

Ribosomal RNA (rRNA) is one of the most conserved genes, meaning that it changes very little between organisms. Because rRNA is so similar among organisms, this strongly suggests a single origin.

2. Amino Acid Evidence

Amino acids are the building blocks of proteins. The three-dimensional structure of proteins is vital to their function. However, amino acids exist in two structures that can be described as left or right “handed.”

chirality = orientation of molecules into left or right “handedness” A left hand is identical to a right hand except for its chirality. Likewise, an L-amino acid (left orientation) is identical to a D-amino acid (dextral, or right orientation) except for its chirality.

Both L and D-amino acids are found on Earth and in organic materials from meteorites. Theoretically, either form should work equally well to build proteins. However, biochemical processes only use L-amino acids. This strongly suggests that life arose once, and by happenstance employed the L-amino acid configuration.

Another hypothesis is that if the earliest forms of life used both L and D-amino acids, then this binary system would have greatly complicated nutrition. Imagine that your cell needs R-amino acids, but what you eat is a combination of R and L; only half of your food can be used to make proteins--a very inefficient system. It would be much more efficient if everything you ate or recycled already had the orientation you needed. If an early organism evolved to utilize just one form (L), this would have conferred a great benefit, allowing the L species to drive its binary rivals into extinction.

[Rare bacteria employ D-amino acids in a kind of chemical warfare to defeat antibiotics. This works because antibiotics are specific for L-amino acids. However, these D-amino acids are added outside the normal protein manufacturing process by specialized enzymes.]

Nature of Scientific Disagreement

Sidebar: The nature of scientific disagreement

Explore Evolution makes a big deal of their single tree/orchard analogy:

Some see evidence of an orchard of separate trees; others see a single, continuous, branching tree.
Explore Evolution, p. 34

Scientists see evolution as a continuous, branching tree, not as separate trees. This statement is simply a misrepresentation and does not cite any sources for its claim.

We have seen that scientists disagree over how to interpret the fossil evidence.
Explore Evolution, p. 34

While there can certainly be disagreement over interpretation, Explore Evolution has not cited any specific argument among legitimate scientists. Who are these mysterious dissenting "scientists"?

But how can there be disagreements? Facts are facts, right? How can qualified scientists disagree over evidence?
Explore Evolution, p. 34

This statement is one of the most egregious of in this chapter. This is wrong in so many ways it is hard to know where to begin to parse this, but first let us examine some assumptions here:

1. The Nature of Evidence

Explore Evolution seems to think that the word evidence means something clear and unchallengeable. However, in the scientific sense, new evidence is often fiercely challenged. Evidence is rarely 100% clear.

By way of analogy, think of this question in Hamlet: Is Hamlet insane, or merely pretending to be insane? The answer, of course, is yes. And no. One can cite passages of Hamlet where the prince talks about pretending to fake insanity. One can also cite passages where Hamlet sees things no one else sees (the ghost of his father in his mother's bedroom, for example). The "evidence" found in the play isn't clear, and a bald statement--Hamlet is not insane--will certainly be challenged. This analogy is a better way to think of the nature of scientific evidence than Explore Evolution's false assumption.

2. Scientists Shouldn't Disagree.

Anyone who has ever attended a scientific conference knows that speakers rarely get far into their prepared talks before some member of the audience challenges them. As soon as one makes any claim in a scientific conference or scientific paper, other scientists pounce with questions that are substantive and challenging. Such criticism isn't necessarily personal, but rather is part of the process of science. Explore Evolution incorrectly assumes that if good evidence exists, scientists will not disagree. Explore Evolution misunderstands science.

Malcolm Gordon

Does Biologist Malcolm Gordon thinks that tetrapods arose multiple times and are therefore "polyphyletic"?

Summary of problems with claim:

Gordon and Olson's point is far narrower than Explore Evolution presents it, and is marred by the authors' inexperience with the field. Even if the problems raised were valid when the paper was written, substantial new material has been found which clarifies many of the issues, and which has spawned new research.

Full discussion:

Explore Evolution introduces this sidebar with a blatant error:

Scientists have long thought that amphibians were a transitional form between aquatic and land-dwelling life forms. Why? Because amphibians can live in both the water and on land. Yet, the fossil record has revealed at least two problems with this idea.
Explore Evolution, p. 28

Tetrapod crown groups:  with some fossil stem groups added, with an attempt made to map the Linnaean classes onto the stem groups.  Fossil stem groups are very problematic for Linnaean ranks such as "class."  Graphic by Nick Matzke.  May be reproduced freely for nonprofit educational purposes.Tetrapod crown groups: with some fossil stem groups added, with an attempt made to map the Linnaean classes onto the stem groups. Fossil stem groups are very problematic for Linnaean ranks such as "class." Graphic by Nick Matzke. May be reproduced freely for nonprofit educational purposes.

Tetrapod crown groups with some fossil stem groups added, with an attempt made to map the Linnaean classes onto the stem groups. Fossil stem groups are very problematic for Linnaean ranks such as "class." The use of the term "transitional form" here is so vague as to be meaningless. As discussed above, this use of the term is hopelessly mired in a way of categorizing life that does not incorporate evolutionary thinking, and has been rejected by biologists precisely because of its ambiguity. For more on this shift in the way groups are named, see Appendix 2 and the figure at right. A traditional Linnaean classification would treat all the species in the area shaded pink as amphibians, while a modern classifications regard the amphibians as the major lineage branching off at the base of the phylogeny in the figure, and the species below that branch are regarded as "stem tetrapods," neither amphibians, reptiles, nor mammals. Similarly, the species before the split between reptiles and mammals are neither mammals nor reptiles, and are no longer referred to as "mammal-like reptiles," despite the use of that term in Explore Evolution.

This shift in terminology invalidates the first sentence of the sidebar (since the transitional form would not have been an amphibian, but a stem tetrapod from before the main split shown in the figure above). This also helps clarify the first supposed problem raised by Explore Evolution. The authors cite a paper by Gordon and Olsen authors who are not phylogeneticists and used terminology vaguely. When they make comments like, "no fossils are known that relate directly to the vertebrate transitions to land. No amphibious rhipidistian crossopterygians have been identified," they’re speaking in the context of direct ancestors, a single fossil which has the properties of a certain group of fish ("rhipidistian crossopterygians") and the tetrapods. The tetrapods, however, share many traits with those fish, and treating these groups as totally separate is an inaccurate holdover from non-evolutionary classification schemes. Tetrapods are members of the same lineage as those fish, making the distinction Gordon and Olsen draw very ambiguous.

The book with the paper by Gordon and Olsen was published in 1995, with Everett Olson dying in 1993, meaning these chapters were written well over 15 years ago. Paleontologists these days do not speak in terms of direct ancestors – i.e., that taxon ‘x’ is the common ancestor of all tetrapods. There are 2 problems with such a claim: it is very difficult to demonstrate direct ancestry; and the fossils we have almost always have features uniquely derived within that group, telling us they were their own lineage. We are more likely to find something like an 'aunt' or 'cousin' as opposed to a 'parent,' 'child' or 'grandparent'. In other words, paleontologists do not claim to find direct ancestors, but instead find what are referred to as collateral ancestors or sister groups. Gordon and Olson working in an old and outdated methodology of viewing fossils as direct ancestors and their claim that no direct ancestor have been named in the vertebrate transition to land is meaningless — no one claims there has been! The authors of Explore Evolution obscure these methodological revisions (either intentionally or through their own outdated understanding) and use Gordon and Olsen's claims to discredit recent research of the numerous sister groups that document this transition quite nicely. These sister groups are identified because they possess traits predicted to be present in the stem groups between modern forms and other known fossils. The sequence of changes in the anatomy of the skull, the legs and the shoulders match the sequence of hierarchal changes predicted by common descent.

There are thus two major problems with Explore Evolution’s representation of tetrapod origins: (1) Gordon and Olson is long outdated, and Explore Evolution is using old quotes to discredit recent research they only vaguely mention – "More recently, paleontologists have found fossils that seemed to show a connection between fish and tetrapods"; and (2) Gordon and Olson were operating in a scheme of classification which was not rooted in evolutionary relationships, and viewed the world in terms of direct ancestors, a view long abandoned by paleontologists. Explore Evolution's description of Gordon and Olsen's claims show exactly why it's important to stay up to date with recent research — if you do not, you run the risk of misrepresenting a field and confounding long-outdated remarks with well established data. If the job of science education is to expose students to scientific methodology and hypotheses that explain the best and most recent data available, Explore Evolution certainly falls short of achieving such goals.

The second point Explore Evolution raises is that the earliest fossil tetrapods are too widely scattered, in Greenland, South America, Russia and Australia. Again, the evidence they cite is long outdated. In the words of Jenny Clack from a 1997 paper describing the evidence of South American tetrapods,

A single, isolated print from the Ponta Grossa Formation of Brazil was interpreted by Leonard (1983) as the left manus… and its date was given as probably the base of the Upper Devonian. As an isolated block, there is room for doubt about this print's provenance and thus its date. As a natural cast, there is doubt about the circumstances in which the print was formed. Further doubt has been cast recently on its identity as a footprint. Rocek and Rage (1994) have commented on the description of this specimen working from a cast and photographs, and suggest that it is more plausibly interpreted as the resting trace of a starfish. … until further material from the same locality comes to light, it should be treated with extreme caution as a record of a Devonian tetrapod. Furthermore, the specimen derives from an apparently marine environment which contains brachiopods (Rotek and Rage, 1994). Thus it would normally be considered as subaqueous in origin. This specimen provides no convincing evidence of terrestriality among Devonian tetrapods.
Jennifer Clack (1997)

There is indeed good tetrapod evidence from the other locations. The current hypothesis is that tetrapods originated in the northern continents, explaining the fossil occurrences in Greenland and Russia areas which were, at the time, equatorial. But what about Australia? The Australian evidence consists of a lower jaw and trackways — evidence that seems to be clearly of tetrapod origin. However, we don’t exactly know where Australia was back 360 Ma. We have a good approximation, but of course in science, details matter! Thus, we’re still working on establishing this question — but that’s how science works. New data opens new questions and gets people thinking. Far from being the unsolvable problem Explore Evolution presents, requiring the evolution of tetrapods multiple time in multiple places, this is an area where ongoing research in geology, and new paleontological digs, are allowing scientists to test hypotheses and refine our understanding. Explore Evolution presents a vision of science trapped by unanswered questions, the exact opposite of an inquiry-based approach, and the opposite of the way scientists work. [say more]

Phylogeny & the Nature of the Fossil Record

Explore Evolution misunderstands and misrepresents the nature of phylogeny and the fossil record.

Stability of Phyla

Does the stability of phyla means phyla do not evolve?

Summary of problems with claim: Explore Evolution misunderstands the definition of phyla.

Full discussion:

But stability also characterizes the body designs of the organisms representing the higher categories of life--the orders, classes and phyla.(13)
Explore Evolution, p. 26

and in footnote #13 continues:

Technically, to say that phyla remain stable is almost redundant. After all, scientists define phyla by referring to an unchanging set of anatomical characteristics. In another sense, however, the stability of phyla is remarkable.

Think of the different phyla as though they were arranged like bars on a bar chart. Each bar represents a unique body plan. The farther apart two individual bars are from one another, the more different the anatomical characteristics are.

In nature, an animal body plan could theoretically fall anywhere along this continuum, even in the gaps between bars. Individual animals either falls [sic] within one of the existing phyla, or in some instances new animals are found that represent radically new body plans altogether.
Explore Evolution, p. 26

This is problematic in many respects. By giving this analogy to phyla arranged horizontally as bars in a bar chart, and arguing that one can "fall within" these bars, really misses the whole point of what phyla are.

Phyla are "body plans." They are the most fundamental ways that bodies can be put together. Phyla are based upon the internal, rather than external, arrangement of organisms. Because of this, many seemingly-similar animals (a number of phyla are "worms") are grouped into separate phyla, while many seemingly-different animals (jellies, anemones, corals are all Phylum Cnidaria) are grouped together.

An analogy for phyla can be made for cars. Think of all the different types of cars you see. They all have four wheels, an engine, a windshield, and so on. But beyond this, imagine that you were to classify cars into different automobile phyla. You could make a phylum for convertibles. Another for SUVs. Sedans get their own, as do coupes. Are two-door sedans different enough from four-door sedans that they deserve their own phylum? These kinds of questions, when applied to animal bodies, help scientists classify animals.

In recent years, advances in molecular biology have shed even more light on phylogeny. DNA-DNA hybridization, for example, takes single-strand DNA from two different organisms and measures how well the single strands bond together; the better the bonding, the more closely the DNA pairs match. The advent of PCR (polymerase chain reaction) allow DNA sequencing from living and some extinct organisms. DNA sequencing directly compares DNA at the base-pair level, yielding even more information. Some proteins--for example, cytochrome c--can be used as a "molecular clock" to judge phylogenetic relationships.

Depending on the exact definition of phylum used, the animal world can be divided into about 38 phyla. These are

# Phylum Features Example
1. Chordates spine or notochord fish, humans
2. Mollusca calcareous shell, muscular foot clams, octopi, nautiloids
3. Arthropods jointed, segmented exoskeleton crabs, spiders, insects
4. Echinoderms calcareous exoskeleton sea stars, sea urchins, sand dollars
5. Acanthocephala parasitic worm thorny-headed worm
6. Acoelomorpha no disgestive tract flatworms
7. Annelida complete digestive tract segmented worms
8. Brachiopoda similar to bivalves lamp shells
9. Chaetognatha long, streamlined body arrow worms
10. Cnidaria stinging cells (nematocysts) jellies, anemones, corals
11. Ctenophora no head, central nervous system comb jellies
12. Cycliophora lives in lobster mouths discovered 1995
13. Echuira unsegmented spoon worm
14. Entoprocta sessile goblet worm
15. Gastrotricha microscopic Meiofauna
16. Gnathostomulida hermaphroditic, 0.5-1.0 mm jaw worms
17. Hemichordata similar to worms acorn worms
18. Kinorhyncha <1 mm mud dragons
19. Loricifera sediment-dwelling, marine brush heads
20. Micrognathozoa <0.1mm, one of smallest animals known similar to Rotifera
21. Monoblastozoa "primitive" multicellular
22. Nematoda molting cuticle, 6 lips round worms
23. Nematophora parasites in arthopods horsehair worms
24. Nemertea unsegmented worms ribbon worms
25. Onycophora relatively large brain velvet worm
26. Orthonectida marine invertebrate parasite
27. Phoronida similar to worms
28. Placozoa pressure-filled body cavity tablet animal
29. Platyhgelminthes unsegmented worms flatworms
30. Porifera sessile suspension feeders sponges
31. Priapula marine worm "penis worm"
32. Rhombozoa cephalopod parasite
33. Rotifera microscopic
34. Siboglinidae no digestive system deep-sea vent worms, beard worms
35. Sipuncula mouth of tentacles peanut worms
36. Tardigrada four pairs clawed legs water bears, recently demonstrated to be able to survive in the vacuum of space
37. Xenoturbellida no brain, no digestive tract similar to flatworm

These represent the full diversity of animal body plans. But perhaps the most important thing about these is that they are all found very early in the Cambrian (542-488) fossil record (Gould, 2002, p. 1155). Only Phylum Bryozoa developed after Cambrian times, during the Ordovician (488-443 Ma).

Paleontologist Mike Foote points out that, although we continue to find new fossils, those we find belong to phyla and other major groups that we already know about.
Explore Evolution, p. 30

Trilobite: Elrathia (sp.) from the Burgess Shale. Photo by Steven Newton.Trilobite: Elrathia (sp.) from the Burgess Shale. Photo by Steven Newton.

This statement implies that the fact that we only find organisms that fit within our definitions of phyla is a circular reasoning problem. This misunderstands the fundamental tenet of common descent--that an animal has to evolve from something rather than spontaneously popping into existence.

According to Gould (1989), the fact that only 1 new phylum has originated since the Cambrian means that animal diversity has actually decreased since Cambrian times, since in early fauna such as the Burgess Shale all of today's major phyla exist plus many other phyla that are now extinct. There is considerable disagreement over Gould's argument.

One implication of this is that the majority of phyla came into being in a relatively short period of time, the ten million years between 535-525 Ma, followed by a dearth of new phyla. If a new body plan did not get in at the very beginning, at the "ground floor," then there would be little chance of its development at a later time.

Molecular phylogeny suggest a rather different story for the origin of the major phyla, in which:

1. echinoderms and chordates split ~ 670Ma (Ayala, 1998)

2. protosomes (arthopods, mollusks) and deuterostomes (chordates, echinoderms) split ~ 1.0-1.2 Ga (billion years ago) (Wray, 1996; Bromham, 1998)

A problem with these estimates, based primarily on protein-coding genes, is that rocks from the period of 1.2 Ga-0.67 Ga show little signs of active life at all. Bioturbation, the mixing of sediment layers by burrowing organisms, and trace fossils are not well expressed in the fossil record until early Cambrian times.

Sudden taxonomic levels

Do taxonomic levels appear too suddenly?

Not only do new mammalian orders appear suddenly, but when they appear, they are already separated into their distinctive forms. For example, during the Eocene epoch (just after the Paleocene), the first fossil bat appears suddenly in the fossil record. When it does, it is unquestionably a bat, capable of true flight. Yet, we find nothing resembling a bat in the earlier rocks.
Explore Evolution, p. 24

Flowering plants appear suddenly in the early Cretaceous period, 145-125 million years ago.
Explore Evolution, p. 24
A bat: from WikicommonsA bat: from Wikicommons

Summary of problems with claim: Even if true, this claim does not undermine evolution. This is simply the way evolution proceeds.

Full discussion: Explore Evolution wants to make it seem as if the sudden appearance of new, well-formed organisms is problematic. In fact, this is exactly what punctuated equilibrium predicts.

Onychonycteris finneyi: a transitional bat described by Simmons et al. (2008). Modified image used with permission. Scale bar = 1 cm.Onychonycteris finneyi: a transitional bat described by Simmons et al. (2008). Modified image used with permission. Scale bar = 1 cm. Explore Evolution is inaccurate, however, in its claim that there are no transitional bat fossils. Simmons et al. (2008) describe a transitional bat, Onychonycteris finneyi, from the Eocene of Wyoming (52.5 Ma) that has clawed digits and lacks ears suitable for echolocation. O. finneyi has short wings and long legs.

The existence of O. finneyi shows two things: 1) bats evolved with intermediate, transitional forms, and 2) continued creationist usage of bats to bolster their claims of "sudden appearances" reflects more on creationist unfamiliarity with the subject material than the actual fossil record.

Flowering plants are called angiosperms. The oldest angiosperm fossil--an aquatic plant named Archaefructus liaoningensis--dates not from 145 Ma, but from 125 Ma. This discovery was described in 2002.

Explore Evolution, quoting a 2005 paper in Trends in Ecology and Evolution, goes on to say:

Angiosperms appear rather suddenly in the fossil record…" This contradiction was so perplexing that Darwin himself referred to it as "an abominable mystery.
Explore Evolution, p. 24

The sudden appearance of a new group in the fossil does not constitute a "contradiction." Rather, this is simply the way in which many organisms--either by rapid evolution or a sparse fossil record--show up in the fossil record.

Simmons, N.B., Seymour, K.L., Habersetzr, J., and Gunnell, G.F., 2008. "Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation." Nature 451, 818-821 (14 February 2008).

Fossil Preservation

The nature of fossil preservation

Sometimes the fossilized organism was buried in sediment.
Explore Evolution, p. 16

Fossils do not occur in igneous rock or metamorphic rock. So by default, then, fossilized organisms always--not "sometimes"--occur in sediment. Explore Evolution seems to misunderstand a basic tenet of taphonomy (the study of how organisms decay and become fossilized). Explore Evolution fundamentally misunderstands geologic processes.

Most paleontologists would argue that we have plenty of fossils
Explore Evolution, p. 30

No paleontologist would argue that we have enough fossils; no paleontologist would say that the fossil record is so complete that we should stop looking for new discoveries. Explore Evolution has no citation for this claim and is simply making it up.

Could it be that the intermediates weren't fossilized because they didn't have hard body parts like teeth or exoskeletons? Some defenders of Common Descent say yes, and point out that small structures and soft tissues are more susceptible to decay and destruction, and are, therefore, harder to preserve. This would explain why they are absent from the fossil record.
Explore Evolution, p. 31

Critics agree that soft, small structures are more difficult to preserve. However, they point out that Cambrian strata around the world have yielded fossils of entirely soft-bodied animals representing several phyla.
Explore Evolution, p. 31

Trilobite: Olenoides serratus from the Burgess Shale. Note the dark lines extending from the shell; these are rarely-preserved soft tissues, an indication of the unique preservation conditions of the Burgess Shale. Photo by Steven Newton.Trilobite: Olenoides serratus from the Burgess Shale. Note the dark lines extending from the shell; these are rarely-preserved soft tissues, an indication of the unique preservation conditions of the Burgess Shale. Photo by Steven Newton.

It is true that the mid-Cambrian Burgess Shale (~515 Ma) and the Chengjiang fauna (525-520 Ma) preserve soft body parts. But the conditions which allowed this preservation were unique.

In the Burgess Shale, a combination of submarine topography and anoxic oceans combined to preserve soft tissues. Approximately 86% of the animals in the Burgess Shale did not have a biomineralized skeleton (Briggs, 1994, p. 33). Walcott's Quarry, where the animals of the Burgess Shale are found, is a ~150 meter long pocket of thin shale between the Cathedral Formation dolomites and the Stephen Formation shales (Briggs, 1994, p. 21). It is located between Mt. Wapta and Mt. Burgess, near Field, Canada. Rocks just a few meters away on either side do not show the same quality of preservation, suggesting that this was a very small pocket of unusual conditions.

The Burgess Shale formed at the bottom of an undersea cliff (Briggs, 1994, p. 25). The steep escarpment allowed Burgess animals to be transported quickly from higher, more productive marine conditions into deeper water. Normally, this is not enough to preserve soft tissues; animals decaying on the bottom of the current ocean floor are usually completely scavenged in a matter of hours or days. However, the water at the base of this undersea escarpment was highly anoxic--meaning, it did not have enough oxygen to sustain scavengers. So Burgess animals that fell very close to the cliff were well preserved, while those slightly further away were not preserved at all. Sediment also accumulated rapidly at the base of the escarpment, effectively sealing the undecayed Burgess animals in mud.

If the Precambrian rocks can preserve microscopic soft-bodied organisms, why don't they contain the ancestors to the Cambrian animals?
Explore Evolution, p. 31

This presents false logic. If-->Can does not equal If-->Must. The rarity of rocks from this period, combined with the rarity of soft-bodied organisms being turned into fossils at all, means that in only a few places in the world can paleontologists even look for the ancestors to Cambrian animals.

If lots of soft-bodied animals existed before the Cambrian, then we should find lots of trace fossils. But we don't. Precambrian sedimentary rock records very little activity.
Explore Evolution, p. 31

Trace fossils:: Planolites trace fossils from the Middle Member of the Deep Springs Formation, just above the Cambrian-Precambrian boundary, White-Inyo Mountains, California. Photo by Steven Newton.Trace fossils:: Planolites trace fossils from the Middle Member of the Deep Springs Formation, just above the Cambrian-Precambrian boundary, White-Inyo Mountains, California. Photo by Steven Newton.

This makes the false assumption that if any animals existed, then those animals should have left trace fossils. Precambrian soft-bodied organisms such as Ediacarans did not leave copious trace fossils because they were most likely sessile; they simply did not move or burrow into sediment, as later forms of life would.

If you go to a place such as the White Mountains of California, you can walk a sequence of rocks that takes you from Precambrian sediment completely devoid of trace fossils (Wyman Formation), through carbonate assemblages (Reed Dolomite) into the early Cambrian and into shales in which you see increasing numbers and complexity of trace fossils. On top of these, you find trilobites and archaeocyathids.

Paleontologists define the boundary of the Precambrian from the Cambrian by the first appearance of the trace fossil Treptichnus pedum.

According to Jensen (2003), we find the earliest, and simplest, trace fossils at 560 Ma. By 550 Ma, we start to see more complex three-dimensional burrowing. At 542 Ma, we find Treptichnus pedum burrowing three-dimensionally in a complex pattern that suggests an active hunt for food. This behavior is radically different from the passive Ediacarans.

Possibly the earliest trace fossils are short unbranched forms, probably younger than about 560 Ma. Typical Neoproterozoic trace fossils are unbranched and essentially horizontal forms found associated with diverse assemblages of Ediacaran organisms. In sections younger than about 550 Ma a modest increase in trace fossil diversity occurs, including the appearance of rare three-dimensional burrow systems (treptichnids), and traces with a three-lobed lower surfaces.

Absence of Fossil Evidence

Does an absence of fossil evidence shows that ancestral species did not exist?

Summary of problems with claim:

The fact that a particular species at a given place and time didn't fossilize doesn't mean that the species didn't exist.

Full discussion:

Explore Evolution states:

…critics argue that Darwin's theory has failed an important test. Just as students are tested by exams, theories are tested by how well they match the evidence. In the overwhelming majority of cases, Common Descent does not match the evidence of the fossil record. A student who gets a correct answer only once in a while does not deserve a passing grade. In the same way, critics say that a scientific theory that only rarely matches the evidence fails the test of experience.
Explore Evolution, p. 27

Firstly, taphonomy and earth processes also help us understand why, where, and under what conditions fossils form – and explain low abundance (or absence) of fossils in certain situations. Just because paleontologists do not find fossils in certain rocks (or certain preservational environments) does not mean nothing ever lived there. There are many contingencies that explain fossilization, and any 'absence' of fossils is not – by default – positive evidence against evolutionary theory. There are two different hypotheses/processes at work, taphonomy and evolution, and fossil absence is also very well explained/understood by taphonomic data. Secondly, when fossils are preserved, there is a lot of evidence for common descent. See section on 'transitional fossils' above.

Punctuated Equilibrium

Is there a problem with Punctuated equilibrium?

Summary of problems with claim:

Full discussion:

Explore Evolution claims punctuated equilibrium is a more accurate description of the fossil record, but species selection doesn't work as a mechanism so punctuated equilibrium can't explain the origin of new body plans or new structures. So punctuated equilibrium confirms that there are few transitional forms, but leaves no mechanism for explaining transitions.

On this page, Explore Evolution finally tackled punctuated equilibrium, a major evolutionary idea first proposed by Niles Eldredge and Stephen Jay Gould in 1972.

Explore Evolution says:

In the traditional view, the fossil record was always to blame for the missing pieces of the evolutionary puzzle… Eldredge and Gould decided to take a different approach. Instead of blaming the fossil record, they accepted the fossil data at face value. They agreed that the fossil record really does show many groups of organisms appearing abruptly, continuing unchanged for millions of years, then going extinct.
Explore Evolution, p. 32

Explore Evolution's tone in this quote is one of gloating: Here Darwin has been corrected by real scientists. If Darwin was wrong on one point, Explore Evolution suggests, Darwin might have been wrong on every point. This is, of course, false logic. Moreover, Explore Evolution fails to understand that science is replete with corrections and clarifications of existing theories; ongoing research and critical testing, far from being a sign of the weakness of the theory of evolution, is a sign of its strength.

This is one of the ways in which science is fundamentally different from other human endeavors. In science, no idea is unquestionable, no expert beyond criticism, no theory safe from new evidence. There are no authorities, no equivalent of a clergy to whom one can turn for infallible answers.

In a sidebar, Explore Evolution says:

The Vendian Fossils: Was the 'Cambrian Explosion' Really Explosive? … Some scientists have suggested that those odd creatures may well be the fossilized intermediates that neo-Darwinists have been looking for.
Explore Evolution, p. 32

The exact relationship of the Ediacarans to modern animals is very unclear. Some of the Ediacarans do not even appear to be animals, as they lack features such as mouths and anuses and digestive tracts. But if there is any phylogenetic relationship between the Ediacarans and modern phyla, then this means they probably weren't "intermediate," but rather first.

Explore Evolution says:

Many critics of the theory pointed out that punctuated equilibrium has never explained how the major changes recorded in the fossil record could have taken place in such a short time.
Explore Evolution, p. 33

Eldredge & Gould's punctuated equilibrium concept is based on observations of the fossil record. The "how" or "why" of changes is not required to understand the "what" of the observations.

In fact, arguing that a concept must be wrong if it does not contain a ready explanation of how it occurs is an exercise in teleology. Teleology is concerned with design of things and their inherent purpose. This presupposes, however, that there is a design, that there is a purpose, and such an assumption is not part of science.

As an analogy, imagine that a teleologist argued against a quantum physicist about the structure of the proton. Sure, the teleologist might say, you can prove with your fancy machines that a proton is composed of two up-spinning quarks and one down-spinning quark, but if you cannot say why, then this invalids your observation. Such an argument would, of course, be absurd--yet this is precisely the argument Explore Evolution makes about punctuated equilibrium.

[Punctuated equilibrium] does not explain the origin of higher taxonomic groups (like phyla or classes). To describe how one species of trilobite evolved into another is not the same as explaining how trilobites arose in the first place.
Explore Evolution, p. 33

Eldredge and Gould never claimed that punctuated equilibrium explained the origin of the phyla. It does, however, do a darn good job of explaining the changes in trilobites.

If the theory of Punctuated Equilibrium is right about the rate of evolutionary change… then it has no mechanism that can produce new structures as rapidly as the fossil record shows.
Explore Evolution, p. 33

Eldredge and Gould never claimed that punctuated equilibrium could explain the rate of new body structures. Punctuated equilibrium focuses on what we can see in the fossil record, leaving broader explanations for subsequent research.

Recent discoveries involving the Hox and Pax genes have, in fact, shown how major body plan changes can be made from relatively minor genetic variation. The Pax-6 gene, for example, is common to both invertebrates and vertebrates, and small changes determine whether and organism develops a compound eye (like a fly) or a eye with a cornea and lens (like a human eye) (Zuker, 1994).

It is hard to refute unnamed, anonymous "critics." This is like being accused of a crime, but being unable to question witness against you. If Explore Evolution were serious about this, each one of these three statements would have several examples from the peer-reviewed literature to back up each claim. A search of the peer-reviewed literature turns up, however, zero peer-reviewed papers showing "critics of both views" agreeing that there are fewer than "expected" transitional fossils.

Other Errors in Chapter 3

Four miscellaneous problems found in Chapter 3.

Time Represented in Outcrops

Time Represented in Rock Outcrops

The strata in Figure 1:1 show a relatively small segment of rock. Figure 1:1 also shows four fossils--a one-toed horse, a frog, a trilobite, and a coral.

While the one-toed horse (genus Equus) dates from less than 5 million years ago (Ma), the coral could be Cambrian (>500 Ma). This makes a several meter outcrop of rock appear to show a half-billion years of rock deposition. While there are certainly gaps (unconformities) of this much time, what one would tend to see would be the old corals set right below the younger horse, without trilobites and frogs in between.

Figure 1:1, therefore, is misleading in that it suggests a very long span of geologic time can be shown in a few layers on the side of a cliff. This might be a tenet of Young Earth Creationism, but geologists would tend not to find such a range of fossils in such a short succession of strata.

Explore Evolution claims:

Another problem is that fossils don't always appear in the order they're predicted to.
Explore Evolution, p. 27

This is blatantly false. In fact, fossils show a great uniformity in terms of their stratigraphic position in rock outcrops. In every case where, for example, an older fossils is set stratigraphically above a younger fossils, this can be explained by features such as reverse faulting.

The fossil record seemed to show a trend from simple to complex.
Explore Evolution, p. 17

Complexity in organisms can be subjective. In many ways, fossils from the middle Cambrian show features as complicated as modern animals: eyes, teeth, claws, digestive tracts, articulated limbs, exoskeletons. While we can discern an increase in brain size and complex behaviors in our own species as it evolved from earlier hominids, complexity in body design is more problematic.

Geologic "Closeness"

How much time is shown in a rock outcrop?

Explore Evolution says:

Textbooks also frequently fail to mention that the different skeletons shown in transitional sequences (including the mammal-like reptiles) were not found close together geologically.
Explore Evolution, p. 27

The problem with this idea is the definition of "close." To a Young Earth creationist, close might mean hundreds or perhaps thousands of years. To a geologist or paleontologist, gaps of tens of millions of years are commonplace.

To give you an idea of the scale gaps involved, let's examine the layers (stratigraphy) of the Grand Canyon. The oldest rocks of the Grand Canyon, called the Vishnu Schist, began forming about 2 Ga (billion years ago) as marine sediment that was then metamorphosed and intruded by the younger Zoroaster Granite. All this completed by about 1.7 Ga.

The next sequence of rocks in the Grand Canyon, the Grand Canyon Supergroup, is a set of highly-tilted sediments deposited between 1.2 and 0.8 Ga.

The third sequence involves the relatively younger, flat-lying rocks that make up the majority of what one sees in the Grand Canyon's cliffs. These were deposited between ~500 Ma to ~250 Ma.

To summarize:

Sequence Age Range Time Gap
Upper Sequence 500-250 Ma 250 Ma missing above, 300 Ma missing below
Grand Canyon Supergroup 1.2 - 0.8 Ga 300 Ma missing above, 500 Ma missing below
Vishnu Schist 2.0-1.7 Ga 500 Ma missing above

These kinds of sequences--where more time is missing than is shown--are common in the rocks of the world. Geologists call these gaps "unconformities"; unconformities are so common that it is rare to find a continuous, uninterrupted sequence of rock. Therefore, to argue that fossil finds not being "close together geologically" is evidence against them is to misunderstand the nature of how rock layers are actually deposited.

Explore Evolution goes on to quote Henry Gee:

As zoologist Henry Gee writes, referring to fossil vertebrates in general, "The intervals of time that separate the fossils are so huge that we cannot say anything definite about their possible connection through ancestry and descent."
Explore Evolution, p. 29

Gee's full quote is:

It is impossible to know, for certain, that the fossil I hold in my hand [found at LO5] is my lineal ancestor. Even if it really was my ancestor, I could never know this unless every generation between the fossil and me had preserved some record of its existence and its pedigree…It might have been, but we can never know this for certain… We cannot know if the fossil found at LO5 was the lineal ancestor of the specimens found at Olduvai Gorge or Koobi Fora. It might have been, but we can never know this for certain. The intervals of time that separate the fossils are so huge that we cannot say anything definite about their possible connection through ancestry and descent.
Henry Gee, 1999, In Search of Deep Time 068485421x, p. 22-23

Gee was therefore not, as Explore Evolution claims, talking about fossils in general, but about a specific hominid tooth, which he recognized to have some relationship to his own species. The real doubt in his mind was exactly how direct the connection was. Moreover, Gee explains that the only way he could know for sure would be to have some preserved record of the entire family sequence, and he recognizes that this would be an unreasonable standard of evidence.

Gee makes a broader point, which he summarizes as:

The disconnection and isolation of events worsens further as centuries turn into millennia, tens of millennia, and finally into millions of years: intervals so vast that they dwarf the events within them… This is geological time, far beyond everyday human experience.
Henry Gee, 1999, In Search of Deep Time, 068485421x, p. 26

Gee is correct to point out that the fossil record does not contain an exact, year-by-year sequence of evidence, which is how most people think of time. By acknowledging his personal connection to the hominid tooth he is discussing, Gee posits that despite the gaps in time, we may still understand relationships between fossils, even if "we cannot say anything definite."

The Three Domains

3 DOMAINS

The 3 Domains

Page 23 is a sidebar showing "Biological Classification." The page correctly points out that the most fundamental taxonomic split of organisms is into the three domains: Bacteria, Archaea, Eukaryota. Of these domains, Explore Evolution says, "Each of these has a fundamentally different cell structure."

While true, this is only half the story--the most important differences are genetic, not morphological. In fact, bacteria and archaea have such a close superficial resemblance that for a long time they were not distinguished into different domains.

The 3 Domains model is relatively new; it was proposed by Carl Woese in 1990. (Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci USA 87 (12): 4576–9.)

Weasel Words

"Weasel Words"

Chapter 3 is replete with "weasel words" --phrases that imply something without explicitly stating it, that make statements without backing, that cite sources without naming those sources.

The type of weasel word most commonly used in Explore Evolution involves making statements attributed to "some scientists" or "some critics." In almost every case, Explore Evolution does not name who these critics are. Even when Explore Evolution does cite a scientist, as in the case of Paul Chien (as discussed at length here ), Explore Evolution misrepresents his credentials, calling him a "paleobiologist," a description that does not match his education, research, or publications.

"Some critics" think Explore Evolution is, according to "some sources," a work of fraud that can be debunked simply by looking at its language. You might want to know who these sources and critics are--but if I refuse to identify them, you cannot verify that I have represented their positions correctly. I could be lying. I could have made up the sources. I could have used real sources but used them incorrectly. Science needs a mechanism for checking sources.

A few examples from Explore Evolution, with weasel words italicized:

p. 20: "Recently, some scientists think they have discovered a transitional fossil sequence…"

p. 20: "[unnamed] Paleontologists have identified many gaps…"

p. 21: "[unnamed] Advocates of Common Descent also point out…"

p. 22: "Most critics of the fossil succession argument agree…"

p. 22: "For this reason, many scientists think…"

p. 24: "Critics of the fossil succession argument point out…"

p. 24: "As a result, critics say the pattern of fossil appearances does not support Darwin's picture…"

p. 26: "Critics of fossil succession point to a second feature…"

p. 26: "No, say the critics…"

p. 26: "In much the same way, critics point out…"

p. 27: "For this reason, critics argue that Darwin's theory…"

p. 27: "In the overwhelming majority of cases, Common Descent does not match the evidence…"

p. 27: "Scientific critics of the Fossil Succession…"

p. 27: "Some critics are unpersuaded…"

p. 27: "Given the millions of different fossil forms in the fossil record, critics argue…"

p. 27: "Some textbooks alter the scale of pictures…"

p. 30: "Many paleontologists would argue…"

p. 31: "Critics agree that…"

p. 33: "And that's the dilemma, say the critics."

p. 34: "Critics of both argue…"

p. 34: "We have seen that scientists disagree over how to interpret…"

p. 35: "For example, some scientists say…"

p. 35: "Even so, some advocates of punctuated equilibrium…"

Explore Evolution seems afraid to name specific sources for its information, and with good reason.

Anatomical Homology

Nested patterns of shared similarities between species play an important role in testing evolutionary hypotheses. "Homology" is one term used to describe these patterns, but scientists prefer other, more clearly defined terms. Explore Evolution would have done well to accurately present the way scientists talk about this issue, instead of building two chapters around a misguided attack on a particular word with a meaning that dates to pre-evolutionary attempts at understanding the diversity of life. Explore Evolution's use of the term promotes confusion and obscures the actual ways in which scientists use the term, and more modern concepts. Explore Evolution's authors could have found those modern concepts clarified in the writing of David Wake, work they cite and quote inaccurately, obscuring the point he and others have made about the importance of using concepts which reflect modern biology, not a term which predates evolutionary thinking. The chapter badly mangles key concepts, and repeats creationist canards, without presenting the actual state of science.

p. 40-41: Homology is defined only by implication

Despite using the word "homology" or "homologous" over 80 times, Explore Evolution never provides a clear and consistent definition of homology. Their use of the term confuses and obscures the actual ways in which scientists analyze the morphological evidence of common descent. Homology is not simply similarity, nor is similarity in development the sole basis for assessing homology. A focus on "homology," as opposed to terms and concepts with clearer meanings and less historical baggage, only adds to the confusion.

A shovel, a mole paw, a human hand, and a mole cricket forelimb: Which structures are homologous?  Which share functional constraints?A shovel, a mole paw, a human hand, and a mole cricket forelimb: Which structures are homologous? Which share functional constraints?

p. 43, 45-48: Homology "exists for important functional reasons … not due to shared ancestry"

Homology is similarity in structure and position that occurs because a trait occurred in a common ancestor. If the similarity is not due to common ancestry, the structures would not be homologous. Biologists test alternative explanations, including shared function, natural laws, and other constraints. Like homology, these effects are all testable. Furthermore, similarity in shape, as between mole cricket forelimbs and the paws of a mole, is not homology. No one has ever suggested such a thing, and Explore Evolution is grossly misleading in suggesting otherwise. The errors Explore Evolution promotes are common only in the creationist literature. Once more, Explore Evolution confuses students rather than bringing clarity to a subject. A good textbook would explain that, and show how scientists test these hypotheses; Explore Evolution does not.

p. 44-45: "the development of non-homologous structures should be regulated by non-homologous genes"

Explore Evolution's premise is simply false, and does not reflect the state of developmental biology. The study of how genes control the development of structures changes rapidly. An important lesson scientists are learning is that developmental pathways are modular and redundant; it is possible to replace or alter one module without changing the end result. Putting the differences in developmental pathway into an evolutionary context clarifies how homologous adult structures could be produced by slightly different pathways.

p. 49: "the concept of homology [is] circular"

This claim has a long history in the creationist literature, but is rooted in basic misunderstandings and is therefore rejected by biologists. Because homology is not the same as similarity, the mere similarity of a single trait in two species would not be treated as evidence of common descent. By examining multiple traits, and identifying a shared nested hierarchy of modifications of a common starting point, scientists can test hypotheses about common descent. There is nothing circular about this process.

Major flaws:

Defining homology: Despite using the phrase over 80 times, Explore Evolution never defines "homology." The term is used as a synonym for similarity in places, is treated as if it required a given sort of developmental recapitulation elsewhere, and finally treated as if it were circularly defined and useless. These are all simply restatements of long-discredited creationist falsehoods.

Convergence: Explore Evolution wrongly treats homology as if it were mere similarity, and then claims that the existence of similarity without common ancestry were evidence that no similarities are results of common descent. In fact, homology is one hypothesis among many which scientists can test, and hypotheses like convergence can also be readily tested. There is no excuse for confusing students by mixing up basic biological concepts.

Development: Explore Evolution assumes that developmental similarities are necessary for homology, and assumes that students are well versed in developmental biology. To understand the issues they raise, a student would need to have taken a college-level developmental biology class, and the student would then realize that this book's presentation is consistently false. Structures can in fact be homologous without sharing every step in their development.

Misquoting: Prominent scientists like David Wake and Brian Goodwin are misquoted and misrepresented in an attempt to portray homology as invalid. Wake has written that "Homology is the central concept for all of biology," a far cry from the claim in Explore Evolution that Wake holds that "homology is not evidence of evolution, nor is it necessary to understand homology in order to accept or understand evolution." Similarly, Goodwin relies on homology for his research, which investigates restrictions on the sorts of variation which is likely to be seen. Explore Evolution misleads students by misrepresenting these and other scientists.

Defining "homology"

Understanding why certain sorts of similarities stretch across large swaths of the biological world is a question that has fascinated biologists since before evolution provided a unifying theme for biology. It is hardly surprising that explanations drawn from the pre-evolutionary thinking of the early 19th century would have flaws in the modern evolutionary context. "Homology" is one such concept, and biologists debate the meaning and significance of that particular term because of its historical baggage. To clarify discussions of similarity and difference in an evolutionary context, biologists have coined new terms which avoid the confusions that Explore Evolution's chapter on homology chooses to wallow in.

The central error in the homology chapter lies in the authors' narrow focus on that particular word, rather than discussing the more modern concepts that scientists actually use to study morphological similarities and differences. The focus on outmoded terminology will only confuse students, a result which may not be inadvertent. It is doubly troubling that the chapter about homology never offers a definition of the term, and the attempts made at describing its scientific usage are simply wrong. Despite leaving the word's definition up in the air, EE repeatd the erroneous creationist canard of claiming that homology's definition is circular. The supposed circularity is simply a reflection of the authors' inaccurate presentation of the concept they are writing about, and the claim that an unspecified definition of homology is circular strains credulity in any event.

Unlike Explore Evolution, biologists do not treat homology as if each part of an organism existed in isolation. The pattern of similarity in genes controlling eye proteins reflect the same evolutionary history as the shape of bones in the leg and the genes controlling the development of the embryo. Biologists compare dozens, hundreds, or even thousands of different traits in many different species to develop a model of the evolutionary history of the group. With that model, they can test whether a structure is shared by two species because of shared evolutionary history, or because of shared selective pressures. This process of building a hypothesis, making predictions, and testing those predictions against data is critical to scientific inquiry, and its absence from Explore Evolutionfurther belies the book's claim to be inquiry-based. Its erroneous treatment of homology belies any claim that it accurately explores evolution.

Homology and similarity

Summary of problems:

Despite using the term in the title of two chapters, and using the word "homology" or "homologous" over 80 times, EE never provides a clear and consistent definition of homology. Their usage is inconsistent and vague, promoting confusion and obscuring the actual ways in which scientists use the term. Furthermore, the focus on "homology," as opposed to terms and concepts with clearer meanings and less historical baggage, introduces confusion to the discussion of the morphological evidence of common descent.

Full discussion:

In the glossary, "homologous structure" is [mis]defined as "a body part that is similar in structure and position in two or more species but has a different function in each; for example, the forelimbs of bats, porpoises and humans" (EE, p. 146). "Molecular homology" is defined in the glossary as "similarity of the nucleotide sequences of DNA or RNA molecules, or the amino acid sequences of proteins." In the text of this chapter, homology is never explicitly defined, but is referred to in the context of "similarities," without any restrictions regarding function. As discussed below, similarity of developmental pathways is treated as a requirement of anatomical homology, but is not included in any definitions. None of these definitions match the actual way scientists define and use the term homology, let alone how scientists evaluate the anatomical evidence for common descent.

To choose a trivial example, evolutionary biologists agree that the hooves of a cow and the hooves of a deer are homologous. By the definition EE offers, they could not be homologous structures since they share the same function. Badly misdefining the term that is central to two chapters, and then using it inconsistently throughout, is not a good way to increase student comprehension.

The glossary in Futuyma's Evolutionary Biology defines homology as "Possession by two or more species of a trait derived, with or without modification, from their common ancestor." West-Eberhard defines it as "similarity due to common descent," but adds that "homology, like 'fitness' and 'species', is an elusive concept. There is unceasing debate within evolutionary biology regarding its meaning and use" (M. J. West-Eberhard, 2003, Developmental Plasticity and Evolution Oxford University Press:Oxford. p. 485 of 794).

While the first mistake Explore Evolution makes in this chapter is its failure to define "homology" (correctly), the far greater error is that they do not engage with the ways that modern evolutionary biologists use the concept, and the ways in which the term "homology" has been superseded by clearer concepts.

Here is how biologist Günter Wagner explained the situation in 1989:

Among evolutionary biologists, homology has a firm reputation as an elusive concept. Nevertheless, homology is still the basic concept of comparative anatomy and has been used successfully in reconstructions of phylogenetic history. A large number of characters are certainly derived from the same structure in a common ancestor and are therefore undoubtedly homologous. One simply cannot escape the conclusion that the brain of a rat and a human are actually the "same" in spite of their obvious differences.
G. P. Wagner (1989) "The biological homology concept." Annual Review of Ecology and Systematics. 20:51–69

The phenomenon is real, but teasing out how to identify "homology" has proven difficult. As EE mentions, "homology" was originally coined by Robert Owen to describe a sort of Platonic ideal which individual species drew upon to produce their forms. This non-evolutionary treatment of the concept can promote confusion when thinking about a structure that evolved in stages, and various of those stages are still present. For an example, see our discussion of eye evolution below.

A term that many scientists prefer is "synapomorphy," or "shared, derived characteristic." This concept was crafted by Willi Hennig specifically to describe a trait of an organism which is shared by all of the descendants of a common ancestor, and which is not shared with other groups — it is newly derived within that lineage. Examining the pattern of shared, derived traits allows scientists to develop hypotheses about common descent, and examining additional traits allows scientists to test those ideas.

Tetrapod limbs provide an example of the way that scientists develop and test hypotheses about synapomorphy. Many different aspects of tetrapod limbs unite tetrapods as the descendants of a species like Tiktaalik (discussed in the critique of chapter 3). Such a species possessed certain novel traits that were passed on to their descendants. Within the various lineages, those traits changed, and those changes were passed on to their descendants. Using only synapomorphic concepts, we can make the following observations and hypotheses:

  1. Observation: Bats, seals, and birds are tetrapods (have four limbs) and the particular bones in their limbs share many of the same traits.
  2. Hypothesis: Bats, seals, and birds share a common ancestor.

  1. Observation: Bats share more limb traits with seals than they do with birds. The limb traits that bats share with birds are the same traits that seals share with birds.
  2. Hypothesis: The common ancestor of bats and seals is more recent than the most recent common ancestor of bats, seals, and birds.

The examination of limb morphology allows scientists to propose an hypothesis about the evolution of the groups which possess those limbs. That hypothesis can be tested by examining other traits, such as skull morphology, or DNA sequences. The hypothesis of common descent allows scientists to predict that the hierarchal arrangement of novel traits in each part of the organism should match the pattern derived from the other parts. Hypotheses about the synapomorphy of a trait can be tested by examining that trait in additional species which share the same common ancestor, as discussed below in the context of eye evolution.

By omitting any discussion of the way that scientists propose and test evolutionary hypotheses, Explore Evolution obscures the ways in which scientists actually use concepts like "homology" and "synapomorphy." Misdefining "homology" in the glossary is bad scholarship or an attempt to further confuse the issue at hand.

Homologous structures, genes, and developmental pathways

Summary of problems with claim:

Similarities in developmental pathways are one of several criteria scientists use for "homology." Presenting it as the sole criterion is incorrect.

Full discussion:

As noted elsewhere, the authors of Explore Evolution first create a "strawman" in generating their "Case For". Specifically, for anatomical homology, the authors draw the following conclusion: two different animals can be said to have "homologous structures because they were built by homologous genes" through "developmental pathways" that are homologous (p. 41). To add support to their conclusion, the authors quote two "neo-Darwinian biologists" Alfred Romer and Thomas Parsons who believed "[T]he identity between homologues is based upon the identity or similarity of the developmental properties…[and] hereditary units, the genes" (EE, p. 41). The source cited is a textbook originally published in 1949, with the latest edition published in 1977. Biologists’ understanding of genes and development has advanced dramatically in the past 30 years, and it is irresponsible of the authors to rest their discussion on such an outdated source.

Closer examination of the "Case For" reveals many problems with assuming the above conclusion. Darwin did not know about genes and developmental pathways. Darwin’s theory of common descent and thoughts regarding homologous structures make no predictions about what we expect to find at the developmental and genetic level. Numerous evolutionary biologists have addressed this assumption. Wagner (1988) stated that there is no simple congruence between anatomical characters and genotypes and hypothesized that only those features of the developmental system that cause a restriction in the possible phenotypic consequences of genetic variation (i.e., developmental constraints) are important. Even de Beer (1951), quoted by the EE authors as a critic of anatomical homology, believed that "the homology of phenotypes does not imply the similarity of genotypes".

Certainly, similarity in developmental control can be helpful in establishing structures as homologous (similar in structure and position as the result of common ancestry). Development, however, is far more complex than the EE authors would have their readers believe.

Developmental plasticity plays a major role in our modern understanding of biology and evolution. Processes such as the change in timing or location of developmental events may lead to changes in size and shape, and may alter the relationship between a developmental pathway and morphology without altering homologous relationships. In general, variations in the expression of a gene (late versus early, prolonged versus brief, constant vs. intermittent, spatially contiguous vs. discrete locales) can influence developmental and phenotypic outcomes.

Mindell and Meyer (2001) point out that reticulate (lateral) evolution and the dissociation among traits at different hierarchies (e.g. genes, morphology, development) can result in genes having complicated histories. Orthology, paralogy, and xenology all describe similarities between genes that arise from processes of organismal lineage splitting, gene duplication, and horizontal transfer of genetic material, respectively. The dissociation of traits can result in the co-option of genes for different functions. For instance, Mindell and Meyer (2001) hypothesize a dissociation has occurred between the developmental mechanisms and the digit primordia in the avian hand. In theropods, developmental mechanisms acted on primordia 1-3, whereas the same mechanisms act on primordia 2-4 in birds. Mindell and Meyer (2001) argue this might explain why the digits do not appear to be phylogenetically homologous in theropod dinosaurs and birds, in conflict with many other characters that suggest they are sister taxa.

The issue is not whether homologous structures exist, but why developmental and genetic processes inadequately account for homology. The authors of Explore Evolution want you to believe that the lack of correspondence between some phenotypic structures hypothesized to be homologous and genetic\developmental pathways underlying these structures is evidence against common ancestry. Recent scientific research in evolutionary developmental biology (evo-devo) is providing data in support of other, more parsimonious, and even wondrous, explanations, as well as proposals of new terms such as homocracy, to describe organs/structures which are organized through the expression of identical patterning genes. Hence, many homologous structures are in all probability homocratic, whereas only a small number of homocratic structures are homologous. And while intuitively one might expect that the historical continuity of morphological characters should be underpinned by the continuity of the genes that govern the development of these characters, Wagner (2007) points out that things are not that simple. Instead, regulatory networks of co-adapted transcription factor genes may be more important in orchestrating the development of homologous characters.

In a major work synthesizing developmental biology and its effects on evolution, Mary Jane West-Eberhard lists various major criteria which have been used to propose homologous relationships. These include "similarity in position and structural detail"; "presence of connecting intermediates or transitional forms, including in ontogeny [development]"; "similarity in development, taken to mean shared developmental pathways, shared developmental constraints, or evoked by the same stimuli"; "lack of conjunction, or lack of coexistence in a single organism"; or "genetic similarity" (M. J. West-Eberhard, 2003, Developmental Plasticity and Evolutionary Biology, Oxford University Press:Oxford, p. 489 of 794, references and quotation marks omitted).

Any of these criteria can be applied in a given situation, depending on the information available and the interests of the researcher. West-Eberhard observes:

As pointed out by Donoghue (1992) "The choice of a [specialized] definition is, at least in part, a means of forcing other scientists to pay closer attention to whatever one thinks is most important" (p. 174). It also invites endless argument over what the "correct" definition should be. The choice of criteria is partly a pragmatic matter. The most powerful procedure is to recognize that there are numerous criteria, and given the difficulty of tracing homologies, as many as possible should be used.
Mary Jane West-Eberhard (2003) Developmental Plasticity and Evolutionary Biology, Oxford University Press:Oxford, p. 489 of 794, and quote from Donoghue (1992), "Homology" in Keywords in Evolutionary Biology, E. F. Keller and E. A. Lloyd (eds.). Harvard University Press: Cambridge, MA, pp. 170-179.

These criteria are the ground for initially proposing homology, but are not the final step. The scientific process rests on repeated inquiry and testing, using new lines of evidence to test the evolutionary history of a lineage, and to understand the detailed history of a particular structure. Developmental pathways are one line of evidence examined, but are not the only basis for identifying homology, nor for testing a hypothesis of homology. Explore Evolution fails here by misleading students about the way scientists assess homology and by misrepresenting the scientific method of proposing and testing hypotheses.

Circular definitions

Summary of problems:

This claim has a long history in the creationist literature, but is uniformly rejected by biologists as rooted in basic misunderstandings. The apparent homology of a single trait would not be treated as evidence of common descent. By examining multiple traits, all showing the same nested hierarchy of modifications of a common starting point, scientists can test hypotheses about common descent. There is nothing circular about this process.

Full discussion:

The argument that homology is defined in a circular manner was a centerpiece of Jonathan Wells's creationist book Icons of Evolution. Wells, an uncredited co-author of EE, undertook graduate studies in biology at the behest of his religious leaders. He explained to a Unification Church ("Moonie") publication "Father [Sun Myung Moon]'s words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism."

EE reuses Wells's figure 4.1 as its figure 2:1, merely adding color to the figure. Similarly, the discussion of homology as a circular argument is a lightly rewritten version of what Wells wrote. Compare EE:

Some biologists suggest that the problems of understanding homology stem from Darwin himself, who re-defined homology as the result of common ancestry.

This made the concept of homology circular, say many critics. If homology is defined as "similarity due to common descent," then to say that homology provides evidence for common descent is to reason in a circle.
EE, p. 49

Wells writes:

before Darwin (and for Darwin himself), the definition of homology was similarity of structure and position …. But similarity of structure and position did not explain the origin of homology, so an explanation had to be provided.

But for twentieth-century neo-Darwinists, common ancestry is the definition of homology as well as its explanation.

[E]volution was a theory, and homology was evidence for it. With Darwin's followers, evolution is assumed to be independently established, and homology is its result. The problem is that now homology cannot be used as evidence for evolution except by reasoning in a circle.
Jonathan Wells (2000) Icons of Evolution, Regnery Publishing, Inc.:Washington, DC. pp. 62-63

The restatement of these claims in EE does not require any different response than Wells received, since it adds nothing to the argument. Reviewer Alan Gishlick responded to Wells's treatment of homology:

Wells claims that homology is used in a circular fashion by biologists because textbooks define homology as similarity inherited from a common ancestor, and then state that homology is evidence for common ancestry. Wells is correct: this simplified reading of homology is indeed circular. But Wells oversimplifies a complex system into absurdity instead of trying to explain it properly. Wells, like a few biologists and many textbooks, makes the classic error of confusing the definition of homology with the diagnosis of a homologous structure, the biological basis of homology with a procedure for discovering homology. In his discussion, he confuses not only the nature of the concept but also its history; the result is a discussion that would confuse. What is truly important here is not whether textbooks describe homology circularly, but whether homology is used circularly in biology. When homology is properly understood and applied, it is not circular at all.

Today, biologists still diagnose homologous structures by first searching for structures of similar form and position, just as pre-Darwinian biologists did. (They also search for genetic, histological, developmental, and behavioral similarities.) However, in our post-Darwin period, biologists define a homologous structure as an anatomical, developmental, behavioral, or genetic feature shared between two different organisms because they inherited it from a common ancestor. Because not all features that are similar in two organisms are necessarily inherited from a common ancestor, and not all features inherited from a common ancestor are similar, it is necessary to test structures before they can be declared homologous. To answer the question, "could this feature in these groups be inherited from a common ancestor?" scientists compare the feature across many groups, looking for patterns of form, function, development, biochemistry, and presence and absence.

If, considering all the available evidence, the distribution of characteristics across many different groups resembles a genealogical pattern, it is very likely that the feature reflects common ancestry. Future tests based on more features and more groups could change those assessments, however — which is normal in the building of scientific understanding. Nevertheless, when a very large amount of information from several different areas (anatomy, biochemistry, genetics, etc.) indicates that a set of organisms is genealogically related, then scientists feel confident in declaring the features that they share are homologous. Finally, while judgments of homology are in principle revisable, there are many cases in which there is no realistic expectation that they will be overturned.

So Wells is wrong when he says that homology assumes common ancestry. Whether a feature reflects common ancestry of two or more animal groups is tested against the pattern it makes with these as well as other groups. Sometimes, though not always, the pattern reflects a genealogical relationship among the organisms — at which point the inference of common ancestry is made.

Evolution and homology are closely related concepts but they are not circular: homology of a structure is diagnosed and tested by outside elements: structure, position, etc., and whether or not the pattern of distribution of the trait is genealogical. If the pattern of relationships looks like a genealogy, it would be perverse to deny that the trait reflects common ancestry or that an evolutionary relationship exist between the groups. Similarly, the closeness of the relationship between two groups of organisms is determined by the extent of homologous features; the more homologous features two organisms share, the more recent their common ancestor. Contrary to Wells's contention, neither the definition nor the application of homology to biology is circular.

Some formulations of the concept of homology appear to be circular, but as discussed above, because there is an external referent (the pattern that characteristics take across groups) that serves as an independent test, the concept, properly defined and understood, is not. Wells's claim that homology is circular reveals a mistaken idea of how science works. In science, ideas frequently are formulated by moving back and forth between data and theory, and scientists regularly distinguish between the definition of a concept and the evidence used to diagnose and test it.

Gishlick here is using "homologous features" in the sense of a "shared derived character," as discussed above. There are several important points that bear emphasizing.

First, biologists do not look at only one line of evidence to infer common descent; it is the agreement of multiple lines of evidence about morphological, genetic, behavioral, ecological and developmental similarity which allows that inference.

Second, that inference is a testable hypothesis. The addition of new lines of evidence allows a test of evolutionary hypotheses. For instance, biologists will test evolutionary hypotheses produced based on skull morphology with information from the DNA sequence of a particular gene. A common test for the accuracy of an evolutionary inference is to run the same analysis while excluding part of the data, and using those excluded data to confirm the accuracy of the results.

Third, the hypothesis of homology (which follows from an evolutionary hypothesis) is testable. In reconstructions of the common ancestry of a group, it is not uncommon to find that certain traits evolved more than once, or appear and disappear at various points on the tree. Those characters are then subject to greater scrutiny, since their disagreement with other traits suggests that there may be more that needs to be understood about that trait. Some traits which appear similar are deemed not to be homologous as a result of this analysis, but to be the result of parallel evolutionary pressure.

Fourth, the evolutionary hypothesis can be tested by reference to previously unexamined species. If the evolutionary hypothesis is correct, new species ought to fit easily into the pattern predicted. Since the evolutionary hypothesis is based on nested groups sharing certain novel traits, that hypothesis would be challenged if newly described species had a mosaic of traits that did not fit into that nested hierarchy.

Explore Evolution, like other creationist books before it, makes the mistake of treating the structures of organisms in isolation. While it would be circular to use a single trait to infer an evolutionary history and then to use that history to infer the common ancestry of that trait, scientists do not do that. In presenting homology and common descent as a circular construct misused by scientists, EE misinforms students about basic concepts, bringing confusion rather than clarity.

Scientists build on earlier hypotheses with new data, and build new hypothesis from that new data. This advance in knowledge adds a third dimension to what EE treats as two-dimensional. Rather than a flat circle, the scientific process spirals upward.

Convergence

The authors' misunderstanding of basic concepts is particularly obvious in their presentation of convergence. They treat the similarity of the bones musculature, nerves and development of hands in humans and moles as if it were no different than the gross similarity in the outlines of mole paws and mole cricket forelimbs. This sort of basic misunderstanding is what a biology textbook is supposed to clarify, not promulgate. The arguments presented in the discussion of convergence have no basis in the scientific literature, but trace back to the beginnings of modern creationism.

Common function vs. common ancestry

Summary of problems:

We determined above that homology, as defined by Darwin, is similarity in structure and position that occurs because species share a common ancestor that also exhibited the basic structural motif. If the similarity is not due to common ancestry, the structures would not be homologous. As Wagner (1988) pointed out, homologs are expected to have a similar position with respect to other structures in different species and their component parts are expected to have a similar position with respect to each other. Furthermore, homologs should be historically contingent in the sense that common descent is the only way to explain the presence of this invariant feature. Hence, before structures meet the criteria for homology, biologists evaluate alternative explanations of similarity, in particular, similarity as a result of function, common materials, and/or limitations of design.

Full discussion:

The authors of Explore Evolution provide their evidence on pages 46-47 that function rather than ancestry may better explain the humerus-radius-ulna pattern of the vertebrate limb. Specifically that it’s a functional optimum for vertebrates with limbs to have one bone, the humerus, in the part of the limb closest to the trunk (body) and two bones, the radius and ulna, in the next portion of the limb. If the arrangement were reversed, functional problems would arise, particularly with range of motion.

The example the authors use to explain the restrictions placed on the two-to-one arrangement involves exploring the two differing arrangements using a ball of clay and two straws. However, a serious design flaw occurs when using their model. The example may recreate the structural arrangement of the bones, but provides an incredibly inadequate model of the connections between the bones. The ball and socket arrangement of the humero-scapular joint, the pivot of the radius-ulna, the hinge of the humero-radial joint are all important in determining function. Hence to really test their hypothesis, that function would be limited given another arrangement of bones, we would also have to rearrange the points of connection, which I suspect would rectify the problem. After all, the two-to-one arrangement works fine for the forearm, and allows the radius and ulna to rotate around the humerus.

Another problem with the authors’ argument is that vertebrate forelimbs actually function in a wide variety of habitats including running on land, swinging in trees, flying in the air, swimming in the water, and as the case is with penguins, flying in the water. It hard to believe that each of these habitats would place the exact same functional requirement on the design of the vertebrate limb. And in fact, to accommodate these different functional requirements, vertebrate limbs show incredible modifications. For example, the horse has a fused radius and ulna (see figure below), disproving the hypothesis that the one-two arrangement is a result of functional optimization for each vertebrate species. In fact, the vertebrate forelimb provides an amazing example of how function has influenced modifications to the same h-r-u pattern.

Diagram showing how the pentadactyl (five-fingered) limb is adapted for a variety of habitats by different animals, including bats for flying, dolphins for swimming, moles for digging, anteaters for tearing, horses for running, pigs for walking, and monkeys for graspingHomology of vertebrate limbs: Image produced by Jerry Crimson Mann, and released under the GFDL.

The pattern of limb bones called pentadactyl is found in all classes of tetrapods (i.e. from amphibians to mammals). It can even be traced back to the fins of certain fossil fishes from which the first amphibians are thought to have evolved. The limb has a single proximal bone (humerus), two distal bones (radius and ulna), a series of carpals (wrist bones), followed by five series of metacarpals (palm bones) and phalanges (digits). Throughout the tetrapods, the fundamental structures of pentadactyl limbs are the same, indicating that they originated from a common ancestor. But in the course of evolution, these fundamental structures have been modified. They have become superficially different to serve different functions in adaptation to different environments and modes of life. This phenomenon is clearly shown in the forelimbs of mammals. For example:

  • In the monkey, the forelimbs are much elongated to form a grasping hand for climbing and swinging among trees.
  • In the pig, the first digit is lost, and the second and fifth digits are reduced. The remaining two digits are longer and stouter than the rest and bear a hoof for supporting the body.
  • In the horse, the forelimbs are adapted for support and running by great elongation of the third digit bearing a hoof.
  • The mole has a pair of short, spade-like forelimbs for burrowing.
  • The anteater uses its enlarged third digit for tearing down ant hills and termite nests.
  • In the whale, the forelimbs become flippers for steering and maintaining equilibrium during swimming.
  • In the bat, the forelimbs have turned into wings for flying by great elongation of four digits, and the hook-like first digit remains free for hanging from trees.

Vertebrate limbs

Summary of problems:

Common function can explain certain similarities of form, but cannot explain similar developmental pathways, or the particular components that make up certain structures in different species.

Full discussion:

The discussion of functional constraints in Explore Evolution is nearly impossible to state in a way which does not refute itself. They do not deny the remarkable similarity between the structures of species within various taxonomic groups. They do not deny that one can produce a hierarchal (branching) arrangement of the ways these structures vary within and among these groups, and that the branching pattern is consistent regardless of which particular structure you examine. In other words, their response to the evidence of the branching pattern predicted by the tree of life is to agree that it is all accurate. They simply argue that it is possible to invoke special explanations for each such structure, multiplying causes needlessly. This practice violates basic scientific and logical principles. By treating structures in isolation, they obscure the actual evidence examined by scientists.

For instance, EE cites biologists from 150 years ago, biologists whose arguments were tested and found lacking.

Agassiz, for example, explained homologies as the result of the necessity of using similar structures to solve similar functional problems. On this view, the pattern we see in the vertebrate forelimb — a single bone closest to the trunk, two bones in the next segment, and a variety of bones in the segment farthest out — exists for important functional reasons.
EE, p. 43

It is worth noting, to begin with, that vertebrate limbs do not have "a variety of bones in the segment farthest out." The number of fingers and toes is consistent. The numbers of bones in each finger and toe are consistent. The number of wrist bones is consistent. Even if functional constraints could predict the broad pattern, they do not explain why no living species has more than 5 fingers or toes, nor the consistency of the number and developmental histories of the wristbones.

Furthermore, functional constraints do not explain the broad pattern. Robotic arms do not typically have one element nearest the base, two further out, and a number in the "hand." They employ various sorts of joints and connections which do not exist in living species. The argument of functional constraints only make sense if you assume some evolutionary process acting on some common starting point. That explains vestigial fingers and toes in the legs of deer, it explains why our two legs, and all four legs in a deer, still have two bones in the middle segment, despite having no need to twist. It explains why no species has more than five fingers or toes, and why vestiges of all five can be found in vertebrates which seem to have fewer. These results would be surprising if there were not some common starting point, but are predicted and found because of evolutionary hypotheses.

Wing morphology: Pterosaurs, bats and birds produced wings with functionally similar shapes from a homologous organ (the forelimb) in three distinct ways.  The bones in each wing are homologous, but because the different arrangement of bones within the wing, the wing itself is independently derived within each group.  Image by J. Rosenau.Wing morphology: Pterosaurs, bats and birds produced wings with functionally similar shapes from a homologous organ (the forelimb) in three distinct ways. The bones in each wing are homologous, but because the different arrangement of bones within the wing, the wing itself is independently derived within each group. Image by J. Rosenau.

The claim of consistency because of functional constraint also does not match the actual evidence. Because of the basic physics of flight, bird wings, bat wings and pterosaur wings must all be similarly shaped. If they were shaped much differently, flight would be (or have been) impossible. If the functional constraint hypothesis were the sole explanation for wing structure, we might predict that all three types of vertebrate wings would be similar in their anatomical structure, but this prediction fails. Pterosaurs have a wing consisting mostly of skin stretched between the 4th finger and the body, with the thumb and three fingers free of the wing. Bat wings consist of skin stretched across all 4 fingers and attaching to the leg, with the thumb free of the wing. Bird wings (like chicken wings you've eaten) do not have skin stretched across them, have fused the bones of the 2nd and 3rd fingers together for strength, and cover the structure with feathers.

Within each group, these traits are consistent, indicating that the wing can be treated as homologous within each group, but not across groups. All three wings share the same bones (the bones are homologous), but they are arranged very differently. Bats use all four fingers in the wing; birds use two, have lost one finger almost completely, and another is nearly functionless; pterosaurs used only one finger in flight, but adapted other fingers to different purposes. Since the anatomy of these wings is so different, this falsifies a prediction of the functional constraint hypothesis.

It confirms what we would expect from evolutionary explanations. Because vertebrates share a common ancestor, all three groups shared ancestors which possessed the basic vertebrate limb. Each group took steps toward flight at different times and from different ancestors with different initial traits. The differences in starting conditions meant that different sorts of genetic and structural changes were advantageous in each different group. Within each group, the structure of the wing is consistent, indicating common descent within pterosaurs, within bats and within birds. The differences in the structure of each type of wing indicates that wings evolved independently in each group. The similarity of the bones in the wings (and elsewhere in the body) indicate that all three groups share an ancestor farther back in their history. This nested pattern of shared characters is exactly what common descent predicts, and has not successfully been explained by other means.

Functional constraints cannot explain why vertebrate wings should consist of skin stretched over bone, since birds do not use skin for the flight surface. Indeed, insect wings do not have bones or skin, and are not derived from legs. Insect wings are structurally similar (homologous) to gills. Again, this pattern of similar structure is unexpected under the predictions of common functional constraint, but entirely predictable based on evolution and common descent.

An inquiry-based textbook could turn a discussion like that above into a fascinating exercise. Students could generate predictions based on various potential explanations, and then test them using data from various biological structures. Explore Evolution, despite its claim to be inquiry-based (and despite the nonsensical and meaningless exercise on pp. 46-47), does not invite students to examine any evidence at all, nor does it explain why students should ignore the research conducted in over a century since Agassiz defended his position. Inquiry-based instruction invites students to discuss the topic, but no useful discussion could possibly proceed from such a flawed foundation.

Similarity of shape vs. similarity of form

Summary of problems:

Similarity of the structure of mole cricket forelimbs and the paws of a mole does not, in any sense, suggest homology between those structures. No one has ever suggested such a thing. Homology consists of more than similarity of shape, but similarity of underlying structures.

Full discussion:

It is worth noting in passing that only a few pages after complaining about the presentation of different fossil skulls without showing the different sizes of the skulls, every graphic in this chapter compares organisms and structures of very different sizes without any indication of the relevant scale. Human arms are 3 feet long, horse legs are generally around 5 feet long, bat wings are a foot or two long, and a whale flipper can stretch close to ten feet long (fig. 2:1). Mammal eyes are generally between half an inch and an inch deep, insect eyes are fractions of an inch across, and cephalopod eyes can be a foot and a half wide (fig 2:2). Ichthyosaurs were 3-6 feet long while the baleen whales EE compares them to are 40-50 feet long (fig. 2:3). A mole cricket is an inch long, a mole is closer to 8 inches long (fig. 2:4). This point is minor, but emphasizes the inconsistent approach Explore Evolution takes to its subject.

EE's attempt to claim some deep meaning for the similarities between the mole cricket's forelimbs and mole hands would be entertaining if it were not obvious that EE intends that comparison to be taken seriously. EE wonders:

are there some similarities not due to common ancestry? Surprisingly, nearly all biologists say there are. … The flippers of a whale and an ichthyosaur have very similar shapes, even though the whale is a mammal and the ichthyosaur was a reptile. … The forelimb of a mole cricket is very similar to a mole's forelimb, even though the mole is a mammal and the mole cricket is an insect.

Even biologists who take a monophyletic view of life's history will tell you that the similarity we see in these structures is not the result of common ancestry. They contend that the last common ancestor of these creatures did not possess the similar structure. In other words, the similar structures arose separately on independent lines of descent.
EE, p. 46-48
Spade or hand?: A shovel, a mole paw, a human hand, and a mole cricket forelimb.  Which structures are homologous?  Which share functional constraints?Spade or hand?: A shovel, a mole paw, a human hand, and a mole cricket forelimb. Which structures are homologous? Which share functional constraints?

It is not clear why anyone, let alone textbook authors, should be surprised that certain basic shapes recur in nature. The shape of a flipper or a wing or a digging implement is constrained not only by the evolutionary history of that structure, but by the nature of the work it is used to do. Limbs shaped more like a flipper tend to make animals better swimmers, whether they are birds (penguins), mammals (whales), or reptiles (ichthyosaurs). The question a biologist asks in assessing homology is not whether the shape of a structure is similar, but whether the composition and developmental origins of the structure are homologous. On that front, there is simply no basis for claiming any homology between cricket limbs and mole paws, any more than there is a homology between mole paws and a spade. An examination of the anatomy of a mole paw, cricket limb, shovel, and a human hand makes it clear why the similarities in the basic outline of three of these structures is less evolutionarily significant than the clear anatomical similarities between the human hand and the mole paw.

This example is so obvious an instance of functional constraints creating similarities in structures that biologists have been using it to illustrate this point since at least the 1950s. Michael Novikoff wrote in 1953:

the concept of analogy includes two different categories of phenomena. One clearly corresponds to the accepted definition of this term, according to which analogous forms are understood to be those that have been secondarily acquired by animals or plants in adaptation to similar environmental situations. As an appropriate example of such an analogy one may cite the front appendages of such widely different animals as the mole, Talpa europaea, and the mole cricket, Gryllotalpa vulgaris. The ends of the front legs of both the mammalian burrower and the insect burrower are shovel-like, well suited to digging underground. Another example, the acquisition of a snow-white fur or plumage by various animals of the northern regions, may be mentioned. This analogy is concerned with a purely physiological phenomenon and is therefore in contrast to homology, which is a morphological or phylogenetic phenomenon.
Michael M. Novikoff (1953) "Regularity of Form in Organisms" Systematic Zoology 2(2):57-62.

It is not the least surprising that certain shapes recur in nature, coming from disparate origins. The surprise expressed by Explore Evolution is truly disappointing. A textbook is not supposed to encourage confusion among students, but to clarify misconceptions. EE's befuddled efforts to cast doubt on evolution merely reflect the authors' own misunderstandings; misunderstandings that no school board nor teacher should wish its students to perpetuate.

Convergence vs. natural selection

Summary of problems:

There is nothing mysterious about convergence. Species facing similar selective pressures would be expected to be similar in certain ways. There is no reference to any particular scientist who would support the claims EE advances, but it is an argument commonly advanced in the creationist literature.

Full discussion:

Explore Evolution says the following about convergence:

Neo-Darwinian biologists use the term "convergence" or "homoplasy" to describe similar structures that are not due to common ancestry but which are found in different types of organisms. They call these features convergent because they think that the evolutionary process has come together (converged) on the same structure two or more times in creatures that exist on very different branches of the Tree of Life. Convergence is a deeply intriguing mystery, given how complex some of the structures are. Some scientists are skeptical that an undirected process like natural selection and mutation would have stumbled upon the same complex structure many different times.
EE, p. 48

No citation is given to the scientists who are supposedly skeptical about the ability of natural selection to explain convergence. Indeed, it's difficult to imagine how anyone who thinks a structure could evolve in one lineage in response to a set of selective pressures would be surprised that the same selective pressures would produce a functionally similar structure in another lineage. Furthermore, in the examples of convergence offered in EE, the convergence does not involve any complexity. The mole paw is a simple modification of shape of the paws found in other mammals. Similarly, the mole cricket's forelimbs are simple modifications of the basic anatomy of the insect forelimb. No new structures are involved, merely the rearrangement of pre-existing structures.

Even though scientists cannot be readily identified making the argument EE presents, that argument is easy to locate in the writings of creationists. In 1925, young earth creationist George McCready Price made a very similar argument to that in EE:

we become convinced that these many similar or identical structures, which must have been evolved quite independently (if evolved at all), make too great a draft on our credulity. At least, these hundreds of examples of "parallel evolution" greatly weaken our confidence in homology, or similarity of parts and organs, as a proof of blood relationship.

There are several distinct types of eyes, each type being quite efficient as organs of seeing. But if we take the eye of the higher animals, we become amazed to find an almost identical structure in the cuttlefish or devilfish, which is really a mollusk. Its eye has all the parts found in the human eye, a retina, a sclerotic, a choroid, a vitreous humor, an aqueous humor, and an adjustable lens, just as in the eye of one of the higher vertebrates. Now I can believe that these similar organs could have been created independently for these very distinct classes of animals. But I cannot believe that this marvelous organ was evolved independently in these two instances by any process of natural development or evolution. … I do not think that [Darwin's] mental equilibrium would have been restored if he had considered that this organ must have been evolved quite separately in at least these two instances. Indeed, this process must have been repeated also once more; for the pecten, another kind of shellfish wholly different from the cuttlefish, has two rows of almost equally perfect eyes around the edge of its body. I cannot force myself to believe that these complete organs of sight were separately and independently evolved by any natural development in these three instances.

The argument has been repeated many times by many creationists. In 1970, Evan Shute wrote:

Many resemblances between animals and plants of different genera, families and orders defy evolutionary explanation. There are both differences and similarities between creatures of different kinds. The evolutionist must decide what features are useful as true species criteria and what features are spurious or misleading. A small but interesting sampling of strange similarities between widely diverse living forms is given here, from a study of spinal tracts, ears, placentae, electric organs, kidney function, fern vessels, milk, brown fat, sweat glands, and other systems: It is asserted that these puzzling resemblances are best explained by special creationism rather than by evolutionary convergence.
Evan Shute (1970) "Puzzling Similarities," Creation Research Science Quarterly, 7(3):147-151.

More recently, the newsletter for the old earth creationist group Reasons to Believe claimed:

No known evolutionary mechanism can account for the nature of biological convergence. Convergence has been far too common throughout life’s history, has involved exceedingly complex structures, and has occurred in situations in which the forces of natural selection have been vastly different. Biological convergence is an important component in the argument that life, throughout earth's history, is a result of the supernatural activity of a Creator.

In the scientific literature, convergence is far from surprising. In Futuyma's Evolutionary Biology, the second of seven "principles of evolutionary change" is "homoplasy [convergence] is common in evolution":

When a similar character (or character state) in two organisms has not been derived from a corresponding character (or state) in their most recent common ancestor, it is said to be homoplasious. An example of a homoplasious character is the superficially similar eye of vertebrates and of cephalopods (squids, octopods). Both have a lens and retina, but their many profound differences indicate that they evolved independently: for example, the axons of the retinal cells arise from the cell bases in cephalopods, but from the cell apices in vertebrates.

Three more or less arbitrarily distinguished kinds of homoplasy are recognized. In convergent evolution (convergence), independently evolved features are superficially similar, but arise by different developmental pathways. The eyes of vertebrates and cephalopods are an example. Parallel evolution (parallelism) is thought to involve similar developmental modifications that evolve independently (often in closely related organisms, because they are likely to have similar developmental mechanisms to begin with). … Evolutionary reversals constitute a return from a [derived] character state to a more … ancestral state.

Homoplasious features are often (but not always) adaptations by different lineages to similar environmental conditions. In fact, a correlation between a particular homoplasious character in different groups and a feature of those organisms' environment or niche is often the best initial evidence of the feature's adaptive significance.
Douglas Futuyma (1998) Evolutionary Biology 3rd ed., Sinauer Associates:Sunderland, MA. p. 110-111

There is nothing the least bit surprising about convergence or homoplasy in general. Shared selective pressures ought to produce some degree of similarity in structures. Characteristics used to identify evolutionary relationships are selected to avoid traits likely to be result of convergence, so homoplasy is not, in general, a problem for reconstructing evolutionary history. Convergence, far from being a surprise, is a predicted result of evolutionary processes.

Convergence and common descent

Summary of problems with claim:

This is another instance where Explore Evolution uses ambiguous language to confuse students, rather than bring clarity to a subject. It is entirely predictable that shared selective pressures would produce superficial similarities from dissimilar anatomical structures. We expect the underlying anatomy to reveal underlying evolutionary relationships; superficial similarities are not expected to be evolutionarily informative.

Full discussion:

Explore Evolution claims:

For other scientists, the phenomenon of convergence raises doubts about how significant homology really is as evidence for Common Descent. Convergence, by definition, affirms that similar structures do not necessarily point to common ancestry. … But if similar features can point to having a common ancestor — and to not having a common ancestor — how much does "homology" really tell us about the history of life?
EE, p. 48

It is not clear who the "scientists" are who advance this argument. As discussed above, scientists see nothing surprising about similar selective pressures producing superficial similarities between structures. The similarities that scientists consider evidence of common descent are similarities of underlying structures and developmental processes.

The point that EE raises here is not a terribly complex point, and closing the chapter with that question is hardly educational. Indeed, EE here passes up an opportunity for genuinely inquiry-based learning. It would not be difficult to prepare an exercise in which students would be asked to examine actual organisms, and to propose investigations which would test whether certain traits are homologous. Scientists perform such tests routinely, and a simplified example would allow students to understand that process. In doing so, students would come to understand that identifying similarities or differences between a particular structure in two species is the first step in a scientific inquiry. Students would learn that testing a hypothesis about homology requires comparison with other structures in other species. Students would also see that certain traits tend to vary rapidly in response to an organism's environment (coloration, for instance), while other traits are remarkably consistent (the number of bones in the limb). Students could then be given a new set of organisms to examine, and see how scientists use knowledge from previous research to inform new assessments of homology and homoplasy.

Instead of encouraging scientific inquiry, EE misuses terminology, makes false claims about the current state of the science, and then closes the discussion with a question to the students, without having given any indication of how students ought to go about addressing the question. This is a poor model of how science works, and a poor way of teaching any subject.

Development

In addition to its profoundly misleading treatment of concepts like homology and of convergence, the book's handling of basic biological facts is often simply wrong, and as frequently is so confusing as to be meaningless. The book uses an example from differences in the developmental pathways in insects without first introducing basic concepts in insect development (a subject high school biology texts also do not cover). The authors do not give students the background to assess how a such a pathway works, or what consequences changing it might have. Students have no choice but to take the author's word that these and other phenomena are in fact inexplicable; a result that is not consistent with EE's claim to use an "inquiry-based" approach. In fact, the authors have simply ignored the existence of clear explanations for the developmental processes in question.

Presenting these examples as unanswered and unanswerable problems for evolution is simply wrong. In fact, the problem in this chapter derive from the book's inaccurate and inadequate presentation of basic concepts, and the authors' incomplete presentation of the existing knowledge on the topics they present. The consequence of this problematic treatment is an totally erroneous vision not only of the current state of scientific knowledge, but of how scientists gather and test new ideas, and how scientists use evolution to study similarities and differences between species.

Primer

Because the arguments advanced in Explore Evolution require readers to have a level of knowledge beyond that offered in the book or in standard high school or college introductory biology texts, this primer on developmental biology and evolutionary developmental biology may be useful for some readers.

The genetic regulation of segmentation: On the left, patterns of gene expression in a developing Drosophila embryo. On the right, a diagram of the regulatory interactions between the genes which produce this patterning. Arrows indicate positive regulatory interactions, a line ending in a flat line indicates negative feedback.    Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Blackwell Publishing:Cambridge, MA, p. 59, fig. 3.5The genetic regulation of segmentation: On the left, patterns of gene expression in a developing Drosophila embryo. On the right, a diagram of the regulatory interactions between the genes which produce this patterning. Arrows indicate positive regulatory interactions, a line ending in a flat line indicates negative feedback.

Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Blackwell Publishing:Cambridge, MA, p. 59, fig. 3.5

A good resource for the basic background necessary is From DNA to Diversity by Sean Carroll, or his book Endless Forms Most Beautiful. Carroll describes developmental biology in terms of "tool kits" of genes. A group of genes which interact and regulate one another's expression would form such a tool kit, and such kits can operate as somewhat independent modules. "Modularity," explains Rasmus Winther, "is central to the current evolutionary developmental biology synthesis" (R. G. Winther, 2001, "Varieties of Modules: Kinds, Levels, Origins, and Behaviors," J. Exper. Zool. (Mol. Dev. Evol.) 291:116–129). How those modules interact is controlled by other toolkits, producing a hierarchy of kits. For example, in Drosophila, five hierarchal tiers of regulation (maternal effect, gap, pair-rule, segment polarity, and homeotic) are involved in organizing the body pattern along the axis from head to tail of the developing embryo. Each segment of the body is produced through interactions between gene products translated from mRNAs deposited in the egg by the mother, transcriptional activation of genes in the egg by such maternal activators, and combinatorial action of segmentation gene products (tool kits) to refine the expression patterns of many zygotic genes.

Explore Evolution skips any presentation of this regulatory network of tool kits and invites the students to compare the regulation of body segmentation in fruit flies and wasps, declaring: "The body segments of some wasps arise from developmental pathways that are entirely different from those of fruit flies, and even from other wasps" (EE, p. 44). The student has no way to evaluate this claim, nor to judge its significance, because high school biology texts rarely cover developmental biology, and EE certainly doesn't offer that background. In the diagram of Drosophila segmentation shown above, the seven stripes that make up the expression patterns of the primary pair-rule genes hairy and even-skipped are controlled independently. That is, different regulatory elements control the expression of different stripes.

Wasp vs. fly development: A hypothesis about the evolution of the the developmental role of the even-skipped (eve) gene.  The gene is present in all insects, and in most it plays a role in defining the embryonic segments.  It does not play that role in some species, either because that role evolved later, or because it has been independently lost in two lineages.  In one lineage, the early development is constrained because the wasp lives as a parasite within another insect, and another gene regulates segment development.Image from Gregory A Wray and Ehab Abouheif (1998) "When is homology not homology?" Current Opinion in Genetics and Development. 8(6):675-680Wasp vs. fly development: A hypothesis about the evolution of the the developmental role of the even-skipped (eve) gene. The gene is present in all insects, and in most it plays a role in defining the embryonic segments. It does not play that role in some species, either because that role evolved later, or because it has been independently lost in two lineages. In one lineage, the early development is constrained because the wasp lives as a parasite within another insect, and another gene regulates segment development.

Image from Gregory A Wray and Ehab Abouheif (1998) "When is homology not homology?" Current Opinion in Genetics and Development. 8(6):675-680

In the wasp species mentioned in Explore Evolution, the same segments are produced even though the even-skipped gene is not expressed at the point when it would be in Drosophila. Nevertheless, the gene which normally follows the expression of even-skipped (engrailed) is not affected, and instead, acts to facilitate normal patterning and segmentation. The wasp species lays its eggs in other insects, and the egg develops as a parasite within the other insect. In order to survive in this environment, the egg structure is modified in many ways, and expression of even-skipped during early development is apparently affected by these changes. The gene still exists, and is expressed at other times. Because of the modular nature of developmental toolkits, the eve toolkit can be switched off early on without affecting later stages in development.

Examining the details of this evolutionary process led researchers to make specific predictions. Observing that the eggs of other parasitic wasps have similar adaptations, and noting the similarities of later developmental patterns across insect species:

we would predict that changes in patterning mechanisms will occur in other … insect taxa that exhibit shifts in life history that favor the loss of yolk or early cellularization. By contrast, … insects with ectoparasitic or free-living life histories will exhibit patterning mechanisms that resemble those of Drosophila.
Miodrag Grbić and Michael R. Strand (1998) "Shifts in the life history of parasitic wasps correlate with pronounced alterations in early development," Proceedings of the National Academy of Sciences. 95(3):1097-1101

Not only does an understanding of the full complexity of developmental patterning clarify the evolutionary basis for this variation in developmental pathways, it yields new, testable hypotheses. The process of scientific inquiry rests on that cycle of proposing hypotheses, making predictions, and testing those predictions. An inquiry-based textbook would revel in those opportunities, would show students how scientists construct new hypotheses and test them, and would encourage students to make and test their own hypotheses. Explore Evolution is not inquiry-based. Their discussion of subjects of active research consistently gives the impression that unanswered questions must be unanswerable. This attitude is not merely unscientific, it is anti-scientific.

Gene regulation in insect wings and vertebrate limbs: Changes in the set of genes targeted by a conserved selector gene explain the divergence of homologous structures: insect hindwings (a) and vertebrate forelimbs (b). The conserved expression of selector genes Ubx (insect hindwings) and Tbx5 (vertebrate forelimbs) indicates that ancestral forelimbs of vertebrates also expressed these genes and the ancestral hindwings of insects. While the selectors regulated certain target genes (colored boxes) in the ancestral appendage, a different set of genes came to be activated in different lineages, resulting in the evolution of morphologically and functionally divergent homologous structures in modern taxa.    Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Blackwell Publishing:Cambridge, MA, pg. 5.16, 144Gene regulation in insect wings and vertebrate limbs: Changes in the set of genes targeted by a conserved selector gene explain the divergence of homologous structures: insect hindwings (a) and vertebrate forelimbs (b). The conserved expression of selector genes Ubx (insect hindwings) and Tbx5 (vertebrate forelimbs) indicates that ancestral forelimbs of vertebrates also expressed these genes and the ancestral hindwings of insects. While the selectors regulated certain target genes (colored boxes) in the ancestral appendage, a different set of genes came to be activated in different lineages, resulting in the evolution of morphologically and functionally divergent homologous structures in modern taxa.

Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Blackwell Publishing:Cambridge, MA, pg. 5.16, 144

Observations of the way that genetic changes can affect development of homologous structures have led scientists to make many fundamental and testable hypotheses about the evolution of the shape of the body. Some developmental biologists argue that the independent control of distinct regulatory tool kits is one of the most important concepts in the spatial regulation of gene expression in animal development, and plays a central role in the evolution of morphological novelty. Certain tool kits may be more modular than others, which could explain the pattern Wagner (2007) observes, that developmental variation in homologous characters is not randomly distributed, but affects some aspects of development more than others.

On the topic of the evolution and diversification of homologous body parts, Carroll offers two excellent examples, the insect hindwing and the vertebrate forelimb (figure at right). He explains how homologous structures, such as the fly haltere and butterfly hindwing are determined by different genes. There is conservation of selector gene expressions, in both cases the insect hindwing is ultimately controlled by Ubx. The same regulator gene acts on different sets of target genes to create variation in morphology in these lineages. Development of the vertebrate forelimb is much the same, with the same selector gene Tbx5 controlling different target genes to produce different morphologies in birds and humans, which are homologous in their basic structure but show variation in the developmental pathways.

The inadequacies in Explore Evolution are especially apparent in its treatment of gut development. They fail to cite the source for their claims about the different origins of the vertebrate gut (though it is presumably Gavin de Beer, 1971, Homology: an Unsolved Problem. Oxford: Oxford University Press; 1971). Because they are citing a passing reference in a 37 year old summary, their terminology is imprecise, failing to clarify what cells they are talking about, or to provide any background information that students might need to understand what the embryonic cavity might be, or how the gut develops from it. Students have no hope of understanding the example. This would be surprising in any other textbook, but confusion seems to be an objective of Explore Evolution.

[The paragraphs in italics may be too speculative, and might be worth cutting. I'm leaving them in so that I remember what I figured out about this, but won't weep if they're deleted.]

[The cavity they refer to is formed early in embryonic development. When the embryo has only a few hundred cells, it forms a hollow sphere with walls one cell thick. One wall pushes in, leaving two walls (the outer cells are called the ectoderm, the inner are endoderm) with a gap between them, and a central cavity (called the yolk sac). The gap between the walls fills with a third type of cells, called mesoderm. The gut forms when a tube of endoderm closes off from the rest of the yolk sac. Different groups of vertebrates form that tube in different locations within the yolk sac. This does not mean that homologous cells are not involved, nor that homologous genes are not involved. Because the endoderm forms when the outer wall pushes in, a small shift in the location of the beginning of that endoderm could mean that descendants of homologous cells (cells which originated from similar patterns of cell division, or which express the same toolkit genes because of a shared developmental trajectory early on) would wind up in very different parts of the embryo.]

[Another possibility is this simply illustrates the modularity of the developmental tool kits that control gut development. Because the genetic tool kit controlling gut development has not been fully worked out, it is not known what signal initiates the formation of that tube, nor how that signal differs between different lineages of vertebrates.]

[These and other hypotheses about the formation of the gut are subjects of ongoing scientific inquiry.] The development of the vertebrate gut has not been as intensively studied as other structures, and the process by which scientists gain new knowledge and test new hypotheses can be easily presented to students with some background in developmental biology. As Didier Y. R. Stainier observes:

[The gut's] location deep within the body has until recently hampered investigation into its formation. The patterning of the gut … is one of the fascinating issues that pertain to the development, function, and homeostasis of this understudied organ.

At first glance, the gut looks deceptively simple …. Yet in evolutionary terms, the gut, as an endodermal organ, predates any mesodermal organ, and it has reached a level of complexity and sophistication that is only starting to be appreciated.

Over the past decade or so, studies in a number of invertebrate and vertebrate model systems … have provided insights into the genes and cellular mechanisms regulating endoderm formation. These studies have revealed a high degree of conservation in some of the transcriptional regulators of endoderm formation; for example, members of the Gata and Forkhead transcription factor families have been implicated in this process across the phyla, although the intercellular events regulating endoderm formation appear to be more divergent. The Wnt signaling pathway has been implicated in the formation of the endoderm in [invertebrates], whereas transforming growth factor–b (more specifically Nodal) signaling has been implicated in the formation of the endoderm in vertebrate embryos. However, this apparent lack of conservation of the signaling pathways regulating endoderm formation probably reflects our incomplete understanding of the process. Indeed, we have not yet gained sufficient knowledge to control the efficient differentiation of mammalian stem cells into endoderm, meaning that the investigation of endoderm formation must proceed using multiple approaches in multiple model systems.

Compared to readily accessible organs such as the limb, or to organs such as the heart and pancreas that are the focus of resourceful charities, the gut has been left behind. However, it is clear from the few vignettes presented here that the many fascinating developmental, evolutionary, and medical aspects of the gut will continue to attract much attention and generate pertinent information.
Didier Y. R. Stainier (2005) "No Organ Left Behind: Tales of Gut Development and Evolution" Science 307(5717):1902-1904

New technologies and improved techniques are only beginning to allow us to investigate the forces driving the development of the vertebrate gut. Scientists know that situations like this are thrilling chances to dramatically increase our understanding of the world. The aversion to inquiry that runs throughout Explore Evolution could not be clearer than in its brief, dismissive and submissive handling of this area of active research.

Fortunately, scientists can refer to the development of other structures to help inform this research. Mary Jane West-Eberhard describes one example:

Formation of the notochord and spinal cord: Because of the modularity of developmental processes, homologous morphological structures can be produced through divergent pathways. As West-Eberhard notes: "comparative development can be used to trace homology, but developmental differences do not negate it" (p. 496).    Image from p. 495 of Mary Jane West-Eberhard (2003) Developmental Plasticity and Evolution, Oxford University Press:Oxford. 794 p.Formation of the notochord and spinal cord: Because of the modularity of developmental processes, homologous morphological structures can be produced through divergent pathways. As West-Eberhard notes: "comparative development can be used to trace homology, but developmental differences do not negate it" (p. 496).

Image from p. 495 of Mary Jane West-Eberhard (2003) Developmental Plasticity and Evolution, Oxford University Press:Oxford. 794 p.
Perhaps the most impressive illustration of endpoint conservation despite different developmental pathways occurs in the ontogeny of the chordate neural tube. The neural tube is a distinctive embryonic trait at the phylum level — a "phylotypic" or "archetypical" trait. Not only is it present in all chordates, but it is essential to normal development of the nervous system and other structures. In most chordates, the neural tube of the head and trunk is formed when an epithelial sheet, the pre-ectoderm, rolls inward to form a tube, whereas the neural tube of the tail forms by coalescence of cells as a solid rod that then becomes hollow to form a tube (figure [at right]). In teleost fish and lampreys the latter mode of neurulation prevails over the entire body length. Clearly the chordate neural tube can be formed by quite different morphogenetic means, and the exact path and means of morphogenesis are not linked closely to the developmental fate of cells.

Because of highly flexible developmental interactions … that include such devices as induction by an organizer of multipotent cells, and highly flexible cell migration, this major difference in developmental origin of the neural tube does not affect the ability of the embryo to organize itself into the standard chordate body plan. The neural plate always arises near the notochord, and the notochord is always surrounded by the neural tube, somites and gut. This arrangement in turn accommodates numerous specializations of later development. Even though neural tube formation and other processes may undergo circuitous evolutionary change, the chordate body plan is conserved.

Given the developmental divergence, should we regard the neural tubes as homologous in all chordates? On one level, yes: the phylotypic stage is conserved by flexible mechanisms held in common due to common descent. On another level, no, because developmental sequence may reveal convergent derivations of such structures as the neural tube. Examples like this support the conclusion that "the similarity of homologous characters cannot be explained or caused by the invariance of developmental pathways" (Wagner, 1989, p. 1163), even though developmental pathways may illuminate homology.
Mary Jane West-Eberhard (2003) Developmental Plasticity and Evolution. Oxford University Press:Oxford. 794 p., pp. 495-496. Citations omitted, except for Wagner, G. P. (1989) "The origin of morphological characters and the biological basis of homology." Evolution 43:1157-1171.

The modularity of developmental toolkits allows these changes in the timing or location of development. Redundancies in the developmental pathway allows the removal of certain stages in development without preventing development of the final form, and the self-sufficiency of tool kits allows the same structure to originate at a different stage in development or from a different part of the organism. This does not undermine the assessment of homology, it merely shows that the definition of homology offered in Explore Evolution is inadequate, an error which, once again, undermines their treatment of an important topic.

Homology via different genes or developmental pathways

Summary of problems with claim:

The study of how genes control the development of structures is changing rapidly. An important lesson scientists are learning is that developmental pathways are modular, and that it is possible to replace one module in a pathway without changing the end result. Putting the differences in developmental pathway into an evolutionary context clarifies how homologous adult structures could be produced by slightly different means.

Full discussion:

Explore Evolution claims:

other scientists simply dispute the neo-Darwinian explanation of homology. They contend that there are important facts about homologous structures that Common Descent cannot explain.

They point out that when two or more adult structures appear to be homologous, neo-Darwinism tells us that those structures should have been built by homologous developmental pathways and homologous genes.

Contrary to these predictions, biologists are learning that homologous structures can be produced by different genes and may follow different developmental pathways.
EE, p. 44

These observations would only create a problem for common ancestry if EE were correct to assert that "homologous … structures should have been built by homologous developmental pathways and homologous genes." Like so many other statements in EE, this assertion is wrong, and to understand the examples Explore Evolution gives, it is necessary to provide more of a background in developmental biology than the authors do. See the Primer subsection for more detail.

In brief:

  • Redundancies in developmental pathways allow the removal of certain stages in development without preventing development of the final form;
  • The self-sufficiency of genetic "tool kits" allows the same structure to originate at a different stage in development or from a different part of the organism.

These evo-devo findings do not undermine assessments of homology, it merely shows that the definition of homology offered in Explore Evolution is inadequate, an error which, once again, undermines their treatment of an important topic.

For more on this issue, see the entry at the Index of Creationist Claims.

Non-homology via homologous genes

Summary of problems with claim:

The basic problem with this claim, as with the one before, is it relies on a fabricated simplistic assumption, a strawman, that, "[a]ccording to neo-Darwinian theory, the development of non-homologous structures should be regulated by non-homologous genes." (pg. 44)

Full discussion:

Explore Evolution presents this example:

Consider, for instance, the eyes of the squid, the fruit fly, and mouse. The fruit fly has a compound eye, with dozens of separate lenses. The squid and mouse both have single-lens camera eyes, but they develop along very different pathways, and are wired differently from each other. Yet the same gene is involved in the development of all three of these eyes.
EE, p. 44

Darwin admitted the evolution of a structure as complex as the eye was difficult, but not impossible, to imagine. Darwin hypothesized that a complex eye could develop through a gradual transition from some type of prototype or simple eye. In fact, anatomists have discovered numerous intermediates between the more primitive prototype and the vertebrate eye. The full range of transitional structures has been observed within living snails (see Salvini-Plawen and Mayr, 1977, "On the evolution of photoreceptors and eye," Evolutionary Biology 10:207-263).

If indeed the vertebrate eye developed from intermediates found in other groups, wouldn’t we expect to find some of the same genes involved in the organization of these structures? At the developmental level, according to Carroll, both the mouse Pax6 and the fruit fly ortholog eyeless are involved in regulatory networks that direct eye development. It is therefore not surprising that we find the same gene involved in eye morphogenesis, even when the general morphology of the eye shows variation.

The ancestor of insects and vertebrates would have had light sensitive organs of some sort, and some regulatory gene would have controlled the development of such structures. That gene is a shared, derived trait uniting many groups of animals, including insects and vertebrates. From that ancestral population, one group went on to produce the compound eyes associated with insects, a trait that is a synapomorphy within the arthropods (a group including insects, lobsters and similar species). The vertebrate eye's particular anatomy is a shared, derived characteristic within that group. The consistency of such hierarchies of synapomorphies is what evolutionary biologists use to identify the patterns of common descent within living things.

Responding to a claim similar to that in EE, David Cannatella explained:

Here the faulty logic lies in equating different hierarchical levels, the beginning and ends (genes and eyes) of the developmental cascade. The presence of the Pax-6 gene is probably a synapomorphy of a large group of metazoans, and thus the Pax-6 genes are homologous. But the distribution of the character state "eyes present" on the phylogeny of metazoans requires homoplasy, and the eyes of insects and vertebrates are independently evolved.
David Cannatella (1997) "Review of Homology. The Hierarchical Basis of Comparative Biology. by Brian K. Hall and Homoplasy. The Recurrence of Similarity in Evolution. by Michael J. Sanderson; Larry Hufford", Systematic Biology 46(2)366-369.

According to Wagner (2007) the more parsimonious interpretation of the genetic similarity between the vertebrate and insect eyes is that Pax6 is part of the ancestral cell-differentiation pathway for photoreceptors and was then separately incorporated into the identity networks for both types of image forming eyes.

Evolution of eye development: The pattern of species in which Pax-6 is involved in eye evolution indicates that it played a role in the development of light-sensitive structures in the common ancestor of modern bilaterians.    Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Blackwell Publishing:Cambridge, MA, Fig. 3.5 pg. 59Evolution of eye development: The pattern of species in which Pax-6 is involved in eye evolution indicates that it played a role in the development of light-sensitive structures in the common ancestor of modern bilaterians.

Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee (2001) From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, Blackwell Publishing:Cambridge, MA, Fig. 3.5 pg. 59

The above observation also allows biologists to form some testable predictions, an important part of any inquiry-based process, disappointingly absent from the supposedly inquiry-based Explore Evolution. We should expect to find Pax6 expression involved in eye morphogenesis in all the descendants of Urbilateria, the common ancestor of insects and vertebrates. The figure at right shows Pax6 that is indeed expressed during eye development in many bilaterian phyla, confirming the evolutionary prediction.

Detailed research on the genetic control of eye development has revealed that the role of pax6 and eyeless is far from the simple story that Explore Evolution presents. A review in 2006 explained that:

Historical views on eye evolution have flip-flopped, alternately favoring one or many origins. Because members of the opsin gene family are needed for phototransduction in all animal eyes, a single origin was first proposed. But subsequent morphological comparisons suggested that eyes evolved 40 or more times independently; this finding is based on, among other things, the distinct ontogenetic origins of eyes in different species. For example, the vertebrate retina arises from neural ectoderm and induces head ectoderm to form the lens, whereas cephalopod retinas result from invaginations of lateral head ectoderm, ultimately producing an eye without a cornea. Multiple origins were also supported by an elegant simulation model. Starting from a patch of light-sensitive epithelium, the simulation, under selection for improved visual acuity, produced a focused camera-type eye in less than 4 x 105 generations. For animals with generation times less than a year, this would be less than a half million years.

>The idea that eyes arose multiple times independently was challenged by the discovery that a single developmental gene, pax6, can initiate eye construction in diverse species. However, subsequent work has shown that pax6 does not act alone and that building an eye requires suites of interacting genes. Discussion about the evolutionary origins of eyes was invigorated by the discovery that homologous genes can trigger construction of paralogous systems for photodetection, just as homologous hox genes do for paralogous body parts across phyla.

For Drosophila photoreceptor arrays, it is now known that seven genes [eyeless (ey), twin of eyeless (toy) (both of which are pax6 homologs), sine oculus (so), eyes absent (eya), dachshund (dac), eye gone (eyg), and optix] collaborate. These genes, in combination with the Notch and receptor tyrosine kinase pathways and other signaling systems, act via a complex regulatory network.

Deletion of any one of the seven genes causes radical reduction or complete loss of the Drosophila eye. Yet in collaboration with certain signaling molecules, any one of them, except sine oculus, can cause ectopic expression of an eye. Like other developmental cascades, a network of genes is required for organogenesis. Six1, Dach, and Eya are important in the formation of the kidney, muscle, and inner ear, as well as eyes, which suggests that this suite of genetically interacting gene products may have been recruited repeatedly during evolution for formation of a variety of structures.

Appearance of photodetection systems probably happened many (possibly hundreds of) times, until selection produced at least the two independent, main types of photoreceptor types known today—ciliary and rhabdomeric.
Russell D. Fernald (2006) "Casting a Genetic Light on the Evolution of Eyes" Science 313(5795): pp 1914-1918

The pax6 gene family is not the only gene with a role to play in eye development, and the particular combination of genes which produce eyes in modern species was assembled by a process of gene duplication, mutation, recombination, and natural selection. Parts of those developmental pathways are homologous across many species, but other aspects were assembled from preexisting combinations of interacting genes active elsewhere in the body which were drawn together independently, perhaps as many as 40 different times over the evolutionary history of life.

This means that the possession of pax6 is a shared, derived character across the bilaterians, but the particular expression of pax6 in the development of the eye is a shared, derived character within smaller subgroups, a trait which evolved several times, built on the nested hierarchy of evolutionary histories of all those groups.

Misquoting

The flaws in this chapter go deeper than merely deepening confusion over basic concepts and omitting references to work which address questions they raise. At critical points, EE quotes biologists in ways which misrepresent their views and distort the state of scientific and philosophical discourse about homology and related concepts. To present the discredited 19th century quibbles of Louis Agassiz as if they had never been addressed is ahistorical and absurd. Claiming that Brian Goodwin rejects evolution as a force which explains homology is plainly wrong. David Wake's concerns over the philosophical definition of homology does not reflect any objection to the use of biological similarity and difference to develop and test hypotheses about evolution. This merely reflects EE's needless focus on a single word, rather than the way that evolutionary biology is actually practiced in the 21st century.

Brian Goodwin

Summary of problems:

Some similarity of shape might be explained by "natural laws," more commonly referred to among evolutionary biologists as constraints. Such constraints arise through restrictions on the range of variation capable of being produce. Brian Goodwin researches ways in which fundamental mathematical principles place limits on evolution. Such constraints will not be evolutionarily informative, since natural selection can only operate on available variation. EE wrongly claims that Goodwin's research is an alternative to homology, when it actually relies on homology and common descent.

Full discussion:

The authors of EE move their inaccurate presentation of homology forward from irrelevant discussions of 19th misunderstandings of evolution to the 20th century in this brief account of Brian Goodwin's process structuralism. They cite Goodwin's work as a challenge to evolution, but this misrepresents his views. Goodwin views evolution through a different lens, but does not deny universal common descent nor the power of the full range of naturalistic evolutionary processes. Goodwin suggests that there are biological rules constraining the sorts of growth patterns that are possible. These limits to the available forms of morphological variation explain various recurring evolutionary patterns. Natural selection acts on a restricted number of possibilities, which explains why evolution has produced less diversity than he might otherwise expect. The authors misrepresent Goodwin's work. Goodwin debates the processes important in evolution, not whether evolution has occurred or whether organisms share common ancestry, let alone the validity of homology.

Goodwin's recent discussion of the vertebrate limb provides a clear sense of his concerns:

An extraordinary thing about our limbs is that they are essentially the same as those of all other tetrapods … Given th[e] diversity of uses [in various tetrapods], one might have expected that natural selection would have designed each limb to optimally serve its functions. Why doesn't the bat's wing start with two bones to anchor it firmly to the shoulder? Why does the horse have that tiny extra bone running like a splint down the side of its main "toe," with another similar one on the other side of the toe? What possible function can they serve? Why not get rid of them altogether? Given their extraordinary utility and the fact that [ancestral tetrapod] Ichthyostega had seven, why don't we have six digits on each hand and banish that rather useless little toe that is so prone to getting stubbed? The answers to these questions usually take the form: Natural selection has to make do with what is given by ancestral form, molding it as best it can to a variety of purposes. But then we are left with the problem: Where does this ancestral form come from, and why is it as it is? Is it just a historical accident, or is there a deeper reason for the basic pattern of tetrapod limbs that provides a rational unity of structure underneath the diversity of functional expression?

Selection has no intrinsic principles that can explain why a structure such as the tetrapod limb arises and is so robust in its basic form: it just appeared in a common ancestor. This leaves a very large hole in biology as an explanatory science … But only in this century have the mathematical tools … been developed allowing us to address the issues of invariance, symmetries and symmetry breaking in complex nonlinear dynamic processes, and giving us insight into the origins of the structural constraints that can explain distinctive features of biological form such as tetrapod limbs. No blame to Darwin for shifting biology onto a different track and sacrificing rational unity for historical unification. There is no reason we cannot have both.
Brian Goodwin (2001) How the Leopard Changed Its Spots Princeton University Press:Princeton, NJ, 252 p., pp. 142-147

Goodwin does not object to the Darwinian explanation, he wishes to supplement it, and to explain why certain forms of variation are available to natural selection, and others are not. A bat could only evolve a more efficient wing hinge (like that found in insects) if there were a way to produce a second anchor point, and Goodwin's objective is to explain why that variation does not come about, but the variation which we do see in tetrapod limbs could and did come to be. This work provides a mathematical basis for research into the ways in which developmental tool kits (discussed in the following claim) operate to organize morphology.

Explore Evolution incorrectly claims that Goodwin "explain[s] homology in another way," saying that "homology does not reflect a process of historical change, but instead reflects constraints imposed by the laws of nature" (EE, p. 43). The passage above clearly demonstrates this to be false. He not only grants, but celebrates, the historical explanation that evolutionary explanations offer. His work offers a set of explanations on top of those historical explanations.

Goodwin's ideas remain controversial, and the links between his mathematical models and the underlying biological processes remain incomplete. Earlier attempts at the sort of unification he is offering have failed on those same grounds. Alan Turing, the father of modern computer science, did some of the earliest work seeking mathematical models which would explain morphological change in terms of simple mathematical concepts. While his math was correct, later work on the molecular basis of development revealed that his models were oversimplified and biologically incorrect. They remain useful in other settings (including manufacturing), and provide a philosophical basis for Goodwin's approach.

For reasons discussed in the previous claim and below in the section on convergence, the sort of similarity that Goodwin's models might predict would not be sufficient to explain homology. His discussion of eye evolution acknowledges and relies on this shortcoming. The consistency of the basic form of the eye is evidence of developmental and functional constraints, but differences in developmental pathways and morphology (structure) provide evidence of multiple origins of the eye in multiple lineages. Eyes, he explains have "evolved independently in at least 40 different lineages. Eyes seem to pop up all over the evolutionary map, and each time they present the same challenge … How could random, independent events ever generate such an inherently improbable, coherently organized process as that required to generate a functional visual system in the first place? What I suggest is that eyes are not improbable at all. The basic processes of animal morphogenesis lead in a perfectly natural way to the fundamental structure of the eye" (Goodwin, 2001, p. 162). EE summarizes Goodwin by claiming that "we should expect to see similarities in the anatomical structures of even different types of organisms" (EE, p. 43). There is a difference between similarity of form (Goodwin's topic) and similarity of structure (the topic of interest in studying homology). In conflating these topics, Explore Evolution confuses the issue of homology, misrepresents the scientist they cite, and skips a chance to help students understand cutting edge research in biology. This is not acceptable for a textbook.

David Wake

Summary of problems with claim:

Wake's point is that the term "homology" was coined in a pre-evolutionary context, and that it has proven difficult to construct a definition of homology which fully incorporates what we understand about the evolution of anatomical structures. He argues that we ought to "stop talking about homology" because there are other terms which better capture our current understanding of how phenotypic characters pass from generation to generation.

Full discussion:

From Exploring Evolution:

Faced with the difficulties in explaining anatomical homology, some evolutionary biologists have given up on the notion. They argue that "the only way out of this dilemma is to stop talking about homology." One such biologist, David Wake of the University of California—Berkeley, argues that "homology is not evidence of evolution, nor is it necessary to understand homology in order to accept or understand evolution."
EE, p. 49

In the abstract to the paper quoted by Explore Evolution, David Wake explains his concerns about the word "homology":

Our attempts to recycle words in science leads to difficulty, and we should eschew giving precise modern definitions to terms that originally arose in entirely different contexts. Rather than continue to refine our homology concept we should focus on issues that have high relevance to modern evolutionary biology, in particular homoplasy — derived similarity — whose biological bases require elucidation.
David Wake (1999) "Homoplasy, homology and the problem of 'sameness' in biology," Novartis Foundation Symposium. 222:24-46.

Far from minimizing the importance of homology, he is arguing that the existence of biological similarity in related species is less interesting than the parallel or convergent evolution of similar forms in different species. In many ways, Wake's research parallels Brian Goodwin's interests in the forces which drive similarity in the absence of common ancestry (discussed elsewhere in this critique).

Wake has spoken out against the view that homology is not important to biology:

Homology is the central concept for all of biology. Whenever we say that a mammalian hormone is the "same" hormone as a fish hormone, that a human gene sequence is the "same" as a sequence in a chimp or a mouse, that a HOX gene is the "same" in a mouse, a fruit fly, a frog, and a human — even when we argue that discoveries about a roundworm, a fruit fly, a frog, a mouse, or a chimp have relevance to the human condition — we have made a bold and direct statement about homology.
Wake, D. B. (1994) "Comparative terminology. [Review of] Homology: The Hierarchical Basis of Comparative Biology (B. K. Hall, ed.). Science 265:268-269.

In that same review, Wake explains his concerns with the use of the term homology:

My conviction is that evolutionary biologists are making ancient words serve too many masters. We take pre-Darwinian terms like "species, "adaptation," and "homology" and try to give them exact modern meanings, but technical meanings require technical terms, and it is time to abandon idealism in favor of pragmatism and utility. It is sufficient to "know" that homology, like truth, exists, and to proceed to use, or coin, more appropriate terms for specifying what we mean in a modern scientific context.
Wake, D. B. (1994) "Comparative terminology. [Review of] Homology: The Hierarchical Basis of Comparative Biology (B. K. Hall, ed.). Science 265:268-269.

As discussed above, the problems with the concept of homology have been a subject of debate since the term was coined, and remain topics of ongoing discussion. The issue is not whether patterns of shared descent are important for documenting evolutionary history, but whether the word "homology" is the best way to describe how we identify those patterns. In the discussion above, we have described some of the ways that biologists have resolved these problems, the ways that Explore Evolution misrepresents scientists' views, and the ways that scientists formulate and test evolutionary hypotheses, including hypotheses about homology.

Explore Evolution badly misrepresents their views in asserting that the problem with "homology" has any connection to "difficulties in explaining anatomical homology" (EE, p. 49).

Molecular Homology

Molecular homology is an important concept in modern evolutionary biology, used to test the relationships between modern taxa, and to examine the evolutionary processes driving evolution at a molecular level. It is a rapidly changing field, and one that students who wish to "explore evolution" should surely understand. Explore Evolution will not provide that understanding.

The book focuses too narrowly on peripheral topics, without giving students an appreciation of the techniques and concepts central to molecular biology and molecular systematics. Explore Evolution only considers homologies in DNA sequence, but scientists also examine homologous amino acid sequences in proteins (which can result from several different DNA sequences), and homologous protein folds (which can result from numerous different amino acid sequences). Before it was practical to sequence genomes, scientists also used simpler measures like molecular size and electrical charge to identify similarities and differences between molecules.

Rather than surveying this range of homologies, Explore Evolution focuses on a few minor points: the consistency of the code for translating between nucleic acids and amino acids, the ability to estimate the timing of evolutionary divergence based on molecular divergence, modest and predictable differences between the patterns of homology in different genes, and genes that seem to have no homologs in other species. In each case, the account given is misleading and inaccurate, reflecting creationist misconceptions rather than the best science.

p. 58: "Biologists have long thought that the genetic code is basically the same in all organisms."

Since the genetic code was first identified, biologists knew that small variants were possible, and existed. Such small variants do not undermine the basic consistency of the code.

p. 59: "advocates of universal common descent have always assumed that a change in code was not survivable"

Scientists have known that the code does vary since at least 1968. Such variants do not undermine the evidence for common ancestry, and understanding the mechanism by which such variants evolve strengthens the evidence for a common source of the genetic code.

p. 58: "It's very hard to see how an organism could have survived a transformation from the standard code"

Mechanisms for this transformation are understood and have been studied in the lab.

p. 57: "A 'family history' of organisms based on their anatomy should match the 'family history' based on their molecules"

There are many well-studied evolutionary processes that can cause a molecular phylogeny to differ from a phylogeny based on anatomy. These well-understood processes are unmentioned.

p. 57: "Michael Lynch has noted that creating a clear picture of evolutionary relationships is 'an elusive problem'"

Lynch was not referring to all evolutionary relationships, only to distant evolutionary connections. He explains: "Given the substantial evolutionary time separating the animal phyla, it is not surprising that single-gene analyses yield … discordant results." In such distant relationships, "Statistical noise" can make "inferences based on single genes… very misleading."

p. 58: "Carl Woese…now thinks that biology must abandon what he calls Darwin's 'Doctrine of Common Descent'"

Woese is engaged in a technical dispute which Explore Evolution misrepresents consistently. Woese does not question the common ancestry of all animals and plants, nor does he think it unlikely that all modern life descended from a common population of organisms with extensive gene swapping. This is a different form of common ancestry, not a rejection of common ancestry in all forms.

p. 57: "the rate of mutation varies in response to a number of environmental factors"

The citation offered to justify this claim offers no support. The claim is a staple of creationist writings, but has no basis in modern evolutionary biology.

Parents for ORFans: Ongoing research finds homologues for supposed ORFansParents for ORFans: Ongoing research finds homologues for supposed ORFans

p. 60: "a large number of genes code for proteins whose functions we don't understand… ORFan genes"

This is not how ORFans are defined. Some have known functions, others do not code for proteins. While coding sections of DNA with no known homologues were identified early in whole-genome sequencing, continued sequencing efforts have revealed homologues for ever more such sequences.

p. 61: "conflicting phylogenetic trees or ORFans … undermine … Universal Common Descent"

Modern evolutionary biologists have addressed these issues, and the incomplete and inaccurate account in Explore Evolution fails to address the current state of the science, or current thinking on the shape of the tree of life.

p. 61: "Michael Syvanen… Michael Gordon"

Syvanen and Gordon have explored some possible alternative shapes for the tree of life, but neither scientist has changed the state of scientific opinion, nor do either challenge the basic principles of common ancestry of all animal and plant life, or the likelihood that all life descends from a united population of cells at some point, however many lineages entered that population.

Major Flaws:

A Universal Tree of Life: The scientists cited by Explore Evolution do not dispute that multicellular life shares a common ancestry, nor the likelihood that all modern life descended from a single population of ancient organisms that swapped their genes widely.

Evolving Codes and Novel Genes: Explore Evolution cites minor variations in the universal genetic code to undermine common ancestry. The mechanisms behind such variations are well-understood and in fact strengthen our understanding of common ancestry. ORFans, sections of DNA that have the structure of genes but lack homologues in other species, do not undermine claims of common ancestry. As new genomes are sequenced, ever more homologues are found.

Molecular Clocks: Common ancestry, contrary to the claims in Explore Evolution, is not dependent on molecular clocks. Nonetheless, some potential problems cited by the book have been addressed by working scientists. Others are based on creationist misconceptions about molecular clocks, and simply lack scientific basis.

A Universal Tree of Life

Molecular homology, genes shared due to common ancestry, is a powerful tool for reconstructing the history of life. A small fraction of the research in molecular phylogeny is concerned with tracing all life to a common ancestor, or population of ancestors. Explore Evolution ignores the bulk of research in molecular evolution to focus on this narrow topic.

Even within this overly-narrow focus, the treatment is deeply inaccurate. The farther back in time a common ancestor would be, the more opportunities there have been for statistical noise to obscure the evolutionary signal. Explore Evolution emphasizes these more complicated issues, and misrepresents the views of scientists like Michael Lynch, Carl Woese, Michael Syvanen, and Michael Gordon who have addressed the shape of the early tree of life.

Whether or not there was one origin of life or several, the best available science indicates that all modern life descended from a single population of organisms. The species in this ancestral population would have shared genes so readily that the entire population can be treated as the ancestor of modern life. Explore Evolution muddles this new field of research, proposing instead a set of entirely separate trees, a vision of life tendered only by creationists, not by any active researchers in the field.

Do Different Genes Mean Different Phylogenetic Trees?

Phylogenetic trees based on single genes (or small numbers of genes) can differ from one another, but Explore Evolution overstates both the extent of the inconsistencies and their implications for phylogenetic reconstruction. Inconsistencies are most common when analyzing phylogenetic events in the very deep past (such as separation of the main animal groups in the pre-Cambrian), and occur for reasons that are well characterized and indeed predicted based on statistical and evolutionary considerations (changes in evolutionary rates, convergent evolution, etc.). In addition, the recent exponential increase in available sequence data has been shown successfully overcoming these artifacts, generating consistent trees with high confidence. Most importantly, the authors' claim that these discrepancies mean that "molecular evidence cannot be reconciled with the theory of Universal Common Descent" (p. 57) is entirely unsupported.

Yhe authors of Explore Evolution reveal a major gap in their understanding of phylogeny and of much of modern biology when they state:

… if Darwin's single Tree of Life is accurate, then we should expect that different types of biological evidence would all point to that same tree. A "family history" of organisms based on their anatomy should match the "family history" based on their molecules (such as DNA and proteins).
Explore Evolution, p. 57

Phylogenetic trees based on a specific gene (gene trees) and those based on several genetic and anatomical traits map the relationships of different entities, genes and organisms. Inconsistencies in phylogenetic tree reconstructions are a fascinating issue and research addressing these inconsistencies has led to a better understanding of complex evolutionary processes.

Phylogenetic trees reconstructed from different genes in the same organism can differ. The possible causes of such differences are understood, ranging from methodological issues (such as different parameters being applied to the algorithms used to weigh sequence similarities) to bona fide biological phenomena. The latter are more interesting and significant, and are generally due to the effects of recognized evolutionary processes on the history of individual genes: convergence, the same sequence change appearing independently in different lineages either because of similar selective pressures, or by chance; changes in evolutionary rates , certain organisms evolve faster than others; horizontal gene transfer, sequences being transfered from one species to another by mechanisms other than vertical, linear descent; and timing, two lineages radiate from a third in relatively close succession, before enough differences mayhave accumulated between them to be able to discern the order of emergence. Thus, even in the best scenarios, absolutely congruent phylogenies from the analysis of individual genes are not expected. The authors of Explore Evolution make it seem as if biologists are surprised and stumped by these inconsistencies:

Evolutionary biologist Michael Lynch has noted that creating a clear picture of evolutionary relationships is "an elusive problem." He also notes that "analyses based on different genes - and even different analyses based on the samegenes — [yield] a diversity of phylogenetic trees."
Explore Evolution, p. 57

But in the very next paragraph of the same paper, Lynch makes the main underlying issues clear:

Given the substantial evolutionary time separating the animal phyla, it is not surprising that single-gene analyses yield such discordant results. Under such circumstances, the statistical noise associated with the substitution process leads to a high probability that phylogenetic analyses based on different molecules will yield different topologies (Philippe et al. 1994; Ruvolo 1997), so that inferences based on single genes can potentially be very misleading (leaving aside for now the additional problem of orthology).[emphasis added]
Lynch M. "The Age and Relationships of the Major Animal Phyla." Evolution. 1999; 53:319-325.

In Lynch's paper the phrase "elusive problem" and the issue of multiple phylogenetic trees applied specifically to the "phylogenetic relationships of the major animal phyla", i.e. very distant evolutionary events; the Explore Evolution authors craftily presented it as if Lynch was referring to all "evolutionary relationships".

Another example of the issues encountered in phylogenetic reconstruction, and their misrepresentation in Explore Evolution, comes from the following paragraph:

A "family tree" based on anatomy may show one pattern of relationships, while a tree based on DNA or RNA may show quite another. For example, one analysis of the mitochondrial cytochrome b gene produced a "family tree" in which cats and whales wound up in the order Primates. Yet, an anatomical analysis says that cats belong to the order Carnivora, while whales belong to Cetacea – and neither of them are Primates.
Explore Evolution, p. 57

The authors are talking about a review paper by Michael Lee (Lee MSY, 1999 Trends Ecol Evol 14:177-178), in which he refers to data obtained on one of the proteins involved in the respiratory chain in mitochondria, cytochrome b. The figure below shows the tree as presented in Lee's review paper: Cytochrome b phylogenetic tree: from Lee, 1999 Trends Ecol Evol 14:177-178Cytochrome b phylogenetic tree: from Lee, (1999) Trends Ecol Evol 14:177-178

The phylogenetic inconsistency here is the misplacement of a single branch, that of tarsiers (a primitive group of primates), as if they had separated from other primates before cats and fin-back whales. Actually, the data in the original publication (see figure below, Andrews et al. 1998 "Accelerated Evolution of Cytochrome b in Simian Primates: Adaptive Evolution in Concert with Other Mitochondrial Proteins?" J Mol Evol. 47:249–257) gives a slightly different picture, namely that the analysis of cytochrome b sequence is statistically incapable of resolving the phylogenetic relationship of most of the species in the tree (the numbers in the figure represent a measure of the statistical confidence in each branch of the tree, and numbers below 30 generally indicate lower confidence; the statistically robust values are underlined). In other words, cytochrome b is simply not a good protein to choose for constructing the evolutionary tree of these species. But why is that?

Cytochrome b phylogenetic tree: from Andrews et al., 1998; adapted to match layout and nomenclature in Lee, 1999 (see prevoius figure)Cytochrome b phylogenetic tree: from Andrews et al., 1998; adapted to match layout and nomenclature in Lee, 1999 (see prevoius figure)

Both the Andrews and Lee papers suggested, based on other data, that the phylogenetic incongruence in this tree was caused by cytochrome b and other respiratory chain proteins having evolved much faster in some primate lineages compared to other mammals, possibly following unique selective pressures. As mentioned above, both accelerated and adaptive evolution can cause errors in phylogenetic tree reconstruction, masking or enhancing the similarities of related genes, depending on the circumstances. And indeed, in more recent years the accelerated adaptive evolution of respiratory chain proteins in monkeys and apes (but not tarsiers and lemurs) has been extensively confirmed (see for instance Grossman LI, et al. 2004 "Accelerated evolution of the electron transport chain in anthropoid primates." Trends Genet. 20:578-585). Thus, the inconsistency in the cytochrome b tree, rather than highlighting hopeless phylogenetic confusion as alleged in Explore Evolution, is the result of real biological and evolutionary processes. The existence of this extensive literature offers opportunities for an inquiry-based lesson on molecular evolution and evolutionary processes. Instead of offering that lesson, the supposedly inquiry-based Explore Evolution throws up its hands in confusion at any sign of difficulty.

Although molecular phylogenetic tree inconsistencies are hardly a fundamental theoretical concern for evolutionary biology, if persistent they could still cause practical problems in assessing certain evolutionary relationships. However, a number of new approaches have recently emerged that address these difficulties. These methods include the combination of large sets of sequence information from genomic databases, as well as the use of genetic features, such as large-scale structural changes or the mapping of mobile genetic elements, that are less prone to convergence and selection-related artifacts. For a thorough discussion of the potential of these approaches, see Lokas A and Carroll SB, (2006) "Bushes in the Tree of Life" PLoS Biol 4:e352.

Finally, the authors of Explore Evolution conclude:

Critics point out that the real problem may be that Universal Common Descent is wrong. In other words, maybe the reason the family trees don't agree is that the organisms in question never did share a common ancestor. Even some evolutionary biologists agree. Carl Woese of the University of Illinois, for instance, now thinks that biology must abandon what he calls Darwin's "Doctrine of Common Descent".
Explore Evolution, p. 58

Woese argues that the earliest history of life may show multiple early lineages which swapped genes extensively, making reconstruction of the early tree of life difficult. This is very different from the strictly non-overlapping trees Explore Evolution suggests as an alternative to universal common ancestry. Woese argues that these multiple lineages converged into a single population from which modern life, and would absolutely reject the claim that molecular data cannot discern the pattern of common ancestry linking all primates, or the relationship between primates, carnivores, and whales, or indeed the common ancestry of all multicellular organisms.

Phylogenetic Trees and Molecular Family Histories

The authors do not understand phylogeny, and have a very limited understanding of the biological vocabular and issues. They propose that if common descent is correct, then:

A "family history" of organisms based on their anatomy should match the "family history" based on their molecules (such as DNA and proteins).
Explore Evolution, p. 57

This is simply wrong.

Genes and organisms are very different things; gene family trees and organism family trees can, and do, differ. Contrary to the book's statements, evolutionary biology does not expect these trees to match up exactly. Rather, the relationship between genes and organisms is an issue in biology that is under active research in a wide range of fields.

The Last Universal Common Ancestor

Explore Evolution claims that certain scientists dispute the existence of a single universal ancestor, citing authors would not actually dispute universal common descent. They just disagree about the form it took, and the nature of the population of organisms from which modern living things evolved.

An Uprooted Tree of Life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5.  Note that distances are not necessarily to scale in this image.  This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor.  They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.An Uprooted Tree of Life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5. Note that distances are not necessarily to scale in this image. This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor. They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.

As discussed in the critique of the Introduction, there is ongoing research into the nature of the Last Universal Common Ancestor. Scientists traditionally envisioned an ancestral population of a single species which branched and gave rise to the modern diversity of life. More recently, researchers are suggesting that that ancestral population of bacteria was not composed of a single species, but of multiple species which swapped genes freely.

This is the point Michael Syvanen is making when he is quoted by Explore Evolution

Do the puzzles of conflicting phylogenetic trees or ORFans … undermine the theory of Universal Common Descent? Most evolutionary biologists say no. …Others are not so sure. Molecular evolutionist Michael Syvanen of the University of California-Davis argues that, "there is no reason to postulate that a LUCA (Last Universal Common Ancestor) ever existed."
Explore Evolution, p. 61

Once again, Explore Evolution misrepresents the views of a scientist by selecting a phrase that sounds as though evolution were on shaky ground. This 'mined' quote suggests, incorrectly, that Syvanen is arguing against Universal Common Descent. Here is what Syvanen actually wrote, in a paper indicating that genes for certain biochemical pathways had been transferred between lineages long after their divergence:

There has been recent discussion that horizontal gene transfer is so frequent that it may never be possible to reconstruct the last common ancestor. However, if biochemical unities could be achieved after speciation events by horizontal gene transfer, then there is no reason to even postulate that a LUCA ever existed. If horizontal gene transfer is as common as I am implying, the modern cell could have evolved in multiple parallel lineages. Earliest life could have been truly polyphyletic.
Michael Syvanen (2002) "On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes," Journal of Molecular Evolution, 54:258-266

Syvanen is not necessarily disputing Universal Common Descent; he is disputing the existence of a Last Universal Cellular Ancestor [LUCA]. Syvanen is participating in an ongoing debate about the shape of the trunk of the tree of life. As shown in the figure above, some scientists see the evidence of extensive gene flow between ancient bacterial species as a sign that, at the base of the tree of life, lines between lineages were less clear, and that the branches didn't begin separating until a later point. Syvanen explained his views in some more depth in a post at the Panda's Thumb blog, pointing out that our increasingly detailed knowledge of the order in which certain ubiquitous genes evolved places greater and greater constraints on the composition of LUCA, and that "if we accept the existence of this LUCA there are a variety of reasons to believe that the LUCA itself was the product of an evolutionary process that employed horizontal transfer events." The full details of this debate require students to have a grasp of biological details that they will not have until after their high school biology classes, but an inquiry-based textbook might work with students to explain what sorts of research is under way to resolve some of these unresolved issues. Instead, Explore Evolution claims the existence of the discussion as proof that nothing is known, a profoundly unscientific attitude, and an unacceptable approach for a textbook to adopt. The existence of horizontal gene transfer, a major topic in discussions of the early tree of life, is not mentioned in the book's index, glossary, or relevant sections.

Malcolm Gordon

Explore Evolution claims that the common ancestry of life is disputed because:

Biologist Michael Gordon of UCLA argues that the single branching-tree picture of life's history is not accurate, but that life must have had multiple, independent starting points.
p. 61

Malcolm Gordon is an expert in the functional morphology of fish, not the origin of life. His argument in "The Concept of Monophyly: A Speculative Essay." (1999, Biology and Philosophy 14:331–348) is that there was likely to be many different environments where life could have arisen (almost certainly true), and that the mobilities of the first organisms would be limited (also likely to be true), that it is probable (note that he never says must as Explore Evolution claims) there would be sufficient time for more than one origin of life event to occur. However, he vastly underestimates the spreading capacity of even slow growing non-motile bacteria. Anyone who has had the misfortune to have a sterile solution contaminated with a few bacteria can attest to how rapidly they grow, and in the prebiotic environment there would be no competition for them. So again, unless the origin of life is astoundingly easy, the first living organism would have had the field to itself. The near universality of the genetic code is consistent with this scenario, but universal common descent does not require a single origin of life, nor have evolutionary biologists ever required only a single origin of life.

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one …
Charles Darwin, The Origin of Species, 1859, Final paragraph

As that quotation from Darwin demonstrates, the theory of evolution does not, a priori, demand that life could not have more than one independent origin. However, there are several lines of evidence that compellingly suggest that the origin of life was limited to a very few, most probably one, initial population serving as an "organism." The strongest evidence for this idea is the nearly universal genetic code. This does not argue that the genetic code used by current organisms was found in the first life form; there are several alternative codes that would work. But if there were multiple origins for present-day life, we would expect to see significantly different genetic codes. However, all we see are minor mutational variants of the standard code.

Also, the basic biochemistry of organisms is fairly universal. If life had developed multiple times, we would expect to see at least some organisms with a radically different biochemistry, but we just don't see that.

Furthermore, unless the origin of life was exceptionally easy, it took some time for "living organisms" to develop. Hundreds of thousands to millions of years (even if they were simple self-replicating molecules) were likely required. Once the first living organism had developed, within the space of a few decades its descendants would have monopolized the prebiotic Earth, preventing the development of competitor organisms. It is unlikely, even if the origin of life were astoundingly simple, that a second form of life developed within a few years of the first one to prevent the first's monopoly. Even if a second organism had developed independently a few years after, the first organism with its head start would be much fitter, and would likely out-compete the second.

Evolving Codes and Novel Genes

The genetic code, the translation between each sequence of three nucleotides to an amino acid, is shared widely across the tree of life. Explore Evolution seizes upon some small variations in that translation to claim that common ancestry must be wrong.

Contrary to claims in Explore Evolution, the genetic code is still considered to be universal, in that the known exceptions are very minor variations on the same basic code found in all organisms. Long before the discovery of variant codes, it was known that the genetic code can in fact change, and how it can change, based on laboratory findings in bacteria and yeast mutants. We also have a good understanding of the kind of mutations and selective forces that can allow the genetic code to evolve new variants.

We also have a growing understanding of so-called ORFans, coding DNA sequences which don't seem homologous to genes in any other lineage. In the account of Explore Evolution, these are insuperable challenges to evolution, but this misrepresents the current state of knowledge. The more of these apparently unique sections of coding DNA we study, and the more genomes we sequence, the fewer of these ORFans actually seem unique. Many of what were thought to be ORFans actually have families, and Explore Evolution misinforms students by treating these sequences as unsolvable problems.

The Genetic Code

Explore Evolution wrongly state that biologists originally maintained that the genetic code is absolutely universal (invariant); that this absolute universality was considered evidence for common descent; that this would be a reasonable inference because changing the code would be invariably lethal ("not survivable"); and finally, that the claim of universality fell apart in the 1980s with the discovery of variant genetic codes. Thus, the authors claim, the genetic code is not universal and the inference of common descent is in question and life must have "multiple separate origins." They cite physicist Hubert Yockey to justify the claim: "Some scientists think this is a possibility, saying that the evidence may point to a polyphyletic view of the history of life." (p. 59)

There are many problems with this argument, which is based on misunderstanding and misrepresentation of the available knowledge and of the scientific record.

First, contrary to the key assertion, scientists have been aware of natural genetic code mutants since at least the 1960s, and the actual molecular mechanism of some of these mutations (such as "suppressors of amber") was elucidated in both bacteria and yeast (Goodman HM, Abelson J, Landy A, Brenner S, Smith JD. (1968) "Amber suppression: a nucleotide change in the anticodon of a tyrosine transfer RNA." Nature 217:1019-24; Capecchi MR, Hughes SH, Wahl GM. (1975) "Yeast super-suppressors are altered tRNAs capable of translating a nonsense codon in vitro." Cell 6:269-77.) Amber suppressor mutations change the read-out of certain codons from STOP to an amino acid by altering the structure of one of the transfer RNAs. This tRNA recognizes the codons in messenger RNAs and allows the addition of the correct amino acid during protein synthesis. These mutants showed how new variant genetic codes can evolve, and what kind of selective pressures can favor such changes (in this case, the need for reversion of point mutations which introduce deleterious STOP codons in critical genes). Therefore, it was recognized fairly early that the genetic code did not need to be absolutely invariant to be fundamentally shared between all organisms ("universal"). Already in 1966, Francis Crick stated in his Croonian lecture:

The best evidence to date [for the universality of the code] is probably the excellent agreement between the code deduced for E. coli and the mutagenic data … derived from tobacco plants or human beings. There is thus little doubt that the genetic code is similar in most organisms. Whether there are any organisms which use a slightly modified version of the code remains to be seen.
Crick, FH (1967) The Croonian Lecture. "The Genetic Code." Proc R Soc Lond B Biol Sci. 167:331-47
Code Variants: from Knight RD, Freeland SJ, Landweber LF. "Rewiring the keyboard: evolvability of the genetic code." Nat Rev Genet. 2001; 2:49-58Code Variants: from Knight RD, Freeland SJ, Landweber LF. "Rewiring the keyboard: evolvability of the genetic code." Nat Rev Genet. 2001; 2:49-58

Second, the small number of organisms with variant genetic codes and the limited extent of the changes (involving a few codons at most) strongly support the view that these represent new variations of the "standard," universal code, as opposed to independently originated codes. Moreover, the known code variants themselves offer in many cases evidence for common descent, being shared by related organisms according to the established phylogenetic hierarchy, as shown in the figure below, from Knight RD, Freeland SJ, Landweber LF. (2001) "Rewiring the keyboard: evolvability of the genetic code." Nat Rev Genet. 2:49-58, which contains a thorough discussion on the phylogenetic distribution and mechanisms of genetic code variation.

In particular, the authors of Explore Evolution mention the specific example of organisms in which 2 of the 3 "stop codons" have been reassigned to encode for amino acids (change "a" in the figure above). They argue:
It's very hard to see how an organism could have survived a transformation from the standard code to this one. Changing to this new code would cause the cell to produce useless strings of extra amino acids when it should have stopped protein production.
Explore Evolution, p. 58

However, the mechanisms that underly this particular kind of code change in some organisms are known, and undermine the authors' argument. The studies have been performed mainly in Ciliates, a group of unicellular eukaryotes belonging to the Protozoans, which include Tetrahymena, the organism specifically cited by the authors. Notably, Ciliates have a peculiar genomic organization, with hundreds of very small chromosomes, often containing a single gene, organized in two distinct nuclei; moreover, their genes tend to have unusually short sequences past their termination codons. This is important because it means that mutations that suppress termination (such as that mentioned by the authors) are less likely to generate very long amino acid stretches past the normal protein end, and hence to cause deleterious phenotypes. Consistent with this possibility, Ciliates comprise the majority of organisms with alternative genetic codes containing termination suppressors (Knight RD, Freeland SJ, Landweber LF. (2001) "Rewiring the keyboard: evolvability of the genetic code." Nat Rev Genet. 2:49-58; Lopuzone CA, Knight RD, Landweber LF. (2001) "The molecular basis of genetic code change in ciliates." Curr Biol. 11:65-74).

The particular genetic code mentioned by the authors, in which the UAG and UAA codons are used to encode the amino acid glutamine instead of STOP, results from two sets of changes. The first involves a reassignment of the transfer RNA for glutamine to recognize UAG and UAA. Interestingly, this kind of change can occur through intermediates with only partial effects ("wobble") (Schultz DW, Yarus M. 1994 "Transfer RNA mutation and the malleability of the genetic code" J. Mol. Biol. 235(5):1377-80). The second set of changes affects eRF1, one of the proteins involved in recognizing STOP codons (Lopuzone CA, Knight RD, Landweber LF. 2001 "The molecular basis of genetic code change in ciliates." Curr Biol. 11:65-74). Because of this, it is not "very hard" at all, and in fact very possible, to envision gradual evolution of this new genetic code through intermediates in which the codon interpretation is ambiguous; "hybrid codes" in a sense.

To justify the claim that some scientists see variation in the genetic code as evidence against a single tree of life, the authors quote a sentence from a 1992 book by Hubert Yockey, a physicist with an interest in information theory of biological systems. Interestingly, the quote in question is absent from the latest edition of the book. More importantly, in the current edition, Yockey approvingly quotes Francis Crick's suggestion that all extant life forms descended from a small interbreeding population (i.e. common descent), and once again prophesizing the possibility of organisms with variant codes:

Crick (1981), in one of those marvelous intuitions that have led him to so many discoveries, and without the mathematical argument above, has proposed: “What the code suggests is that life, at some stage, went through at least one bottleneck, a small interbreeding population from which all subsequent life has descended… Nevertheless, one is mildly surprised that several versions of the code did not emerge, and the fact that the mitochondrial codes are slightly different from the rest supports this.
Yockey H, (2005) Information Theory, Evolution, and The Origin of Life. Cambridge University Press, 2005, p.102

Here, the authors of Explore Evolution make the fundamental mistake of conflating (either on purpose or due to a misunderstanding of the underlying issues) two very different questions: common descent, whether extant organisms can trace their ancestry to a single population at some point in the past, and abiogenesis, whether life originated only once. Quite obviously the two issues are distinct. It is entirely possible that life originated more than once, but that early life forms were so promiscuous in sharing genetic material that they constituted, from a genetic standpoint, a single population from which all later organisms evolved. Essentially no scientist at this point objects to the possibility of the latter proposition, although some disagree as to the pattern in which various lineages arose from the original population. These differences may affect the extent to which linear, vertical descent lineages can be unequivocally identified when analyzing the deepest phylogenetic relationships (such as the separation of life into the Domains of Eubacteria, Archaea, and Eukarya), but do not change the view that all organisms ultimately are phylogenetically related.

ORFans

Explore Evolution claims:

[Molecular biologists] have been surprised to learn that a large number of of genes code for proteins whose function we don't understand yet. They call these ORFan genes.
Explore Evolution, p. 60

This is not the definition of ORFans. ORFans are "open reading frames," sections of a chromosome with a start codon followed by a stretch of nucleotide triplets and ended by a stop codon and which do not match a known coding DNA sequence in other species. There is no guarantee that these sections even code for a protein, let alone that they have any function. More importantly, these merely have no currently recognized relatives. (Siew N, Fischer D. (2003) "Analysis of singleton ORFans in fully sequenced microbial genomes." Proteins. 53:241-51) Function is not a consideration in defining ORFans. Some of these proteins with no known relatives do have recognized functions (e.g. bacterial virulence factor staphostatin B (1nycA)).

In contrast, we do have many genes that are in recognizable gene families, but whose functions are not clear from their sequence alone. For example, alpha-beta barrel family proteins have a wide variety of functions, and it is difficult to deduce the function of a member from simple inspection. The incorrect definition given in Explore Evolution artificially inflates the purported number of ORFans.

According to evolutionary theory, new genes arise from old genes by mutation … . New genes should resemble the older "ancestor genes." However, these newly discovered genes do not match any sequence that codes from a known protein.
Explore Evolution, p. 61

Most ORFans have relatives found for them rather rapidly as new genomes are sequenced. With the larger databases available now, old ORFans are finding relatives (e.g. in 2004 hypothetical protein Apc1120 was an ORFan, now several relatives have turned up) and fewer new ORFans are being found. Also, we know that proteins can be generated de novo, so not all proteins must be traced back to older ancestor genes.

Thus, there are two claims here:

  1. There are a substantial number of ORFans have no similarity to other sequences and
  2. Common descent assumes all (or a very high proportion) of current proteins all originated with the Last Universal Common Ancestor.

The first claim is deeply misleading and the second is wrong.

Explore Evolution gives the impression that there are many genes with no relation to any other genes (especially by selectively quoting from older papers). In fact while initially many putative genes in a newly sequenced organism may appear to be unrelated to any then known gene, relatives are usually found rather rapidly. When H. influenzae was first sequenced, 64% of its Open Reading Frames (ORF's, putative genes) were ORFans, as of 2003, only 5.2% were. When Mycoplasma genitalium was first sequenced, roughly 30% of its predicted genes were ORFans, and now all have homologues in other lineages.

Explore Evolution quotes the brief review N. Siew, D. Fischer. 2003 "Twenty Thousand ORFan microbial protein families for the biologist?" Structure 11:7-9.

If proteins in different organisms have descended from common ancestral proteins by duplication and adaptive variation, why is it that so many today show no similarity to each other? Why is it that we do not find today any of the necessary “intermediate sequences” that must have given rise to these ORFans?
Explore Evolution, p. 62

This citation ignores the following sentences from that paper:

Regardless of their origin, ORFans may be of two types. Some ORFans may correspond to newly evolved (through a yet unknown mechanism) or to unique descendants of ancient proteins, with unique functions and three-dimensional (3D) structures not currently observed in other families. Alternatively, ORFans may correspond to highly diverse members of known protein families, but with functions and/or 3D structures similar to proteins already known.

As well as the prescient observation:

More sensitive computational methods, such as fold recognition or sequence-to-profile comparisons, may succeed in assigning some ORFans to known families, and thus, their roles and functions may be gained.

This is what has turned out to be the case. By ignoring work in this area since 2003, (including papers from Siew and Fischer published after this mini-review, such as Siew N, Fischer D. (2003) Proteins. 53:241-51), Explore Evolution gives a highly distorted picture of our current understanding of ORFans.

ORFans versus Genome Number: The proportion of ORFans in the genome, as compared to the total number of sequenced genes. As we increase the number of genes sequenced, the percent of ORFans fall. As of 2003, only 5% of long ORFans (ORF's that are unlikley to be simple sequencing artefacts) were unaccounted for. Figure 1, C from Siew, N and Fisher D, PROTEINS: Structure, Function, and Genetics 53:241–251 (2003)ORFans versus Genome Number: The proportion of ORFans in the genome, as compared to the total number of sequenced genes. As we increase the number of genes sequenced, the percent of ORFans fall. As of 2003, only 5% of long ORFans (ORF's that are unlikley to be simple sequencing artefacts) were unaccounted for. Figure 1C from Siew N, Fischer D. (2003) "Analysis of singleton ORFans in fully sequenced microbial genomes." Proteins. 53:241-51). Figure 1, C from Siew, N and Fisher D, PROTEINS: Structure, Function, and Genetics 53:241–251 (2003)

In an inquiry-based class, a teacher might ask the students to suggest reasons why some putative genes appear to be ORFans. Once students generated that list, the teacher could encourage students to generate testable hypotheses and even to test those hypotheses. Instead of guiding students and teachers along that path, Explore Evolution encourages students simply to surrender in the face of the unexplained, a decidedly inquiry-averse approach. Some of the reasons scientists have offered for genes to remain ORFans includ:

  1. Some ORFans may be artefacts: Many ORFans are very short, 100-150 codons long. It is likely that many of these represent database or annotation errors. Also, in any genome, one would expect some random ORFs being formed. Fukuchi S and Nishikawa K. ("Estimation of the number of authentic orphan genes in bacterial genomes." DNA Res. 2004 Aug 31;11(4):219-31, 311-313.) closely examined sequences and estimated that about half of all short ORFans are sequencing or other errors.
  2. Some ORFans may have relatives, but we haven't sampled enough genomes yet. As of 2003, when most of the ORFan comparisons were done, something like 60 complete bacterial genomes had been sequenced. Note the diagram above, with the continuing fall of ORFans as more genomes are sequenced. By 2006 the percentage of ORFans fell by a further 5% (Marsden RL, et al., "Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space." Nucleic Acids Res. 2006 34:1066-80). More genomes have been sequenced since then, but there are many, many more bacteria that are not yet sequenced, and will have genomes quite divergent from the human pathogens that form the majority of current sequences. This will be especially important because a horizontal transfer from a distantly related bacteria that has not been sequenced will look like an ORFan (until that distantly related bacteria is sequenced). A recent paper shows that many E. coli ORFans are the result of horizontal gene transfer from bacteriophages (Daubin and Ochman, 2004; "Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli". Genome Res. (6):1036-42.). Bacteriophages are viruses, which is why they didn't turn up in bacterial database comparisons.
  3. Some ORFans may have relatives, but our tools aren't good enough to detect these relatives yet. Rapidly evolving proteins, especially small proteins, can have have their evolutionary history obscured by multiple substitutions during their evolution. More sensitive techniques are needed to find the relatives of these proteins, usually based on structural recognition. For example, using improved fold recognition software and a large database of fold family structures, Siew et al. have found that in Bacillus sp., some related ORFans are members of the of the alpha/beta hydrolase superfamily, and most likely derive from the haloperoxidases (N. Siew, H. K. Saini and D. Fischer. (2005) "A Putative Novel Alpha/Beta Hydrolase Family in Bacillus." FEBS Letters, 579:3175-82.).

    So most ORFans have been accounted for, and as we study more genomes with better tools we will resolve the status of many more. In an inquiry-based approach, students could recheck Escherichia coli ORFans from 2003, and would find that the vast majority now have resolved relatives. Indeed, if some of the non-artefactual ORFans are due to horizontal transfer from bacteriophages, as recent experiments suggest (Daubin and Ochman, 2004), then they may prove to be a valuable tool in understanding the phylogeny of bacteria, in the same way that families of LINES, SINES and pseudo genes have been. Far from being a threat to common descent, the patterns seen of the nested hierarchies of singleton, lineage specific and family specific ORFans are those you would expect from common descent.
  4. Some ORFans may be de novo generated proteins. We fully expect a modest proportion of new genes to be generated de novo during evolution. We even have examples of proteins that are so generated. The most famous of these is the nylonase gene, which allows bacteria to metabolise the artificial polymer nylon. This was produced by a mutation in a piece of non-coding DNA which generated a transcribable protein (Okada H, et al., (1983) "Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers." Nature. 306(5939):203-6.). The sperm-specific dynein intermediate chain gene (Sdic) was generated by a fusion mutation between two genes (so strictly speaking it falls under the gene duplication rubric), but the coding region of the new Sdic gene is generated from the non-coding intronic regions, so protein homology studies would have a hard time identifying it (Nurminsky DI, et al., (1998) "Selective sweep of a newly evolved sperm-specific gene in Drosophila." Nature. 396(6711):572-5). Formation of new genes poses no problem for evolutionary biology or common descent, as we do not demand that all, or the vast majority of genes originate in the Last Common Universal Ancestor. Furthermore, we are quite able to trace common ancestry with some genes being generated de novo, as this does not disturb the trees generated from other genes.

Molecular Clocks

Explore Evolution's arguments against molecular clocks are a bungled mishmash of actual facts, misinterpretations and completely spurious claims. First, the authors raise the issue of calibration of the molecular clock. This is an acknowledged potential problem in using the clock to date certain evolutionary events, especially those in the very deep past. Nevertheless, when appropriate methodology and controls are used, molecular clock dating has been shown to be reliable and consistent.

Contrary to the authors' statement, "environmental factors" such as magnetic field changes and mass extinctions are thought to play a minor role, at best, in molecular clock variation, as opposed to intrinsic differences in generation times/molecular substitution rates and selective forces across lineages and time. Significantly, the author's use and misattribution of this "environmental factors" claim appears to have resulted from their reliance on secondary creationist sources, instead of the primary scientific literature they cite.

Regardless of the claims in Explore Evolution, common ancestry is not dependent on any particular molecular clock. At best, this is again dependent on creationist sources. At worst, it is simply irrelevant.

Environmental Influences

The authors of Explore Evolution raise another issue, that of variations of clock rates along lineages due to "environmental factors", which if true would be more problematic because they would be harder to control for. However, while mutation rates in individuals can of course change according to environmental factors (e.g radiation exposure), for this change to noticeably affect substitution rates in populations and species (which is what the molecular clock measures), the change in mutation rates would have to be very substantial, to be sustained over many generations, and to affect a very large proportion of individuals in a species. These are not a common occurrence, even on a paleontological scale, and indeed environmental changes are not counted by experts among major hurdles in molecular clock studies. The authors provide the following citations for their statements:

16 James W. Valentine, David Jablonski, and Douglas H. Erwin, "Fossils, molecules and embryos: new perspectives on the Cambrian explosion," Development 126 (1999):851-859.

17 According to James W. Valentine, David Jablonski, and Douglas H. Erwin, these environmental factors might include the collapse of magnetic fields, ad mass extinctions (which may create environmental niches).

p. 62

Nowhere in the paper by Valentine, Jablonski and Erwin do the authors find that magnetic field changes and mass extinctions affect clock rates. In fact, while the idea that inversions of the Earth’s magnetic field could correlate with accelerated evolution by effects on cosmic radiation levels was considered early in the 1960s, it was quickly shown to be very unlikely based on physical and biological principles.

Explore Evolution wrongly attributes this idea to Valentine and his collaborators, and gives no basis for this attribution.

Molecular Clock Rates

Explore Evolution's arguments against molecular clocks are a bungled mishmash of actual facts, misinterpretations and completely spurious claims. First, the authors raise the issue of calibration of the molecular clock. This is an acknowledged potential problem in using the clock to date certain evolutionary events, especially those in the very deep past. Nevertheless, when appropriate methodology and controls are used, molecular clock dating has been shown to be reliable and consistent.

Explore Evolution is wrong to present molecular clocks as "evidence for Common Descent" or to claim that such a link constitutes circular reasoning. The authors do not bring any specific example of this usage of the molecular clock by biologists, so it is hard to evaluate in what context it has been made, if at all. Again, however, allegations of this claim being made by unspecified "evolutionists" and its refutation are found in several Creationist sources.

Explore Evolution claims:

Critics also dispute both the accuracy and the importance of the "molecular clock." They dispute the accuracy because of many known problems with calibrating such clocks. To time something accurately, you must know that your watch runs at a constant rate—that it doesn't speed up or slow down. Unfortunately, say the critics, the rate of mutation varies in response to a number of environmental factors. As a result, even if we knew when species diverged, we couldn't be sure that the molecular clock was "ticking" at a constant rate.
Explore Evolution, p. 59

There are several problems in this paragraph. First, it illustrates a rather grating habit found throughout Explore Evolution: the appropriation of arguments made by evolution scientists as if they were made by "critics," followed by the misrepresentation of such arguments. In this case, it is not anonymous "critics" who have pointed out that the molecular clock can perform unevenly, it is the very same scientists who then improve and continue to use the molecular clock approach.

More specifically, scientists have identified two main potential sources of error in molecular clock studies. The first is unevenness in the "ticking" rate. The finding that different proteins evolve (indeed, must evolve) at different rates was already known in the 1960s, and it was incorporated into the early theoretical formulations of molecular clocks by Jukes, Dickerson, Kimura and others. Differences in clock rates for the same protein between evolutionary lineages became clear with the advent of large-scale gene sequencing in the 1980s (Wu CI, Li WH. 1985 "Evidence for higher rates of nucleotide substitution in rodents than in man." Proc Natl Acad Sci U S A. 82:1741-5. Li WH, Tanimura M. 1987 "The molecular clock runs more slowly in man than in apes and monkeys." Nature. 326:93-6). Both these kinds of differences are generally measurable, and can be accounted for using appropriate calibration methods and adjustments.

The choice and statistical evaluation of calibration points has been more difficult. In order to accurately date events, scientists must set the clock based on events that are recognized as being accurately dated based on independent fossil or (for more recent events) archaeological evidence. Once one or more such events (for instance, the separation of the lineages giving rise to birds and mammals) are identified, genetic differences in a specific set of proteins between relevant species (in this case, birds and mammals such as humans and chickens) can be measured to "set" the clock, which can then be applied to the separation of other lineages in comparable time frames. Calibration points, especially for analyses in the deep past, have been a source of sometimes heated debate among scientists (Graur D, Martin W. 2004 "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision." Trends Genet. 20:80-6.; Hedges SB, Kumar S. 2004 "Precision of molecular time estimates." Trends Genet. 20:242-7; Glazko GV, Koonin EV, Rogozin IB. 2005 "Molecular dating: ape bones agree with chicken entrails." Trends Genet. 21:89-92). Still, the consensus is that application of the molecular clock with the appropriate controls and cautions can be useful and reliable.

References

References

Knight RD, Freeland SJ, Landweber LF. Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet. 2001; 2:49-58,

Embryology

The new field of "evo-devo"–an integration of evolutionary biology with our growing understanding of embryonic development–is an exciting a fruitful area of intense scientific research. A book purporting to "explore evolution" would do well to address this exciting field, yet the discussion in Explore Evolution is mired in disputes about what Darwin thought about embryos 150 years ago, and the legitimacy of illustrations by Ernst Haeckel 100 years ago. Current work that shows how the developmental process can evolve, and how that understanding deepens our understanding of the common ancestry of modern species, goes unmentioned.

Instead, Explore Evolution obsesses over whether certain illustrations of embryos from textbooks are or are not legitimate, and whether actual photographs of embryos confirm or disconfirm comments made by Darwin or by Haeckel. Modern evolutionary biology does not stand or fall on the views of people a century ago, but on the current evidence and research, research and evidence the book omits.

p. 66: "Darwin thought… similarities in … embryos revealed what the[ir] ancestors would have looked like."

This view that "ontogeny recapitulates phylogeny" was stated by Haeckel, not Darwin, and historians generally agree that Darwin did not accept that view. Darwin, like modern evolutionary biologists, preferred a much broader view advanced by von Baer: that characters acquired earlier in a species' evolution tend to develop earlier in an embryo.

Yolked into it: Removing yolk from photographs of embryos makes them look much more like Haeckel's drawings.Yolked into it: Removing yolk from photographs of embryos makes them look much more like Haeckel's drawings.

p. 66: Haeckel … show[ed] that [vertebrate] embryos … were very similar during their earliest stages.

Historians have shown that Haeckel meant something different by "earliest stages" of an embryo than modern authors, but the book uses the confusing translation to create a straw man. Haeckel was aware of divergence in early stages of embryos, and like modern embryologists, was aware that these divergences are driven in part by factors like the amount of yolk, not by fundamentally different developmental processes.

p. 69: "[Haeckel's] pictures were faked and the facts were distorted."

Historians investigating Haeckel's drawings have shown that he used the best illustrations available at the time, and continued to update the illustrations in his books as better ones became available. Comparisons to Richardson's photographs are flawed because Richardson, unlike Haeckel, did not remove the yolk from all of his embryos. This distorts the shape and outline of the embryos and makes it difficult to compare lineages with the yolk removed and those without. As one prominent Haeckel biographer concludes: "fraud not proven."

p. 68: "In 1894, Adam Sedgwick…challenged Darwin's two claims…"

Sedgwick's essay is not a reply to Darwin, as shown by the title of the cited essay: "On the Law of Development commonly known as von Baer's Law." Darwin, who died 12 years before Sedgwick's essay was published, did accept von Baer's results and, like modern biologists, found them bourn out by his own experience. To attribute those laws to Darwin, or to claim Sedwick was responding to Darwin, is simply false.

p. 68: "chickens and ducks[] display specific differences very early in development."

Researchers find that, other than a small difference in the rate of development, early chicken and duck embryos are "nearly identical."

p. 68: Sedwick claims: "There is no stage of development in which the unaided eye would fail to distinguish [chicken and shark]."

Sedwick acknowledges that these embryos are "superficially" not similar, but notes "striking similarities" of embryos, shared traits "which the adults do not exhibit." Rather than relying on a single paper from over a century ago, a truly inquiry-based book would lay out those structures and encourage students to explore their evolutionary implications.

p. 69: "This error [in Haeckel's drawings] remains in many modern high school and college biology textbooks."

Most textbooks in use today do not show Haeckel's drawings. They either use photographs, or redraw the embryos to correct errors. Evolutionary biologists' agreement about evolution's impact on development is hardly driven by a reliance on century-old illustrations, but on their experience with actual embryos in the lab. Explore Evolution gives students no understanding of that research.

p. 71: "To explain … adaptations in embryos, … evolutionary biologists invoke 'macromutations'"

This is simply false. Richard Goldschmidt's ideas were never widely accepted when he proposed them in the 1940s, and play no role whatsoever in modern evolutionary developmental biology. Explore Evolution later acknowledges this rejection in a passage plagiarized from a creationist website.

p. 70: "Darwinists have effectively made it impossible to challenge the theory with counterevidence"

Embryological evidence can and does challenge specific hypotheses of common ancestry. They also know that explanations of embryonic morphology must incorporate our knowledge of common ancestry and the species' immediate adaptive history. Finding that embryos differ because of adaptions specific to different environments is a prediction of evolution, not a falsification of it.

Major Flaws:

History of embryology: Rather than focusing on modern evolutionary developmental biology, this chapter rehashes arguments from the 19th century. Darwin's own views are serially misrepresented. A single essay from 1894 is transformed into a scientific attack on Darwin and evolution, despite the original author's narrower focus and the subsequent research which has invalidated his claims. Errors in a century-old illustration are dolled up as a evidence that the illustrations, and all of evolutionary developmental biology since, are frauds. This despite extensive research by biologists and historians showing that the illustrations were the best available at the time, and that the evolution of development is well-documented.

Philosophy: The authors misrepresent science by comparing the scientific process to how a jury operates. Students cannot be a jury if they are not given adequate background in the modern state of the field. This book does not give that background, and neither do many high school biology texts. Students are thus not qualified to sit in judgment on evolution, and this book does not give them the investigative tools they would need to be qualified. The authors also misrepresent the way evolutionary developmental biology works by pretending that the only force operating on embryos ought to be common ancestry. A falsification of evolutionary biology must address its totality, including both the constraints of common ancestry and divergences driven by other evolutionary mechanisms.

Embryology: Remarkably, this chapter simply does not discuss modern evolutionary developmental biology. While this means it is devoid of factual errors on that point, it also means that the chapter's title is inaccurate, and the content uninformative for students.

History of Embryology

Evolutionary developmental biology is a vital and active field of study. High school biology textbooks rarely cover it in detail, so Explore Evolution might have done a service by offering a brief exploration of that modern field. Instead, it focuses on creationist hobbyhorses from the history of biology. Most prominent of these historical arguments is a debate over illustrations by Ernst Haeckel.

Later illustrations from Haeckel: Haeckel continued to update his illustrations as better ones became available.Later illustrations from Haeckel: Haeckel continued to update his illustrations as better ones became available.

These century-old drawings, like any historical illustrations, have errors. Historians reviewing Haeckel's life and work are confident that he used the best illustrations available to him, and that he did not intend to mislead his readers. Contrary to claims in Explore Evolution, a comparison between that illustration and more recent photographs does not show a stark difference. Haeckel's drawings omit the yolk, while illustrations by Michael Richardson do not do so consistently. When the yolk is digitally removed from the images, the similarites become clear again. Nonetheless, Explore Evolution claims these illustrations are "possibly fraudulent," and implies that all of modern evolutionary developmental biology depends on those illustrations' fate. In fact, Haeckel's illustrations, like his idea of recapitulation (which the book wrongly claims Darwin accepted), have been superceded by more recent research.

This is also true of the book's discussion of Adam Sedgwick's writings against von Baer's law. That single essay from 1894 does not invalidate all the subsequent research of the last century. Recent research has specifically addressed many of the claims quoted from Sedgwick's essay, and it is foolish and inaccurate for students to be presented with Sedgwick's essay as if it were the last word on the matter. Inquiry-based eduation requires providing students with enough information that they can conduct their own inquiry, yet this chapter does not give even a basic understanding of modern embryology, and its account of the history of embryology is profoundly inaccurate.

Darwin on Dissimilarities

Explore Evolution focuses excessively on the details of what Darwin argued 150 years ago, rather than informing students about the dynamic field of evolutionary developmental biology. Whether or not Darwin argued that dissimilarities in early development do not cause a problem for evolution is less important than helping students understand how modern scientists view these issues. Explore Evolution fails to explain that the amount of yolk in an egg has adaptive value and is responsible for differences in embryogenesis. Instead of explaining a concrete example such as this, Explore Evolution makes a vague reference to Richard Goldschmidt's work from the 1930's and 1940's on macromutations – a hypothesis rejected by modern biologists.

From Explore Evolution:

Darwin was aware of these dissimilarities, but he argued that they do not disprove Common Descent. As Darwin explained, some groups of embryos have been "so greatly modified [by adaptations]* as no longer to be recognized."
Explore Evolution, p. 70

Darwin did argue that adaptations to embryonic life would result in the dissimilarities of embryos, as Jerry Coyne observes:

Darwin himself noted that embryos must adapt to the conditions of their existence, and the earliest stages of vertebrate embryos show adaptation to widely varying amounts of yolk in their eggs.
Jerry Coyne, 2001. "Creationism by Stealth," Nature, 410, p. 475-476

The early cleavage embryos of humans and chickens are quite different due to constraints imposed by the large yolk of chickens. The amount of yolk in an egg varies depending on how long the embryo will rely on the yolk for energy and nutrients. In amniotic mammals such as humans, relatively little yolk is needed because the developing embryo is able to get continual nutrition from maternal sources. Other organisms, such as chickens, have a large and yolk-rich egg as they lack constant maternal nutrition and lack feeding larval stages. Because yolk does not divide as the cells in the egg divide, the pattern of embryonic cell cleavage in chickens is necessarily different from the pattern in humans in order to accommodate their large amount of yolk.

Gastrulation is the process by which the embryo is converted from a single layer of cells to three different layers by a series of coordinated cellular movements. How these cell movements occur is dependent upon the earlier cleavage patterns. Therefore, embryos can differ significantly in their morphology at the gastrula stage. PZ Myers explains this relationship between yolk, cleavage patterns and gastrulation here..

Instead of explaining a concrete example of how the amount of yolk is an adaptation to embryonic life and how it affects the early development, students are referred to Richard Goldschmidt's work from the 1930's and 1940's.

*To explain what might cause these adaptations in embryos, some evolutionary biologists invoke "macromutations," large-scale changes in form that occur in one generation. One such biologist, the late University of California at Berkeley geneticist Richard Goldschmidt, believed that such macromutations could produce what he called "hopeful monsters."
Explore Evolution, p. 71

Notably, Richard Goldschmidt's macromutation hypothesis is not included in modern evolutionary biology. As Michael Dietrich notes:

Richard Goldschmidt is remembered today as one of the most controversial biologists of the twentieth century. Although his work on sex determination and physiological genetics earned him accolades from his peers, his rejection of the classical gene and his unpopular theories about evolution significantly damaged his scientific reputation.
Michael Dietrich, 2003. "Richard Goldschmidt: Hopeful Monsters and other heresies." Nature Review Genetics, 4, p. 71.

The mention of macromutations to explain adaptations to embryonic life by Explore Evolution is yet another failure to use "current evidence and arguments for and against the key ideas of modern Darwinian theory." The book is too focused on trying to attack Darwin to properly examine modern biology.

Ontogeny & Phylogeny

There is no question that the study of development played an important role in Charles Darwin's thinking on evolution, and that it continues to play an important role in modern evolutionary biology. Ernst Haeckel's early suggestion that ontogeny (development) recapitulates phylogeny (evolution) was far less influential and is rejected by modern biologists. Alternative views on the relationship between development and evolution include Baer's Laws, which simply state that general characteristics of the group to which an organism belongs often develop earlier than special characters of a species, and that organisms tend to become more divergent through their development. This formulation remains valid today, and (unlike Haeckel's proposal) has a straightforward relationship with evolutionary mechanisms. Despite these simple facts, Explore Evolution invests substantial effort trying to tie Darwin to Haeckel's views, rather than exploring the modern state of evolutionary developmental biology. In doing so, the book mangles both history and biology.

Intelligent design proponents have a tradition of flogging embryology in order to attack common descent (Wells 2000, 2003, 2005). Explore Evolution continues this tradition of misrepresenting embryology and evolution. The first misrepresentation is the claim that Darwin accepted Haeckel's Biogenetic Law. In this case, Explore Evolution presents a minority position among scholars who have studied this question. This claim is the first move by Explore Evolution to link Darwin and Haeckel as closely as possible, so as to tarnish Darwin's arguments for common descent with the controversy about Haeckel's embryos. It is notable that the only embryological data Explore Evolution offers students in support of common descent is a modified diagram of Haeckel's embryos from 1894. In protecting their anti-evolution viewpoint, the authors omit recent research showing evolutionary conservation of the genetic pathways regulating animal development (e.g., Carroll et al. 2005, Davidson, 2005).

Intelligent design proponents have attacked the idea of common descent through promoting a misunderstanding of embryology and the new field of evolutionary developmental biology (evo-devo):

There is a whole stable of intelligent design creationist writers associated with the Discovery Institute, and we will see more slick books of bogus science produced to influence the teaching of biology, and even federal funding of research. Evo-devo data have become a part of the creationist rhetorical weaponry, and as evo-devo grows in prominence, the problem will grow in severity.
Rudolf Raff, 2001. "The Creationist Abuse of Evo-Devo," Evolution and Development, 3:6, p. 374

From Explore Evolution:

Darwin noticed certain similarities in the embryos of vertebrate animals, similarities he thought were especially great during the embryo's earliest stages of development.
Explore Evolution, p. 66

This short statement in Explore Evolution makes two significant mistakes, one of omission and one of commission. Darwin considered that similarity of early embryos provided very strong support for common descent. However, he never personally examined vertebrate embryos. Instead he relied upon Karl von Baer’s observation in 1828 that early vertebrate embryos were more similar to each other than when fully developed. Failing to distinguish von Baer from Haeckel later allows Explore Evolution to present Adam Sedgwick's erroneous criticism of Baer's Laws as if they were criticism of Haeckel.

In addition, Explore Evolution falsely asserts Darwin thought the similarities between embryos were greater at the earliest stages of development. This begins a relentless pattern of suggesting that common descent and Haeckel's Biogenetic Law require that the earliest stages of animal development are most similar. However, as Jerry Coyne notes, that is not what Darwin actually thought, embryos at the earliest stages of development can vary signficantly from one another depending upon the amount of yolk in their eggs.

Darwin himself noted that embryos must adapt to the conditions of their existence, and the earliest stages of vertebrate embryos show adaptation to widely varying amounts of yolk in their eggs.
Jerry Coyne (2001) "Creationism by Stealth," Nature, 410,p. 476

While Darwin accepted von Baer's Law, it is much less clear whether Darwin accepted Haeckel's Biogenetic Law, proposed in 1866, which claimed that embryonic development recapitulates the adult stages of their ancestors ("ontogeny recapitulates phylogeny"). Nonetheless, Explore Evolution claims:

Darwin thought that the observable similarities in different embryos revealed what the ancestors to these organisms would have looked like.
Explore Evolution, p. 66

This claim by Explore Evolution contradicts the majority view of prominent Darwin scholars (including Ernst Mayr, Stephen Jay Gould, David Hull, and Peter Bowler) who have argued that Darwin did not accept the Biogenetic Law.

most authors (including Darwin) rejected the claim that ontogeny is the recapitulation of the adult stages of the ancestors.
Ernst Mayr (1982), Growth of Biological Thought, , p. 475.
Darwin saw that ancestral groups in an established community of descent would differ least in their adult form from the embryonic state common to all members of the community. The gill slits of the human fetus represent no ancestral adult fish; we see no repetition of adult stages, no recapitulation.
Stephen Jay Gould, Ontogeny and Phylogeny, p. 72
belief that ontogeny (individual growth) recapitulates phylogeny (the history of the type) thus owes little to Darwinism and is more characteristic of the non-Darwinian, or developmental, view of evolution.
Peter Bowler (1988), The Non-Darwian Revolution: Reinterpreting a Historical Myth, , p. 11.

Not all historians of science who have studied embryology and evolution are in agreement that Darwin was not a recapitulationist (Roberts, 1990). However, this fails to warrant the claim by Explore Evolution that Darwin accepted Haeckel's Biogenetic Law.

Haeckel's Drawings

Explore Evolution incorrectly asserts that Haeckel’s Biogenetic Law claims that the earliest stage of embryos are most similar. Haeckel's concept of caenogenesis fully acknowledged that there can be signficant differences between embryos including at the earliest stages of development. This misrepresentation of the Biogenetic Law allows Explore Evolution to set up erroneous claims that Haeckel committed fraud and that the distinctions between the early stages of development of different classes of vertebrates argue against common descent.

Following Darwin's lead, Haeckel tried to discover the evolutionary history of various animals by studying their embryos. He produced a set of influential drawings showing that the embryos of various classes of vertebrates were very similar during their earliest stages of development.
Explore Evolution, p. 66. Emphasis added.

This claim is false. Haeckel was aware of significant departures in the morphology of early embryos from what would be predicted by his Biogenetic Law. These differences in order, timing and pattern of embryogenesis were termed as caenogenesis by Haeckel. He also understood that a prominent reason for why embryos showed a signficant difference in their cleavage and gastrulation patterns was due to the amount of yolk in their eggs. As Michael Richardson (the developmental biologist whose work re-ignited the interest in Haeckel's embryos) and Gerhard Keuck observe:

The early divergence, which violates some of von Baer's laws, is due to differences in egg size and patterns of cleavage and gastrulation among species. Recent explanations of the conservation of midembryonic stages, despite variations in early development, include the idea that they are subject to strong stabilizing forces (e.g. selection, pleiotropy; see Wagner & Misof, 1993; Raff, 1996; Wagner, 1996). Haeckel was aware of these early differences, and they were included among his caenogenetic exceptions.
Richardson and Keuck, 2002. "Haeckel's ABC of Evolution and Development," Biol. Rev. 77 , p. 507

Why are Haeckel's embryos focused upon in this section? Most likely because this diagram was found in many high school biology textbooks, and that Michael Richardson's research on vertebrate embryos rekindled an old controversy about whether the early embryos in the diagram are accurate. However, as Richardson and colleagues note, this hardly undermines the strong support for common descent from embryology, despite the claims of Creationists and ID proponents.

Data from embryology are fully consistent with Darwinian evolution. Haeckel’s famous drawings are a Creationist cause célèbre (3). Early versions show young embryos looking virtually identical in different vertebrate species. On a fundamental level, Haeckel was correct: All vertebrates develop a similar body plan (consisting of notochord, body segments, pharyngeal pouches, and so forth). This shared developmental program reflects shared evolutionary history. It also fits with overwhelming recent evidence that development in different animals is controlled by common genetic mechanisms. (4)
Richardson et al. (1998) "Haeckel, Embryos and Evolution." Science, 280:983

Finally, given that Explore Evolution claims:

This book is one of the first textbooks ever to use the inquiry based approach to teach modern evolutionary theory. It does so by examining the current evidence and arguments for and against the key ideas of modern Darwinian theory.
Explore Evolution, preface

it is remarkable that Explore Evolution fails to include recent work in evo-devo in the Embryology: Case For section. We now know there is an evolutionarily conserved "genetic toolkit" - a set of genes responsible for constructing all animals, from sea anemones to fruit flies to humans (Carroll et al. 2005, Davidson 2005). The only mention of the genetic regulation of development refers to the outdated macromutation theory from the 1940's by Richard Goldschmidt. So while Explore Evolution generally acknowledges that modern biologists consider embryology to provide strong support for common descent, students are at a high risk of incorrectly concluding that this support is from the diagram of Haeckel's embryos.

Accuracy in embryo illustrations

It has been widely noted that a number of the embryos in top row of the Tables 6 and 7 from Haeckel's Anthropogenie (1874) are not realistic representations. However, the assertion by Explore Evolution that Haeckel claimed that top row represented earliest embryos is false. Nor are the book's claims that Haeckel engaged in fraud justified by current historical scholarship.

Haeckel's Diagrams: embryonic development, as drawn by Ernst HaeckelHaeckel's Diagrams: embryonic development, as drawn by Ernst HaeckelIllustrations from Ernst Haeckel, Anthropogenie, 4th ed. (1891): Reproduced from Richards (2009)Illustrations from Ernst Haeckel, Anthropogenie, 4th ed. (1891): Reproduced from Richards (2009)

When considering Haeckel's embryos, it is important to note that Haeckel compared embryos of different groups in several publications. For example, in Naturliche Schopfungsgeschichte (1868), Haeckel compared vertebrate embryos including human and dog. But his most famous diagram are Plates 4 and 5 from Anthropogenie (1874). Explore Evolution uses a version of this diagram from Romanes (1894) that is not completely identical to Haeckel's original (1874) diagram. Haeckel himself updated his illustrations over several editions (compare figures at right).

A diagram showing real vertebrate embryos by Michael Richardson and colleagues (used in Figure 4.2 of Explore Evolution) suggest that Haeckel took considerable license in portraying the earlier embryos in the series, particularly in the top row. Scholars who have studied Haeckel generally think the reason why Haeckel exaggerated similarities of early embryos was not to mislead his readers. A key difference between Richardson's figures and Haeckel's is that Richardson did not remove the yolk from his embryos. The yolk distorts the comparative outline of the embryos and alters the posture of the embryo in ways with no evolutionary or developmental significance.

Explore Evolution also claims that Haeckel misled his readers into thinking that the top row of embryos is the earliest embryonic stage. This charge about mislabeling the top row embryos as earliest was first made by Jonathan Wells in 2000 and has been refuted by Alan Gishlick at the National Center for Science Education. Nonetheless, Explore Evolution continues this false charge.

The stage that Haeckel labeled first is actually midway, through development. Embryologists such as Sedgwick knew this, but their publications challenging the Darwinian interpretation were lost beneath the popularity of Haeckel's inaccurate (and possibly fraudulent) drawings.
Explore Evolution, p. 68

It is notable that none of Haeckel's contemporary critics, including Sedgwick, accused him of claiming that the embryos in his famous diagram were at the earliest stage. (Richardson and Keuck, 2002; Sedgwick, 1894)

Nick Hopwood, an historian of science, has comprehensively explored the production of Haeckel's embryos diagram (Hopwood, 2006) and shows that Haeckel's own writings would not have been taken by contemporaries to represent the earliest stages of development. Hopwood describes the original diagram with the following figure legend from Hopwood's paper in Isis. Quotation marks below are in the original and represent the English translation of Haeckel's description of the diagram.

"Comparison of the embryos” of various vertebrates “at three different stages of development.” This expanded double plate shows fish (F), salamander (A), turtle (T), chick (H), pig (S), cow (R), rabbit (K), and human (M) embryos at “very early” (I), “somewhat later” (II), and “still later” (III) stages… Lithograph by J. G. Bach of Leipzig after drawings by Haeckel from his Anthropogenie (Leipzig: Engelmann, 1874), Plates IV–V.
Nick Hopwood, 2006. "Pictures of Evolution and Charges of Fraud: Haeckel's Embryological Illustrations"Isis: 97:292

What did Haeckel mean by "very early" embryos? The definition of embryos has changed over the last 100 years. Unlike the modern definition of embryos, which refers to any stage after the fertilized egg, the 19th century definition of embryo was more restricted.

In present English usage, the term "embryo" includes even the earliest stages. The German tradition, however, largely established by von Baer, restricts the term "embryo" to the basic rudiment of the body or its later stages (the "embryo proper" in English usage). This is evident from many remarks by von Baer, for instance: "The germ ["Keim", blastodisc] during its growth transforms into two parts; [… ] the middle forms the embryo, the much wider periphery the Keimhaut [extraembryonic blastoderm]" (von Baer, 1828, p.44).
Klaus Sander and Urs Schmidt-Ott, 2004. "Evo-Devo aspects of classical and molecular data in a historical perspective," J. Exp. Zool. (Mol. Dev. Evo) 302B:69–91.

Thus, Haeckel's "very early" embryos are midway through development and were not meant to represent the earliest stages of development.

When Explore Evolution claims that "the pictures were fabricated and the facts were distorted" (p. 69), the authors are ignoring recent scholarship. In addition to Hopwood's reassessment of Haeckel's original writings, historian Robert Richards has reexamined the drawings and their sources, finding no support for the claim of intentional fraud. Richards notes that Anthropogenie was a popular work based on a series of lectures Haeckel presented. The figures began as visual aides for his lecture, and represented the best illustrations available at the time. In Haeckel's subsequent writings, he replaced those illustrations as newer and better illustrations became available.

Richardson and his colleagues selected images from the first edition of Haeckel’s Anthropogenie, which was hastily drawn together from his lectures. The book, though, went through five further editions. With each new edition the text grew fatter as Haeckel deployed more evidence; and the illustration in question expanded the comparison from 8 species of embryo to 20 by the 5th edition (1905). In the subsequent editions, the images grew ever more refined, so that even by the 4th edition (1891), the differences among them became more pronounced. The refinements were a function of more material available and better instrumentation (embryos at the earliest stages are invisible to the naked eye). Had the Science article compared Richardson’s photos with illustrations from Haeckel’s later editions, the argument for fraud would have withered.
Robert J. Richards (2009) "Haeckel's embryos: fraud not proven" Biology and Philosophy 23:147-154.

This level of historical detail would be irrelevant to a class covering modern biology, but if Explore Evolution is to use this obscure debate to attack evolution, it behooves them to accurately describe the history. The best available historical research shows that Haeckel's drawings of embryos represented the best available illustrations, and were not a fraud.

The Earliest Stages

Explore Evolution claims:

both Darwin's and Haeckel's comparisons left out the earliest stages of development.*

Whether this omission was intentional is a matter of some debate.

Explore Evolution, p. 68
Eggs, cleavage stages, and gastrula stage embryos Eggs, cleavage stages, and gastrula stage embryos

Vertebrate embryos (in the modern definition - after fertilization) have a number of stages such as the cleavage and gastrula stages which precede the embryos shown in Haeckel's diagram. Darwin's Use of Embryonic DrawingsDarwin's Use of Embryonic Drawings Nick Matzke at Panda's Thumb has pointed out that comparisons of these earlier stage embryos are actually shown in Anthropogenie. Indeed, Anthropogenie has over 20 figures showing gastrula embryos from different groups. This does not reconcile with Explore Evolution's implication that Haeckel intended to deceive his readers.

Shown below are Plates 2 and 3 from Anthropogenie comparing eggs, cleavage stages, and gastrula stage embryos from different animals. As discussed earlier, Haeckel used von Baer's convention for embryo as the stage in which a body form is first apparent. Instead of describing these earliest stages of development as "embryos", Haeckel uses terms which include "keim" (meaning "germ"). For example, morula embryos are called "maulbeerkeim", and blastula embryos are referred as "blasenkeim".

In Descent of Man (1871), Darwin compared drawings of a human and dog embryo at the same stage (originally from Bischoff and from Ecker). However, nowhere does Darwin imply that this is the earliest stage of development. In fact, because dogs and humans are mammals and have very small eggs, their earliest stages of development are extremely similar. So it is absurd to suggest that Darwin purposefully left out the earliest embryonic stages of humans and dogs in order to mislead his readers.

Sedgwick's Two Challenges

Explore Evolution asserts that in 1894, Adam Sedgwick challenged Darwin's two claims about embryos, 1) early embryos of related organisms are more similar than adults and 2) the younger the embryos, the greater the resemblance. A comprehensive comparison of vertebrate embryos does not support Sedgwick's challenges about the similarity of embryos. Explore Evolution also neglects to mention that the section of Sedgwick's paper quoted by Explore Evolution is actually challenging von Baer's Law (that development proceeds from a more general to a more specific morphology such that taxa-specific features are added later in development), and not Darwin or Haeckel.

From Explore Evolution:

In 1894, Adam Sedgwick, an embryologist at Cambridge University, challenged Darwin's two claims: 1) that vertebrate embryos were more alike than the vertebrate adults, and 2) that the younger the embryos, the greater the resemblance.
Explore Evolution, p. 68

Adam Sedgwick's critique was directed not against Charles Darwin, but Karl von Baer:

The generalization commonly referred to as v. Baer’s law is usually stated as follows: - Embryos of different members of the same group are more alike than the adults, and the resemblances are greater the younger the embryos are examined.
Adam Sedgwick, 1894. "On the Law of Development commonly known as von Baer’s Law; and on the Significance of Ancestral Rudiments in Embryonic Development," Quart. J. Microscopy , 36, p. 35

Darwin did think that the Karl von Baer's observations provided strong support for descent with modification. However, this does not merit the inaccurate statement that von Baer's claims can be attributed to Darwin.

Explore Evolution cites Sedgwick to challenge the first of von Baer's claims:

Even the embryos of "closely allied animals," such as chickens and ducks, display specific differences very early in development. "I can distinguish a [chicken] and a duck embryo on the second day," he wrote.
Explore Evolution, p. 68

A more recent and comprehensive analysis of embryogenesis of poultry shows that morphological differences between two day duck and chick embryos are only because duck embryonic development is slower than chick embryonic development. Otherwise, their development is "nearly identical". Hence, Sedgwick's first challenge to von Baer is not supported.

Chicken, turkey, Japanese quail, and Pekin duck blastoderms from oviductal eggs showed differences in the rate of development that were inversely correlated with egg size. … Although it is recognized that the temporal rate of development will differ between different species and strains, the external features of any embryo in any given stage will be nearly identical.
Sellier, et al., 2006. "Comparative Staging of Embryo Development in Chicken, Turkey, Duck, Goose, Guinea Fowl, and Japanese Quail Assessed from Five Hours After Fertilization Through Seventy-Two Hours of Incubation." J. Appl. Poult. Res., 15, p. 219

Explore Evolution also cites Sedgwick to challenge the second claim of von Baer, that younger embryos of different groups have a greater resemblance than older embryos.

Comparing the embryos of a chicken and shark, he continued, "There is no stage of development in which the unaided eye would fail to distinguish them with ease."
Explore Evolution, p. 68

Sedgwick does observe clear differences between these dogfish and chick embryos.

According to law of v. Baer these embryos (fowl and dogfish) ought to be closely similar in the younger stage. Do these embryos, developing under similar conditions, conform to the law? Superficially, clearly not. There is no stage of development in which the unaided eye would fail to distinguish between them with ease- the green yolk of one, the yellow yolk of the other; the embryonic rim and blastopore of the fish, the absence of these in the chick; the six large gill-slits bearing gills on the one hand, the four rudimentary clefts on the other; the small head, straight body and long tail, as opposed to the enormous head, cerebral curvature , short tail, and so on.
Adam Sedgwick, 1894. "On the Law of Development commonly known as von Baer’s Law; and on the Significance of Ancestral Rudiments in Embryonic Development." Quart. J. Microscopy, 36, p. 36

However, Sedgwick also admits that there are "striking similarities" between these embryos which are not found in adults.

These embryos are not closely similar, but it is maintained that the law is justified by certain remarkable features of embryonic similarity which the adults do not exhibit, and of which the most important are the presence in the chick of pharyngeal clefts, a tubular piscine heart and a similarity in the arrangement of the cardiac arterial system, a cartilaginous endo-skeleton, oro-nasal grooves and a notochord. Now I freely admit that these are striking similarities, but I question whether they are sufficient to justify the law of v. Baer.
Adam Sedgwick, 1894. "On the Law of Development commonly known as von Baer’s Law; and on the Significance of Ancestral Rudiments in Embryonic Development." Quart. J. Microscopy, 36, p. 36

Explore Evolution asserts that Sedgwick had successfully disproved von Baer's second claim that younger embryos show a greater resemblance to each other than older embryos. However, when considering the major differences between the fully developed dogfish and chick embryos (presence or absence of limbs, feathers, teeth etc.) as well as the shared features of these embryos at earlier stages that are not found in adults (heart structure, cardiac arterial system, notochord etc.), it is apparent why biologists consider the early embryos to be more similar than later embryos. Interestingly, Explore Evolution does not ask students to specifically examine the early and late dogfish and chick embryos shown in Figure 4.2.

Michael Richardson's photographs

Michael Richardson and colleagues in 1997 were instrumental in pointing out the discrepancies between Haeckel's popular diagram and genuine embryos. However, Explore Evolution simply accepts a flawed creationist interpretation of Richardson's work. The claim that the common ancestry of vertebrates requires that embryos be most similar at the earliest embryonic stage was not accepted by Darwin nor Haeckel nor any modern evolutionary or developmental biologist. This is simply a straw man argument that was set up by the misrepresentations of Haeckel's and Darwin's view of embryology and development discussed above.

From Explore Evolution:

Critics of the argument from embryology agree that common descent might be a reasonable inference to draw from the similarity of embryos - if embryos really were similar in their earliest stages of development. But they're not, say most embryologists.
Explore Evolution, p. 68

The inference that earliest embryos of various groups must be similar if they shared a common ancestry is a claim of intelligent design proponents such as Jonathan Wells in Icons of Evolution. Darwin certainly never made such a claim. In his review of Icons of Evolution Jerry Coyne addresses this particular fallacy:

Wells also notes that the earliest vertebrate embryos (mere balls of cells) are often less similar to one another than they are at subsequent stages when they possess more complex features. According to Wells, this counts as evidence against biological evolution, which supposedly predicts that the similarities among groups will be strongest at the very first stages of development. But Darwinism makes no such prediction. Darwin himself noted that embryos must adapt to the conditions of their existence, and the earliest stages of vertebrate embryos show adaptation to widely varying amounts of yolk in their eggs.
Jerry Coyne, (2001) "Creationism by Stealth." Nature, 410, p. 475-476

Michael Richardson and Gerhard Keuck find that Haeckel also did not imply that the earliest stages of embryos must be similar if they share a common ancestor. His concept of caenogenesis, the adaptations to embryonic life which blur recapitulation, also applied to early stages of development, particularly with respect to the size of eggs.

Haeckel was aware of these early differences, and they were included among his caenogenetic exceptions. With regard to egg size for example, he noted that ova of different species look very similar at early stages of maturation (although he did acknowledge that they must show molecular differences; see Haeckel, 1896b: 1, p. 137).
Richardson and Keuck, 2002. "Haeckels ABC of Evolution and Development." Biol. Rev., 77, p. 507

Explore Evolution repeats another false claim from Wells.

This error even crept into the Encyclopedia Britannica, and remains in many modern high school and college biology textbooks.
Explore Evolution, p. 69

This is incorrect. A recent survey of 36 biology textbooks, dating from 1980 to the present and covering high school biology, college introductory biology, advanced college biology, and developmental biology books, found that only 8 of these textbooks mentioned Haeckel or the biogenetic law. Two of these 8 were creationist/ID books (Of Pandas and People, and Biology for Christian Schools from Bob Jones University Press). Of the 6 mainstream textbooks that mentioned Haeckel or the biogenetic law, two are advanced college-level books. In all cases where Haeckel is mentioned (except for the creationist/ID books), the text discussion does not reproduce Haeckel's mistakes.

Explore Evolution emphasizes data from the 1997 paper by Michael Richardson and colleagues that strongly challenged a literal interpretation of Haeckel's diagram.

In 1997, an international team of scientists, led by the embryologist Michael Richardson, compared Haeckel's drawings to photographs of actual embryos at various developmental stages. They found that Haeckel had distorted the evidence at every turn, leading Richardson to tell Science that "it looks like it's turning out to be one of the most famous fakes in biology."
Explore Evolution, p. 69

However, the claim that Haeckel "distorted the evidence at every turn" is untrue. As Michael Richardson and colleagues also point out, there is, in fact, compelling similarity of early embryos which provides strong support for common descent.

Data from embryology are fully consistent with Darwinian evolution. Haeckel’s famous drawings are a Creationist cause célèbre (3). Early versions show young embryos looking virtually identical in different vertebrate species. On a fundamental level, Haeckel was correct: All vertebrates develop a similar body plan (consisting of notochord, body segments, pharyngeal pouches, and so forth). This shared developmental program reflects shared evolutionary history. It also fits with overwhelming recent evidence that development in different animals is controlled by common genetic mechanisms (4)
Richardson, et al., 1998."Haeckel, Embryos and Evolution." Science, 280, p. 983

Furthermore, historians comparing Richardson's images to Haeckel's find other problems. Robert Richards observes:

Richardson and his colleagues selected images from the first edition of Haeckel’s Anthropogenie, which was hastily drawn together from his lectures. The book, though, went through five further editions. With each new edition the text grew fatter as Haeckel deployed more evidence; and the illustration in question expanded the comparison from 8 species of embryo to 20 by the 5th edition (1905). In the subsequent editions, the images grew ever more refined, so that even by the 4th edition (1891), the differences among them became more pronounced. The refinements were a function of more material available and better instrumentation (embryos at the earliest stages are invisible to the naked eye). Had the Science article compared Richardson’s photos with illustrations from Haeckel’s later editions, the argument for fraud would have withered.
Robert J. Richards (2009) "Haeckel's embryos: fraud not proven" Biology and Philosophy 23:147-154.
Richardson vs. Haeckel: Reengineered photographs of embryos with yolk material removed, comparable scaling, and orientationRichardson vs. Haeckel: Reengineered photographs of embryos with yolk material removed, comparable scaling, and orientation

Furthermore, Richardson's own images display disturbing inaccuracies:

several (but not all) of the photographed embryos retain the attached yolk sack and other maternal material; this exaggerates their differences from Haeckel’s images. Haeckel explicitly indicated that he pictured his specimens without yolk, allantois, and amnion (Haeckel 1874, p. 256). The bulge of the salamander is not part of the embryo; rather, it is the yolk sack, as is the case for the fish and the human embryos (though not for the chick and the rabbit, from which the yolk sacks have been removed); moreover the salamander photo is obviously not reduced to the same scale as the others (despite the assertion in the caption for the figure in Science). The chick was photographed in a highly circumflex orientation, which occurs at a somewhat later stage of development than that represented by Haeckel. Again, Haeckel expressly stated that he oriented his embryos all in the same way for ease of comparison. I have used a computer program to remove the yolks in the photographs, scale back the salamander, and straighten out the chick. The result is a bit crude, but one can clearly see that the differences between photograph and illustration are not nearly as great as presented in the Science article. Shorn of yolk, the photographed embryos would not have provided the kind of graphic evidence upon which the Science article was premised.
Robert J. Richards (2009) "Haeckel's embryos: fraud not proven" Biology and Philosophy 23:147-154.

This error is significant, and demolishes Explore Evolution's claim that Haeckel's drawings are inherently unreliable. The inconsistency among Richardson's own images, however, makes them unreliable for use with students, and nothing in this historical dispute offered by Explore Evolution undermines modern evolutionary developmental biology.

Philosophy

Rather than presenting an account of how embryology is studied in the 21st century, the "Embryology" chapter concludes by exhorting students to pretend they are jurors in a court case against evolution. It's unclear what the charges might be, but it is certain that the students would be diverted from a fair verdict by the chapter's studious avoidance of current science in the field.

Rather than a scientific argument, the book offers a philosophical charge, that evolution has been rendered unfalsifiable. This charge rests on a misrepresentation of how science works, and what evolutionary developmental biologists actually claim. It is one thing to argue that there is no evidence which currently falsifies common ancestry, and quite another to say that no such evidence could ever exist. Scientists agree to the former statement, but not the latter.

Evolutionary Predictions of Common Ancestry

Explore Evolution argues that if common descent predicts both similarity and dissimilarity of embryos, it is impossible to challenge the theory. The similarity of embryos is best explained by common descent. The dissimilarity of embryos can be explained by environmental adaptations under natural selection, and while it can cause scientists to re-evaluate particular claims of common ancestry, no embryological evidence now available would cause scientists to reject universal common ancestry.

Explore Evolution insists

By arguing that common descent predicts both embryonic similarity and dissimilarity, Darwinists have effectively made it impossible to challenge the theory with counterevidence. When the case is stated this way, common descent would be consistent with whatever we observe in embryos.
Explore Evolution, p. 70

In this claim, Explore Evolution fails to distinguish two main threads of modern evolutionary biology; common descent and the role of natural selection in adaptation. As noted earlier, Darwin realized that embryos would show differences if they had adaptations to different environmental circumstances. Perhaps the most important adaptation is the amount of yolk, which affects the egg size and the amount of stored nutrition available for the developing embryo. One of the most striking differences is between animals that undergo metamorphosis from a feeding larval stage and animals that undergo direct development, bypassing the larval stage. The comparative analyses of sea urchin embryos and larvae has shed light upon the adaptive strategies of these different modes of development.

Observations of a [sic] sea urchin larvae show that most species adopt one of two life history strategies. One strategy is to make numerous small eggs, which develop into a larva with a required feeding period in the water column before metamorphosis. In contrast, the second strategy is to make fewer large eggs with a larva that does not feed, which reduces the time to metamorphosis and thus the time spent in the water column. The larvae associated with each strategy have distinct morphologies and developmental processes that reflect their feeding requirements, so that those that feed exhibit indirect development with a complex larva, and those that do not feed form a morphologically simplified larva and exhibit direct development.
Smith, Zigler and Raff, 2007. "Evolution of direct-developing larvae: selection vs loss." Bioessays, 29:6, p. 566

Significantly, these different modes of development are found in closely related species who diverged relatively recently, about 4 million years ago, and have occurred in multiple instances in other echinoderm lineages. The comparison of indirect and direct development has demonstrated that the earliest stages of development are relatively plastic (Raff ref).

Shared features of organisms are normally most parsimoniously explained by inferring common descent. The support for common descent, which is disputed by Explore Evolution but accepted by the vast majority of biologists, arises from the independent convergence of evidence from a wide variety of fields including biogeography, biochemistry, molecular biology, and embryology. One such shared feature of primate embryos, including human, is a tail. Primates which lack a tail as adults, such as humans and chimps, resorb the tail during later embryogenesis. Primates which have a tail as adults, do not resorb the embryonic tail. Phylogenetic analysis have unambiguously demonstrated that the ancestors to primates were tailed. The vast majority of biologists would consider human embryonic tails to be best explained by common descent. How would Explore Evolution explain it to students?

Students as Jurors

Explore Evolution claims that many scientists who criticized Haeckel's embryos still support common ancestry; but students, as good jurors, should keep an open mind. Students are learners, not jurors. Their science class is a chance to gain enough context to continue their science education in college and graduate programs, where they will get the background necessary to challenge well-established science. To suggest that students should reject such science at the beginning of their scientific careers is irresponsible.

Keeping an open mind is a virtue when coupled with skepticism and critical analysis. Such skepticism and analysis requires accurate information, which Explore Evolution fails to offer.

Asking students, at the very start of their biological studies, to keep an open mind about the views of an extremely small minority of biologists has questionable pedagogical value. This is particularly problematic because Explore Evolution suffers from so many distortions.

In Explore Evolution, students are exposed to a set of arguments from authority presented in a courtroom-like "he said/she said" fashion. This is not "inquiry-based" education, but rather a rhetorical exercise.

In science, there are not always two diametrically-opposed sides to every issue. When measuring the velocity of objects falling in gravity fields, there is no "dissenting view" or other side that can claim equal time. In areas of active scientific research, there are often more than two sides or interpretations. The courtroom-like approach of this book is an inaccurate representation of how science works.

References

References

Carroll, S. (2005) Endless Forms Most Beautiful.

Davidson, E. (2005). The Regulatory Genome.

Richards, RJ. (1990) The Meaning of Evolution.

Richards, RJ. (2008) The Tragic Sense of Life.

Wells, J. (2000) Icons of Evolution.

Wells, J. (2003) "Survival of the Fakest." American Spectator.

Wells, J. (2005) The Politically Incorrect Guide to Intelligent Design and Evolution.

Biogeography

Explore Evolution mangles the tiny fraction of biogeography covered in this chapter. It is largely dedicated to an historical debate about whether early creationists disputed the fixity of species, a topic falling outside biogeography, and indeed the biology curriculum. The biological examples used are all instances of adaptive radiations on islands, an interesting topic, but not representative of the whole field.

Biogeography is an active field, exploring how geographic distribution of life is affected by history, climate, geology, and behavior. As predicted by evolution, the geographical arrangements of related species repeats in different groups. This comparison of multiple lineages shows how the shared history of an area produces similar patterns of common ancestry, and allows us to test hypotheses about evolution. The rapid ecological and morphological diversification of organisms on islands shows how quickly evolution can produce novelty. Explore Evolution ignores or dances around these points.

p. 75: "Galápagos Islands, seen from Earth orbit"

Technically speaking, this image shows the Yucatán peninsula on Mexico's eastern shore. The Galápagos are roughly 1500 miles south, in a different ocean.

p. 76: "Darwin was using [biogeography] to challenge the fixity of species."

Biogeography yields clear evidence for evolution not only of new species, but of new genera, families, etc., and examples of rapid evolution of morphological novelty. This is exactly opposite to the erroneous conclusion that Explore Evolution presents.

p. 76: "The evidence is just as consistent with … the orchard picture … as with the monophyletic view.

The same techniques that allow us to reconstruct evolutionary trees for a single lineage apply equally well to the entire tree of life. Biogeographic studies of a small family of insects may allow us to look deep into the evolutionary history of other branches of the tree of life. The consistency of these trees cannot be explained without reference to common descent. The creationist "orchard" is scientifically vacuous.

p. 78: "a mechanism … that can transform one type of animal into a fundamentally different type of animal.

These very different species descended from a single ancestor in the last ten million years. Steve Olson (2004) Evolution in Hawaii. The National Academies Press:Washington, D.C.Hawaiian Honeycreepers: These very different species descended from a single ancestor in the last ten million years. Steve Olson (2004) Evolution in Hawaii. The National Academies Press:Washington, D.C.

The adaptive radiations of honeycreepers in Hawaii (and many other groups) represent a range of variation that meets any fair definition of "fundamentally different." Explore Evolution never defines this term, and its use in a definition of "macroevolution" is scientifically inaccurate.

p. 78: "Marsupials are not restricted to … Australia and South America … the opossum live[s] in the northern hemisphere … the oldest marsupial fossil [was found in] China."

The best evidence is that marsupials originated in Asia, migrated across a land bridge to the Americas, and across Antarctica to Australia. The Asian and North American marsupials went extinct, while the Australian and South American populations speciated and radiated in behavior, ecology and morphology. Extinction, migration and diversification are important parts of biogeography and evolution, and Explore Evolution does students a disservice by ignoring or misrepresenting these processes. The total omission of plate tectonics from this discussion is inexcusable.

p. 79: "Scientists … disagree about how to interpret the … evidence we have examined."

Scientific inquiry takes disagreement as a basis for new research, not as a chance to declare that "there may not be much further debate" and "the issue is likely to remain exactly where it is." This is not inquiry; it is surrender. It not only misleads students about the actual state of scientific knowledge, it misinforms them about the way science works.

Major Flaws:

Fixity of species and common descent: Biogeography allows powerful tests of particular hypotheses about evolutionary histories. Explore Evolution wrongly claims that biogeography is only relevant to tests of species fixity, but offers no testable claims to justify arguing that the biogeographic evidence is equally consistent with common ancestry or with creationist orchards.

Evolution on Islands: Studying island biogeography is important, but biogeography encompasses much more than Explore Evolution offers readers. What the book covers omits crucial information about the motion of the continents over time, falsely claims that island biogepgraphy does not show novel features evolving on islands, and introduces confusing and erroneous information about the few examples examined in detail.

Fixity of species and common descent

Studying the biogeographical links between different parts of the world can deepen our understanding of the evolutionary relationships between different populations within a species, between different species, and among higher taxonomic groups. Because different groups diversify at different rates, the evolutionary history of a single species revealed by biogeography might help clarify the relationship between entire families of some different group. These testable predictions about biogeography are powerful tools for scientists.

By the account in Explore Evolution, this predictive power is nonexistent, and biogeography only allows us to reject the notion of species fixity, nothing more. Instead of examining the many ways that biogeographic studies can inform our understanding of evolution, Explore Evolution simply dismisses the field as irrelevant. In particular, the authors claim that biogeographic evidence cannot distinguish between common ancestry and creationist "orchard" models. Such "orchards" have no scientific basis. Despite the book's claim to be "inquiry-based," Explore Evolution never clarifies how readers might themselves investigate such an orchard.

Fixity of Species

As John Wilkins explains, "The idea that species were universally thought to be fixed prior to Darwin is simply wrong — many creationist thinkers of the classical period through to the 19th century thought that species could change." Linnaeus, the father of modern taxonomy, began his career committed to the fixity of species, but began accepting the evidence against such fixity approximately a century before Darwin's ideas were published. Nor was fixism widely accepted within the scientific community by the time Darwin wrote: "No sooner had natural history established a tradition of fixism of species [in the 1700s] than it was immediately under challenge, for example by Pierre Maupertuis in Vénus Physique in 1745," according to Species: A History of the Idea, by John Wilkins (p. 104). It was not Darwin's intention simply to refute the discredited notion of species fixity, but to describe the way that life on earth is related. Biogeography helps us see how that process works over longer time periods.

Despite that history, Explore Evolution claims:

Darwin was using this evidence [biogeography] to challenge a theory that was popular in his day but is almost unheard of now: the fixity of species. The fixity of species was the idea that each species is fixed in its physical form which it doesn't change (at least not enough to constitute a new species) and placed in its current habitat from which it doesn't move (at least not beyond significant geographic barriers such as mountain ranges or oceans). Nowadays, the idea of the fixity of species isn't even a blip on the radar.
Explore Evolution, p. 76

Regardless of this rejection of fixism, Explore Evolution cites unnamed "critics" who assert that biogeography does not demonstrate "macroevolution," idiosyncratically defined as "the origin of new large-scale features such as organs or body plans." This, like the later arguments about the limits on the evolution of finches (see discussion of chapter 8), is an argument for fixity of something. They are merely following the lead of creationists like George McReady Price in the 1930s, who replaced the notion of species fixity with fixity of Biblical "kinds."

In fact, biogeography is a powerful illustration of macroevolution (as it is conventionally defined: "Evolution on the grand scale. The term refers to events above the species level. The origin of a new higher group, such as vertebrates, would be an example of a macroevolutionary event." from Ridley's Evolution, 2nd ed., p. 669). Adaptive radiations of flies, finches or marsupials all demonstrate how rapidly a small population can speciate and diversify, producing the the sort of diversity normally associated with "higher taxonomic groups" in geologically brief periods of time. The few genera of Darwin's finches occupy as many ecological niches as several families of birds; African cichlids exhibit morphologies and ecologies greater than can be found in the many orders of fish found on coral reefs, and all from an ancestor a few million years ago.

Deeper evolutionary insights can come from comparisons of multiple groups with a shared evolutionary history. For instance, both rodent, bat, and insect populations in the Philippines show similar evolutionary connections between certain island populations. One recent study summarized:

The Philippine archipelago is an exceptional theatre in which to investigate the roles of past history and current ecology in structuring geographic variation. The 7000 islands originated as a set of de novo oceanic islands … of varying ages and geological histories… It is an area of high biotic diversity … [A]t least 111 of the 170 native species of terrestrial mammals (64%) are endemic, it is still more striking that 24 of 84 genera (29%) are endemic, implying much in situ diversification, and phylogenetic studies suggest that several large endemic clades are present among fruit bats and murid rodents. Each oceanic island that has remained continuously isolated from its neighbouring islands is a unique centre of mammalian endemism, with 25–80% of the non-volant mammals [mammals other than bats] endemic, even on islands of only a few hundred square kilometres. Similar patterns are evident among butterflies (Holloway, 2003) and trichopteran insects.

Lawrence Heaney, Joseph Walsh, Jr., and A. Townsend Peterson (2005) "The roles of geological history and colonization abilities in genetic differentiation between mammalian populations in the Philippine archipelago," Journal of Biogeography 32(2):229-247

The similarity of these results allows researchers to make predictions about other groups, and where in one case a researcher might look at the biogeography of a single species, in other cases the same pattern may be seen in the biogeography of an entire taxonomic family. Thus, if biogeography undermines the fixity of species, it also undermines the fixity of higher taxonomic groups (as often advocated by proponents of a creationist "orchard") by showing that all taxonomic groupings have responded to the same evolutionary pressures.

Biogeographic predictability

Explore Evolution asserts "the evidence [from biogeography] is completely consistent with other views of the history of life, in which small-scale changes in form and features do occur within separate but disconnected groups of organisms" (p. 79). In order for a claim to be good science, it is not enough that it be "consistent" with the evidence, it must actually make testable predictions. In the terms stated, this "orchard" model offers no testable predictions, as it is infinitely malleable. It can be adjusted to fit any evidence, but Explore Evolution never offers enough details on the "orchard" to allow any predictions. Given the book's claim to be "inquiry-based," this is at best a sad oversight.

By contrast, the consistency of multiple lines of biogeographic evidence is exactly what would be predicted if all life were evolving in response to the same events throughout earth's history. As discussed above, in standard textbooks, and in the extensive (and uncited by Explore Evolution) scientific literature on biogeography, biogeography generates powerful testable predictions, predictions generated by comparing the biogeography of one group to that of another with shared geography. Biogeographers can predict where new species will be found, and can predict the diversity of communities in areas never before investigated because of the power of biogeography and evolution.

Such tests are impossible for the neo-creationist "orchard" model hinted at by Explore Evolution. The book simply gives too little detail of such a model to allow readers to make any prediction. Since the neo-creationist advocates of this model state forthrightly that they believe that God created each tree in the orchard of life, and since God can do anything, this is a model which is consistent with everything, and predicts nothing. The authors of Explore Evolution, perhaps in order to hide the book's creationist heritage, chose not to explain where they think the many trees of life come from (who planted the "orchard"?), how many trees there are, or why the trees are "separate but disconnected" (who prunes them?). This lack of specificity makes the model potentially consistent with anything, but only because they have chosen to specify nothing.

The "Further Debate" section of this chapter (pp. 79-80) repeats one of the great failings of this text. It highlights two sets of views, presents a weak explanation of one side, anonymous critics on the other, and then simply abandons the students to decide for themselves what to think. The authors might claim that this is consistent with an inquiry-based approach, but as discussed in the critique of chapter 1, this is false. An inquiry-based approach would present a real source of scientific uncertainty (and not a lightly repackaged creationist attack on science) and would provide the students with the tools to investigate the subject further. An inquiry-based textbook would not simply declare "scientists sometimes disagree about how to interpret the various classes of evidence we have examined" (p. 79). That is not inquiry, that is surrender. Scientific inquiry takes disagreement as a starting point for further research, not as a chance to declare that "there may not be much further debate" and "the issue is likely to remain exactly where it is."

Not only does this chapter (and the book as a whole) mislead students about the actual state of scientific knowledge, it misinforms them about the way science works.

Doubting Common Ancestry

Explore Evolution claims that some people who doubt common ancestry accept fixity of species, so biogeography doesn't prove anything to them. One such 19th century scientist:

accepted that migration and adaptation would alter the features of species. Nevertheless, he doubted that species could undergo unlimited change, and did not accept that all species shared a common ancestor. Many modern critics of neo-Darwinism share this view.
Explore Evolution, p. 78

Cuvier shares little with the modern creationists he is being compared with here. Cuvier wrote in the early 19th century, decades before Darwin and Wallace, and the understanding of genetics and the fossil record which Darwin had, let alone which modern scientists enjoy. He can be excused for thinking species appeared from some unknown source and remained fixed in form thereafter. If this is the most recent genuine scientist Explore Evolution can cite who holds this view, it is hardly a ringing endorsement. Cuvier's claims had there day, but research in his day and since then have falsified his views.

This small aside at the chapter's end takes back the small concession to critics of creationism offered at the chapter's beginning. Before, the authors acknowledge that species fixity "isn't even a blip on the radar" today. But again, biogeography is not simply an exercise in disputing species fixity: it demonstrates that taxonomic ranks above the species level are not fixed, and shows the process by which species diversify, and by which the branching process of evolution has produced those higher taxonomic levels.

Nor is biogeography simply concerned with speciation and adaptive radiation (a process the authors denigrate in the following chapter). Biogeography shows a great deal more than that species can change. Even within the limited subset of biogeography that Explore Evolution chooses to address (adaptive radiation), there is clear evidence for evolution of new species, genera, families, etc., and illustrations of the power of evolution to produce morphological novelty with great speed, given the right conditions. This is exactly the opposite conclusion from the one Explore Evolution draws. That does not mean that a debate is underway, only that the selective use of evidence can produce misleading results. When this book declares it impossible for evolution to accomplish a task, and then ignores instances where evolution does explain how that impossible thing happened, it calls the book's credibility, not evolution's, into question.

Evolution on Islands

Biogeography, contrary to what readers of Explore Evolution might think, encompasses more than just adaptive radiation on islands. Studying the biogepgraphic effects of rivers and mountain ranges also informs our understanding of evolution. Our understanding of relationships between distantly related groups is often informed by comparing the distributions of modern species and their fossil ancestors with our understanding of continental drift. Such comparisons allow scientists to predict the whereabouts of important fossils and to trace back the distant shared ancestry of modern groups.

Explore Evolution never discusses plate tectonics and its impacts on biogeographic study, and in some cases erroneously dismisses common ancestry based on the current distribution of continents. For the most part, the book focuses on the rapid diversification seen on many isolated island populations, but wrongly claims that evolution in these adaptive radiations has produced no novelties, and only represent loss of genetic information. In fact, studies on islands show the evolution of novel anatomical structures and complex adaptations to new ecological niches.

The Breadth of Biogeography

The vision of biogeography in Explore Evolution is shockingly narrow. The examples of biogeography discussed are: the Galá Islands, the Hawaiian Islands, and island continents Australia and ancient South America. The discussion of marsupial biogeography across South America and Australia bizarrely omits any discussion of plate tectonics, a central theme in any discussion of biogeography over long time scales. No discussion at all is offered of many crucial biogeographic concepts that bear on evolutionary biology.

Biogeography generally focuses on finding repeated geographical patterns across multiple taxonomic groups. For instance, in the 1850s, Alfred Russel Wallace (who independently discovered natural selection) found in his travels through the East Indies that there was a sharp line between the species found in Southeast Asia and the islands as far east as Borneo and Bali, while islands only a few miles away had communities of species with closer affinities to the Australian fauna. The same pattern could be found in a range of groups, including mammals and birds, indicating that some common process acted to allow diversification of groups within regions. He summarized the significance of this result by stating "Every species has come into existence coincident both in space and time with a closely allied species" (Wallace, 1855, "On the Law Which Has Regulated the Introduction of New Species," Annals and Magazine of Natural History 16:184-196.)

By comparing macroevolutionary patterns between different groups, we find that the same patterns repeat. This strongly suggests that the same forces drove the diversification of those different groups. This also makes it possible to compare rates of evolution of those groups. For instance, a recent study of the global biogeography of mites allows unique insights into the processes driving diversity within and across various groups of mammals.

Mite Biogeography: Modern and historical locations of mites.  Because these species do not move long distances, the current locations of species change principally because of continental drift, not because of migration.  "By studying a group of organisms with not only an ancient origin, low vagility and restricted habitats but also a present global distribution, we have been able to test biogeographical hypotheses at a scale rarely attempted."  Sarah L. Boyer, Ronald M. Clouse, Ligia R. Benavides, P. Sharma, Peter J. Schwendinger, I. Karunarathna, G. Giribet (2007) "Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids," Journal of Biogeography (OnlineEarly Articles). Figure from Carl Zimmer (2007) "A Daddy Longlegs Tells the Story of the Continents’ Big Shifts," The New York Times, 8/28/2007.Mite Biogeography: Modern and historical locations of mites. Because these species do not move long distances, the current locations of species change principally because of continental drift, not because of migration. "By studying a group of organisms with not only an ancient origin, low vagility and restricted habitats but also a present global distribution, we have been able to test biogeographical hypotheses at a scale rarely attempted." Sarah L. Boyer, Ronald M. Clouse, Ligia R. Benavides, P. Sharma, Peter J. Schwendinger, I. Karunarathna, G. Giribet (2007) "Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids," Journal of Biogeography (OnlineEarly Articles). Figure from Carl Zimmer (2007) "A Daddy Longlegs Tells the Story of the Continents’ Big Shifts," The New York Times, 8/28/2007.

The authors of the mite research explain that "To date, few conclusive empirical studies of the worldwide historical biogeography of terrestrial organisms are available, because the members of clades [groups containing all descendants of a single common ancestor] with global distributions tend to present dispersal abilities that obscure historical biogeographical patterns. To find a group of land organisms with an ancient global distribution, and therefore suitable for a study of historical biogeography on a global scale, one needs to look among the earliest colonizers of terrestrial environments" (Boyer, et al. 2007, "Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids," Journal of Biogeography, OnlineEarly Articles).

These data establish a context within which other groups' diversity can be examined. While the mites those researchers were studying have a long history, and can be traced back nearly to the beginning of life on land, other groups evolved much later, and exist only in the subset of the world that was connected at the time they evolved. Not only is biogeography evidence against the fixity of species, it is evidence against the fixity of larger taxonomic categories, since groups of much different taxonomic rank follow the same biogeographic patterns. Marsupial biogeography, discussed below, fits well with part of the pattern seen in the mites. The biogeography of extant mammals matches a large portion of the mite data, and the inclusion of fossilized mammalian ancestors results in a biogeography that matches yet more of the mite data. This biogeographic pattern can not be explained without reference to common descent.

Explore Evolution does not even mention major areas of biogeographic research such as gradients in species diversity found as one travels from the poles to the equator, or from sea level to the tops of mountains. Such studies are central to our understanding of the origins not just of individual species, but the evolutionary processes which generate species diversity, and the book's silence on these topics does students a disservice.

Island Diversity

The adaptive radiations of marsupials in Australia, finches in the Galápagos, honeycreepers in Hawaii, or cichlids in Africa's Rift Valley (to choose but a few examples) produced a range of variation equivalent to that seen within vastly larger taxonomic groups. Explore Evolution wrongly demands infinite variation, but that is not a requirement of evolution, and the variation we see in island adaptive radiations is more than enough to account for the diversification of life on earth from a single ancestor.

Explore Evolution states:

Critics note that the examples of mockingbirds in the Galápagos and fruit flies in the Hawaiian Islands show only small scale variations in existing traits. … Since critics of the argument from biogeography see no evidence of large-scale change, or of a mechanism that can produce the new genes needed to cause such change, they doubt that the biogeographical distribution of animals supports Universal Common Descent.
Explore Evolution, p. 77

The issue here of Universal Common Descent is a bit of a red herring. Biogeography is a powerful way to illustrate the power of evolutionary processes, but since all of the parts of the planet have been connected at one point or another, the earliest biogeographic evidence tends to be obscured by subsequent extinction and evolutionary change. Biogeography does reveal the speed with which evolution can operate, and comparing the biogeographic histories of different groups, we can better understand the timing and processes by which various groups evolved. As with the research on mite biogeography discussed earlier, researchers can test predictions of common ancestry by examining overlapping biogeographic patterns, and research on island adaptive radiations provide powerful examples of the power of evolution to generate evolutionary novelties. Explore Evolution claims that these radiations do not demonstrate a mechanism which can "transform one type of animal into a fundamentally different type of animal" (p. 77), but never offers a definition of "fundamentally different." By any reasonable standard, though, island radiations do indeed show exactly such novelty.

Hawaiian Honeycreepers: A phylogeny of a few of the Hawaiian honeycreepers.  These species descended from a single species of finch in the last ten million years.  Figure 14 from Steve Olson (2004) Evolution in Hawaii: A Supplement to Teaching About Evolution and the Nature of Science. The National Academies Press:Washington, D.C.  (Paintings copyright H. Douglas Pratt, The Hawaiian Honeycreepers: Drepanidinae. Oxford: Oxford University Press, 2003. Diagram adapted from T.J. Givnish and K.J. Sytsma, eds., Molecular Evolution and Adaptive Radiation. Cambridge: Cambridge University Press, 1997.)Hawaiian Honeycreepers: A phylogeny of a few of the Hawaiian honeycreepers. These species descended from a single species of finch in the last ten million years. Figure 14 from Steve Olson (2004) Evolution in Hawaii: A Supplement to Teaching About Evolution and the Nature of Science. The National Academies Press:Washington, D.C. (Paintings copyright H. Douglas Pratt, The Hawaiian Honeycreepers: Drepanidinae. Oxford: Oxford University Press, 2003. Diagram adapted from T.J. Givnish and K.J. Sytsma, eds., Molecular Evolution and Adaptive Radiation. Cambridge: Cambridge University Press, 1997.)

Most of the examples that Explore Evolution discusses are poor examples of the breadth of biogeography, since they are really illustrations of adaptive radiation (and not the most striking examples of that phenomenon, either). For instance, rather than addressing the classic case of the adaptive radiation of Darwin's finches on the Galápagos, Explore Evolution focuses on the less diverse Galápagos mockingbirds. Of the 14 species of finches which evolved from an ancestral population blown to the islands several million years ago, the range in sizes is vast, and the ecologies range from vegetarianism to carnivory, from tool-using insect hunters to bills which can crush seeds and to bills that probe into tiny holes to draw out insects. The range of ecologies generated from a small starting population in a few million years is tremendous. Similar ecological diversity evolved among a population of finches which blew onto the Hawaiian islands between 5 and 10 million years ago. Their descendants, known as honeycreepers, show a range of variation in morphology and ecology which falsifies any claim that evolution on islands does not produce fundamental differences. Some authors consider that group to represent a separate family of birds which evolved in a their short time in Hawaii, others regard it as a subfamily within the finches; all agree that their diversity is stunning.

Cichlid Evolution: (from http://evolution.berkeley.edu/evosite/evo101/VIIB1aAdaptiveRadiation.shtml) A few of the many mouth morphologies found in Lake Malawi's cichlids].  Based on geological evidence, the nearly 1000 species of cichlid in Lake Malawi evolved in the last few million years, coming to occupy [http://malawicichlids.com/mw01100.htm a range of ecological niches].Cichlid Evolution: A few of the many mouth morphologies found in Lake Malawi's cichlids. Based on geological evidence, the nearly 1000 species of cichlid in Lake Malawi evolved in the last few million years, coming to occupy a range of ecological niches.

http://evolution.berkeley.edu/evosite/evo101/VIIB1aAdaptiveRadiation.shtm

http://malawicichlids.com/mw01100.htm

Similarly, in three lakes of Africa's Rift Valley, a member of a family of fish named cichlids has evolved a range of ecologies and sizes unmatched anywhere else. Those lakes are known to have formed no later than 1.5-2 million years ago, and the hundreds of species of fish in those lakes occupy ecological niches, and exhibit biological forms, unheard of elsewhere. (One species specializes in eating the eyes of other fish.) The range is greater than what you might find at a coral reef, and all from a small number of evolutionary starting points.

In Hawaii, there are about at least a thousand species of flies — many still waiting to be described — in the genus Drosophila and they all share a common ancestor that separated from the mainland Drosophila tens of millions of years ago. Islands known to be less than 500,000 years old have species which exist only on that island, and which must have evolved in less than half a million years. Those flies represent roughly one third of the members of the genus in the world, and the species found in Hawaii exhibit evolutionary novelties: anatomical traits and behaviors seen nowhere else. This diverse group is not the only adaptive radiation on the islands.

In most of the world, damselfly larvae are aquatic hunters of other invertebrates, breathing through gills on their tails. In Hawaii, some have evolved to live on land, hunting through the leaf litter. In the course of their evolution from aquatic to terrestrial habitats, their gills evolved into air-breathing structures, and representatives of various intermediate stages in this transformation can be found on the islands. Others have adapted to live near the water that collects at the bottom of leaves, but actively avoid being actually soaked in that water, requiring a different set of adaptations. Again, these are structures which are fundamentally different than anything found in other damselflies, and these adaptations have occurred in remarkably short amounts of time.

Hawaiian Silverswords: A few examples of the diverse morphologies of Hawaiian silverswords.  Within 30 species and 3 genera, the group includes trees, shrubs, vines, palm-like stalked plants, aloe-like rosettes, and low-growing ground-cover (not shown).  Images by Gerald Carr, University of Hawaii, made available for educational purposes.Hawaiian Silverswords: A few examples of the diverse morphologies of Hawaiian silverswords. Within 30 species and 3 genera, the group includes trees, shrubs, vines, palm-like stalked plants, aloe-like rosettes, and low-growing ground-cover (not shown). Images by Gerald Carr, University of Hawaii, made available for educational purposes.

Though Explore Evolution constrains itself to discussing animals, adaptive radiations can also be found in the plants of Hawaii. The silverswords, three genera in the sunflower family found in Hawaii have evolved a range of structures, ranging from short plants with spiky leaves to trees, shrubs, vines and low ground-cover. As Futuyma explains, "They vary greatly in the form and anatomy of the leaves and in the size, color and structure of the flowers. In many features their range of variation exceeds that among families of plants, yet almost all of them can be crossed, and the hybrids are often fully fertile. They all appear to have been derived from a single ancestor that colonized the Hawaiian Islands from western America" (Futuyma, 1997, Evolution, Sinauer Associates, Sunderland, MA, p. 118).

The appearance of such diversity from a known starting population demonstrates the incoherence of Explore Evolution's "criticisms". Adaptive radiations have often generated variations exceeding that seen within whole families within a geological flash, yet the authors call these "only small-scale variations in existing traits." By making such a sweeping and imbalanced generalization, Explore Evolution misinforms students about the actual evidence at hand. By making the claims without explaining the basis for them, Explore Evolution makes it impossible for students to explore these ideas in any additional depth, once again hindering inquiry, rather than encouraging and supporting true scientific investigation. If such new structures can be generated in the space of a few milllion years, it's not hard at all to envision the same processes producing the diversity of all life in the space of billions of years.

Marsupials

The marsupial faunas of South America and Australia are at least as ecologically diverse as placental mammals worldwide (with some exceptions, see the discussion of developmental constraints in our response to chapter 8). The convergent evolution of Australian mammals and placentals found in comparable habitats elsewhere shows the power of evolution to adapt species to similar conditions. That they have similar adaptations to those found in placentals, but achieve such adaptations by different means, indicates how flexible evolutionary processes can be. Because of the ecological diversity of South American and Australian marsupials, and the biogeographic history which made such diversity possible, marsupials could serve as a useful exploration of the interplay of evolution and biogeography.

Unfortunately, the discussion of marsupial biogeography in Explore Evolution is laughably bad: too brief to education, and so inaccurate as to be utterly useless. It begins with a mischaracterization of the evolution of marsupials:

The first mammals with the marsupial's distinctive mode of reproduction arose on the ancient southern super-continent of Gondwanaland. Later, after this great land mass broke up into separate continents, the ancestors of marsupials were separated from other mammals and evolved in isolation on the new continents of Australia and South America.
Explore Evolution, p. 75.

This is a straw man. Textbooks and researchers in the field do not claim that marsupials originated in Australia or South America. The best evidence is that marsupials originated Asia, migrated to North America via a land bridge, and that the co-existed with placental mammals in the northern hemisphere for some time. Marsupials colonized first South America, and from there moved on to Antarctica and then Australia. The marsupial populations in Asia and North America went extinct, possibly as a result of competition with placental mammals among other factors, and the populations on southern continents remained in those safe havens.

Explore Evolution's perfunctory and inaccurate coverage of this basic biogeography does students a disservice. Students cannot be guaranteed to have a background to know what Gondwanaland was, nor to appreciate that the supercontinent was already largely broken up by the time marsupials were crossing landbridges between the continents. If students do not have the background to appreciate the interplay of diversification and continental drift, the book's explanation will not help.

Having created the straw man, Explore Evolution proceeds to knock it down:

Critics of the marsupial argument insist that it, too, fails to establish Universal Common Descent or even the descent of all marsupials. At best, it shows that various groups of marsupials first originated in the same general area in the Southern Hemisphere and were then distributed more widely as the Southern continents separated from one another. But even this is questionable, some critics say. They point out that marsupials are not restricted to the southern continents of Australia and South America. Marsupials such as the opossum live in the northern hemisphere. And, in a recent development, paleontologists have unearthed the oldest marsupial fossil of all … in China.
Explore Evolution, p. 77-78.

Marsupials exist in North America because of migration, a process described in this very chapter, but ignored now when the authors find it inconvenient. Around 3 million years ago, a combination of continental drift and the rising Andes brought South America into contact with North America. For the first time in 50 million years, North American species and South American species came into contact. Some marsupials (like the opossum) spread north. Some placentals from North American spread south. For reasons that scientists continue to investigate and discuss, the ability of North American placentals to persist and diversify in South America was much greater than the ability of South American marsupials to diversify in the north, or to outcompete the northern invaders (Stehli and Webb, eds. 1985. The Great American Biotic Interchange. Plenum Press: New York). Today, half of South American mammals are descended from North American ancestors. South American descendants represent no more than 20 percent of modern North American species, and most of those are in Central America, near the point of initial contact (Marshall, et al. 1982. "Mammalian evolution and the Great American Interchange," Science 215:1351-1357). This helps explain the confusion of the apparently biogeographically illiterate authors of Explore Evolution about why "marsupials such as the opossum live in the northern hemisphere." It is because of migration, a process they described as uncontroversial only a page earlier. It is not a mystery, and it is unclear why the authors would regard it as such.

The claim that North American opossums are evidence against the common ancestry of marsupials bears striking similarities to a critique of biogeography by young earth creationist Kurt Wise:

There are very few examples of macrobiogeographical evidences for macroevolution, and none of them is very strong. The best-known claim is the concentration of marsupials in Australia. But there are several reasons that marsupials in Australia are actually a poor example. First, all marsupials are not in Australia. The Virginia opossum of North America, for example, is a marsupial. It is thought to have come from South America, not Australia. Thus not all similar organisms are known from every continent. Third, marsupials are the oldest fossil mammals know from Africa, Antarctica and Australia—in that order. The fossil record seems to show a migration of marsupials from somewhere around the intersection of the Eurasian and African continents and then a survival in only the continents farthest from their point of origin (South America and Australia).
source Wise, Kurt (1994) "The Origins of Life's Major Groups," ch. 6 in J. P. Moreland (ed.) The Creation Hypothesis: Scientific Evidence for an Intelligent Designer, Intervarsity Press:Downers Grove, IL, p. 223).

Wise's confusion over the status of the Virginia opossum perhaps reflects his confusion of the New World order Didelphimorphia — commonly called opossums — with the Australian order Diprotodontia — some of which are commonly called possums (without the first "o"). The groups are morphologically and molecularly distinct, with well-established paleontological histories. If the opossum truly had roots in Australia, it would indeed be a biogeographic conundrum. In fact, the only close link between opossums and Australia is Wise's typo.

Similar misunderstandings plague the discussion of the marsupial fossil record in Explore Evolution and its creationist source material. It is not surprising, the breathless tone of Explore Evolution notwithstanding, that "paleontologists have unearthed the oldest marsupial fossil of all … in China." The authors wonder "If the ancestors of the marsupials originated in the Southern Hemisphere, why has the oldest known member of the group been discovered in the Norther Hemisphere?" The answer is simple: paleontologists do not claim that marsupials originated in the Southern hemisphere, only that they migrated there.

Mammal Taxa: A phylogeny of fossil and extant mammalian taxa, combined with the known ages of fossils.  The earliest fossils are found in Asia, with more modern fossils found in North America, and then spreading to South America and Australia.  This pattern is consistent with known land connections between the continents at the times of apparent interchange.  Zhe-Xi Luo, Qiang Ji, John R. Wible, Chong-Xi Yuan (2003) "An Early Cretaceous Tribosphenic Mammal and Metatherian Evolution", Science, 302(5652):1934-1940.Mammal Taxa: A phylogeny of fossil and extant mammalian taxa, combined with the known ages of fossils. The earliest fossils are found in Asia, with more modern fossils found in North America, and then spreading to South America and Australia. This pattern is consistent with known land connections between the continents at the times of apparent interchange. Zhe-Xi Luo, Qiang Ji, John R. Wible, Chong-Xi Yuan (2003) "An Early Cretaceous Tribosphenic Mammal and Metatherian Evolution", Science, 302(5652):1934-1940.

Marsupials and placental mammals separated roughly 125 million years ago, according to the most recent fossil data. Several lines of evidence indicate that the marsupials originated in Asia, spread to North America over a land bridge, which can be seen in the figure. The ages and characteristics of fossils found in Europe, South America, Africa, Australia and Antarctica suggest that marsupials spread to Europe and South America from North America. South America, Africa, Australia and Antarctica still had linkages at that time, allowing species on the Southern continents to spread easily.

Despite the feigned confusion of Explore Evolution's authors, the fossil record gives a very clear picture of the biogeographic history of marsupials, though there are many questions scientists continue to investigate. The earliest marsupial fossils (and the earliest placental fossils) are found in Asia. Fossilized marsupials are found in North America in rocks that are only a few million years younger than the Chinese fossils. During that period in geological history, plate tectonics had brought North America and Asia close enough together to forge a land bridge, allowing many species to migrate between those continents.

Cretaceous Continents: Christopher Scotese's reconstruction of the continental arrangement 94 million years ago.  The land bridge between North America and Asia is indicated at the upper left.  The connection between North and South America is also visible.  Africa is drifting away from other southern continents, but Australia, Antarctica and South America are linked.  Africa split off from this southern supercontinent beginning around 140 million years ago.Cretaceous Continents: Christopher Scotese's reconstruction of the continental arrangement 94 million years ago. The land bridge between North America and Asia is indicated at the upper left. The connection between North and South America is also visible. Africa is drifting away from other southern continents, but Australia, Antarctica and South America are linked. Africa split off from this southern supercontinent beginning around 140 million years ago.

At that time, the southern continents were all connected, North America and Europe were still very close, and South America had not drifted far from North America, allowing dispersal during periods when ocean levels dropped. Marsupials related to North American species colonized Europe briefly, through a northern land bridge, and others colonized South America. Africa was in the process of separating from the supercontinent which also included Antarctica, Australia and South America, so the presence of marsupial fossils in Africa gives a good measure of how quickly they entered South America and dispersed across the supercontinent Gondwana. Fossilized marsupials in Antarctica also allow us to track their dispersal to Australia. This pattern is consistent with the fossil record of placental mammals, and with other lines of evidence (John P. Hunter and Christine M. Janis. 2006. "'Garden of Eden' or 'Fool’s Paradise'? Phylogeny, dispersal, and the southern continent hypothesis of placental mammal origins," Paleobiology, 32(3):339–344).

As the southern continents drifted apart as well, the marsupial faunas in each isolated continent followed a different path. As Antarctica drifted south towards its current polar position, it became colder and colder, ultimately driving its resident marsupials and palm trees extinct. South American and Australian marsupials produced diverse radiations which filled many of the same ecological niches occupied by placental mammals elsewhere. In the northern continents, which were periodically linked by land bridges, biotic interchanges resulted in periods of intense competition, which seem to have driven the native marsupials extinct.

When South America drifted north again and connected with North America around 3 million years ago, the Great American Biotic Interchange had the same devastating effect that biotic interchanges had on other marsupial faunas.

The same pattern of diversification and migration seen in marsupials can also be seen in other groups of plants and animals. That consistency between biogeographic and evolutionary patterns provides important evidence about the continuity of the processes driving the evolution and diversification of all life. This continuity is what would be expected of a pattern of common descent. The creationist orchard scheme gives us no reason to predict this pattern.

"Lost" Genetic Information

True biological novelty can be found in many of the adaptive radiations that Explore Evolution describes. Despite this, the authors insist "There are many examples of isolated islands that are home to flightless birds and insects that have clearly lost some of the genetic information necessary to produce the traits possessed by their ancestors. Large-scale macro-evolutionary change requires the addition of new genetic information, not the loss of genetic information" (p. 77). No evidence is offered of research on the genetics of flightlessness, and it is far from obvious that flightlessness must represent a loss of information. It is not generally true that loss of a structure involves loss of genes; eyeless cave fish lose their eyes because certain genes are over-expressed. Furthermore, there is no basis for their claim that macroevolution requires the addition of new genetic information, nor is new genetic information beyond the capacity of normal evolutionary processes. For a fuller discussion of the problems with Explore Evolution's treatment of "information," please see chapter 8.

We saw previously that the variation within Hawaiian Drosophila and other adaptive radiations is far greater than the variation found within some much broader taxonomic groups. It is difficult to say what genetic information the authors of Explore Evolution believe was lost. For instance, in the example of damselflies above, here is how one researcher put it in 1970:

This change from aquatic to semi-aquatic to arboreal to terrestrial habit has demanded considerable morphological and physiological change in the gills, and there is a beautiful transition series displayed by the gills of the various species from the long, thin, delicate, highly tracheated gills of the aquatic forms to the short, thick, opaque, densely hairy gills of the terrestrial species. There must also be changes in the function of the spiracles.
Elwood C. Zimmerman (1970) "Adaptive Radiation in Hawaii with Special Reference to Insects." Biotropica, 2(1):32-38.

"It would appear," he concludes, "that it is from such extraordinary adaptive radiation that new major taxa might be produced, and the phenomenon is here demonstrated most lucidly before our eyes."

While the full set of genetic changes underlying this evolution are not fully known, there is no reason to believe it required any new genes, nor that any existing genes were lost along the way. Like many cases of the evolution of new structures (for instance, those discussed by Armin Moczek. 2008. "On the origins of novelty in development and evolution," Bioessays, 30(5):432-447), the evolutionary process most likely operated by rearranging and reusing existing genes and regulatory systems, making changes to the places where genes were expressed, or the times when they turned on or off. Such subtle changes can produce dramatic effects on the final form of an organism.

Understanding the precise genetic basis for those sorts of changes has been an important area of research over the last few decades, as new technology made it possible to examine the ways that genes control development. Explore Evolution presents such open areas of research as a reason to abandon all hope of resolving the underlying issues, but this is not how science works. Scientists are actively investigating the ways in evolution actually works, and students who hope to participate in the active research under way as researchers, doctors, or patients need to understand the process by which scientists produce and evaluate new knowledge. A competent textbook would use these areas of active research to invite true exploration of novel ideas. The fact that Explore Evolution despairs of finding explanations for unresolved issues in science is a damning indictment of the book's inadequacies.

Natural Selection

Natural selection is one of the major mechanisms of evolution, but where most evolution textbooks discuss several such mechanisms, often devoting separate chapters to each, Explore Evolution ignores nearly all of them, devoting a chapter and a half to misrepresenting natural selection. The chapter devoted to this concept inaccurately describes natural selection, mischaracterizes several widely-known examples of natural selection at work, misconstruing howthe significance of those examples.

Students need to understand natural selection, and there are many inquiry-based techniques for teaching about it. Explore Evolution fails to offer any new additions to this literature. Worse yet, it neglects to even draw on that literature to help students deepen their understanding of this basic aspect of evolutionary biology.

p. 95: "changes in the sub-population take place as genetic information is lost to that population"

Ongoing research by geneticists and evolutionary biologists shows that evolutionary processes (including natural selection) do increase information, including through the evolution of new genes, and of genes that are better able to operate under novel conditions. Explore Evolution fails to confront this ongoing research, preferring to criticize decades-old experiments.

Field data vs. Explore Evolution: An illustration of the evolution of finch beaks from Explore Evolution shows no relationship with actual data from the field.  The former restricts its period of analysis to exclude periods of intense change, adding a line of "extrapolation" with no relatField data vs. Explore Evolution: An illustration of the evolution of finch beaks from Explore Evolution shows no relationship with actual data from the field. The former restricts its period of analysis to exclude periods of intense change, adding a line of "extrapolation" with no relationship to anything predicted by working scientists. Explore Evolution uses these inaccuracies to argue for a fallacious extrapolation: limits on the variation possible through natural selection.

p. 94: "not only does the experiment [on peppered moths] not show what the story says it's supposed to, the experiment itself is highly questionable"

While Explore Evolution was being written, a researcher re-ran Kettlewell's classic experiment on peppered moths, correcting various criticisms offered of the original. The new research confirmed the original findings, and those findings affirm the importance of natural selection as an evolutionary mechanism.

p. 90: "definite, discoverable limits on what artificial [and therefore natural] selection can do"

Shortly before decrying extrapolation from short periods to long-term trends, Explore Evolution claims that limits on what animal breeders can accomplish over a century or two demonstrate that evolution could not produce the diversity of life we see over life's 4 billion year history. In fact, intensive selective breeding over a few hundred years has produced a range of sizes and morphologies among domestic dogs that exceeds the diversity of all other members of the family Carnivora. Whatever limits evolution reaches after intense selection, they are much smaller than what the diversity of life requires us to explain.

p. 87: "Is it possible that something like [artificial selection] occurs in nature – only without any intelligence to guide it?"

Explore Evolution plays a slight of hand here, treating "intelligence" interchangeably with the practices of animal breeders, when the difference between artificial and natural selection lies not in the application of intellect, but the application of selective pressures other than those which would occur naturally. Natural selection will tend to be messier than artificial selection, zigging and zagging to match changing environmental conditions, but the practical aspects of each are identical. Explore Evolution wrongly treats artificial selection as an analogy for natural selection, when natural selection is just a more general process.

Major Flaws:

Natural and Artificial Selection: The nature of natural selection is obscured, confusing natural selection's use in evolutionary explanations, the relationship between natural selection and artificial selection, and the way in which evolution from generation to generation produces new genes and new anatomical structures.

Experiments: It is true that many textbooks describe classic experiments on the evolution of beak size in Galápagos finches and peppered moths in England, they also discuss many other examples. Rather than further supplementing textbooks with new knowledge, Explore Evolution devotes itself to factually misleading accounts of those classic experiments, confusing students rather than deepening their understanding.

Extrapolation: Explore Evolution criticizes scientists for extrapolating from evolutionary changes over short timespans to long-term processes like speciation. Instead, the book encourages students to extrapolate from apparent limits to artificial selection to the existence of absolute limits to evolution. While the book's extrapolation is unjustified, the scientific study of evolution is not rooted in extrapolation but in detailed experimentation, mathematical modeling, and experimental hypothesis testing.

Artificial and Natural Selection

Explore Evolution begins its discussion of natural selection with a discussion of artificial selection. Artificial selection, in which differential survival and reproduction in animals, plants, or other organisms is driven by the choices of human breeders selecting among natural variations in a population, is treated as an analogy for natural selection, in which differential survival and reproduction of organisms is driven by natural processes acting on natural variation in a population.

This is a dubious beginning, as natural and artificial selection are, in fact, different aspects of the same process. While Darwin's early understanding of natural selection was influenced by his ability to draw analogies between natural observations he made and the actions of humans breeding pigeons and dogs for special traits, it is wrong to suggest that our modern understanding of these processes is merely analogical, rather than treating artificial selection as a special application of the principles behind natural selection.

Explore Evolution further errs in presenting results from a few hundred years of intensive breeding in dogs and horses as evidence for limits in evolutionary processes over thousands, millions, and indeed billions of years. Even if horses and dogs demonstrated the limits claimed by the authors, it would be foolish to extrapolate limits found under the special conditions of horse-breeding and dog-breeding to the longer-term and more complex conditions which natural selection must confront in its more general form. Given the track record of Explore Evolution, it is hardly surprising that artificial selection in dogs and in horses has not actually reached clear limits, and what limits can be inferred from those cases shows that the variation which can be produced in even a thousand years or so is greater than that seen in all of the members of the mammalian family Carnivora other than dogs. If such extrapolation is legitimate, the actual evidence undermines the point Explore Evolution seeks to make with those data.

Artificial vs. Natural Selection

Summary of problems:

Artificial selection and natural selection are different forms of the same process. Treating the relationship as a mere analogy assumes that differences are greater than they actually are.

Full discussion:

Natural selection simply requires certain conditions. When they occur, natural selection will occur:

  1. There must be variation within the population of organisms.
  2. That variation must be heritable.
  3. There must be differences in reproductive success based on those heritable differences.

The only difference between natural selection and artificial selection is whether the difference in reproductive success is driven by naturally occurring processes, or whether the selection is imposed by humans. Explore Evolution obscures this in two ways. First, by asserting that the relationship is an analogy, rather than a generalization from the human activity. Second, by referring not to a human activity, but to the action of "intelligence."

This shift is subtle, but is a powerful rhetorical opening move. After introducing an example of shepherds selectively breeding woollier sheep, Explore Evolution asks:

Is it possible that something like this process occurs in nature—only without any intelligence to guide it?
Explore Evolution, p. 87

The same question could as easily be posed whether "something like this process occurs in nature—only without any [human] to guide it," but would seem much less profound. And as Explore Evolution acknowledges, it is easy to see how forces other than humans could exert selective pressure on populations of living things.

Horses and Dogs

Summary of problems:

The claim that there are limits on evolution – as evidenced by the limits on the speed of horses or the size of domestic dogs – is essentially a restatement of the creationist doctrine that types (or baramins) cannot evolve into one another. Explore Evolution argues that if natural selection cannot produce a certain change in a matter of decades, it could never produce that change. This is nonsensical on its face, and does not accurately reflect basic knowledge about natural selection and population genetics stretching back to the 1920s. It also misstates the effects that animal husbandry has been shown to have on domestic species.

Full discussion:

Explore Evolution invites readers to imagine a dog as small as a pair of glasses, or larger than a horse, concludes "this is comical," and states that unnamed "critics" think "there are limits to how much an animal can change [via natural selection]" (p. 90). Setting aside that natural selection does not change "an animal," but operates over many generations of a population or species of animals, plants or other organisms, the claim that limits on natural selection are such that they would prevent speciation or other "large-scale changes" is simply not correct.

Explore Evolution states that "Horse breeders have not significantly increased the running speed of thoroughbreds, despite more than 70 years of trying" (p. 90), a claim which is inaccurate on at least one count, and which misrepresents the source they cite. Gaffney and Cunningham (1988), the paper they cite to justify the sentence, do find that winning race times have not changed, but end the paper stating, "We conclude that the explanation for the lack of progress in winning times is not due to a lack of genetic gain in the thoroughbred population as a whole." Genetic gain in the population as a result of selective breeding is the very definition of selection. Furthermore,

breeders and horse-racing enthusiasts state they pay little attention to winning times. Instead, riders, horse owners, breeders, and bettors are rewarded for horses that win races, regardless of time, and little effort is made to "beat the clock." Furthermore, "fast tracks" are notoriously bad for the health of horses, causing damage to bones and tendons. Consequently, track surfaces are often treated to be softer, slower, and less likely to cause stress on the horse. Thus, modern racetracks may be slower than the tracks of 50 years ago.
Ernest Bailey (1998), "Odds on the FAST gene," Genome Research, 8(6):569-571

Thus, it is not the case that horse breeders have tried to increase the absolute time in which their horses complete races, but to ensure that their horses run faster than the other horses in a given race. It is therefore impossible to know whether contemporary horses would run faster than famous racehorses like Seabiscuit or Secretariat if they ran against one another, or whether contemporary horses as a whole are faster in absolute terms than horses were 70 years ago.

The book's dismissal of variation within dogs is, if possible, even more disingenuous.

Dog limbs vs. wild canids: Fig. 7 from Wayne (1986), "Limb morphology of domestic and wild canids: The influence of development on morphologic change," Journal of Morphology 187(3):301-319. It shows an analysis of limb measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5) and other species: la) Canis lupus, the grey wolf; 6a) Speothos venaticus, the bushdog; 6b) Nyctereutes procyonoides, the raccoon dog; 6c) Atelocynus microtis, the short-eared dog; A) Chihuahua; B) Irish wolfhound. It shows that dog limbs are much more varied than those of all other members of the family Canidae, including foxes, wolves, and coyotes.Dog limbs vs. wild canids: Fig. 7 from Wayne (1986), "Limb morphology of domestic and wild canids: The influence of development on morphologic change," Journal of Morphology 187(3):301-319. It shows an analysis of limb measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5) and other species: la) Canis lupus, the grey wolf; 6a) Speothos venaticus, the bushdog; 6b) Nyctereutes procyonoides, the raccoon dog; 6c) Atelocynus microtis, the short-eared dog; A) Chihuahua; B) Irish wolfhound.

It shows that dog limbs are much more varied than those of all other members of the family Canidae, including foxes, wolves, and coyotes.
Dog skulls vs. wild canids: Fig. 3 from Robert K. Wayne (1986) "Cranial Morphology of Domestic and Wild Canids: The Influence of Development on Morphological Change," Evolution, 40(2):243-261. It shows an analysis of skull measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5), other species (labeled 6), and Canis lupus, the grey wolf (labeled 1a).Dog skulls vs. wild canids: Fig. 3 from Robert K. Wayne (1986) "Cranial Morphology of Domestic and Wild Canids: The Influence of Development on Morphological Change," Evolution, 40(2):243-261. It shows an analysis of skull measurements from several species of domestic dogs (dots), other members of the genus Canis (labeled 1), fox-sized species (labeled 2-5), other species (labeled 6), and Canis lupus, the grey wolf (labeled 1a). As with limb morphology, the variability in skull size and shape in dogs exceeds that found within all other canids. Morphometric studies of dog limbs and skulls have found that the variation within the domestic dog, Canis familiaris, is greater than the variation within the entire family to which that species belongs, and indeed greater than the variation within the order Carnivora. The range of sizes is many times greater (axis 1 in both figures). The shapes of the dogs' limbs (axis two in the first image) only slightly overlap the shapes found in other canids, including other members of the genus Canis. The shapes of the skulls (axis two in the second figure) completely overlap the shapes of non-Canis canid skulls, and the range of dog skull shapes is matched only by variation among other members of the genus.

There is no evidence in these data to suggest that dogs have reached any inherent limits to their evolution or to the powers of natural selection. What these data show is that dog breeders have already managed to produce animals which break new morphological ground. Whatever limits might seem to exist if we look at the shapes and sizes of wild canids have been surpassed by the work of dog breeders. Whatever limits natural selection has, they have prevented the evolution of variation beyond that seen within the rest of the entire order Carnivora (dogs, cats, bears, foxes, weasels, etc.), all within the last few thousand years. Natural selection may well have limits, but if the limits are that loose, they would not prevent the diversification of life as we know it over the course of several billion years.

There is little doubt that limits on natural selection do in fact exist. Because selection operates on existing variation, there is a balance between the rate of mutation and the force of selection. This balance was first described in the 1920s, and modern textbooks describe this mutation-selection balance (e.g., p. 115 in Ridley's Evolution, p. 438 in Futuyma's Evolutionary Biology, or p. 461 in Campbell and Reece's Biology). In a hypothetical case where mutation does not occur, strong enough selection would eventually stabilize all of the genes relevant to a given trait. Similarly, in the absence of selection, mutation would gradually increase the number of mutants in the population to some equilibrium. Depending on the amount of selection and the amount of mutation, the amount of variation available to select on will vary.

The limits selection might face because of limited natural variability within a single generation will get progressively broader as the number of generations increases. Modern racing horses can trace over half of their genes to 10 horses of the late 18th century, and over 80% to only 31 ancestors from that era. Despite that highly constrained gene pool, the speed of horses has risen (whether or not it plateaued in the 1950s as discussed above). Similarly, much of the morphological evolution in dogs took place over a similar time period, beginning in the 18th century as breeders began paying more careful attention to studbooks.

Experiments

In its effort to debunk natural selection, Explore Evolution reiterates the debunked claims from the creationist book Icons of Evolution. That book claimed that textbooks misrepresented evolution by incorrectly characterizing certain popular experiments. Explore Evolution repeats the earlier book's arguments, reuses several of that books images without change (or attribution), and does not update its arguments to reflect more recent research.

The most fundamental error here is the claim that research on peppered moths and work on the Galápagos finches are the only, or at least major, examples offered for natural selection in textbooks. Those examples are frequently cited, but modern textbooks cite many other examples to show how natural selection works. Nor do modern textbooks cite those bodies of research for the purposes claimed in Explore Evolution. The treatment of natural selection in this book focuses exclusively on whether natural selection can generate biological novelty. That is an interesting topic, but not the only relevant topic for students to learn about natural selection, and Explore Evolution does students a disservice by treating an important and multi-faceted topic like natural selection through such a limited lens.

Turning to the details of the critiques offered for the peppered moth work and the Galápagos finch research, one finds that Explore Evolution describes that research inaccurately, and ignores recent work which directly contradicts the book's claims. For instance, it presents a graph of finch evolution which bears no relationship at all with any measurements reported by any researchers in the field, and criticizes the 50 year old work of Bernard Kettlewell on peppered moths without any discussion of research from the 1990s which tested several of the authors' criticisms of Kettlewell, and found that Kettlewell's results were unaltered by those criticisms.

Biology Texts

Summary of problems:

Darwin's finches and peppered moths are unquestionably examples of natural selection. They are far from the only examples offered in biology textbooks.

Full discussion:

Explore Evolution claims:

Biology textbooks cite two classic examples to support the claim that natural selection can produce small-scale change over a short time.
Explore Evolution, p. 88

Campbell and Reece's Biology (6th edition) has a section in the chapter on evolution entitled, "Examples of natural selection provide evidence of evolution." It begins:

Natural selection and the adaptive evolution it causes are observable phenomena. As described in the interview at the beginning of this unit, Peter and Rosemary Grant of Princeton University are documenting natural selection and evolution in populations of finches in the Galápagos [Darwin's finches]. We will now look at two additional examples of natural selection as a pervasive mechanism of evolution in populations.
Neil A. Campbell and Jane B. Reece, Biology, 6th ed.

Those examples include the evolution of HIV and insects in response to drugs and insecticides, yet neither HIV nor insecticide even rates a mention in the index of Explore Evolution. In Chapter 9, Explore Evolution addresses antibiotic resistance, but only to discuss the origins of mutations conferring resistance, not to point out that natural selection is what causes that resistance to spread.

Sickle cell anemia also makes an appearance in Chapter 9, again purely as an example of a mutation. In Raven and Johnson's Biology (5th edition), however, it is the first example of natural selection described in the section entitled "Natural selection explains adaptive microevolution." Explore Evolution mentions that sickle cell anemia can be beneficial under some circumstances, but misses the chance to either discuss how natural selection makes it more common in human populations traditionally occupying malarial areas, or to employ a truly inquiry based approach by inviting students to develop and test hypotheses about malarial resistance in order to actually explore evolution.

Earlier, Raven and Johnson discuss examples of natural selection including its ability to maintain persistent latitudinal gradients in the oxygen-carrying hemoglobin molecule in ocean fish, differences which make northern fish more efficient in cold water and southern fish more efficient in warmer water. They also describe how selection improves the camouflage of butterfly caterpillars and allows snail populations to adapt to different local ground coloration, as well as pesticide resistance in tobacco budworms and agricultural weeds. Only later do they discuss industrial melanism in peppered moths or the beaks of Darwin's finches.

That introductory textbook authors tend to focus on a few common examples does not detract from the fact that natural selection is commonplace, easy to observe, and widely documented. Specialized textbooks on evolutionary biology present an even wider array of examples of natural selection. For instance, the chapter on natural selection in Futuyma's Evolutionary Biology discusses how selection produces a north-south gradient in the frequency of alleles of a certain gene in Drosophila flies, a pattern repeated on multiple continents. Similar patterns exist for field crickets. Later, Futuyma describes how guppies in streams without predators have brighter coloration than closely related guppies in streams with predators. In the example of snail shells also used by Raven and Johnson, Futuyma points to paleontological studies showing that the genetic polymorphism seen in the population today has persisted for thousands or millions of years — clear evidence of stabilizing selection — and studies of broken snail shells allow an evaluation of rates of predation on various color morphs — allowing an assessment of the selective pressures acting on the population.

The emphasis on two examples of natural selection, and the complete disregard for the myriad other examples in active use by introductory and advanced textbooks, reflects a common creationist strategy. Jonathan Wells, a creationist author at the Discovery Institute, has made a career of attacking the Galápagos finches and the peppered moth, perhaps in the belief that all of the other examples of natural selection would go away if he could disprove one or two well-known examples.

It is noteworthy that several figures in this chapter are drawn from Jonathan Wells' Icons of Evolution, a creationist work aimed at critiquing the content of common biology textbooks and common examples used to illustrate and explain evolutionary processes. While Wells is not credited in this chapter, many of the arguments are the same as in his earlier work (critiqued by NCSE's Alan Gishlick), as are the illustrations. Explore Evolution repeats many of the errors previously identified in Wells' work. Just as the authors of Explore Evolution have a well-documented religious agenda which belies the scientific appearance of their book, Wells is famous for his religious reasons for obtaining a PhD in biology and attacking evolution, rooted in his involvement with the Unification Church (better known as "Moonies"), led by Sun Myung Moon, or, as Wells refers to him, "Father":

I asked God what He wanted me to do with my life, and the answer came not only through my prayers, but also through Father's many talks to us, and through my studies.…

He also spoke out against the evils in the world; among them, he frequently criticized Darwin's theory that living things originated without God's purposeful, creative activity.…

Father's words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle.

Explore Evolution, like Wells' earlier work, is rooted in a religious aversion to evolution, not in actual science. Scientists have sought to correct the erroneous claims displayed in Explore Evolution in their earlier incarnations, and the refusal to accept those corrections, or even to acknowledge those criticisms, recommends strongly against adopting this work into science classes.

Modern Galapagos Finches

Summary of problems:

The hybridization observed in the finches is not enough to merge two species, and observations in the field have actually shown substantial evidence of incipient speciation.

Full discussion:

Explore Evolution argues that
…after the rains returned [to the Galápagos], the Grants notices that several separate species of finches were interbreeding. No only were no new species springing forth, but existing varieties actually seemed to be merging. Critics therefore conclude that the finch beak example of microevolution actually suggests that biological change has limits.
Explore Evolution , p. 93

Explore Evolution versus the data: Actual measurements of G. scandens finches compared to Explore Evolution's presentation of data over the same time period.  EE arbitrarily compresses the Y-axis to minimize actual variability, introduces an "extrapolation" which bears no resemblance to what any scientist has predicted, and uses the unjustified claim of oscillation in the data to produce their own extrapolation &mdash; limits on the power of evolution.Explore Evolution versus the data: Actual measurements of G. scandens finches compared to Explore Evolution's presentation of data over the same time period. EE arbitrarily compresses the Y-axis to minimize actual variability, introduces an "extrapolation" which bears no resemblance to what any scientist has predicted, and uses the unjustified claim of oscillation in the data to produce their own extrapolation — limits on the power of evolution.

Given that this passage follows right after their complaints about the dangers of extrapolation, it is rich to find them claiming that anything that didn't happen in a 30 year study could never happen. The sole basis for the claim that limits exists seems to be that something did not occur in the course of a single study. By that standard, I could predict that I will never die, since I am thirty and have not been observed to die.

Furthermore, the citation the authors use to explain that hybridization occurred points out that genetic novelty accompanies such unusual matings, and explains why those matings do not mean that the species are merging. The ongoing changes in beak shape (shown in part F of the figure above) cannot be explained by natural selection alone. They can only be explained by invoking the combination of two of the 4 major evolutionary mechanisms: natural selection and gene flow. Natural selection explains the initial changes, but the flow of genes between species provided the ongoing evolutionary pressure towards blunter beaks. Peter and Rosemary Grant explain:

The proportionally greater gene flow from G. fortis to G. scandens than vice versa has an ecological explanation. Adult sex ratios of G. scandens became male biased after [the extremely hot and wet] 1983 as a result of heavy mortality of the socially subordinate females. High mortality was caused by the decline of their principal dry-season food, Opuntia cactus seeds and flowers; rampantly growing vines smothered the bushes. G. fortis, more dependent on small seeds of several other plant species, retained a sex ratio close to 1:1. Thus, when breeding resumed in 1987 after 2 years of drought, competition among females for mates was greater in G. fortis than in G. scandens. All 23 G. scandens females paired with G. scandens males, but two of 115 G. fortis females paired interspecifically. All their F1 offspring later bred with G. scandens because choice of mates is largely determined by a sexual imprinting-like process on paternal song.
Grant, P. R. and B. R. Grant (2002), "Unpredictable evolution in a 30-year study of Darwin's finches." Science 296:707-711

There are two important things to understand about that. First, that the hybridization was a result of unusual environmental conditions and an excess in the number of males of one species. Those males competed for access to any female at all, and were prepared to overcome pre-mating barriers to hybridization. Second, the main force limiting hybridization is that different species of finches select mates with songs similar to those of their fathers. Elsewhere, the Grants explain:

Hybridization occurs sometimes as a result of miscopying of song by a male; a female pairs with a heterospecific male that sings the same song as that sung by her misimprinted father. On Daphne Major island, hybrid females bred with males that sang the same species song as their fathers. All G. fortis × G. scandens F1 hybrid females whose fathers sang a G. fortis song paired with G. fortis males, whereas all those whose fathers sang a G. scandens song paired with G. scandens males. Offspring of the two hybrid groups (the backcrosses) paired within their own song groups as well. The same consistency was shown by the G. fortis × G. fuliginosa F1 hybrid females and all their daughters, which backcrossed to G. fortis. Thus mating of females was strictly along the lines of paternal song.
Peter R. Grant and B. Rosemary Grant (1997). "Genetics and the origin of bird species," Proceedings of the National Academy of Sciences, 94:7768–7775

The Grants go on to discuss how this helps explain the speciation of Galápagos finches.

Experiments show that birds are less responsive to the songs of conspecifics from different islands than to songs from their own island. Even though the changes are small, the process of cultural drift is enough to begin isolating these populations. In addition, the finches show a preference for the morphology of birds from their own island to members of the same species from other islands, even independent of song differences. The forces driving natural selection on different islands will differ, and that will produce morphological differences, which will combine with differences in songs to make hybridization less likely.

Thus, the observation of hybridization does not provide evidence that two species will merge into one. Instead, it helps test the process by which species separate. Furthermore, the hybridization observed had an effect which directly contradicts the claim that novelty cannot originate through evolutionary processes. Because of genes flowing in from another species, G. scandens experienced substantial evolutionary change, and acquired novel traits.

The Grants point out that this sort of gene exchange is important to understanding speciation and evolution in general:

Introgressive hybridization [as seen in Darwin's finches] has the potential of leading to further evolutionary change as a result of enhancing genetic variances, in some cases lowering genetic covariances), introducing new alleles, and creating new combinations of alleles, some of which might be favored by natural selection or sexual selection. Svärdson believed that introgression in coregonid fishes has replaced mutation as the major source of evolutionary novelty. Introgression and mutation are not independent; introgressive hybridization may elevate mutation rates.



The relevance to speciation lies in the fact that regions of introgression are peripheral areas, which could become isolated from the main range of the species through a change in climate and habitat: they are potential sites of speciation.
Grant, P. R. and B. R. Grant (1997)

Far from demonstrating limits to the power of evolution, the rare hybridizations between species demonstrate how strong pre-mating isolation is, illustrate an important source of variation, and provide evidence about the process of speciation and the origins of genetic novelty. The fact that Explore Evolution never mentions two of the four major mechanisms of evolution (gene flow and genetic drift), speaks poorly of the authors' commitment to a serious examination of evolutionary biology.

Peppered Moths

Summary of problems with claim:

Textbooks do not use peppered moths as an example of something new being created, they use it to demonstrate what natural selection can do in mere decades.

Full discussion:

Explore Evolution claims:
Critics question whether the peppered moth story shows that microevolution can eventually produce large-scale change. They point out that nothing new emerged.
Explore Evolution, p. 93, emphasis original

Textbooks which present this example typically use it to illustrate the process by which biologists investigate natural selection, not to demonstrate the origins of biological novelty. In Raven and Johnson's Biology (5th edition), the discussion of peppered moths and industrial melanism is in a section titled "Natural selection explains adaptive microevolution," and never claims that the example illustrates anything other than the process by which scientists have investigated the effects of natural selection. Ridley's Evolution (2nd ed.) discusses peppered moths first in a section explaining how "Natural selection operates if some conditions are met," and later in a chapter entitled "The Theory of Natural Selection," in a section discussing how "the model of selection can be applied to the peppered moth." Ridley first demonstrates the reasons why natural selection was invoked by observers of a pattern, and then proceeds to describe the particular ways in which researchers investigated the hypothesis: determining the heritability of coloration, experimenting to determine the fitnesses of various genotypes under different conditions, and concluding with a discussion of ways in which "the details of the story are now known to be more complex."

As Ridley explains:

In conclusion, the industrial melanism of the peppered moth is a classic example of natural selection, and illustrates the one-locus, two-allele model of selection. The model can be used to make a rough estimate of the difference in fitness between the two forms of moth using their frequencies at different times; the fitnesses can also be estimated from mark-recapture experiments. However, the one-locus, two-allele model is only an approximation to reality. In fact, several alleles are present (and their dominance relations are not simple); selection is not simply a matter of bird predation in relation to camouflage; and it seems that migration, as well as selection, is needed to explain the geographic pattern of gene frequencies.
Mark Ridley (1996), Evolution, 2nd ed., p. 109

Explore Evolution claims that "the experiment [does] not show what the story says it's supposed to," but misrepresents what scientists claim it illustrates. It is not an experiment meant to illustrate speciation, and Explore Evolution does not discuss those experiments, such as the examples in Drosophila discussed by Ridley in his chapter on speciation.

In fact, Explore Evolution does not even discuss the process by which melanism would have originated in peppered moths. The genetics of melanism have been well understood since the 1960s, when researchers showed how several different mutations to the same genes could produce similar sorts of melanism (Lees, David R., 1968, "Genetic Control of the Melanic Form Insularia of the Peppered Moth Biston betularia (L.)," Nature 220(5173):1249-1250). Natural selection is the process by which those mutations increased in frequency over several generations, exactly what scientists and textbook authors claim this example demonstrates.

Kettlewell's Experiments

Summary of problems:

Research scientists do not find Kettlewell's work invalid because he released moths in the daytime. This claim is found nowhere in the research literature.

Full discussion:

Bernard Kettlewell did several experiments on peppered moths, to explore the factors driving their observed evolution from lighter to darker forms over a relatively short time period. The research most relevant to this claim are the mark-recapture experiments where moths were captured, marked, released onto trees and recaptured the following night.

In these experiments the moths were placed onto trunks and branches at dawn, not day time, and allowed to take up their own resting places, as described in Kettlewell's 1958 paper "The importance of the micro-environment to evolutionary trends in the Lepidoptera" (Entomologist, 91:214-224). This is exactly what the moths do naturally. In one experiment, as a control, Kettlewell released moths earlier, and allowed them to fly on to the trees themselves. The recapture patterns from this experiment were no different from the recapture patterns with the moths placed on branches and trunks (Kettlewell, 1956, "Further experiments on industrial melanism in Lepidoptera" Heredity, 10: 287-301).

As well, some of the moths that were released in the mark-recapture-experiments stayed out for two nights before being captured. That is, they had been flying free at night and had found their own location during the morning. The distribution of those moths that did freely choose their own resting places is no different from those that were placed on trunks and branches (as shown in Kettlewell, 1956, and in his 1955 paper "Selection experiments on industrial melanism in Lepidoptera," (Heredity, 9: 323-342).

While there were legitimate reasons why scientists did criticize Kettlewell’s experiments (including Bruce Grant's 1999 paper "Fine tuning the peppered moth paradigm," Evolution 53. 980-984 and Michael Majerus's 1998 Melanism: evolution in action, Oxford University Press, Oxford, chapters 5 and 6), none of these criticisms (density and resting place choice) involve the moths being sleepy or sluggish, and no serious experimenter suggested that Kettlewell’s results were invalid. Indeed, subsequent experiments to test these criticisms broadly confirmed Kettlewell’s results (again, see Grant, 1999, Majerus 1998, and Majerus' 2007 talk "The Peppered Moth: The Proof of Darwinian Evolution," given at the ESAB meeting in Uppsala on 23 August – also available as Powerpoint, as well as his 2009 paper "Industrial melanism in the peppered moth, Biston betularia: an excellent teaching example of Darwinian evolution in action," Evolution: Education and Outreach 2(1):63-74). Further details of these experiments are discussed in "Where Peppered Moths Rest," below.

Where Peppered Moths Rest

Summary of problems:

Peppered moths do rest on trunks. Kettlewell placed moths on both branches and trunks, covering the spectrum of moth resting places.

Full discussion:

Kettlewell was aware that peppered moths rested on both trunks and branches. In Kettlewell’s experiments, he actually placed the moths on trunks and branches, in relatively unexposed locations, thus covering the natural resting places of the peppered moth.

In a comprehensive study of peppered moth resting places in the wild, fully 25% of moths were found resting on trunks (Majerus, 1998, cited above). Of the remainder, roughly 25% were found on branches, and 50% at branch/trunk junctions. Furthermore, in the branch/trunk junction category, the moths are actually resting on the trunks, 2-3 inches below the branch. In a later, extensive 6 year study 37% of peppered moths were found on trunks (Majerus, 2007, cited above).

Peppered moths in situ: Peppered moths in their natural resting places on horizontal tree branches (above) and vertical tree trunks (below).  From figures 4 and 5 in Michael E. N. Majerus (2009), "Industrial melanism in the peppered moth, Biston betularia: an excellent teaching example of Darwinian evolution in action," Evolution: Education and Outreach 2(1):63-74.Peppered moths in situ: Peppered moths in their natural resting places on horizontal tree branches (above) and vertical tree trunks (below). From figures 4 and 5 in Michael E. N. Majerus (2009), "Industrial melanism in the peppered moth, Biston betularia: an excellent teaching example of Darwinian evolution in action," Evolution: Education and Outreach 2(1):63-74.

It is important to note that Kettlewell performed several different experiments; direct observations, filmed observations of birds taking moths from exposed trunks, indirect observations of moth predation where moths were released onto relatively unexposed trunks and branches and allowed to chose their resting places, and mark-recapture experiments, where again moths were released onto relatively unexposed trunks and branches to choose their own resting places (Kettlewell, 1955, 1956, both cited above). So when Kettlewell put his moths on trunks and branches (Kettlewell, 1955, 1956), he was placing them where the majority of all moths rest naturally, as far as we can tell (even more if we count the trunk-resting moths at the trunk/branch junctions).

Michael Majerus has repeated Kettlewell’s experiments using moths resting on the undersides of branches (Majerus 1998, 2007). In both cases, differential predation was found that confirmed Kettlewell’s original observations. Furthermore, in Majerus’s 6-year experiment, measured predation intensity at the experimental sites predicted the population frequencies of moths found in the wild (Majerus, 2007).

While the authors of Explore Evolution could not have been expected to have had access to Majerus’s 2007 results, Majerus’s 1998 results, as well as Kettlewell’s description of the original experiments (Kettlewell, 1955, 1956) alone are enough to show that Explore Evolution is completely wrong on this point.

Since Kettlewell's original experiments were published, they have been independently replicated at least 6 times (See for example Grant 1999, Majerus 1998, and Majerus 2007, all cited above, for reviews). All of these experiments have addressed one or more criticisms of the original study, and all have broadly confirmed Kettlewell's experiments. Thus we can say that Kettlewell's experiments have stood the test of time.

An inquiry-based book could have used this history of successive investigations to explore the practice of science as a self-correcting enterprise, and the importance of replicability to the scientific process. Students could have been asked to devise their own experiments based on criticisms of Kettlewell's early work, and then teachers could reveal data from experiments like those performed by Majerus to evaluate the results of those new experiments. Instead, students are presented with erroneous critiques of Kettlewell's work, given none of the more recent vindicating evidence, and instructed to believe that this flawed exploration demonstrates a weakness in natural selection. In fact, it reflects only the weaknesses of Explore Evolution, and of its authors' approach to evolution and science in general.

Extrapolation

Natural selection operates at different speeds under different circumstances. Scientists agree that natural selection over long periods of time can produce larger evolutionary change than natural selection can produce in shorter periods, but exactly how much more is a subject of ongoing research.

Explore Evolution claims that there are inherent limits to the amount of change that evolutionary processes can produce, and that these limits make it improper to extrapolate from short-term research on natural selection in explaining the long-term evolutionary change we see in the fossil record. Alas, their argument for inherent limits to evolutionary change is rooted in exactly the sort of fallacious extrapolation they decry. The work scientists do bears little, if any, resemblance to these sorts of erroneous extrapolation.

To illustrate the claim of improper extrapolation, Explore Evolution actually invents data from whole cloth, presenting a graph of finch beak size "extrapolation" vs. "data" which is actually contradicted by the data obtained from field research. Where the text and graph suggest constant oscillations within fixed limits, research on the Galápagos finches show directional change in beak shape in addition to cyclical changes in beak size. Furthermore, those cycles match the cyclical environment the birds live in, so it is inappropriate to treat those oscillations as inherent limits to the birds' evolutionary capacity, rather than a reflection of their ability to rapidly adapt to large environmental changes with equally large evolutionary change.

As always, Explore Evolution passes up any opportunity to give students the data or opportunity to propose their own tests of any of these claims, belying the book's claim to be inquiry-based. Students are expected to learn by rote that limits exist on evolutionary change. They are never told how researchers actually investigate the ways in which various factors do limit evolutionary change.

Exrapolating microevolution to macroevolution

Summary of problems with claim:

The link between evolution on short timescales and longer-term evolutionary processes is thoroughly testable and not a mere extrapolation.

Full discussion:

Anyone who denies the logical link between genetic changes within a population ("microevolution") and speciation ("macroevolution") is similar to someone who watches the sun come up in the east and move west across the sky, but denies that it will set in the west. The only difference between genetic changes within a population and generation of a new species from that population is time. Given enough time, the sun will set in the west. Given enough time, speciation will occur.

This claim is related to the "young earth" creationist belief that the earth is only a few thousand years old. In this belief system, there has not been enough time for speciation to occur, given the rate of change that we can observe in most populations. So it is necessary for them to deny reality (observations of speciation) in order to validate a creationist perspective on the age of the earth. An age, by the way, that is about 0.00000002% of the approximately 3 billion years over which biological evolution has proceeded.

Limits on Evolution

Summary of problems:

Explore Evolution never defines "biological information," except through error-laden analogies to computers. Biologists have no trouble showing how new information (in the sense used by information theorists) originates, nor how new genes, kinds of cells or tissues evolve.

Full discussion:

Nowhere in the discussion of "the information problem" is there any attempt to formally define how students should measure "information." At one point, the authors introduce a strained analogy between upgrading computer software and adding biological information, but never quite explain the analogy. Later they observe that scientists have occasionally referred to DNA as if it were analogous to a computer program. Based on this informal analogical reasoning, they declare "So, biological information is stored in DNA" (p. 94). Teachers who wish to actually discuss this idea in class would be stranded utterly not only by Explore Evolution's treatment of the subject, but by the equally vague attempts by the ID creationists on whose work this section draws.

The field of mathematics known as information theory was developed to address the transmission of information, and it both defines information and describes how information is created. In essence, a mathematically random sequence of symbols (whether letters, DNA bases, or computer bits) has the highest information content possible. A completely predictable sequence contains only as much information as it would otherwise take to accurately predict the sequence. Thus, in information theory, adding random noise actually increases the amount of information being transmitted. Whether that information is useful or not to a listener is a separate matter.

This is where the misuse of "information" throughout Explore Evolution can be confusing. We usually have a very specific expectation for information transmitted over a telephone line, so random static on the line reduces the amount of information we can use. Randomness adds mathematical information, but decreases immediately usable information. A process of selection, mutation, and drift acting on such random information will, in time, extract new elements which are usable.

Evolution itself has no expectations about what data will be transmitted from generation to generation. Random mutations add information to the genome, and natural selection (or artificial selection) acts against those mutations which are not useful at a given moment, promotes those mutations which happen to benefit the organisms possessing them, and has no particular effect on mutations which do not influence the organism's fitness.

Biologists have incorporated this insight into their studies of the evolution of new genes. Gene duplication are common events, resulting from small errors in the process of cell replication. Once a gene is duplicated it is possible for one copy to mutate, adding information without risking the functioning of the pre-existing gene.

The process of gene duplication has been known since at least 1936; its possible significance for producing the raw material for the evolution of genetic novelty was recognized as early as 1951 (see Zhang 2003 for more on this history).

Examples of New Genes of Known Age (from Long, 2003), table 2)
Genes Age Evolutionary feature
Drosophila
jingwei 2.5 my A standard chimeric structure with rapid sequence evolution
Sdic <3 my Rapid structural evolution for a specific function in sperm tails
sphinx <3 my A non-coding RNA gene that rapidly evolved new splice sites and sequence
Cid Function diverged in the past 3 my Co-evolved with centromeres under positive Darwinian selection
Dntf-2r 3-12 my Origin of new late testis promoter for its male-specific functions.
Adh-Finnegan 30 my Recruited a peptide from an unknown source and evolved at a faster rate than its parent gene
Primates
FOXP2 100,000 y A selective sweep in this gene, which has language and speech function, took place recently
RNASE1B 4 my Positive selection detected, which corresponds with new biological traits in leaf-eating monkeys
PMCHL2 5 my Expression is specifically and differentially regulated in testis
PMCHL1 20 my A new exon-intron in the 3' coding region created de novo and an intron-containing gene structure created by retroposition
Morpheus 12-25 Strong positive selection in human-chimpanzee lineages
TRE2 21-33 my A hominoid-specific chimeric gene with testis=specific expression
FUT3/FUT6 35 my New regulatory untranslated exons created de novo in new gene copies; the family has been shaped by exon shuffling, transposation, point mutations and duplications
CGß 34-50 my One of two subunits of placentally expressed hormone; the rich biological data clearly detail its function
BC200 35-55 my A non-coding RNA gene that is expressed in nerve cells.
Rodents
4.5Si RNA 25-55 my A non-coding RNA gene that is expressed ubiquitously
BC1 RNA 60-110 my A neural RNA that originated from an unusual source: tRNA
Fish
Arctic AFGP 2.5 my Convergent evolution; antifreeze protein created from an unexpected source driven by the freezing environment
Antarctic AFGP 5-14 my Convergent evolution; antifreeze protein created from an unexpected source driven by the freezing environment
Plants
Sanguinaria rps1 <45 my A chimeric gene structure created by lateral gene transfer
Cytochrome c1 110 my Origin of mitochondrial-targeting function by exon shuffling
Protozoa
N-acetylenuraminate lyase << 15 my A laterally transferred gene from proteobacteria that recruited a signal peptide

As it has become more practical to trace the sequences of genes in multiple species, scientists have been able to identify genes which went through these processes, acquiring new functions within relatively recent history. That research systematically refutes the claim in Explore Evolution that "whether you're talking about artificial selection or about microevolution that occurs naturally, changes in the sub-population take place as genetic information is lost to that population" (p. 95). In fact, a recent review of the processes by which new genes and new gene functions evolved drew the exact opposite conclusion:

The origination of new genes was previously thought to be a rare event at the level of the genome. This is understandable because, for example, only 1% of human genes have no similarity with the genes of other animals, and only 0.4% of mouse genes have no human homologues, although it is unclear whether these orphan genes are new arrivals, old survivors or genes that lost their identity with homologues in other organisms. However, it does not take many sequence changes to evolve a new function. For example, with only 3% sequence changes from its paralogues, RNASE1B has developed a new optimal pH that is essential for the newly evolved digestive function in the leaf-eating monkey. Although it will take a systematic effort to pinpoint the rate at which new genes evolve, there is increasing evidence from Drosophila and mammalian systems that new genes might not be rare. Patthy compiled 250 metazoan [multicellular animal] modular protein families that were probably created by exon shuffling. Todd et al. investigated 31 diverse structural enzyme superfamilies for which structural data were available, and found that almost all have functional diversity among their members that is generated by domain shuffling as well as sequence changes.
Manyuan Long, Esther Betrán, Kevin Thornton and Wen Wang (2003) "The Origin of New Genes: Glimpses from the Young and Old," Nature Reviews: Genetics, 4:865

The table at the right describes a few well-studied examples of recently evolved genes, and a summary of what scientists have learned about the processes by which those genes evolved. The processes are the same sorts of small-scale mutational changes that we observe in existing populations. It was not necessary to invoke previously undescribed processes, merely to understand how known processes could produce the patterns observed in nature. That is the way scientists typically work, and an inquiry-based textbook ought to teach students to apply those methods. Instead, Explore Evolution ignores actual knowledge, criticizes the scientists who produced that knowledge, and discourages scientific inquiry from students, in favor of vague and untestable speculation.

Biologists do not dispute that limits to evolution may exist, and conduct research to test whether such limits exist. For instance, biologists wonder why no marsupials evolved flight or the sorts of adaptations to swimming seen in other mammals. It is hypothesized that the young marsupials' early crawl to the teat (see our discussion of marsupial reproduction in chapter 12) may place a constraint on the possible final forms the marsupial shoulder can take. While placental mammals give birth to offspring that are self-sufficient, marsupials give birth before major nerves, muscles and bones have formed, and must crawl to the teat (an exception is found in bandicoots of the genus Isoodon, which have a backwards-facing pouch into which the newborn can drop or slither without using its arms). That crawl requires that a functional shoulder exist early in fetal development, and the necessity of forming that functional shoulder so early may prevent the sort of limb diversification seen in other mammals, which range from the bat's wing to the cat's leg and on to the whale's flipper.

To test this, Dr. Karen Sears measured the adult and fetal shoulderblades of a dozens of marsupial and placental mammals, and performed a statistical analysis of the changes in shape.

Ontogenetic Trajectories: Growth of the shoulderblade in marsupials and placentals. The ontogenetic trajectories of individual marsupial and placental species are plotted in a morphospace representing general scapular shape (PC2 and PC3 are the 2nd and 3rd principal component; the first principal component is just size). Marsupials, with the exception of the bandicoot Isoodon, are represented by solid black arrows (w, Macropus [Tammar wallaby] t, Trichosurus [Australian possum] m, Monodelphis [South American opossum]). Isoodon (i) is represented by the white arrow with the black border. Placentals are represented by solid gray arrows. The ontogenetic trajectories of marsupials, with the exception of Isoodon, are remarkably similar, whereas the trajectories of placentals vary greatly.  Isoodon does not crawl to the pouch, and so its fetus does not experience the same developmental constraints as other marsupials. (Figure 7 from Karen E. Sears. 2004. "Constraints on the Morphological Evolution of Marsupial Shoulder Girdles," Evolution 58(10):2353–2370.)Ontogenetic Trajectories: Growth of the shoulderblade in marsupials and placentals. The ontogenetic trajectories of individual marsupial and placental species are plotted in a morphospace representing general scapular shape (PC2 and PC3 are the 2nd and 3rd principal component; the first principal component is just size). Marsupials, with the exception of the bandicoot Isoodon, are represented by solid black arrows (w, Macropus [Tammar wallaby] t, Trichosurus [Australian possum] m, Monodelphis [South American opossum]). Isoodon (i) is represented by the white arrow with the black border. Placentals are represented by solid gray arrows. The ontogenetic trajectories of marsupials, with the exception of Isoodon, are remarkably similar, whereas the trajectories of placentals vary greatly. Isoodon does not crawl to the pouch, and so its fetus does not experience the same developmental constraints as other marsupials. (Figure 7 from Karen E. Sears. 2004. "Constraints on the Morphological Evolution of Marsupial Shoulder Girdles," Evolution 58(10):2353–2370.)

As shown in the figure here, the placental mammals changed shoulder shape in many directions as they grew in size, while all of the marsupial limbs moved in the same direction. All but Isoodon, which doesn't use the shoulder during its move from womb to pouch, and so does not face the same developmental constraints.

This insight that developmental constraints can limit what evolutionary processes can produce is not new, and is well integrated into textbooks on biology and evolutionary biology (for a recent review, see J. L. Hendrikse, T. E. Parsons and B. Hallgrímsson. 2007. "Evolvability as the proper focus of evolutionary developmental biology," Evolution & Development, 9(4):393–401. For examples of textbook coverage, see pp. 352-365 of Ridley's Evolution, with sections titled: "Genetic constraints may cause imperfect adaptations," "Developmental constraints may cause adaptive imperfection," "Historical constraints may cause adaptive imperfection," "An organism's design may be a trade-off between different adaptive needs" and "Conclusion: constraints on adaptation.")

Other scientists confronting apparent biological constraints did not merely criticize, they proposed new evolutionary mechanisms which would not face those same limitations. The origins of mitochondria and other cellular structures is a case in point. The mitochondrion is the part of the cell in which oxygen is converted into usable energy. Without mitochondria, oxygen would poison every cell in our bodies, and without the molecular energy they produce, each of our cells would starve.

Our cells each have several mitochondria within them. Each of those mitochondria has its own circular genome with which it produces the proteins it needs to process oxygen. Each of the mitochondria possess two or more cell membranes, rather than the one found around all of our cells. It is impossible to imagine how a cell could exist with only part of a mitochondria, nor why a cell before the era of oxygen might have any of the unique parts present in the mitochondria found in nearly every eukaryotic cell. Even more mysterious was why the mitochondrial genome should be so different from that of every eukaryote. It is much more similar to that of a bacterium.

In the late 1970s, Lynn Margulis proposed that the mitochondria and several other parts of the eukaryotic cell might actually be the descendants of bacteria which were engulfed by the ancestors of all eukaryotes. This would explain the odd genome, and would explain the multiple membranes. The inner membrane is like that possessed by the free-living ancestor of mitochondria, while the outer membranes are the remnants of the vacuole within which that bacterium was captured to be digested. For whatever reason, it wasn't digested, instead helping process oxygen and cellular waste into useful molecular energy.

This theory proposed an entirely novel evolutionary mechanism, endosymbiosis. While some of the endosymbiotic relationships Margulis proposed are seen as unlikely, her explanation of the origin of mitochondria and chloroplasts have become widely accepted within the scientific community. Again, her discovery could form the basis for an inquiry-based discussion of evolutionary mechanisms, and could be enhanced by evidence of transitional stages in the evolution of endosymbiosis found today. Scientists in Japan recently described one such case (Noriko Okamoto and Isao Inouye. 2005. "A Secondary Symbiosis in Progress?" Science, 310(5746):287), and researchers recently showed that a bacterium which commonly invades insect cells, sometimes integrates its genes into the host cell, exactly like mitochondria sometimes do (Julie C. Dunning Hotopp, et al. 2007. "Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes," Science [DOI: 10.1126/science.1142490]).

Explore Evolution never mentions this process, despite its obvious pedagogical value, and its utility in addressing the limits of more commonly observed evolutionary mechanisms.

Oscillations

Summary of problems with claim:

When the sizes of finch beaks oscillates, it is because of an oscillating environment. The size changes within a species are large enough to explain the differences between the various species of Galápagos finches, species Charles Darwin initially thought belonged to several different families of bird. Not all of these changes oscillate, the evolution of Darwin's finches has been directional in some aspects.

Full discussion:

Finch Sizes: Morphological trajectories of adult Geospiza fortis (A to C) and G. scandens (D to F). In the absence of change, mean trait values should have remained within the 95% confidence intervals (horizontal broken lines) of the estimates from the 1973 samples (body size: G. fortis, n = 115, G. scandens, n = 37; beak traits: G. fortis, n = 173, G. scandens, n = 62). Sample sizes varied from 45 (1997) to 976 (1991) for G. fortis and from 30 (1999) to 336 (1983) for G. scandens. The 1972 sample is composed of the adults (=1 year old) in 1973.  (From [http://www.sciencemag.org/cgi/content/full/296/5568/707 Peter R. Grant and B. Rosemary Grant, 2002, "Unpredictable Evolution in a 30-Year Study of Darwin's Finches," Science 296(5568):707-711].Finch Sizes: Morphological trajectories of adult Geospiza fortis (A to C) and G. scandens (D to F). In the absence of change, mean trait values should have remained within the 95% confidence intervals (horizontal broken lines) of the estimates from the 1973 samples (body size: G. fortis, n = 115, G. scandens, n = 37; beak traits: G. fortis, n = 173, G. scandens, n = 62). Sample sizes varied from 45 (1997) to 976 (1991) for G. fortis and from 30 (1999) to 336 (1983) for G. scandens. The 1972 sample is composed of the adults (=1 year old) in 1973. (From [http://www.sciencemag.org/cgi/content/full/296/5568/707 Peter R. Grant and B. Rosemary Grant, 2002, "Unpredictable Evolution in a 30-Year Study of Darwin's Finches," Science 296(5568):707-711].

The figure shown here illustrates that, as the climate in the Galápagos has changed due to the multiyear El Niño cycle, the finches have changed body size, beak size, and beak shape (a measure of width, length and depth). Some of those measurements have returned to levels that were seen historically (inside the faint horizontal lines in the figure), while other measurements continue to diverge.

As the Grants describe in "Unpredictable Evolution in a 30-Year Study of Darwin's Finches", "The temporal pattern of change shows that reversals in the direction of selection do not necessarily return a population to its earlier phenotypic state." This is the opposite of what Explore Evolution describes:

After the heavy rains of 1983, the depth of the average finch beak went back to its pre-drought size, and the so-called "evolutionary change" was reversed.
Explore Evolution, p. 93

While one species did wind up at roughly the same beak size, the beaks at the end were sharper than they had been at the beginning, while the other species has a smaller and blunter beak than it had to begin with.

Does this demonstrate that evolution has limits? Not at all. We would not expect finches to evolve more rapidly over 30 typical years. Over the thirty years, the environment oscillated within limits, and the finches evolved and adapted to that changing climate. When the climate returned to the state it had been in at the beginning of the study, the finches became more similar, but not identical, to their initial state. Why students ought to assume that finches could not have changed more if the environment had changed more is not at all clear, especially since the size and shape of finches and their beaks continues to change and to cross historical limits.

Of course, the climate is not constant, either. Peter Grant explains:

The climate of the Galápagos has not remained stable over the last 50,000 years. This is known from an analysis of particles and plant products in cores taken from the sediment of El Junco lake on the summit of San Cristobal (Colinvaux 1972, 1984). Inferences can be made about changes in water level, cloud cover, and heat budget from the composition of the cores at different levels.

The present climate has persisted for the last 3,000 years, and it also prevailed about 6,200 and 8,000 years ago. In the intervening period of 3,200 years it was drier, and possibly hotter, than now. Going back further, it was drier before 8,000 years ago. The most different climate regime from the present one occurred from about 10,000 to 34,000 years ago; this was a time of little precipitation or evaporation.
Grant, P. R. (1999) Ecology and Evolution of Darwin's Finches, Princeton University Press, Princeton, NJ, pp. 29-30

We know that finches can and do undergo significant morphological change when the climate changes. We know the climate changes. Explore Evolution simply insists that we should not follow the syllogism to its conclusion, and decide that the finches would have undergone large changes during periods of large environmental change. Explore Evolution invokes limits, but provides no actual evidence that inherent limits on evolution operate beyond those imposed by limited environmental variability. This is not, needless to say, how science proceeds, and it is not what we would expect from an inquiry-based approach to science. Unanswered questions are not places where scientists draw lines, they are opportunities to make new discoveries. An inquiry-based text should invite students to propose hypotheses about finch evolution, and provide teachers with a suite of data for students to test their hypotheses.

Natural Selection & Mutation

Mutation is a crucial component of evolution, as is natural selection. In focusing exclusively on those two mechanisms, Explore Evolution ignores other critical evolutionary mechanisms. Despite those omissions, the book's coverage of mutation is woefully inadequate. "Mutation" itself is misdefined, ways in which mutations influence morphology are omitted, and the effects of mutations on fitness are mischaracterized. Scientists views are described inaccurately, creationists are passed off as legitimate sources and even plagiarized.

In its discussion of developmental biology, the chapter carries out the predictions of biologist Rudolf Raff: "we will see more slick books of bogus science produced to influence the teaching of biology … Evo-devo data have become a part of the creationist rhetorical weaponry, and as evo-devo grows in prominence, the problem will grow in severity." Again, baic knowledge is misrepresented, scientists are misquoted, and students are left without the resources necessary to conduct their own inquiry into one of the most exciting new fields in biology.

p. 98: "Mutations can occur when genes are exposed to heat, chemicals, or radiation"

This is not an exhaustive list of causes of mutation. Errors in DNA copying and chromosomal crossing-over are more significant causes.

p. 101: "structural mutations" are mutations which "ultimately affect an animal's shape or structure"

Evolution of hindwings: Mutations in regulatory genes change the shapes of insect hindwingsEvolution of hindwings: Mutations in regulatory genes change the shapes of insect hindwings

Structural mutations are those which change the structure of a protein, not which change an organism's morphology. This is a trivial misdefinition.

p. 109: "no experimental mutations in hox genes … have proven helpful"

This is a young field, and the absence of evidence would not be evidence that no such mutations exist.

p. 103: Antibiotic resistance "mutation … impairs [bacterial] ability to perform … vital functions"

Compensatory mutations reverse such impairments, and they do not always occur.

p. 103: "The cell cannot endure an unlimited number of mutations"

Many mutations can be tolerated by a cell, and an infinite number is not necessary.

p. 103: "multiple mutations at active sites inevitably do more harm than good"

Compensatory mutations can and do increase fitness.

p. 107: "a reptile laid an egg from which a bird was hatched … two-legged sheep or two-headed turtles"

These odd phrases, and many others on this page, are plagiarized from creationist David Menton.

p. 109: "temperature changes" cause "a whole new fitness cost"

Fitness is always relative to an environment. Changing temperature changes fitness, and may either increase or decrease an organism's fitness.

p. 110: "DNA does not direct how the overall body plan gets built"

This is contrary to the best current research, and is unsupported by the evidence offered.

p. 111: "many scientists doubt that [higher-level assembly instructions] are stored in DNA alone"

The authors cited to support this claim actually dispute it. Alternatives offered are still producedstructured by DNA sequences.

p. 110: "Critics say it's a little like building a CD player."

This analogy makes no sense, and has only ever been offered by creationist sources.

p. 111: "you can mutate DNA 'til the cows come home and you still wouldn't get a new body plan"

The citation offered to support the claim actually rejects this conclusion.

p. 106: "Major mutations &hellip are always harmful or outright lethal"

The authors cited supporting this claim actually reject it. The results may be "tiny, moderate, or large."

p. 104: "In every case … resistance results from small changes to a single protein molecule"

This is not always true.

p. 105: "there is no evidence that one species of bacteria has changed into another"

This is false. New bacterial species have been produced in the lab.

Major Flaws:

Mutations: Mutation is misdefined, major types of mutation are omitted, and the effects of mutation on fitness are mischaracterized. For a chapter about mutation, these basic failures are fairly significant.

DNA: The role of DNA in development is described incorrectly throughout. It has been clear for decades that DNA ultimately controls morphology and development. Explore Evolution wrongly obscures this basic truth.

Morphology: The study of evolutionary changes in morphology – evolutionary developmental biology – is an exciting and rapidly-changing field. Explore Evolution confuses this field, giving students too little background to understand this new field, and misinformiag them about the basics of this dynamic field.

Mutations

Mutation is the raw material of evolution. Understanding what evolution is, what its sources are, and how different forms of mutation operate is crucial for students. Instead of offering that information – information crucial to the inquiry Explore Evolution purports to encourage – the book misdefines and mischaracterizes mutation and ignores basic concepts in mutation.

After providing an inaccurate definition of mutation, and misdefining "structural mutation," the book then fails to describe the most common causes of mutation. Mutation can be caused by crossing-over during production of gametes, by errors in DNA replication, as well as the environmental factors which Explore Evolution describes as the sole causes of mutation. Mutations do not just occur in genes, the description in Explore Evolution notwithstanding.

The book errs in treating mutations as principally altering protein forms, rather than also considering the ways that mutations change the regulation of other genes, including protein-coding genes and other regulatory genes. The ways that genes are regulated is a key concept in modern biology, but these issues are simply ignored by the authors. The book focuses on antibiotic resistance, but even mangles that example, mischaracterizing the way antibiotic resistance evolves and the side-effects of mutations that generate such resistance.

Mutation Definition

Unfortunately, Explore Evolution makes a confusing definition of "structural mutations" which significantly differs from normal scientific usage. Also, Explore Evolution remarkably fails to mention the major cause of mutations, errors in copying DNA.

A straightforward definition of mutation can be found in any genetics or evolution textbook. For example, the recently published Evolution textbook by Nick Barton and colleagues explains:

Mutation, formally defined as a heritable change in the genetic material (DNA or RNA) of an organism, is the ultimate source of all variation. Without mutation, there would be no evolution.
Barton, et al., (2007) Evolution, p. 325

Unfortunately, Explore Evolution takes this straightforward concept and manages to make it incomprehensible:

As we have seen, there are scientists who doubt that natural selection can produce major evolutionary change. Specifically, they question whether there is a source of new information that can produce new genetic traits – the variations needed to produce lasting biological change.

Defenders of the neo-Darwinian position dispute this critique by offering another argument for the creative power of natural selection. they say that the critics have underestimated the power of another type of variation, unknown in Darwin's time, called mutation.

Explore Evolution, p. 98

How are mutations produced?

Mutations can occur when genes are exposed to heat, chemicals, or radiation.
Explore Evolution, p. 98

Remarkably, Explore Evolution fails to mention that errors in copying DNA are a major source of mutations.

Explore Evolution's definitions of mutations are arbitrary and result in outright confusion. "Genetic mutations" are defined by Explore Evolution as:

a change in the sequential arrangement of the information-bearing bases – the "letters" in the genetic text – of the DNA molecule.
Explore Evolution, p. 98

Explore Evolution explains that there are several types of "genetic" mutations including point mutations, gene duplications, and chromosomal inversions. Presumably, chromosomal translocations and insertions would also be "genetic" mutations, although they are not mentioned. In fact, Explore Evolution's definition of "genetic mutations" encompasses every type of mutation.

Why produce an arbitrary and unnecessary definition of "genetic mutation"? Explore Evolution seems to be distinguishing "genetic mutations" from something they define as "structural mutations":

For major changes to occur in more complex, multi-cellular animals, mutations must ultimately affect an animals shape or structure. Are there examples of such structural mutations? Evolutionary biologists say they are, and point to another striking example of the novel variation that mutation can produce: the four-winged fruit fly.
Explore Evolution, p. 101

This distinction between "genetic" and "structural" mutations is found nowhere else in evolutionary biology, it misappropriates the legitimate term of "structural mutation," and it will generate considerable confusion among students. The long-standing legitimate definition of a "structural mutation" refers to a mutation in the protein coding portions of a gene that results in a change in amino acid sequence. An example of a structural mutation in the human serum cholinesterase gene that is a result of a mutation in the protein-coding region is described below.

A point mutation in the gene for human serum cholinesterase was identified that changes Asp-70 to Gly in the atypical form of serum cholinesterase. The mutation in nucleotide 209, which changes codon 70 from GAT to GGT, was found by sequencing a genomic clone and sequencing selected regions of DNA amplified by the polymerase chain reaction.
McGuire et al., (1989), "Identification of the structural mutation responsible for the dibucaine-resistant (atypical) variant form of human serum cholinesterase," PNAS 86, p. 953

According to Explore Evolution, structural mutations "ultimately affect an animal's shape or structure", but this correctly labeled "structural mutation" in human serum cholinesterase does not result in a change in organismal structure. Instead, human serum cholinesterase is involved in controlling the stability of neurotransmitters.

What Explore Evolution refers to as "structural mutations" would be recognized by most biologists as mutations in genes that are used to build animal embryos, the genetic toolkit. For example, the four-winged fruit fly referred to by Explore Evolution is due to mutations of the Hox gene, Ultrabithorax. Are mutations in the protein-coding region of Ultrabithorax responsible for the four-winged fruit fly? No, the mutations are in non-coding regions of Ultrabithorax. Explore Evolution's own example of a "structural mutation" is the opposite of what biologists consider structural mutations.

If the intent of Explore Evolution was to prevent a clear understanding of mutations and their relationship to evolution, they succeed grandly. For teachers and students, however, this treatment of mutations promises headaches.

Protein Coding

Explore Evolution ignores mutations in non-protein-coding cis-regulatory sequences (CREs). Furthermore, research has shown that mutations in the coding regions and in CREs of the genetic toolkit are both responsible for evolutionary change.

Evolutionary developmental biologists argue that mutations in members of the genetic toolkit will be most important for driving morphological change during the evolution of animals. Many genetic toolkit genes, such as Ultrabithorax, a member of Hox gene family, regulate developmental pathways by turning other genes on or off. Hox proteins bind to specific DNA sequences in CREs and control whether or not RNA is synthesized from the adjacent gene.

Explore Evolution claims:

Because hox genes are so important for coordinating the activities of the cell, some researchers think that mutations in these genes can cause large-scale changes in the structure of an organism. Many neo-Darwinists think that influencing the "coach" (hox genes) through mutation can provide a new source of beneficial variation. Critics aren't so sure. They note that, precisely because hox genes are so influential, no experimental mutations in hox genes (so far) have proven helpful to the organism.
Explore Evolution, p. 109

Explore Evolution latches onto the current circumstance that experimental mutations in the Hox genome have yet to result in an advantage to an organism. Then they invoke anonymous "critics" and suggest that evolution does not involve Hox gene mutations. This is the typical creationist ploy of identifying an experimental shortcoming to generate "doubts" about evolution. This time, they raise the bar rather high for evolutionary developmental biologists. Given the hundreds of millions of years in which evolution has been optimizing morphology, Explore Evolution injects "doubt" because researchers have yet to make a further structural improvement in a decade or so of research.

However, we can investigate whether natural mutations in the protein-coding regions of Hox genes have been responsible for changes in body plans. To understand how the changes a Hox gene could result in evolutionary change, evolutionary developmental biologists compare the functions of Hox genes in different organisms. For example, Ultrabithorax is known to repress limb formation in insects, such as fruit flies. However, the abdominal segments of crustaceans, such as brine shrimp, express Ultrabithorax and also have limbs. So, Ultrabithorax is able to repress limb formation in insect embryos but not in crustacean embryos. Notably, a major feature of the insect body plan is their lack of abdominal limbs, unlike crustaceans. Thus the difference between crustacean and insect Ultrabithorax function in repressing limbs could play an important role in arthropod evolution.

Ultrabithorax in Insect and Crustacean LimbsUltrabithorax in Insect and Crustacean Limbs

The comparison of a genetic toolkit gene, Ultrabithorax in insects, crustaceans and velvet worms has established why insects lack abdominal limbs (Galant et al., 2002; Ronshaugen et al., 2002). Changes in sequence at the tail end of Ultrabithorax protein have enabled Ultrabithorax to repress abdominal limbs in insects.

UltrabithoraxUltrabithorax

Genetic experiments in fruit flies has shown that crustacean Ultrabithorax does not repress embryonic limbs, unlike fruit fly Ultrabithorax. An important reason for the difference in Ultrabithorax function is that all modern insects have a "QA motif" - a short 15 amino acid sequence (QAQAKAAAAAAAAAA)at the tail of Ultrabithorax protein. Arthropods, such as millipedes and crustaceans, have a different type of sequence at the tail of Ultrabithorax which has a number of serines (S) and threonines (T). In a functional analysis in fruit flies, Ronshaugen et al. show that the replacement of a few of the serines (indicated by * in diagram below) in the tail of a crustacean Ultrabithorax renders it capable of repressing limbs.

As McGinnis and colleagues explain:

Previous studies led us to propose that gain and loss of transcriptional activation and repression functions in Hox proteins was a plausible mechanism to diversify morphology during animal evolution(12). Here we show that naturally selected alteration of the Ubx protein is linked to the evolutionary transition to hexapod limb pattern.
Ronshaugen et al., "Hox protein mutation and macroevolution of the insect body plan." (2002) Nature 415, p. 914

The evidence for the importance of Hox gene mutations in morphological evolution certainly extends beyond creating a four-winged fruit fly.

Normal Protein

Mutations can improve normal protein function resulting in increased fitness relative to the environment. Many mutations work by generating more effective enzymes or through novel catalytic mechanisms. Explore Evolution is wrong to claim that mutations must impair a protein's normal functioning and impose a fitness cost. Explore Evolution does not even discuss mutations in cis-regulatory elements (CREs), which have minimal fitness costs and are considered by many evolutionary biologists to have the greatest potential for generating evolutionary change (Prud'homme et al., 2007). Explore Evolution also misrepresents the basic notion of fitness, by failing to note that fitness depends on the environment.

After saying that a "resistance gene" does not develop through mutation, Explore Evolution then says mutations do confer resistance but with a "fitness cost."

… [A] mutation [changes] the shape of the active site on the "target" protein so that the antibiotic no longer recognizes the site. … However, that very same mutation also impairs that strain's ability to perform other vital functions like information processing. … Microbiologists refer to this as the "fitness cost" of a mutation.
Explore Evolution, p. 103
… Experiments show that once antibiotics are removed from the environment, the original (non-resistant) strain "out-competes" the resistant strain, which dies off within a few generations.
Explore Evolution, p. 103

Explore Evolution significantly misrepresents how antibiotic resistance arises in this description. For example, methicillin resistance is due to generation of a new binding site for penicillin-like drugs on a protein that previously did not have this activity (Wu et al., 1996, 2001). Vancomycin resistance is due to the generation of a novel enzyme that bypasses the vancomycin-susceptible step. Resistance to extended-spectrum antibiotics is due to the evolution of beta-lactamases with increased catalytic efficiency (Sideraki et al., 2001).

Increased fitness cost is not necessarily related to enzyme "impairment." Consider the example of the methicillin resistance gene. It produces a new protein which binds methicillin, preventing methicillin from acting. However, producing this protein costs energy and resources. In the absence of methicillin, making the protein diverts resources way from growth, and so the methicillin resistant bacteria will grow more slowly than a methicillin sensitive bacteria in the absence of the antibiotic. This slower growth decreases fitness.

One of the best studied examples of antibiotic resistance is the case of resistance to the antibiotic streptomycin. Streptomycin kills bacteria by interfering with protein assembly on the ribosome, turning out garbage proteins, by binding to the S12 subunit of the 30S ribosomal particle in bacteria. The 30S ribosomal particle is a multi-subunit structure which in turn forms part of the protein synthesizing ribosomal particle. The S12 subunit together with 16S RNA forms part of the proof reading centre of the transfer RNA (tRNA) acceptor binding site. A mutation that results in the substitution of threonine or asparagine for lysine at position 42 in the rspL gene results in streptomycin failing to bind to S12, with resulting resistance of the bacteria to the antibiotic streptomycin. This mutant version is actually more accurate, i.e. more specific, than the wild type. The wild-type proof reading center makes a few mistakes even in the absence of streptomycin, and the mutant forms make even fewer mistakes than the wild type, roughly 85% fewer (Bjorkman et al., 1999). This is a classic example of a beneficial mutation. Furthermore it was work on this mutation that determined that mutations were random.

Thus we can see that the mutation that produces streptomycin resistance doesn't impair information processing, it makes it more accurate. However, this increased accuracy slows protein synthesis so overall growth is slower. When you put the threonine or asparagine rspL 42 mutant streptomycin resistant bacteria and wild type streptomycin sensitive bacteria together in head to head competition in the absence of streptomycin, the wild type will out compete-them. It's a classic trade off, make your proteins carefully and grow slowly, or grow quickly and have some messed up proteins.

Importantly, not all mutations produce fitness costs. There are several examples of mutations that produce no fitness cost, or are even fitter than the wild-type antibiotic sensitive bacteria (Andersson, 1996; Zhang 2006).

Equally importantly, compensatory mutations occur that restore the fitness of the bacteria to wild type levels. There are multiple examples of this for streptomycin (Bjorkmann, 1996, 2000; Anderson, 2006) and other antibiotics (Anderson, 2006; Maisnier-Patin, 2002; Zhang 2006). This is a major issue in clinical treatment, as it means that withdrawing use of an antibiotic does not mean that the antibiotic resistant bacteria will go away.

Finally, as discussed elsewhere, mutations in the regions of non-coding DNA that act as genetic switches, CREs, have significantly lower fitness penalties than mutations in protein-coding regions of developmental regulatory genes.

References:

Andersson DI. The biological cost of mutational antibiotic resistance: any practical conclusions?Curr Opin Microbiol. 2006 Oct;9(5):461-5. Epub 2006 Aug 4.

Bjorkman J, Hughes D, Andersson DI. Virulence of antibiotic-resistant Salmonella typhimurium. Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3949-53

Bjorkman J, et al., Novel ribosomal mutations affecting translational accuracy, antibiotic resistance and virulence of Salmonella typhimurium. Mol Microbiol. 1999 Jan;31(1):53-8

Bjorkman J, Nagaev I, Berg OG, Hughes D, Andersson DI. Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance. Science. 2000 Feb 25;287(5457):1479-82

Maisnier-Patin S, Berg OG, Liljas L, Andersson DI. Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol Microbiol. 2002 Oct;46(2):355-66

Sideraki V, Huang W, Palzkill T, Gilbert HF. A secondary drug resistance mutation of TEM-1 beta-lactamase that suppresses misfolding and aggregation. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):283-8.

Wu S, Piscitelli C, de Lencastre H, Tomasz A. "Tracking the evolutionary origin of the methicillin resistance gene: cloning and sequencing of a homologue of mecA from a methicillin susceptible strain of Staphylococcus sciuri." Microb Drug Resist. 1996 2(4):435-4

Wu SW, de Lencastre H, Tomasz A. "Recruitment of the mecA gene homologue of Staphylococcus sciuri into a resistance determinant and expression of the resistant phenotype in Staphylococcus aureus." J Bacteriol. 2001 Apr;183(8):2417-24

Zhang Q, Sahin O, McDermott PF, Payot S. "Fitness of antimicrobial-resistant Campylobacter and Salmonella." Microbes Infect. 2006 Jun;8(7):1972-8. Epub 2006 Mar 31.

Mutation Accumulation

Evolutionary biology does not require that organisms be able to accumulate unlimited mutations. Organisms can and do accumulate large numbers of mutations. Explore Evolution is deeply misleading about the role of mutations and adaptations.

Explore Evolution claims that

The cell cannot endure an unlimited number of mutation-induced changes at these critical active sites. At some point, the cell's information processing system will be damaged so badly that it stops functioning altogether. For this reason, multiple mutations at active sites inevitably do more harm than good.
Explore Evolution, p. 103

There are a number of problems with this claim. First, not all mutations are associated with a fitness cost relative to the wild type in the original environment, and in those mutations that do reduce fitness with respect to the wild type, subsequent compensatory mutations often restore fitness, sometimes to above wild type levels. Therefore, a large number of mutations can be tolerated.

This "loss of fitness" is always in relation to the wild-type organism in the original environment. In an environment with antibiotics, the wild-type organism's fitness is very low, and the antibiotic resistant mutant is much fitter. Accumulation of mutations may indeed mean that an organism is restricted to the new environment, and cannot survive in the old environment. This is irrelevant. Penguins and polar bears have adapted to cold environments, and cannot survive in the environments their ancestors came from. Our ancestors came from the sea, but we are remarkably unfit in the sense of being able to breath underwater. There are many examples like this. Explore Evolution implies there is some universal standard of fitness, but fitness is always relative to the environment the organism is in.

Compensatory Mutations

Compensatory mutations are mutations that correct a loss of fitness due to earlier mutations. In some cases, such mutations bring their own fitness costs, but often they do not. Even when they do, it is irrelevant to the power of mutation and selection to produce novelty.

Explore Evolution claims:

the effectiveness of the second [compensatory] mutation is a limited-time offer, a coupon only good for the exact environment in which it was issued. If the temperature changes in the environment,* or if the salinity changes, a whole new fitness cost comes to light. The compensatory mutation now "codes for" a protein that doesn't fold properly under the new conditions. And if it doesn't fold properly, it doesn't work properly. Or, it may not work at all.

* This is what happens when your body "runs a temperature" when you have a cold. Your body is changing the temperature of the environment, trying to make it less hospitable to the invading bacteria or virus.

Explore Evolution, p. 108-109

In contrast to the claims of Explore Evolution many compensatory mutations do not have hidden fitness costs. Their "example" is a bacterium which has a compensatory mutation that makes it more temperature sensitive, and therefore unable to cope with the increased temperature seen in animals when they have fever. This appears to be an imaginary example, and the compensatory mutations seen in Staphylococcus aureus allow them to infect mice as easily, if not more easily, than the wild type.

But even if there were hidden fitness costs, the main issue is that the mutant is fitter in the altered environment. It does not matter if the mutant is less in the wild type environment unless it is returned to that ancestral environment. Penguins and polar bears are fitter than normal seabirds and brown bears in polar regions, but unfit in temperate and tropical regions. This hardly means that polar species are less fit than their ancestors in more temperate regions.

An inquiry-based textbook could readily present a real example from the scientific literature, and encourage students to predict how compensatory mutations would affect a species' ability to adapt to other environments. Instead, it presents a made-up example with too little detail for students or a teacher to practice inquiry-based learning.

Pre-Existing Resistance

All antibiotic resistance that develops in bacteria can be traced back to mutations in bacteria that were originally susceptible to antibiotics. Explore Evolution is rather incoherent in its discussion of antibiotic resistance. It incorrectly presents antibiotic resistance as due to pre-existing coding in the bacterial population for different varieties of beta-lactamase (an enzyme that breaks down penicillin).

Explore Evolution claims:

In the case of penicillin resistance, critics agree that when penicillin is present in the bloodstream, a bacterial strain that already has a gene coding for penicillinase will have a significant survival advantage over a strain that doesn't. … They do not develop such a gene when penicillin is introduced.
Explore Evolution, p. 102

Before discussing the origin of antibiotic resistance further, a little background is required. Antibiotics revolutionised medicine. For example, prior to antibiotics, 82% of people infected with the bacteria Staphylococcus aureus died. After the introduction of penicillin in 1944, most people infected with this bacterium survived. However, by 1947 the first clinical case of S. aureus resistant to penicillin was described. By 1952, over 75% of S. aureus was resistant to penicillin. A similar history is seen with other antibiotics. Methicillin, an antibiotic developed to be resistant to beta-lactamases (the bacterial enzymes that break down penicillin), was introduced in the 1960’s, by the 1970’s the first reports of resistance to methicillin were coming in. Vancomycin, the antibiotic of last resort for organisms like S. aureus, was introduced in the mid-1950’s but bacterial resistance to vancomycin was first seen in the 1980's and in 2002 vancomycin resistant S. aureus were reported. As can be seen, antibiotic resistance in populations of bacteria develop after a lag phase of some years, which would not happen if antibiotic resistance was just selection of pre-existing variability.

Antibiotic resistance occurs in many ways (Patostini et al, 2007), some bacteria are resistant because they develop enzymes that break down antibiotics, such as the beta-lactamases that break down penicillin, others develop proteins that bind the antibiotics and prevent them acting on their targets, such as the penicillin-binding-proteins that inactivate methicillin, still others develop enzymes that bypass the biological process that the antibiotic targets, such as the alternative cell wall synthesis enzymes that evade vancomycin.

Still other mechanisms involve altering the ability of enzymes to bind the antibiotic, decreasing the antibiotics entry into the cell, or increasing the activity of cell membrane pumps which remove the antibiotic from the cell. Antibiotic resistant bacteria may utilise one or more of these mechanisms.

Antibiotic resistant bacteria gain these mechanisms in one of two ways. They may develop by mutation of one or more genes in previously antibiotic sensitive bacteria, or bacteria may gain resistance genes via horizontal gene transfer from bacteria that are already resistant.

However, the genes that have been transferred were originally the products of mutation. The methicillin resistance gene is a mutant duplicate of a gene that did not originally bind penicillin found in the widely distributed bacteria S. sciuri that was transferred to S. aureus (Wu et al., 1996, 2001). The vancomycin resistance gene is a mutant version of the D-ala-D-ala ligase cell wall synthesis enzyme that has been transfered from Enterococcus faecium to S. aureus. Only a single mutation is required to change the cell wall synthesis enzyme D-Ala-D-Ala ligase to the D-Ala-D-Lac ligase that is the vancomycin resistance gene product (Park et al., 1996).

Explore Evolution treats the variants of beta-lactamase as if they were always present and could not have been produced through mutations, whereas research shows that beta-lactamases are mutant versions of a variety of enzymes (one group are mutant D-ala-D-ala ligases, Knox et al., 1996). As these enzymes originated very early on, their evolutionary history is more obscure than that of the vancomycin or methicillin resistance genes. However, in the continuing “arms race” of humans versus bacteria, new beta-lactamase resistant antibiotics have been introduced, and new beta-lactamases have evolved that can break down these antibiotics. Generally, as newer variants of beta-lactam antibiotics have been introduced, beta lactamase variants active against those beta-lactams have appeared within 2 to 3 years. The study of these mutations is a classic in evolution research (Petrosino et al., 1998).

References:

Knox JR, Moews PC, and Frere JM, Molecular evolution of bacterial beta-lactam resistance, Chemistry & Biology 3, 1996, p. 937-947.

Park IS, Lin CH, Walsh CT. Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B. Biochemistry. 1996 Aug 13;35(32):10464-71.

Pantosti A, Sanchini A, Monaco M. Mechanisms of antibiotic resistance in Staphylococcus aureus. Future Microbiol. 2007 Jun;2:323-34.

Petrosino J, Cantu C 3rd, Palzkill T. beta-Lactamases: protein evolution in real time. Trends Microbiol. 1998 Aug;6(8):323-7.

Wu S, Piscitelli C, de Lencastre H, Tomasz A. Tracking the evolutionary origin of the methicillin resistance gene: cloning and sequencing of a homologue of mecA from a methicillin susceptible strain of Staphylococcus sciuri. Microb Drug Resist. 1996 2(4):435-41

Wu SW, de Lencastre H, Tomasz A. Recruitment of the mecA gene homologue of Staphylococcus sciuri into a resistance determinant and expression of the resistant phenotype in Staphylococcus aureus. J Bacteriol. 2001 Apr;183(8):2417-24.

Protein Changes

Antibiotic resistance comes from a variety of mechanisms, including changes in gene regulation, production of new genes with novel activities, as well as simple point mutations. All these mechanisms are representative of the kinds of mutation involved in the sorts of morphological change that Explore Evolution thinks are important. Explore Evolution misrepresents the basic biology of mutations and their significance in antibiotic resistance in claiming:

In every case where mutations lead to antibiotic resistance, resistance results from small changes to a single protein molecule.
Explore Evolution, p. 104

Explore Evolution tries several times to make distinctions between different kinds of mutations. These distinctions are incorrect. In the case of antibiotic resistance, while the most intensively studied mutations are simple point mutations, such as those responsible for resistance to streptomycin, there are many other mutations that are involved. For example, resistance to some antibiotics is due to mutations that change the expression of drug transporters. Changes in gene expression are important in the evolution of many organismal traits.

Another example is gene duplication. Methicillin resistance originated with the duplication of a gene, which subsequently mutated, gaining a new function, penicillin binding. The first step was duplication of the cell wall synthesis enzyme D-Ala-D-Ala ligase. A single mutation then resulted in a novel cell wall synthesis enzyme D-Ala-D-Lac ligase, which confers vancomycin resistance.

Gene duplication, with duplicates gaining new functions though mutation, is a major source of gene gain in evolution. For example, the expansion of cell signaling systems in evolution is almost entirely through gene duplication and function gain via mutation. Most of what Explore Evolution later refers to as "molecular machines" are aggregates of duplicated genes. By failing to provide students with this background, they hinder any inquiry those students might choose to undertake into these issues.

DNA

A great shame of creationism and intelligent design is their appropriation and mischaracterization of genuine scientific concerns about whether we currently possess a complete explanation for the unity and diversity of life. Explore Evolution thoroughly mixes up scientific issues of gene-centric vs. epigenetic phenomena with much broader unsupported anti-evolutionary claims that genes do not control development and that new body plans need new sets of non-genetic instructions.

The success of developmental genetics in identifying an evolutionarily conserved set of genes that are used to construct organisms can lead to the temptation of restricting explanation of morphological evolution to genes alone. The question of whether nuclear genes were responsible for embryonic development has a long history. In the first half of the 20th century, proponents of nuclear inheritance battled with advocates of cytoplasmic inheritance. More recent authors argue that the metaphor of a genetic program does not take into consideration environmental affects upon development. Some argue that genes alone cannot explain cellular organization in microbes; that self-organizing properties of sub-cellular structures operating in physically constrained environments are also important. Others suggest that physical forces acting upon the earliest multi-cellular organisms played a major role in morphological evolution. A growing body of research indicates that the emergent properties of gene networks and cellular behaviors are also important for explaining morphological evolution. Other research suggests that development does not have the goal of producing an adult form and that the role of genes in regulating animal development is presently overemphasized.

Explore Evolution caricatures the nature of these scientific critiques of a gene-centric biology. Explore Evolution concludes that “something else – some other source of information” besides DNA is necessary to construct an organism and therefore evolution of body plans could not have resulted from mutations. Explore Evolution hints that the something else is still a mystery. They should have described to students how non-genetic processes (such as biomechanical forces and exploratory behavior of cells) contribute to morphological evolution.

Neil DeGrasse Tyson, the Director of the Hayden Planetarium at the American Museum of Natural History has described intelligent design as "a philosophy of ignorance" and his description is exemplified in this section of Explore Evolution.

Information

Explore Evolution is part of a longstanding effort by creationists, many of them authors of Explore Evolution, to mischaracterize and obscure scientific critiques of a gene-centric view of biology. In 1994, an argument was put forth by Jonathan Wells, a Senior Fellow at the Discovery Institute whose discredited arguments are repeated throughout Explore Evolution, in a publication of the Unification Church, often called "Moonies", that genes do not determine the "floor plan" - morphological development - of organisms.

So DNA does not program the development of the embryo… In a developing organism, the DNA contains templates for producing proteins-the building materials.To a very limited extent, it also contains information about the order in which those proteins should be produced-assembly instructions. But it does not contain the basic floor plan. The floor plan and many of the assembly instructions reside elsewhere (nobody yet knows where).
Jonathan Wells (1994) Why I Went for a Second Ph.D

The next year, the Nobel Prizes in Physiology or Medicine was awarded to scientists studying the genetic regulation of fruit fly development and another was awarded in 2002 to scientists studying the genetic regulation of nematode development. Nonetheless, Explore Evolution repeats Wells-like denials of the scientific consensus that genes carry instructions for embryonic development.

From Explore Evolution:

Also, on the cutting edge of research is the noteworthy claim that genes may not do as much as scientists previously thought.
Explore Evolution, p. 109
But some scientists contend that while the genes in DNA carry assembly instructions for building proteins out of amino acids, they do not carry the assembly instructions for building organs out of proteins or for building whole creatures out of organs or other body parts.
Explore Evolution, p. 110
many biologists (embryologists in particular) are beginning to think that genes do not (by themselves) carry the instructions for building a whole organism or animal.
Explore Evolution, p. 110
Scientist are not entirely sure where these higher-level assembly instructions are stored. However, these instructions are clearly necessary, and many scientists doubt that they are stored in DNA alone.
Explore Evolution, p. 111

Explore Evolution ignores the fact that DNA does significantly more than code for proteins, it has regulatory information (such as cis-regulatory elements) that controls when and where genes are expressed. More seriously, Explore Evolution ignores the fundamental unit of life, the cell, when it claims that genes "do not carry the assembly instructions for building organs out of proteins". In order to raise questions about the plausibility of morphological evolution, Explore Evolution must shield students from the uncomfortable fact that critics of a gene-centric view of biology propose viable alternative scientific explanations that are fully compatible with evolutionary biology.

References in the quotations above cite the Origination of Organismal Form, edited by Gerd Muller and Stuart Newman, to assert that DNA: "does not carry out the assembly instructions for … building whole creatures." Muller and Stuart's essay is an introduction, giving an overview of the various issues that the research published in the rest of the book will address. Muller and Newman write:

Organismal evolution is nowadays almost exclusively discussed in terms of genetics. But are genes determinants of form? … The chapters of part III [Relationships between Genes and Form] provide viewpoints on several of the problems that will have to be taken into account in future modeling approaches.
G. Muller and S. A. Newman (2003) The Origination of Organismal Form pp. 5-6

Explore Evolution asserts that the "mutation argument" has serious problems since DNA (alone) does not carry assembly instructions and "scientist are not entirely sure where the higher level assembly instructions are stored," therefore calling into question whether morphological evolution is possible. However, these claims are not supported by Origination of Organismal Form. As the book's back cover explains, the goal is not to remove gene sequences and gene expression from biological consideration, but to introduce another set of factors into biology's toolkit.

By placing epigenetic processes, rather than gene sequence and gene expression changes, at the center of morphological origination, this book points the way to a more comprehensive theory of evolution.
The Origination of Organismal Form, Back Cover

Each paper in Part III of Origination of Organismal Form discusses other factors besides genes which are important for generating form. Mina Bissell and colleagues argue that the 3-D organization of a tissue in the extracellular matrix is important for cellular differentiation. Roy Britten argues that molecular interactions as opposed to "global control mechanisms" are responsible for embryonic development. Scott Gilbert explains that genomes have been selected to respond to environmental cues during embryonic development. Finally, Ellen Larson summarizes how changes in cellular behaviors in development facilitates morphological evolution. Larson explains:

1. Rates of morphological evolution depend upon changes in the coordination of developmental processes

2. The hierarchical organization of biological systems facilitates relatively rapid evolution and change because developmental systems are modular.

3. At the molecular level, surprisingly few genetic changes may lead to change in coupling between genes and their regulatory signal.

4. Genes affect morphogenesis by affecting cell behaviors, including cell behaviors that modify morphogenetic fields.

5. At the tissue level, cell-autonomous genetic behavior in two-dimensional sheets may permit large and evolutionarily rapid changes in morphogenesis, compared to changes in interacting tissues that probably require complementary changes in both interacting tissues to achieve change.

6. Because there are alternative routes to achieve a morphology using different cellular behaviors, the likelihood of having sufficient genetic variation for selection is increased.

E. Larson, (2003), "Genes, Cells and Form" in The Origination of Organismal Form p. 126

Far from denying the importance of DNA, this is an acknowledgment of the importance of genes, and an exploration of the ways that genes vary. Explore Evolution is wrong to offer this book as evidence that biologists do not thing DNA is crucial in establishing morphology. The same passages in Explore Evolution mischaracterize teh views of Alessandro Minelli. Minelli also acknowledges that embryonic development is influenced by genes, but argues that there is too much an emphasis placed upon morphological changes in embryos as a means to generate adults. As with Stuart Newman, Minelli does not think that his arguments are anti-evolutionary.

Development, even in its simplest forms … is the complex networking of cellular behaviors and mechanisms influenced by the expression of all these genes …All of these behaviors, mechanisms, and genes are not there to ensure the deployment of wonderfully complex shapes of living beings. Much more modestly, they are simply there and consequently affect other behaviors, mechanisms or genes and set in place those forms of self-regulation that are the key to avoid developmental bankruptcy.
Alessandro Minelli (2003) The Development of Animal Form pp. 4-5
The non-adultocentric view of development I am advocating here is perfectly compatible with most views of development and evolutionary biology – for example, with the concept of the developmental module, a local cell population with its own developmental dynamics, but also interacting with other modules in a kind of metapopulation of cells (the biological individual or colony).
Alessandro Minelli (2003) The Development of Animal Form, p. 6

In claiming compatibility with "most views of development and evolutionary biology," Minelli is surely not supporting the anti-evolution arguments of Explore Evolution, nor its particular claim that Minelli claims DNA is not crucial to "building whole creatures out of organs and other body parts."

Explore Evolution also wrongly claims support from a paper by Brian Hall, a developmental biologist with a long-standing interest in evolution who thinks that cellular behaviors play an important role in morphogenesis. Is "DNA demoted" according to Brian Hall?

By emphasizing the role of cells, I want to be very explicit and not misunderstood. I am not downgrading the role of genes, either in development or in evolution.
B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219

The diagram below, based upon Figure 8 of Hall (2003), shows how Brian Hall views the relationship between genes (genotype) and organismal structure (phenotype). Notably, these "higher-level assembly instructions" consist of interactions of genes as networks and cascades, and the interactions of cells in aggregation and communication which are fully able to "translate the effects of mutations into phenotypic change."

Genotype to Phenotype: Figure 8 from B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219Genotype to Phenotype: Figure 8 from B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219
This modular and hierarchical cellular organization allows like cells to receive the intra- and extra-organismal environmental and epigenetic signals that allow organisms to develop, adapt to their environment, modify their development and translate the effects of mutations into phenotypic change on both developmental (including regeneration) and evolutionary (including asexual reproduction) time scales.
B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units."Biology and Philosophy, 18, p. 219

Another reference in the quotations above cites a 1990 essay by Fred Nijhout as an example of a scientist who now doubts that "higher-level assembly instructions" are stored in DNA alone. Undoubtedly, Nijhout expresses clear reservations about a gene-centric approach to biology.

The reason that pattern and form exhibit heritability is that they develop under a specific and restricted set of physical circumstances. When these circumstances are altered whether by changes in gene products or by changes in the environment a different pattern, equally heritable, develops. Changes in the heritable phenotype that are cause by changes in the environment are referred to as norm of reaction and have occasionally have been studied from the evolutionary perspective. Since gene do not 'code' for form, but form emerges out of an interaction of gene product and environment, it is clear that the norm of reaction deserves more wide spread study.
F. Nijhout (1990) "Metaphors and the Role of Genes in Development," Bioessays 12, p. 445

Despite this, Nijhout's research can hardly be said to reject DNA's role in morphology. In a recent Science paper, Suzuki and Nijhout show how a mutation in a gene affecting the hormonal regulatory pathway increases the environmental sensitivity to moth larval coloration and the origination of an new adaptive phenotype.

Polyphenisms are adaptations in which a genome is associated with discrete alternative phenotypes in different environments. Little is known about the mechanism by which polyphenisms originate. We show that a mutation in the juvenile hormone-regulatory pathway in Manduca sexta enables heat stress to reveal a hidden reaction norm of larval coloration. Selection for increased color change in response to heat stress resulted in the evolution of a larval color polyphenism and a corresponding change in hormonal titers through genetic accommodation. Evidently, mechanisms that regulate developmental hormones can mask genetic variation and act as evolutionary capacitors, facilitating the origin of novel adaptive phenotypes.
Y. Suzuki and F. Nijhout (2006) "Evolution of a Polyphenism by Genetic Accommodation," Science, 311, p. 650

Science journalist Elizabeth Pennisi explains how the study of reaction norms supports role of mutations in evolution, contrary to the claim Explore Evolution advances.

The study demonstrates how species can mask effects of genetic mutations until an environmental trigger reveals them, an adaptive mechanism that may help organisms survive changing conditions. The work "is a tour de force of experimental evolutionary biology," says Mary Jane West-Eberhard, an evolutionary biologist at the University of Costa Rica. "It [begins] to answer a question of fundamental importance: How does a novel, environmentally sensitive trait originate?"
E. Pennisi (2006) "Hidden Genetic Variation Yields Caterpillar of a Different Color,"Science, 311, p. 591

Explore Evolution also cites a book by Lenny Moss, entitled What Genes Can't Do, published in the MIT Press's Basic Bioethics Series. Moss promotes the ideas of two embryologists, John Gerhart and Marc Kirschner, to explain the formation of multicellular organisms. Gerhart and Kirchner's explanation emphasizes the ways that modular processes can be linked together to generate novelty in evolution.

The evolution of complex, internally differentiated, and yet globally coordinated life forms, including Homo sapiens, was not achieved by the elaboration of a master code or script, but by the fragmentation of functional resources of the cell into many modular units whose linkages to one another have become contingent (Gerhart & Kirschner, 1997). The more contingently uncoupled the molecular and multimolecular constituents of the cell become, the greater becomes the subset of potential specializations that can be achieved.
Lenny Moss (2004) What Genes Can't Do., pp. 188-189

The critique by Gehart and Kirschner provides no support for Explore Evolution's claim that mutations are insufficient to produce morphological change, simply showing that a full understanding of the evolution of morphology will require other levels of explanation beyond stating that a gene was mutated.

Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits.
J. Gerhart and M. Kirschner (2007) "The Theory of Facilitated Variation," PNAS 104, p. 8582
Although recent insights in developmental biology and physiology deepen the understanding of variation, they do not undermine evolutionary theory. Laws of variation begin to emerge, such as regulatory change as the main target of genetic change, the means to minimize the number and complexity of regulatory changes, and the regulatory redeployment of conserved components and processes to give phenotypic variations and selected traits.
J. Gerhart and M. Kirschner (2007) "The Theory of Facilitated Variation," PNAS 104, p. 8588
This is a new and active field of research, and an inquiry-based textbook could take advantage of the field's new results to encourage student exploration. Instead, as elsewhere in Explore Evolution, students are encouraged to treat unanswered questions as unanswerable, as chances to stop investigating. Students are given neither the conceptual background nor the scientific resources to engage with the ideas introduced here, and the book's approach is to encourage intellectual surrender, giving up whenever scientists seem to disagree or scientific questions are unresolved. This is not "inquiry-based," and is not good science.

Other sources

Explore Evolution asserts:

Something else – some other source of information – must orchestrate the assembly of the component proteins into unique cell types and direct the organization of cell types into various tissues and organs, and controls the arrangements of organs and body parts into an overall body plan (18).
Explore Evolution, p. 110

As to the nature of this "other source of information" that is not DNA, Explore Evolution cites a study in the history of science by Jan Sapp, Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics. In one section, Sapp describes how embryologists at the start of the 20th century thought the cytoplasm played the most prominent role in directing development and heredity. A more contemporary topic that Sapp examines is cortical inheritance in ciliates, single celled organisms such as paramecium. Ciliates divide by fission and the two daughter cells are able to inherit the pattern of cilia at their cell cortex. This inheritance of ciliary patterns is an example of cytoplasmic inheritance and appears to be largely independent of direct control by nuclear genes.

As Sapp noted in 1987,

Even some leading neo-Darwinian evolutionists have admitted their concern about the significance of the "the phenomenon of cortical inheritance in ciliates." At a symposium on Development and Evolution held at the University of Sussex in 1982, the centenary year of Darwin's death, John Maynard Smith (1983) p. 39) stated "Neo-Darwinists should not be allowed to forget these cases, because they constitute the only significant threat to our views."
Jan Sapp (1987) Beyond the Gene: Cytoplasmic Inheritance and the Struggle for Authority in Genetics, p. 219-220

However, to date, cortical inheritance has failed to displace nuclear genes as the most important player in regulating embryonic development in the ensuing 25 years after John Maynard Smith's warning to fellow evolutionists. Indeed, in this period there have been two sets of Nobel Prizes for scientists who have been leaders in the genetic analysis of animal development.

As Alessandro Milenni – also cited by Explore Evolution notes:

From the point of animal evo-devo, the question is whether these aspects of cytoplasmic information (cytotaxis sensu, Sonneborn, 1964) are limited to ciliates or are a general property of cells. I am not aware of the inheritance of intracellular patterns in animals, but it is certain that very few biologists have thought it a rewarding topic be investigated.
Alessandro Minelli (2003) The Growth of Animal Form, p. 29

Far from supporting the claim that modern biologists cytoplasmic factors as an alternative to DNA, the citations offered by Explore Evolution actually show that science has rejected various alternatives and all evidence points to DNA as the repository of "instructions" for biological development.

DNA and CD players

According to Explore Evolution:

Critics say it's a little like building a CD player. Even if you have all the information you need to build all the individual electrical components – resistors, capacitors, jumper switches and laser unit – you will still need additional information to arrange all the components and circuit boards. You'll need even more information to coordinate the circuit boards with the mechanical components. Remarkably, many scientists say the same concept is true in biological systems. An organism needs genetic information to build proteins. It also needs higher-level assembly instructions to arrange tissues and organs into body plans.
Explore Evolution, p. 110-111

Arguments from analogy are only as good as the strength of the analogy and this is a terribly wrong analogy. Biologists know that building a multicellular organism has no similarity to the assembly of a CD player. Unlike multicellular organisms, CD players do not grow from a single cell, they are constructed in factories. CD players do not reproduce, and thus have no system of inheritance, no way to pass variation from generation to generation.

While attributed to "many scientists," this technology-based analogy has almost exclusively been used by Stephen Meyer, an Explore Evolution author, to argue that "a purposive intelligence" designed organisms:

Organisms not only contain information-rich components (such as proteins and genes), but they comprise information-rich arrangements of those components and the systems that comprise them. Yet we know, based on our present experience of cause and effect relationships, that design engineers – possessing purposive intelligence and rationality – have the ability to produce information-rich hierarchies in which both individual modules and the arrangements of those modules exhibit complexity and specificity – information so defined. Individual transistors, resistors, and capacitors exhibit considerable complexity and specificity of design; at a higher level of organization, their specific arrangement within an integrated circuit represents additional information and reflects further design. Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies.
S. Meyer (2004) "Origins of Biological Information and the Higher Taxonomic Categories," Proceedings of the Biological Society of Washington 117(2):213-239.

However, this paper was later disavowed by the of Biological Society of Washington.

The paper by Stephen C. Meyer in the Proceedings (“The origin of biological information and the higher taxonomic categories,” vol. 117, no. 2, pp. 213-239) represents a significant departure from the nearly purely taxonomic content for which this journal has been known throughout its 124-year history. It was published without the prior knowledge of the Council, which includes officers, elected councilors, and past presidents, or the associate editors. We have met and determined that all of us would have deemed this paper inappropriate for the pages of the Proceedings.
Biological Society of Washington, 9/7/2004

A critique of Meyer's paper by Alan Gishlick, Nick Matzke and Wes Elsberry of the National Center for Science Education can be found at Panda's Thumb. The paper has enjoyed no support in the scientific community, as revealed by examining papers citing it. Almost all are social, political, or theological critiques or defenses of intelligent design creationism. This argument has made no significant impact on scientific research, and the claim that "many scientists" agree to the analogy simply does not hold up. The analogy is uninformative and will only mislead students reading it.

"Genomic equivalence"

Explore Evolution quotes Jonathan Wells, a senior fellow of the creationist Discovery Institute, in support the claim that "assembly instructions" are not solely in DNA. Inaccurately citing Wells as a "developmental biologist," the footnote quotes from Wells' creationist work Icons of Evolution, critiqued elsewhere on NCSE's website:

Developmental biologist Jonathan Wells has noted: "A skin cell is different from a muscle cell, which in turn is different from a nerve cell and so on. Yet with a few exceptions, all these cell types contain same genes as the fertilized egg. The presence of identical genes in cells that are radically different from each other is known as "genomic equivalence. According to Wells, this equivalence presents us with a paradox. "If genes control development, and the genes in every are the same, why are the cells so different?" Genes, says Wells, "are being turned on or off by factors outside themselves … [C]ontrol rests with something beyond the genes…". Icons of Evolution (Washington, D.C., Regnery Press, 2000):191.
Explore Evolution, p. 112

One could note that Zeno's paradox is not discussed in physics as a major problem in the study of motion, since the calculus of Newton and Leibniz solved the paradox. Likewise, this supposed paradox of "genomic equivalence" is not discussed as a major problem in developmental biology courses since it has been solved by the last 40 years of research in developmental biology.

If the genome is the same in all somatic cells within an organism (with the exception of lymphocytes; see Sidelights and Speculations), how do cells become different from one another?… Based upon the embryological evidence for genomic equivalence (as well as bacterial models of regulation), a consensus emerged in the 1960's that cells differentiate through differential gene expression.
Scott Gilbert (2003) Developmental Biology 7th ed., p. 92

This consensus view of development has been overwhelmingly supported by the discovery of genes such as Ultrabithorax which regulate other genes involved in developmental pathways. The claim by Jonathan Wells that genomic equivalence remains a paradox is another demonstration of how the anti-evolutionary arguments of the intelligent design movement embrace ignorance.

Morphology

Evolutionary developmental biology – evo-devo – is one of the most dynamic fields in modern biology, and is often poorly covered by introductory textbooks. Rather than providing students with background that would let them conduct scientific inquiry into this field, Explore Evolution provides an account that is too brief and deeply misleading. Perhaps the greatest failing of the book is its misrepresentation of authors, citing them in support of claims that they directly disagree with.

The only thing that exceeds this consistent misrepresenting of scientists' views is this chapter's plagiarism of a creationist source. In discussing the views of Richard Goldschmidt, a biologist of the 1940s, Explore Evolution borrows text from a letter to the editor by young earth creationist David Menton. Menton is not credited as the author of the text. Oddly, the plagiarized text adds little to the chapter, as Goldschmidt has no impact on 21st century biology. The plagiarism demonstrates the authors' lack of academic rigor and the book's deep ties to creationism.

In addition to misappropriating the words of a creationist to revive long-forgotten ideas, Explore Evolution mischaracterizes the views of modern scientists. The authors claim that scientists do not think mutations in DNA can explain new morphology, but the sources cited in support of this argument actually support the role of DNA as the repository of instructions for embryological development. This approach to the scientific literature is inaccurate and misleading, and ultimately contradictory to the principles of inquiry-based learning that Explore Evolution purports to exemplify.

The Four-Winged Fly

The four-winged fruit fly is a classic example of how creationists misinterpret the genetic analysis of development. Developmental geneticists try to understand the role of a gene by modifying a gene and analyzing the consequences, so it is of little consequence that four winged flies would not survive in the wild. The importance of the four-winged fruit fly is that it demonstrated that a few mutations in a single gene were able to transform an entire structure. This work by Ed Lewis led to the discovery of Hox genes and other members of the genetic toolkit (genes which play roles in constructing animal embryos) as well as to a Nobel Prize in 1996. An inquiry-based textbook might well use Nobel-winning research as a way to encourage inquiry, rather than as a way to obscure critical scientific concepts.

Explore Evolution explains the importance of the four-winged fruit fly by focusing upon the importance of mutations as opposed to the importance of the function of a gene:

These experiments show that mutations can induce dramatic changes in the anatomical structure of organisms. And, for many evolutionary biologists, they provide a powerful confirmation of the neo-Darwinian claim that mutations provide the novel variations that natural selection needs to build new anatomical architectures and animals.
Explore Evolution, p. 101

However, as Explore Evolution correctly claims, one cannot assume that natural selection in the wild will operate on the same type of mutations that were artificially selected for in the laboratory:

The neo-Darwinian scenario says that new structures are produced by natural selection acting upon purely undirected and random mutations. Yet, the mutants that produce four-winged fruit flies survive only in a carefully controlled environment and only when skilled researchers meticulously guide their subjects through one non-functional stage after another. This carefully controlled experiment does not tell us much about what undirected mutations can produce in the wild.
Explore Evolution, p. 105

No evolutionary biologist would dispute this point.

Have evolutionary biologists been able to actually identify mutations from the wild that cause morphological differences between related species? This work has only recently been undertaken and has already found clear cases in which mutations result in morphological differences between species.

  • Mutations in Pitx1 gene affect pelvic hindlimb structure in sticklebacks (Shapiro et al., 2004, Shapiro et al., 2006).
  • Mutations in the Ectodysplasin gene affecting armor plates in sticklebacks (Colosimo et al., 2005).
  • Mutations in yellow gene affect formation of wing spots in fruit flies (Prud'homme et al., 2006).
  • Mutations in shavenbaby affect trichome pattern in fruit flies (Mcgregor et al.,2007).
  • Mutations in BMP4 affecting beak morphology in “Darwin’s finches" (Abzhanov et al. 2004).
  • Mutations in the KNOT gene in the mustard plant, Arabidopsis, affecting leaf structure(Hay and Tsiantis, 2006).
  • Mutations in the Scute gene in fruit flies affecting sensory bristle formation (Marcellini and Simpson, 2006).

These experiments are not meant to show the exact mechanism by which today's biological structures evolution. Laboratory experiments will not perfectly replicate wild conditions, but by considering simpler circumstances, researchers can gain insights into big questions. Lab work like the work described above allows researchers to refine their understanding and move the research to ever-more complex situations, balancing a desire for greater realism for decreased ability to focus on a single factor. Explore Evolution misinforms students about what the research they are describing was meant to show, and misinforms them about the methods of inquiry employed by scientists. This is the opposite of what an inquiry-based textbook should do.

Survival

Explore Evolution claims that some current evolutionary biologists think that mutations that result in major changes in morphology (such as the mutations in the Hox gene Ultrabithorax, which produce the four-winged fruit fly) are necessary to explain morphological evolution. Modern evolutionary biologists do not suggest mutations in the genetic toolkit must have dramatic effects (as discussed elsewhere in this critique). Explore Evolution falsely asserts that evolutionary developmental biologists doubt the role of mutation in development.

The "mutation argument," according to Explore Evolution is:

even if the existing gene pool doesn't supply enough information to build a fundamentally new organism, new mutations can.
Explore Evolution, p. 98

Explore Evolution finds significant problems with this straw man "mutation argument" and implies that "small, limited mutations" are restricted to genes which do not regulate morphology:

Critics of the mutation argument say these textbook examples point to a kind of Catch-22. Small, limited mutations (like those that produce antibiotic resistance) can be beneficial in certain environments but they don't produce enough change to produce fundamentally new forms of life. Major mutations can fundamentally alter an animal's anatomy and structure, but these mutations are always harmful or outright lethal (12) …. That is why critics say mutations have not turned out to be the information-rich super-variations that neo-Darwinian biologists had hoped for.
Explore Evolution, p. 106

To support their case, Explore Evolution cites four papers in reference 11 as critical of the "mutation argument":

Wallace Arthur, "The effect of development on the direction of evolution: toward a twenty-first century consensus." Evolution and Development 6 (2004) 282-288.

K.S.W. Campbell and C.R. Marshall "Rates of evolution among paleozoic echinoderms," in Rates of Evolution, K.S.W. Campbell and M.F. Day eds. (London, Allen and Unwin, 1987).

Eric H. Davidson, Genomic Regulatory Systems, Development and Evolution (San Diego Academic Press, 2001).

Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff "Resynthesizing evolution and developmental biology," Developmental Biology 173 (1996): 357-372.
Explore Evolution, p. 112

Notably, all of the more recent citations (after 1987) are evolutionary developmental biologists and, as we shall see, the citations of their work by Explore Evolution is another example of "creationist abuse of evo-devo."

As Rudolf Raff, a critic of the "mutation argument" (according to Explore Evolution) notes:

There is a whole stable of intelligent design creationist writers associated with the Discovery Institute, and we will see more slick books of bogus science produced to influence the teaching of biology, and even federal funding of research. Evo-devo data have become a part of the creationist rhetorical weaponry, and as evo-devo grows in prominence, the problem will grow in severity
Rudolf Raff, "The Creationist Abuse of Evo-Devo," (2001), Evolution and Development, 3:6, p. 374

Explore Evolution asserts that mutations in the genes regulating development will only produce major mutations that will be harmful. Does Wallace Arthur actually think about mutations that affect development (ontogeny)? Is Arthur a "critic of the mutation argument"?

Subsequent to the modification of a developmental gene (e.g., a Hox gene) by mutation, the ontogenetic trajectory will in many (but not all) cases be reprogrammed so that it follows a different route. The difference may be tiny, moderate, or large.
Wallace Arthur, (2004) "The effect of development on the direction of evolution: toward a twenty-first century consensus." Evolution and Development 6, p. 282

In other words, not all mutations in a developmental gene (a genetic toolkit gene) need have major affects, such as the four-winged fruit fly. Indeed, evolutionary developmental biologists think that relatively modest changes in genes of the genetic toolkit are more likely to prove useful to organisms.

Scott Gilbert is also cited as a "critic of the mutation theory" according Explore Evolution. Gilbert has explained about his view of evolution, (available at National Center for Science Education) in response to misrepresentations of his work by the Discovery Institute in 2002 in their testimony to the Ohio Board of Education.

My research on turtles and my research into evolutionary developmental biology is fully within Darwinian parameters. My gripe has been that neo-Darwinism has supposed that population genetics was the only genetics needed to explain Darwinian evolution. I claim that developmental genetics is also needed. So my research has been to include developmental genetics into the Darwinian mix.
National Center for Science Education (2002), Analysis of the Discovery Institute’s “Bibliography of Supplementary Resources for Ohio Science Instruction”

In contrast to Explore Evolution's misrepresentation, Eric Davidson actually argues that mutations in the "regulatory genome" (CREs and proteins encoded by the genetic toolkit genes) play important roles in animal evolution.

Since the morphological features of an animal are the product of its developmental process, and since the developmental process in each animal is encoded in it's species-specific regulatory genome, then change in animal form during evolution is the consequence of change in genomic regulatory programs for development.
Eric Davidson, in The Regulatory Genome: gene regulatory networks in development and evolution, (2006), p. 27

None of the recent research cited actually undermines what Explore Evolution refers to as "the mutation argument." They all argue that mutations can and do change developmental trajectories, and that these changes are important in our understanding of evolutionary developmental biology. Explore Evolution misleads students by suggesting otherwise.

"Hopeful Monsters"

The discussion of Richard Goldschmidt and his saltational model of evolution is largely copied (without credit) from an essay by "creationist anatomist" David Menton. Goldschmidt's ideas were widely criticized when first publicized, and their reputation has not improved with time. There's no particular reason to cover them in a modern biology textbook at all.

It is difficult to be sure why Explore Evolution invests a full page in a discussion of Richard Goldschmidt's ideas. His work was rejected by biologists of his own day, and age has not improved his reputation. A recent assessment of his influence on modern biology concluded:

Richard Goldschmidt's research on homeotic mutants is not significant because it was right or paradigmatic. It is significant because it represents one of the first serious efforts to integrate genetics, development, and evolution. As such, Goldschmidt's research reveals the great difficulty of balancing the different contributors to a developmental evolutionary genetics. Consider the major flaws with his different models of macroevolution. Evolution by systemic mutations placed too much emphasis on a model of genetic structure which could not be confirmed or fully integrated with a model of gene action (not every inversion or chromosomal repatterning produces a phenotypic effect). Evolution by developmental macromutations placed too much faith in the ability of developmental processes to create functioning new species from major genetic changes. Goldschmidt needed [Sewall] Wright's counsel to provide a reasonable evolutionary dynamics for major mutations, which in turn made speciation by macromutation a possibility.
Michael R. Dietrich (2000) "From Hopeful Monsters to Homeotic Effects: Richard Goldschmidt's Integration of Development, Evolution, and Genetics" American Zoologist 40(5):738–747

In short, Goldschmidt's erroneous ideas spurred other scientists to consider ideas which did ultimately improve our understanding of evolution. The insight that mutations could have both large and small effects influenced Sewall Wright's "shifting balance" evolutionary model — a major component of modern population genetics. Similarly, evolutionary biologist Stephen Jay Gould wrote an essay on the "Return of the Hopeful Monster," in which he rejected most of Goldschmidt's actual argument, but identified useful insights which could guide modern researchers:

I disagree fundamentally with his claim that abrupt macroevolution discredits Darwinism. For Goldschmidt also failed to heed Huxley's warning that the essence of Darwinism – the control of evolution by natural selection – does not require a belief in gradual change. …

[A]ll theories of discontinuous change are not anti-Darwinian, as Huxley pointed out nearly 120 years ago. Suppose that a discontinuous change in adult form arises from a small genetic alteration. Problems of discordance with other members of the species do not arise, and the large, favorable variant can spread through a population in Darwinian fashion. Suppose also that this large change does not produce a perfected form all at once, but rather serves as a "key" adaptation to shift its possessor toward a new mode of life. Continued success in this new mode may require a large set of collateral alterations, morphological and behavioral; these may arise by a more traditional, gradual route once the key adaptation forces a profound shift in selective pressures …

In my own, strongly biased opinion, the problem of reconciling evident discontinuity in macroevolution with Darwinism is largely solved by the observation that small changes early in embryology accumulate through growth to yield profound differences among adults. Prolong the high prenatal rate of brain growth into early childhood and a monkey's brain moves toward human size. Delay the onset of metamorphosis and the axolotl of Lake Xochimilco reproduces as a tadpole with gills and never transforms into a salamander.

The element that Gould borrowed from Goldschmidt was not the erroneous view of genetics, nor Goldschmidt's model of how large morphological changes could be produced in that bogus genetic scheme. The connection between the sort of developmental biology research Gould describes and Goldschmidt's work is negligible. Hence Dietrich's observation above that the significance of Goldschmidt's work not being that "it was right or paradigmatic."

Neither Goldschmidt nor "hopeful monsters" is mentioned in the index to any of the most common college or high school biology textbooks. Evolutionary biology textbooks mention him only in passing, to note that his ideas were not and are not generally accepted. Ridley's Evolution merely observes that Ernst Mayr's arguments in favor of the Modern Synthesis won out against Goldschmidt's suggestions, and Futuyma rightly noting that Goldschmidt's genetic ideas "have been entirely repudiated by modern geneticists" and that his "saltationism was rejected in favor of gradual change" (even the changes Gould discusses above would be gradual in this sense). The lesson Futuyma draws from the coalescence of the Modern Synthesis, and the consequent rejection of ideas like Goldschmidt's, is that "the rejection of false ideas is an important part of the progress in science" (Futuyma, D., 1998, Evolutionary Biology, Sinauer Associates, Inc.:Sunderland, MA. p. 25).

In the perverted view of science promulgated by Explore Evolution, bad ideas never die. While there might be pedagogical value in leading students on a discussion of the flaws in Goldschmidt's ideas and the advantages of the Modern Synthesis, there is no value in the approach Explore Evolution takes. Simply tossing out a bad idea as if it were generally accepted today is unethical. Presenting an incomplete account of Goldschmidt, and leaving the impression that biologists today rely on his work, simply leaves students with the wrong impression.

An even worse impression will be left if students realize that the first paragraphs of Explore Evolution's page about Goldschmidt are copied without credit from another author. David Menton wrote those words for a young earth creationist group called the Missouri Association for Creation. Menton wrote:

In the 1930s, paleontologist Otto Schindewolf concluded that the missing links in the fossil record were not really missing at all, but rather were never there in the first place! Schindewolf proposed that all the major evolutionary transformations must have occurred in single large steps. He proposed, for example, that at some point in evolutionary history, a reptile laid an egg from which a bird was hatched! This bizarre notion was championed in 1940 by the geneticist Richard Goldschmidt of the University of California at Berkeley. Like Schindewolf, Goldschmidt resigned himself to the fact that true transitional forms were not found despite over a hundred years of searching for them, and that evolutionary theory would simply have to accommodate this fact.

Goldschmidt sought to advance Schindewolf's notion of evolution through single large steps by trying to imagine a plausible mechanism for it. He suggested that the answer might lie in what are known as embryological monsters, such as the occasional birth of a two-legged sheep or a two-headed turtle. Goldschmidt conceded that such monsters rarely survived very long in nature, but he hoped that over a long period of time some monsters might actually be better suited to survive and reproduce than their normal siblings. Goldschmidt named this monstrously hopeless speculation the "hopeful monster theory." Since there was not even the slightest shred of evidence to support the hopeful monster theory, it was dismissed with derision by almost all evolutionists of his time.

Compare this to the material in Explore Evolution (identical passages bolded, paraphrases in italics):

In the 1930s, paleontologist Otto Schindewolf proposed that all the major evolutionary transformations must have occurred in single, large steps. (He proposed, for example, that at some point in evolutionary history, a reptile laid an egg from which a bird was hatched.) In 1940, geneticist Richard Goldschmidt took Schindewolf's idea one step further, suggesting that true evolutionary change takes place in the rare successes of large-scale mutations, not by the accumulation of small changes (as Darwin predicted).

Goldschmidt conceded that the vast majority of large-scale mutations produce hopelessly maladapted freaks like two-legged sheep or two-headed turtles. However, he suggested that on rare occasions a lucky accident might produce a fundamentally new form of life — an organism that was actually better suited to survive and reproduce than its "normal" siblings.

Explore Evolution, p. 107

Teachers know that it is not appropriate to quote so much material from a source without proper credit. Paraphrasing a few passages and correcting some grammatical errors does not excuse the failure to identify the source. Not only does this passage misinform students about the current state of the science, distract from real science, and repeat creationist canards, it is also built on a serious ethical lapse. Students should not be sent the message that plagiarism is appropriate.

Hox & Development

In claiming that developmental processes are too integrated to allow change, Explore Evolution ignores over 10 years of research in evo-devo on the modularity of development. Evolutionary developmental biologists who study Hox genes think that mutations in the CREs of target genes for Hox genes are more likely to be more important for morphological evolution than mutations in Hox genes themselves.

Developmental biologists are investigating another kind of mutation - mutations in "hox genes" - that many neo-Darwinists think can provide a signficant source of major variation in living forms. Hox genes are "master regulator" genes that turn other genes in the cell on and off during the developmental process…Because hox genes are so important for coordinating the activities of the cell, some researchers think that mutations in these genes can cause large-scale changes in the structure of an organism.
Explore Evolution, p. 109

Explore Evolution disregards research on Hox genes that strongly suggest that instead of soley acting at the top of a hierarchy as a "master regulator", they work at many sites in a developmental pathway as "micromanagers".

We still have little idea how the differential expression of one 'master' gene can control the morphology of complex structures, but recent studies suggest that the Drosophila Hox gene Ultrabithorax micromanages segment development by manipulating a large number of different targets at many developmental stages.
Michael Akam (1998) "Hox genes: from master genes to micromanagers," Current Biology 8:676

Explore Evolution gestures towards accuracy in suggesting that there is a challenge in mutating the protein-coding regions of Hox genes. As Sean Carroll and colleagues explain below, developmental regulatory genes, such as Hox genes are pleitropic - they control many different developmental processes, making it more difficult to mutate their protein-coding region without harmful consequences (although the case of the evolution of Ultrabithorax function in limb repression in insects appears to be a notable exception). In contrast to most mutations in the protein-coding regions of developmental regulatory genes, mutations in CRE's minimize the fitness penalty - an important issue which is completely ignored by Explore Evolution.

A clear principle is emerging from the increasing number of case studies: pleiotropy imposes a genetic constraint on the type of changes that can be accommodated in morphological evolution. Highly pleiotropic genes (including most developmentally regulated genes) are more likely to contribute to morphological evolution through cis-regulatory changes than through coding sequence alterations. In contrast, known examples of pigmentation evolution resulting from the alteration of coding sequences affect genes involved in a single process, such as the overall body color in fish, mammals, or birds. Coding sequence changes appear to be better tolerated in minimally pleiotropic genes. This principle of minimizing fitness penalties delimits the scope of what changes are permissible under natural selection and explains why CRE evolution is a pervasive mechanism underlying morphological diversification.
Prud'homme et al., (2007) "Emergining Principles of Regulatory Evolution," PNAS 104:8609

To understand how Hox genes, such as Ultrabithorax, act to regulate developmental pathways, we must consider how CREs act as genetic switches. Recall that the four-winged fruit fly is generated by mutations in Ultrabithorax, (Ubx) that turn the gene off in hindwings (halteres).

A Four-Winged FlyA Four-Winged Fly

The diagram below shows the basic gene network involved in patterning the forewing along the anterior-posterior and dorsal-ventral axes. If Ubx was working as a "master regulator" in the hindwing, Ubx would be predicted to only affect genes at the top of the hierachy, such as selector or short-range signals. Instead, it has been shown by Sean Carroll and colleagues (Weatherbee et al., 1998, Hersh et. al, 2005) that Ubx may directly regulate many wing patterning genes at all levels of the hierarchy, including the primary target genes, demonstrating that Ubx is acting as a micromanager.

Wing PatterningWing PatterningUbx 10Ubx 10

How can Ubx regulate multiple genes involved in wing patterning? Ubx binds to CREs that contain the specific DNA sequence as shown in the diagram below.

This short sequence is present in many different CREs throughout the genome. CREs also have different binding sites for other proteins that can turn genes on or off. In the figure below, future wing cells lack the Ultrabithorax protein, Ubx (U), while future haltere cells contain Ubx. Additionally, there are other proteins (A,B,C,D,E,F) which bind to the CRE to regulate the nearby target gene.

Note that whether or not Ubx can bind to a CRE depends upon whether Ubx is present and if the CRE has a binding site on it for Ubx. For example, Omb does not have a Ubx binding site and is not regulated by Ubx. In contrast, sal and CG13222 have Ubx binding sites and are respectively turned off or on in halteres.

Is there direct evidence that Ultrabithorax binds to CREs of target genes involved in wing patterning? So far Sean Carroll's lab has identified four such genes (Galant et al., 2002; Hersh and Carroll, 2005; and Hersh et al, 2007).

Since the proteins which bind to CREs generally bind to different sites on the CRE, a mutation in a CRE which abolished the binding of Ubx would not affect the binding of A,B,C etc. to their sites on the CRE. This independence of binding sites on CREs means that these binding sites can evolve independently.

Ubx and CREUbx and CRE
As we have seen with four-winged fruit flies, it requires a great many coordinated changes to transform one system into another without losing function in the "in-between" steps. The more the individual parts of a system depend on each other, the harder it is to change any one part without destroying the function of the organism as a whole. Since Hox genes affect so many genes and systems, it seems unlikely that they could be mutated without damaging the way some of the genes are switched 'on or 'off.'
Explore Evolution, p. 109

How is a hindwing transformed into a forewing? In this case, "a great many coordinated changes" are actually mutations in three CREs controlling in which part of the hindwing the Hox gene Ultrabithrox is normally expressed. These three mutations result in the absence of Ultrabithorax in all of hindwing and the conversion of a hindwing into a forewing. As we shall see, mutations of CREs, even in genes that are involved in highly complex networks, such as Hox genes, are very capable of evolving.

Can protein-coding regions of Hox genes be changed? Elsewhere, we examine the case of how Ultrabithorax evolved the ability to repress limbs in insects by the replacement of the amino acids serine or threonine with the amino acid alanine at the tail of Ultrabithorax. In that example, "a great many changes" may involve as much as five such replacements, hardly an insurmountable barrier.

Modularity in Hox genes

To buttress the false claim that developmental pathways regulated by Hox genes cannot evolve Explore Evolution engages in a major error of omission by failing to address the issue of modularity. This is concept is not obscure - a PubMed search of "modularity and evolution" yields over 140 publications in the last ten years. Modularity describes the independent control of hierarchical levels in development and evolution ranging from anatomical structures to signaling pathways to genetic switches.

In 1996, modularity in development and evolution was fully discussed in the influential book on evolutionary developmental biology, The Shape of Life by Rudolf Raff. As a book review of the Shape of Life in the journal Bioscience notes:

Raff defines modules as units "…that are distinct in genetic specification, autonomous features, hierarchical organization, interactions with other modules, location, time of occurrence, and dynamic properties" … Modularity permits change because developmental processes are free to dissociate, duplicate, diverge, and be co-opted to new uses. Although developmental modules themselves are complex, Raff argues that they may often be activated by single or few regulatory genes acting as switches, such as Pax-6 in eye development. The mostly likely changes in ontogeny are those that alter the relative timing, number, or location of preexisting modules rather than those that produce wholly novel modules or structures. This feature of development also helps to explain the essential conservation of body plan.
Terri Williams, "The Modularity of Development" (1998), Bioscience 48 p. 60

As Eric Davidson notes in 2006, the modularity of cis-regulatory elements (CREs) is now well-established.

When cis-regulatory sequences were first proposed to be generally modular in organization (Kirchamer et al. 1996), there were on ly a modest number of examples from work in Drosophila and sea urchins, and the idea was largely inferential. Now there are literally scores of genes for which detailed experimental analyses have demonstrated sharply modular cis-regulatory elements, such that given non-overlapping regions of the genomic DNA each control a specific subcomponent of the overall expression pattern.
Eric Davidson, The Regulatory Genome: gene regulatory networks in development and evolution (2006) p. 33

How does the modularity of CRE's relate to whether the integrated networks regulated by Hox genes can evolve? Consider how Ubx regulates the target genes Sal and CG13222 by binding to their CREs. A mutation that disabled Ubx binding to CG13222 would prevent it from being from turned on in the hindwing, but would not affect Ubx turning off Sal in the hindwing. Similarly, a mutation in Omb that caused it to turned off in the hindwing would not affect how Ubx controls Sal or CG13222.

Hindwing EvolutionHindwing Evolution

Thus Ubx binding sites on CREs of different genes can be gained or lost independently of binding sites for other proteins genes. Although these genes can be involved in a complicated gene network, the modularity of CREs allow specific genes to be independently changed without affecting the rest of the network. Ubx is known to regulate hindwing development in all insects, from beetles to fruitflies, even though the morphology of their greatly differs. These major changes in morphology are easily explained when considering how Ubx binding sites on CREs can evolve.

Body Plans

Explore Evolution completely ignores studies showing that mutations in both protein coding sequences and in non-coding cis-regulatory element sequences (CREs) are responsible for changes in morphology. Explore Evolution muddies the distinction between mutations which affect protein structure and function, and mutations which affect when and where genes are turned on or off.

In its discussion of DNA and mutations, Explore Evolution asserts:

DNA is actually closer to the bottom of the organizational ladder. Yes, it directs the building of proteins, and yes, proteins are important. But DNA does not direct how the overall body plan gets built.
p. 110

In making this claim, Explore Evolution fails to acknowledge the extensive research on mutations in DNA sequences that do not encode proteins, but which have important morphological effects. Explore Evolution thereby misses out on the opportunity to present the genuinely relevant and interesting scientific debate in evolutionary morphology concerning the relative importance of mutations in protein-coding sequences versus mutations in non-coding sequences.

An important tenet of evolutionary developmental biology ("evo devo") is that adaptive mutations affecting morphology are more likely to occur in the cis-regulatory regions than in the protein-coding regions of genes… Although this claim may be true, it is at best premature. Adaptation and speciation probably proceed through a combination of cis-regulatory and structural mutations, with a substantial contribution of the latter.
Hoekstra et al., (2007) "The locus of evolution: Evo devo and the genetics of adaptation," Evolution 61:005

Non-coding regions of DNA contain genetic switches called cis-regulatory elements (CREs). CREs control when and where a gene is turned on (expressed). Mutations in the CREs of Ultrabithorax are responsible for that gene being turned off in fly hindwing resulting in the four-winged fruit fly. As Sean Carroll and colleagues argue, recent analyses have shown that mutations in CREs play an important role in morphological evolution.

A growing number of case studies exploring the mechanisms of morphological changes have provided direct evidence that CRE evolution plays a major role. From these examples, we have identified general rules regarding regulatory evolution, namely how regulatory evolution exploits available genetic components, irrespective of their hierarchical position in gene networks to generate novelty, and minimizes fitness penalties. These rules offer a rationale explaining why regulatory changes are more commonly favored over other kinds of genetic changes in the process of morphological evolution, from the simplest traits diverging within or among species to body-plan differences at higher taxonomic levels.
Prud'homme et al., (2007), "Emerging Principles of Regulatory Evolution", PNAS 104:8611

An example of the Pitx1 gene in the marine stickleback fish is shown below. Genetic studies of sticklebacks by David Kingsley and colleagues have established the mutations in Pitx1 have played an important role in the evolution of sticklebacks. There two important CREs controlling Pitx1 expression. One CRE is postulated to control Pitx1 expression in the mouth and jaw while another CRE is postulated to control Pitx1 expression in the pelvic hindlimb.

Mutations in the protein-coding region can affect the sequence and the function of a protein. On the other hand, mutations in the CRE can affect when and where a gene is turned on. Have mutations in CREs or in protein-coding regions of genes been involved in morphological evolution? This question has been addressed in a number of different studies described below.

David Kingsley and colleagues (Shapiro et al., 2003) have studied the evolution of sticklebacks. Over the last 10,000 years, marine sticklebacks have invaded freshwater lakes and have undergone an extensive adaptive radiation. One important adaptation in freshwater stickleback has been the reduction of pelvic spines that helps to reduce predation from arthropods. To address what gene(s) are responsible for pelvic spine reduction, Kingsley and colleagues conducted genetic experiments on sticklebacks and showed that mutation in the Pitx1 gene was responsible.

Recall that Pitx1 is expressed in development of the pelvic spine and of the mouth and jaws in marine sticklebacks. However, in freshwater sticklebacks with reduced pelvic spines, Pitx1 is expressed only in the mouth and jaws. So, although they have not yet identified the precise mutation(s), a technically demanding job of finding a needle in a haystack, this observation strongly suggests that mutations in the CRE controlling pelvic spine expression of Pitx1 are responsible for this reduction. Note that a mutation in the protein-coding region of Pitx1 would affect Pitx1 function in both the mouth, jaw and pelvic spines. This type of mutation is fatal in mice. However, because mutations in one CRE do not affect the function of a different CRE, Pitx1 function can be lost in the pelvic spine and retained in the mouth and jaw of freshwater sticklebacks.

As Kingsley and colleagues show, the mutations in a CRE can cause the loss of Pitx1 function in pelvic spines, but can mutations generate new CREs? Sean Carroll and colleagues (Prud'homme et al., 2006) have addressed this question by focusing upon how wing spots have evolved in fruit flies. Wing spots play an important role in mating behaviors of fruit flies and would be predicted to be under strong natural selection. By a functional analysis of wingspot CREs of different fruit fly species, Prud'homme et al. show that CREs responsible for wing spots in fruit flies have been independently gained as shown below. Interestingly, these new CREs have been generated by the modification of pre-existing CREs.

David Stern and colleagues have examined a different type of morphological evolution in fruit flies, trichome formation on limbs. They have recently discovered that multiple mutations in the CREs controlling the genetic toolkit gene, shavenbaby, are responsible for the evolution of this morphological feature.

Here we examine the genetic basis of a trichome pattern difference between Drosophila species, previously shown to result from the evolution of a single gene, shavenbaby (svb), probably through cis-regulatory changes(6),,, Our results demonstrate that the accumulation of multiple small-effect changes at a single locus underlies the evolution of a morphological difference between species. These data support the view that alleles of large effect that distinguish species may sometimes reflect the accumulation of multiple mutations of small effect at select genes.
McGregor et al., "Morphological evolution through multiple cis-regulatory mutations at a single gene," (2007), Nature 448:487

Mutations in CREs in fruit flies and sticklebacks have been shown to play important roles in their morphological evolution. Do mutations in CREs play any role in the evolution of humans? To address this question, Greg Wray and colleagues examined the PDYN gene which is involved in the synthesis of endogenous brain opiates. Through comparing the genomes of chimps and humans, population genetics and experimental analyses, they demonstrate that a 68 base-pair element is important for turning the PDYN gene on at higher levels in human brains and that this element has been under positive natural selection.

Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory.
Rockman et al., "Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans," (2005), PLOS Biology 3, p. 387

This is an important and active field of evolutionary research, and if Explore Evolution aimed to live up to its title, it is a field that could have generated the basis for genuine inquiry. Instead, unsolved questions are offered as unsolvable obstacles, and ongoing scientific research is ignored or obscured to serve the authors' misconceptions.

Mutations & New Body Plans

Explore Evolution claims:

According to Neo-Darwinism, new biological form arises when natural selection acts on randomly occurring mutations and variations in DNA. But new research seeems to say that mutations in DNA assembly instructions will produce, at best, a new protein. Higher-level instructions – for building tissues, organs and body types – are not stored only in DNA. This means that you can mutate DNA 'til the cows come home and you still wouldn't get a new body plan.
Explore Evolution, p. 111

It is outright baffling that Explore Evolution cites Franklin Harold's book, The Way of the Cell, to support the claim that mutations are insufficient to change body plans. Franklin Harold is a microbiologist, and a proponent of the role of self-organization and structural constraints in the spatial organization of cells and does not remotely address the issue of body plans in his book. He's interested in microbes, not higher organisms.

This book celebrates microorganisms, and that requires explanation because with most folks the word "life" does not conjure up the image of a bacteria or protozoa … Microorganisms, the bacteria and protists, can make a biosphere all by themselves, and did so for billions of years when the earth was young. Higher organisms hold mysteries that are of special concern to us humans; the genetic basis of disease, the immune response, embryonic development and the nature of mind are now at the forefront of the research effort. But for the purposes of an inquiry into the nature of life, these are peripheral issues. They represent potentialities inherent in living matter, but they are not required for its existence.
Franklin Harold (2001) The Way of the Cell, Preface, p. xi

Nor is Franklin Harold sympathetic to the special pleading that a mysterious "something else" is needed to explain cellular morphology.

Spatial organization is not written out in the genetic blueprint; it emerges from the interplay of genetically specified molecules, by way of a hierarchy of self-organizing processes, constrained by heritable structures, membranes in particular.
Franklin Harold (2005) Molecules into Cells: Specifying Spatial Architecture, Microbiology and Molecular Biology Reviews, 69 p. 545

Perhaps Explore Evolution meant to include reference 21, Stephen Meyer's paper, "The origin of biological information and the higher taxonomic categories," which was later retracted by the Proceedings of the Biological Society of Washington.

During the Cambrian, many novel animal forms and body plans (representing new phyla, subphyla and classes) arose in a geologically brief period of time. The following information-based analysis of the Cambrian explosion will support the claim of recent authors such as Muller and Newman that the mechanism of selection and genetic mutation does not constitute an adequate causal explanation of the origination of biological form in the higher taxonomic groups.
S. Meyer (2004) "Origins of Biological Information and the Higher Taxonomic Categories," Proceedings of the Biological Society of Washington 117(2):213-239

As in Explore Evolution, Meyer refers to Origination of Organismal Form for support. But, as described elsewhere in this critique, Muller and Newman are not addressing the origin of higher taxonomic categories per se, they are concerned with the origin of the forms of the earliest multi-cellular life and of their embryos.

However, Simon Conway Morris, a paleontoloist who studies Cambrian and pre-Cambrian fossils, does address the issue of body plans in the Origination of Organismal Form:

Despite the seeming welter of body plans emerging in the Cambrian, it is difficult to escape the conclusion that the process and products, far from requiring a radical revision of existing theory, fit comfortably into the neo-Darwinian framework.
S.C. Morris (2003) "Metazoan Phylogeny," in Origination of Organismal Form,, p. 21

The vibrant field of evolutionary developmental biology has generated significant insights into the mechanisms by which mutations in DNA would have generated the morphological novelty that produces tissues, organs, and body types. The only citation the authors offer to support their beliefs to the contrary turns out not to support the claim by Explore Evolution.

Developmental Controls

Explore Evolution insists, contrary to the consensus of developmental biologists, that we don't really know what controls development or whether that mystery force could mutate:

Some developmental biologists now think that two other cellular features – the cytoskeleton and the cell membrane – store structural information that affecdts how the embryo develops, but there is much we do not know yet.

What we do know is that if DNA doesn't control development, something else must. Identifying the "something else" is one of the next great areas of research. Another question, of course, is whether the "something else" can be altered by mutation, which would provide a whole new vista of variations on which natural selection could act. Is this what research will reveal? Or will it reveal even deeper questions? Stay tuned.

Explore Evolution, p. 111

Explore Evolution is not clear whom they are referring to in this passage. If this is truly "the next great area of research," an "inquiry-based" textbook would do well to lead students through the leading hypotheses and the evidence researchers in the field are considering, so that students could engage in their own inquiry. Unfortunately, the citations offered earlier in this chapter are uninformative. Franklin Harold, cited earlier and quoted in this critique observing that "[s]patial organization … emerges from the interplay of genetically specified molecules," takes this position:

I do not mean to imply that eukaryotic cells are the product of intelligent purposeful design, the supposition is that the adaptive evolution of a cytoskeleton and intracellular membranes made possible the proliferation of larger cells displaying varied and elaborate morphologies.
Franklin Harold (2001) The Way of the Cell, p. 121

Another possibility is the creationist pseudoscience of Jonathan Wells:

Jonathan Wells, a molecular biologist with the Discovery Institute, argues that genes, environment, and cell structure all affect development. DNA controls the production of proteins that affect development, but the cytoskeleton (a network of microscopic fibers) and certain features in the cell membrane determine what happens to these proteins after they are made…

"The notion that genes control development is a fallout from neo–Darwinian evolutionary theory," Mr. Wells added. Evolutionists use genetic mutations to explain how organisms could change gradually over time. But if development involves the entire egg, then its complexity is much stronger evidence that a Creator designed life.

Setting aside the absurd implication that evolutionary biologists think that development does not involve the "entire egg," could genes affect how the egg is produced? Indeed they can and do. Fruit fly geneticists have searched for "maternal effect mutations" in such genes and have identified genes necessary for the proper construction of the oocyte, the future egg. One such gene encodes Protein Kinase A (PKA) that has a direct effect upon the organization of microtubules through mediating a external signal from nearby follicle cells.

Microtubule polarity has been implicated as the basis for polarized localization of morphogenetic determinants that specify the anteroposterior axis in Drosophila oocytes. We describe mutation affecting Protein Kinase A (PKA) that act in the germ line to disrupt both microtubule distribution and RNA localization along this axis.
M. E. Lane and D. Kalderon (1994) "RNA localization along the anteroposterior axis of the Drosophila oocyte requires PKA-mediated signal transduction to direct normal microtubule organization," Genes and Development 8, p. 2896

Unfortunately for creationists, the organization of microtubules in the oocyte is under genetic control and will be sensitive to mutation. In this case, a mutation affecting PKA function in the egg can result in an embryo which has heads at both ends, or in more subtle variations. In a similar fashion, if the "certain features of the cell membrane" are due to actions of proteins, either in the cell membrane or involved in generating the cell membrane of eggs, they will also sensitive to genetic control and mutation, since, as Harold observes, those structures are genetically specified.

Bacterial speciation

The study of evolution in the bacterial world is one of the most dynamic and exciting areas of current biological research. New analytical tools from molecular biology and the increasing wealth of data from genomics research are currently offering new insights into the nature of bacterial species and the mechanisms of speciation. These studies also promise to illuminate the early history of life on earth. Explore Evolution obscures this active area of research by claiming:

As British bacteriologist Alan Linton has noted, "Throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.
Explore Evolution, p. 104-5

This claim is made to imply once again that natural evolutionary mechanisms cannot account for speciation. As worded, it again misrepresents what evolutionary biology actually claims, and what research has shown. Explore Evolution ignores the hundreds of papers which address the study of speciation in bacteria. The quotation offered is from a book review by a British microbiologist affiliated with the Biblical Creation Society, hardly a credible source.

Recent research indicates that speciation in bacteria occurs when otherwise relatively frequent and genome-wide genetic recombination events become more limited.

A recent study notes that when eukaryotic organisms become reproductively isolated, their entire genomes become isolated. In bacteria, the situation is very different. Bacteria exchange pieces of DNA, not whole genomes. This study showed that "different regions of the Escherichia coli and Salmonella enterica chromosomes diverged over a ~70-million-year period. Genetic isolation first occurred at regions carrying species-specific genes, indicating that physiological distinctiveness between the nascent Escherichia and Salmonella lineages was maintained for tens of millions of years before the complete genetic isolation of their chromosomes."

Note also that the authors of this paper emphasize that their research on bacterial evolution is important for dealing with urgent practical problems. The proper identification and delineation of bacterial species plays critical roles in medical diagnosis, food safety, epidemiology, and bioterrorism mitigation.

Recent work by Richard Lenski has even shown new bacterial species evolving in the laboratory. Lenski and his student Zachary Blount note that "E. coli cells cannot grow on citrate under oxic conditions, and that inability has long been viewed as a defining characteristic of this important, diverse, and widespread species." They then exposed several identical populations of E. coli to an environment high in citrate and low in other energy sources. "For more than 30,000 generations, none of them evolved the capacity to use the citrate. … [O]ne population eventually evolved the Cit+ function [a gene that could metabolize citrate], whereas all of the others remain Cit− [unable to metabolize citrate] after more than 40,000 generations." Given that the Cit- trait is a defining feature of E. coli, the population that gained Cit+ could be considered a new species.

Bacterial evolution is an interesting and important field. There are also important questions to ask about what it even means for bacteria to speciate. Without offering a clear definition of a bacteria species, it is impossible to know whether it's true that scientists have not seen bacterial speciation, nor what significance that would hold if true. Without giving students that information, there's no way for them to pursue their own inquiry, again falsifying the claim that Explore Evolution is inquiry-based.

References:

Adam C. Retchless and Jeffrey G. Lawrence (2007) "Temporal Fragmentation of Speciation in Bacteria" Science 317(5841):1093-1096. DOI: 10.1126/science.1144876

Christophe Fraser, William P. Hanage, Brian G. Spratt (2007) "Recombination and the Nature of Bacterial Speciation" Science 315(5811):476-480 DOI: 10.1126/science.1127573

Zachary D. Blount, Christina Z. Borland, Richard E. Lenski (2008) "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli" Proc. Nat. Acad. Sci. 105(23):7899-7906

Molecular "Machines"

(from NCSE's critique of Explore Evolution) The chapter in EE called "Molecular Machines" (pp. 115-125) presents a rehash of standard claims made by "intelligent design" promoters, especially Michael Behe. These claims were examined and rejected by expert scientists well before EE's publication. The chapter simply ignores the published scientific literature which refutes its central claims. Unlike a genuine science book, EE makes no effort to correct mistakes made in earlier writings, but simply repeats yet again erroneous statements about the bacterial flagellum. The central claims in this chapter were heard in United States Federal court in the Kitzmiller v. Dover "intelligent design" trial and were decisively rejected there, too.

The chapter fails to make clear that it is essentially promoting intelligent design creationism. While avoiding the phrase "intelligent design," the chapter relies heavily on the work of Michael Behe who is simply called "a biochemist from Lehigh University." The chapter neglects to mention that Behe is a leading intelligent design proponent and testified in favor of teaching ID in the public schools in the Kitzmiller v. Dover case. The chapter also avoids mentioning the significant point that Behe's arguments have been rejected by scientists and also were famously debunked during cross-examination and rejected by the court in the Kitzmiller v Dover trial Bacteria with flagellaBacteria with flagella The "intelligent design" movement presents the bacterial flagellum as a structure that supposedly could not have evolved, and therefore indicates the intervention of an "intelligent designer." Discovery Institute Fellow Michael Behe has been one of the most active promoters of erroneous claims about the bacterial flagellum.

The bacterial flagellum is a complex molecular structure, typically made of about 30 different proteins. Ten more proteins are involved in building it.

The ID/creationist movement claims that the structure requires all of its protein parts to function, and therefore could not have evolved in a stepwise manner, and therefore an "Intelligent Designer" must have been required.

The bacterial flagellum in young earth creationist literature

Before the flagellum was adopted by the ID movment, it was already common in arguments of "creation scientists" (Battson 1986, Anonymous 1992, Anonymous 1994, Lumsden 1994). As Henry Morris, the founder of "scientific creationism," wrote in 2005:
These well-meaning folks [ID advocates] did not really invent the idea of intelligent design, of course. Dembski often refers, for example, to the bacterial flagellum as a strong evidence for design (and indeed it is); but one of our ICR scientists (the late Dr. Dick Bliss) was using this example in his talks on creation a generation ago.
see "The Design Revelation" by Henry M. Morris (2005)


A connection between EE and earlier creationist and ID literature are apparent in the graphical depictions of the bacterial flagellum. The graphics are identical to, or closely resemble, images from previous "ID" works. For example, Figure 8.1 on page 117 (and on pages 115 and 116) is the same graphic used for the cover of DI fellow William Dembski's 2002 ID book No Free Lunch, and in the Discovery Institute's "ID" video Unlocking the Mystery of Life.

Claims about complexity of cells

This chapter attempts to argue that structures like the bacterial flagellum can not evolve through natural evolutionary mechanisms.

EE's Claim: Some scientists claim that features "that could not have been formed by the natural selection/mutation process have been found." (p.116)

Problems with claim: This claim is wrong and/or deceptive in 3 ways. First, no structures have been found in living things that cannot in principle be explained by evolutionary processes. Ongoing research in evolutionary biology is continuing to develop our understanding of the evolution of cell structures. Second, modern evolutionary theory encompasses much more than just mutation and natural selection. Evolutionists have made this point numerous times, but ID promoters and other creationists continue to ignore that fact. Third, EE uses the phrase "some scientists" in a misleading manner. The only scientists who doubt evolution are members of a fringe group of intelligent-design promoters and other creationists who reject evolution.

EE's claim: Molecular biology has shown that cells contain "machines" which can't be explained by evolution. (p. )

Problems with claim: EE highlights a quotation from the distinguished biological scientist Bruce Alberts in which he refers to "protein machines" and "assemblies with highly coordinated moving parts" inside cells (quoted on p. 116). EE uses this quote to imply that cell structures are just like human-made machines which break down if a part is taken out or broken. EE's use of the quote also suggests that Alberts shares ID-creationist doubts about evolution. What does Albert's really think about evolution? In a letter to the New York Times, Alberts objected to the way ID-promoters quote him, writing:

...the majestic chemistry of life should be astounding to everyone. But these facts should not be misrepresented as support for the idea that life's molecular complexity is a result of "intelligent design." To the contrary, modern scientific views of the molecular organization of life are entirely consistent with spontaneous variation and natural selection driving a powerful evolutionary process. In evolution, as in all areas of science, our knowledge is incomplete. But the entire success of the scientific enterprise has depended on an insistence that these gaps be filled by natural explanations, logically derived from confirmable evidence. Because "intelligent design" theories are based on supernatural explanations, they can have nothing to do with science. Bruce Alberts Letter to the New York Times, February 12, 2005

EE's claim: The flagellum is irreducibly complex. It requires 40 proteins -- 30 structural, 10 regulation. "[A]ll 30 parts have to be present together" to function

This claim is factually incorrect. The latest published review, apparently ignored by the authors of EE, showed that only 23 of the 42 proteins found in the bacterium E. coli are universally required in the flagella of all bacteria. This error has occurred repeatedly in ID literature.

Research has shown that the motor only functions after all 30 of the motor's protein parts are in place. All 30 are required for motor function. When experimenters in the laboratory take away even one part of the motor, it stops working. (EE, p. 118, italics original)

Unfortunately, the authors of Explore Evolution do not acknowledge a directly relevant paper by Pallen and Matzke (2006), which specifically debunked this point and was published online in September 2006. The paper debunked directly the ID movement's claims about the bacterial flagellum, for example as made by ''EE'' author Scott Minnich during his testimony on behalf of ID in the Kitzmiller v. Dover case.

Table 1 of Pallen & Matzke (2006) gave a systematic review of the literature on each protein of the bacterial flagellum, examining whether or not the protein was universally required in all functional flagella. The analysis showed that of the 42 flagellar proteins in the standard lab strains E. coli and Salmonella typhimurium only 23 (55%) were actually universally required in all functional flagella. Some proteins can be removed experimentally without removing flagellar function, and other proteins simply aren't found in all flagellated bacteria.

References

W. Ford Doolittle, Olga Zhaxybayeva, Evolution: Reducible Complexity -- The Case for Bacterial Flagella, Current BiologyVolume 17, Issue 13, , 3 July 2007, Pages R510-R512. (http://www.sciencedirect.com/science/article/B6VRT-4P3MFYD-G/2/7acab14271d539cac30d01d5e567a77d)

Pallen MJ, Matzke NJ. (2006). “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. Advanced Online Publication on September 5, 2006

Claims about "cooption"

EE's claim: Evolution via cooption can't really work.

Problems with claim:

EE almost acknowledges that "cooption" is a powerful evolutionary process. Cooption occurs when a given gene (or trait) acquires a new function, different from its original one. Genes can acquire new functions in several ways. Extra copies of genes are sometimes produced by DNA copying errors. These extra copies are free to mutate without disrupting the function of the original gene. Or, sometimes a mutation in a part of a gene can lead to the evolution of a new function in addition to the original one.1 (True JR, Carroll SB, 2003)

EE attempts to cast doubt on the power of cooption by making comments like this:

For one thing, the co-option hypothesis underestimates the problem of coordinating the necessary transformations. How does an undirected process incorporate the "borrowed" parts to form a new system -- without disrupting the old system? What natural process ensures that previously unrelated parts fit together well enough to form a new, functioning system? (EE p. 121)

The old system is not disrupted because a duplicate is modified, not the original. Gene duplication has been a standard part of evolutionary theory for decades.

EE's Claim: The scientist H. Allen Orr thinks cooption doesn't work.

Critics, including many neo-Darwinian biologists, contend that these questions remain unanswered, and are skeptical of the co-option hypothesis. As H. Allen Orr has said, "You may as well hope that half your car's transmission will suddenly help out in the airbag department."

What does Orr think about Behe's argument?

The first thing you need to understand about Behe's argument is that it's just plain wrong. It's not that he botched some stray fact about evolution, or that he doesn't know his biochemistry, but that his argument—as an argument—is fatally flawed.>
1 True JR, Carroll SB. Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 2002;18:53–80.

Claims about evolution of flagella

Claim: "[T]he proteins in the motor are older than those in the pump"

Explore Evolution again misleads readers. This issue is currently debated within the community of flagellum researchers (reviewed briefly in Pallen & Matzke 2006), and about half the papers go each way. The definitive study has not yet been done. Even if it turns out that the type 3 secretion system is derived from the flagellum, it will still prove that (a) Behe was wrong that reduced subsets of "irreducibly complex" systems "are by definition not functional", and (b) that a subset of flagellum parts has a plausible function different from motility. Furthermore, only the ID advocates think that the type 3 secretion system is the only known relative of the flagellum: the actual scientific community, in contrast, knows of several others.

Claim: The pump only accounts for 10 of the 30 proteins

Furthermore, critics of co-option point out that the bacterial motor is a machine with about 30 structural parts. While roughly 10 of these protein parts are found in the needle-nose pump, the other 20 are found in no other known bacteria or organism. They are unique. So, where are you going to 'borrow' them from? they ask.10

This is yet another claim copied straight from the ID literature. Here are several previous examples:

It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.
William A. Dembski (2003). "Still Spinning Just Fine: A Response to Ken Miller." DesignInference.com. February 17, 2003.

With the bacterial flagellum, you're talking about a machine that's got 40 structural parts. Yes, we find 10 of them are involved in another molecular machine, but the other 30 are unique! So where are you going to borrow them from? Eventually you're going to have to account for the function of every single part as originally having some other purpose. So you can only follow that argument so far until you run into the problem of you're borrowing parts from nothing.
Scott Minnich (2003), in the video Unlocking the Mystery of Life, online at The Apologia Project.

Miller's scenario faces at least key three difficulties. First, the other thirty or so proteins in the flagellar motor are unique to it and are not found in any other living system. From where, then, were these protein parts co-opted?

Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system. From whence, then, were these protein parts co-opted?
Minnich (2005) expert report, March 31, 2005 / Scott A. Minnich & Stephen C. Meyer (2004). "Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria." Second International Conference on Design & Nature, Rhodes Greece. Wessex Institute of Technology, September 1, 2004.

With regards to the flagellum at least 2/3 of the parts are not known to be shared with any other structure therefore might not be even a sub-part of another system at all.

In the Unlocking video, Scott Minnich stands in his microbiology lab and quietly assesses the Darwinian TTSS scenario. Yes, he says, it is remotely possible that the TTSS injector came first, and he affirms that its ten proteins do seem to parallel or match the core proteins of the flagellum. But that's where you bump into a huge problem. Where did the cell find the other thirty or so proteins to build incrementally from the TTSS all the way to a rotary-motor flagellum? You come to the point where you are borrowing from nothing, and the plausibility of the scenario fades quickly.

[...]

Many observers watching the shifting battles over Behe's theory feel that Kenneth Miller was premature in loudly declaring victory, insisting that the flagellum could possibly have evolved from the TTSS, when the evidence indicates that the TTSS was the fruit of reverse-evolution. Miller's exercise in hand-waving (arguing that the TTSS led right on to the flagellum) has always depended upon the other thirty proteins – floating in from the cellular environment. But what's the source? Are they just easily bubbling up from day-to-day cellular processes, in wondrous variety, ready to be recruited to build from ten TTSS proteins up to the flagellum's set of forty?here
Thomas Woodward (2006). Darwin Strikes Back: Defending the Science of Intelligent Design. Grand Rapids, Michigan: Baker Books, p. 80. Italics original.

The ID proponents are all telling the exact same story as Explore Evolution. (The difference between 20 or 30 unique proteins depends on whether or not regulatory proteins are included.) And they seem terribly confident that they know what they are talking about. After all, the flagellum is the "icon of ID," the ID movement's flagship example of something that could not have evolved, and must have been intelligently designed instead. Explore Evolution repeats the talking points almost word-for-word, with the only difference being that the "intelligent design" conclusion is tactically left out. Scott Minnich seems to be the original authority for the claim, and he is a published researcher on type 3 secretion systems. Furthermore, Minnich made the same claim in his expert report for the Kitzmiller case. As a named coauthor of Explore Evolution, he presumably checked or edited this section of the textbook, if he made any substantial contribution to the book at all.

Apart from dishonestly pretending that Explore Evolution is not making an ID argument here, the only problem with the "20+ proteins are unique to the flagellum, where did they come from?" argument is that it is wildly, hopelessly, false, and is obviously so to anyone familiar with the actual scientific literature and data on the subject. Pallen & Matzke (2006) reviewed the evidence on this specific point and published a table listing all 42 "standard" flagellar proteins (structural and regulatory) in the most-studied lab strains of E. coli and Salmonella typhimurium.

Here is a summary of the table published in Pallen & Matzke (2006) (the table is freely available online here):

  • Total number of proteins listed: 42

         (this table excludes the chemotaxis proteins; there are ~10 chemotaxis proteins in standard E. coli, but the number can range from 0 to 10+ in various bacteria)

  • Total number thought to be indispensable in modern flagella: 23 (55%)
  • Total number "unique" (no known homologs): 15 (36%)
  • Total number of indispensable proteins that are also "unique": 2 (5%)

Claim about protein synthesis

Claim: Plus, you'd have to explain the origin of protein synthesis too

Summary of problems with claim:

This is a case of "shifting the goal posts," much as we saw in the chapter on fossils. The fact that we do not fully understand everything is not a problem for science. An inquiry-based textbook would not hold these lacunae in our knowledge out as problems, it would hold them out as exciting opportunities for students to explore.

Full discussion:

Explore Evolution, having presented a misleading and even erroneous case against the evolution of one particular structure, responds to the evidence showing that the structure would not be impossible to evolve by simply choosing a new target for their anti-intellectual pseudo-criticism":

In other words, even assuming the presence of all the necessary genes and protein parts, the only way co-option can explain the origin of one irreducibly complex system (the bacterial motor) is by assuming the pre-existence of another irreducibly complex system (the system of protein machines that reads and processes genetic information). Critics of co-option say this is rather like explaining the origin of machines by saying that a machine that makes machines makes them.
Explore Evolution , p. 122

Actually, it is like responding to a question about where heavy elements come from and being told that they are produced from reactions between lighter elements inside of suns. Explore Evolution's "critics of co-option" are doing the equivalent of demanding to know where suns come from before they will accept that nuclear fusion can occur. When three-year-olds ask "why?" until their parents can't (or decide not to) answer, it is cute. It is less cute when grown men attempt the same game.

As shown above, the flagellum is not actually irreducibly complex — it could have been assembled through a stepwise evolutionary process. Research into the evolution of protein synthesis is an ongoing area of research, and progress is indeed being made. If there were a model for that process, the authors of Explore Evolution would undoubtedly inquire about areas where our knowledge was less complete, and present those blank spots as if they were evidence that no knowledge of those subjects was even possible. In doing so, they follow their intellectual godfather, Philip Johnson, who once wondered "why the scientists won't admit that there are mysteries beyond our comprehension," and that phenomena like the origins of protein synthesis, the bacterial flagellum, or the origins of complex multicellular organisms might be among those mysteries (Philip Johnson, 1990. "Evolution as Dogma: The Establishment of Naturalism," First Things 6:15-22, reprinted in Robert Pennock, ed. 2001. Intelligent Design Creationism and its Critics, The MIT Press, Cambridge, MA, ch. 2).

Scientists do not work by that process. Scientists employ a process for asking questions and testing the answers to those questions which is comfortable with uncertainty and does not require that the currently unknown be branded as eternally unknowable. As discussed elsewhere (for instance, Chapter 3), areas once presented as insurmountable problems for evolutionary theory are now well-understood examples of evolution at work. The model of science that the authors endorse here (and elsewhere) is hopeless — and hopelessly wrong.

The idea of inquiry-based learning is to encourage scientific exploration. By getting students to propose their own experiments to test the hypotheses they develop about the world around them, they learn not just the facts of science (e.g., how protein synthesis works), but the process scientists employ (e.g., how scientists test hypotheses about the evolution of protein synthesis). The approach Explore Evolution adopts does not describe that scientific process, and in passages like this, it actively discourages students from those scientific pursuits. This inquiry-averse approach to science is inaccurate and inappropriate.

Natural Selection / Survival of the Fittest

The biological concept of "fitness" is critical to an understanding of natural selection and of evolution in general. While philosophers continue to argue about the best way to define "fitness," there are some generally accepted aspects of biological definitions of fitness.

First, it is a term applied to an allele or genotype, a particular form of the genome. Thus, it is a property not of a single individual, but of a collection of individuals who share certain heritable traits. Fitness then is the contribution of the average individual with that trait to the next generation.

Explore Evolution misdefines this key biological concept, stating that fitness is a property of an individual, and is measured by that individual's contribution to future generations. By shifting from a focus on heritable traits to individuals, EE obscures the way in which biologists employ the concept of fitness, and mislead students.

The central theme of this chapter is a common creationist assertion that natural selection is invalid because it is circularly defined. If natural selection means "survival of the fittest," and the fittest are those that survive, then (they insist) the definitions are circular. Natural selection is the survival of those that survive. Of course, this is not the definition of natural selection, and it is not the definition of fitness. Fitness is defined in terms of the genotypes represented among future generations, not of the current generation, and natural selection is defined in terms of differential reproduction, not as "survival of the fittest." The entire chapter is based on a pair of flawed definitions and trivial wordgames. Philosophers dismissed this creationist argument long ago.

Major Flaws:

Tautology: Creationists have relied on this flawed argument for over a century, but it is no more valid today than it was when first introduced.

Tautology

Circular reasoning

Summary of problems:

Explore Evolution substitutes word games for serious engagement with natural selection. Rather than providing an accurate definition of a key evolutionary concept — fitness — the book defines in in circular terms, then pretends that the fault for this circularity lies with the concept, rather than their own poor writing. This gambit is a long-refuted creationist canard based on a misunderstanding of basic terms. It is irrelevant to the science, and rejected by philosophers of science.

Full discussion:

"Creationists have long argued that natural selection has no predictive value and thus is a mere tautology stating the obvious fact that organisms that 'survive' are thereby decreed to have been the 'fittest.'" Henry Morris, the late president of the young earth creationist Institute for Creation Science, may have been wrong about many things, but that quotation from the preface to Scientific Creationism is an accurate account of this argument's heritage. Later he repeats the claim about natural selection and Herbert Spencer's description of it as "survival of the fittest":

It is tautologous. Those who survive in the struggle for existence are the fittest because the fittest are the ones who survive.
Henry M. Morris (1974) Scientific Creationism, Master Books, El Cajon, CA, p. 7

Explore Evolution doesn't add much:

Just about everyone has heard the popular description of natural selection as "survival of the fittest," a term Darwin credited to Herbert Spencer. The grassroots appeal of this catchphrase was very great, but it sometimes conceals some sloppy reasoning.

For example, someone might say that a particular organism survived because it was more "fit" than its competitors. Unfortunately, when we examine this "explanation" closely, we find that it only takes the very fact that it was supposed to explain and says it in a different way.
EE, p. 126

EE later explains that "Some [philosophers] think that biologists can avoid such circularity by carefully and specifically identifying the trait that is responsible for the competitive advantage and reproductive success of the population being studied" (p. 127), but then dismisses the claim without explaining why.

This is unfortunate, because that discussion would give them a chance to define fitness and to discuss some common misconceptions about it. Instead, the examples given merely deepen those misunderstandings. EE defines fitness as "the ability of an organism to survive and produce viable offspring in a given environment" ("Glossary," p. 146). This definition does not match that used by biology textbooks, and those differences are what allows EE to repeat this creationist error.

Mark Ridley's Evolution defines fitness as:

The average number of offspring produced by individuals with a certain genotype, relative to the number produced by individuals with other genotypes.
Mark Ridley (1996) Evolution 2nd ed., Cambridge, MA, p. 668

Campbell and Reece define it:

the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals.
Neil A. Campbell and Jane C. Reece (2002) Biology 6th ed., San Francisco, p. 457

Futuyma defines two related concepts:

fitness: The success of an entity in reproducing; hence, the average contribution of an allele or genotype to the next generation or to succeeding generations. Relative fitness is the average contribution of an allele or genotype compared with that of another allele or genotype.
Douglas J. Futuyma (1998) Evolutionary Biology 3rd ed., Sunderland, MA, p. 766

Each of these definitions discusses the fitness of alleles or genotypes rather than the fitnesses of individuals. Explore Evolution only talks about the fitness of individuals, and studiously avoids discussing alleles or genotypes. The reason can be seen in the brief example quoted above, in which "someone might say that a particular organism survived because it was more "fit" than its competitors." Later, EE creates a hypothetical situation in which we observe finches and see that some produce more offspring than others. The authors then complain that a study like this "certainly doesn't tell us why. All we can say is that some finches leave more offspring (our definition of 'survival') because they produce and sustain more eggs (our definition of 'fittest')." By ignoring the role of genetics in defining fitness, they trivialized the concept and confused its place in biological evolution.

A student working with an inquiry-based book which properly defined fitness might have been encouraged to propose an experiment which would help determine the "why." The student would propose looking for some genetic factor shared by individuals which produce more eggs. (The student might also suggest examining whether producing more eggs actually produces more offspring which survive to adulthood and contribute genes to future generations, a key component of the accurate definitions of fitness).

Philosophers do continue to seek an broad philosophical account of fitness, but agree that it is not tautological, and that it does describe a general tendency of a trait or organism, not — as EE prefers — a description of the actual performance of an organism. Thus, an individual can be fit (possess traits which ought to increase its reproductive success) but not reproduce. It could be struck by lightning, for instance. Treating fitness as a tendency eliminates any circularity, just as recognizing that salt tends to dissolve in water allows you to describe salt as soluble even if it never is placed in water. A gene can tend to be more fit without making each individual possessing that trait produce more offspring.

What Fossils Tell Us

Platypus: an egg-laying mammalPlatypus: an egg-laying mammal

Unlike the authors of Explore Evolution, many elementary school students are well aware that there are mammals which lay eggs, and that there are snakes which have placentas. Scattered among errors so elementary that grade-school students could correct them, this chapter is laced with statements which requiring a level of knowledge far beyond even typical college biology students. Questions are posed to students which cannot be answered without much more background than the book provides, or than the average high school teacher is trained to provide. The book does not offer such resources, nor suggest ways that students could explore those questions through independent inquiry.

The flaws in the chapter go much deeper than such errors and inconsistencies. The practice of science is misrepresented, and common misconceptions about evolution are actively promoted. Far from encouraging scientific inquiry, this chapter blocks and discourages genuine inquiry. Given that the book parrots creationist misrepresentations of biology, then shuts off inquiry into scientific answers to those questions, it is easy to see that the book's aim is to instill exactly those creationist errors.

p. 130: "any transition from a three-chambered heart to a four-chambered heart requires a series of coordinated … changes."

This is a recapitulation of the fallacious "irreducible complexity" argument of intelligent design creationism. Evolutionary and developmental biologists have clear understandings of how morphological structures can and do evolve in parallel.

p. 137

: "can there even be a transition between a single-opening and a dual-opening system [of lungs]?"

Scientists have good evidence explaining the evolution of bird lungs – with two openings – from reptilian lungs – with only one opening. None of that evidence is offered.

p. 137: "the ancestors of birds almost certainly had a diaphragm breathing system"

This claim is advanced on the basis of a controversial and widely-criticized paper from 1997, and even that paper does not support this claim. No discussion is offered of the subsequent research offering further evidence against this idea.

p. 129: "the superficial resemblance between skeletons [of early mammals and early reptiles]"

The fossil record of early mammals is one of the most continuous records available to paleontologists, and the chain of similarities is hardly superficial.

p. 130: "Transforming a reptile into a mammal … requires the development of completely new organs like the placenta and mammary glands"

Placentas have evolved dozens of different times within modern reptiles, and mammary glands are highly modified sweat glands, so it is wrong to claim either of these are "completely new organs." More significantly, mammals are not "transformed" from reptiles: they share a common ancestor, but neither descended from the other.

p. 129: "Most reptiles lay eggs, while mammals carry fertilized eggs internally in a placenta and bear live young."

There are mammals which lay eggs, and many other mammals which have live birth but lack a placenta. No discussion is offered of the placentas found in several groups of reptiles.

p. 138: "all we can say for sure is that the internal organs of living reptiles, living birds, and living mammals are very different from one another"

We can do far more than just say that different things are different. The patterns of differences and similarities between living species – and between preserved remains of extinct species – gives us insight into the evolutionary processes driving those differences. Explore Evolution fails to provide students with the background to allow them to explore this fascinating field: evolutionary biology.

Major Flaws:

Hearts: In discussing the evolution of the four-chambered mammalian heart from the three-chambered reptilian heart, Explore Evolution omits any reference to existing scientific models of that evolutionary path, and makes gross misstatements about the anatomy of hearts in living animals.

Lungs: In discussing the evolution of bird-like lungs from reptilian ancestors, the authors make inaccurate claims about the lungs of bird ancestors, and misrepresent the biology of modern birds and crocodilians. There is no discussion of existing research on the evolution of bird lungs, research answers the very questions posed by Explore Evolution.

Transitional Forms: Explore Evolution states that all mammals give birth to live young and possess a placenta, while all reptiles lay eggs and lack a placenta. In fact, many groups of reptiles have evolved a placenta, and there are mammals which lack a placenta and lay eggs. Each of those counterexamples represents a living transitional form, and it is possible to study the evolution of placentas, lactation and egg-laying using both modern species and fossils. Explore Evolution obfuscates the truth and confuses students with creationist falsehoods.

Hearts

Worms and other structurally simple animals have simple, single-chambered hearts. Fish have a two-chambered heart. Reptiles and amphibians generally have three-chambered hearts. Mammals and birds have four-chambered hearts, with the four chambers arranged differently in each group. Explore Evolution presents this arrangement as a mystery, unbridgeable by evolutionary means.

Contrary to the account in this chapter, the evolution of the four-chambered heart is no mystery. Many researchers have addressed elements of the question, but rather than addressing these well-tested models, Explore Evolution makes passing reference to their existence and reliance on specific processes in developmental biology, but never gives enough detail for students to understand those models. Having given an inadequate account of mainstream models of heart evolution, the book then criticizes those models, again without offering enough detail for students to evaluate or even fully understand the critique. Rather than encouraging inquiry, this approach forces students to simply learn by rote that certain things cannot evolve, leaving students with no basis for understanding future advances in the evolution of hearts and other anatomical structures.

Mammalian hearts

Summary of problems:

There are good examples of the functional intermediate stages in the evolution of the mammalian heart. Explore Evolution repeats inaccurate and long-debunked creationist claims about the impossibility of evolving a four-chambered mammalian heart from a three-chambered reptilian heart. Though extensive research exists into exactly how this transition took place, Explore Evolution ignores the research, and abandons intellectual inquiry in favor of creationist talking points.

Full discussion:

Explore Evolution claims:

… any transition from a three-chambered heart to a four-chambered heart requires a series of coordinated physiological and anatomical changes, including: 1) lengthening and attaching the existing septum to create a new, separate ventricle chamber, 2) replacing the forked abdominal aorta and two aortic arches with a single aorta, 3) rerouting the pulmonary arteries and veins, and 4) making various secondary structural changes to the walls and valves between chambers.

The need to change so many anatomical features and still maintain function at every step along the way raises some difficult questions about the viability of a series of transitional stages between a three- and four-chambered heart. Would the new chamber arise before the new veins, arteries, and septa? Would it arise before or after the new, single aorta emerged and the new plumbing was rerouted to support it? If the new chamber arose before these other features, how would it work? If it arose after the other features, what are the odd that all these new structures — veins, arteries, septa, and aorta — would fit together properly and function in concert with the new chamber?
Explore Evolution, pp. 130-131
4-Chambered and 3 Chambered Hearts: All that is fundamentally required to get the topology of the mammalian four-chambered heart from a reptile-like three-chambered heart (e.g. B, although this should not be taken as an exact representative of the ancestral state) is extension of the septum (the wall dividing the chambers and lost of the right systemic arch.  The lineage leading to crocodiles evolved a four-chambered heart along a different pathway, keeping both systemic arches.      From Figure 9-5, p. 112 of: Farrell, A. P. (1997). "Evolution of cardiovascular systems: Insights into ontogeny". Development of cardiovascular systems: molecules to organisms. Burggren, W. W. and Keller, B. B., Eds. Cambridge, UK ; New York, NY, USA, Cambridge University Press: 101-113.4-Chambered and 3 Chambered Hearts: All that is fundamentally required to get the topology of the mammalian four-chambered heart from a reptile-like three-chambered heart (e.g. B, although this should not be taken as an exact representative of the ancestral state) is extension of the septum (the wall dividing the chambers and lost of the right systemic arch. The lineage leading to crocodiles evolved a four-chambered heart along a different pathway, keeping both systemic arches. From Figure 9-5, p. 112 of: Farrell, A. P. (1997). "Evolution of cardiovascular systems: Insights into ontogeny". Development of cardiovascular systems: molecules to organisms. Burggren, W. W. and Keller, B. B., Eds. Cambridge, UK ; New York, NY, USA, Cambridge University Press: 101-113.

Rather than addressing the research that has been done on precisely these questions, Explore Evolution changes subjects, discussing hypotheses from evolutionary developmental biology, and citing a series of papers which do not actually address heart evolution. Yet again, this approach is not inquiry-based, and presents students with an inaccurate view about the way to approach uncertainty in science. The question of whether mutations affecting the early development of the heart might allow multiple changes to happen at once is a question which has to be addressed with evidence in that system, not with arguments about the evolution of novel body-plans, or hand-waving discussions of evolution in the Cambrian. There has been substantial work done on the development of the heart, and it is that literature which the authors of Explore Evolution should have reviewed (for example, Antoon F. M. Moorman and Vincent M. Christoffels. 2003. "Cardiac Chamber Formation: Development, Genes, and Evolution", Physiological Reviews 83:1223-1267).

Liem's Hearts: This diagram shows a side view of the organisms, with the head facing left and heart and lungs to the right.  The highly derived patterns of birds and mammals were formed by loss or specialization of the various arches. The order of events leading to each lineage has been reconstructed in some detail.  As the caption says, "One of the hallmarks in comparative anatomy is the discovery and broadly based explanation of the evolutionary pattern of the heart and great vessels of vertebrates.  It still has profound and pervasive implications in comparative biology." From pp. 620-621 of: Liem, Karel F. and Walker, Warren F. (2001). Functional anatomy of the vertebrates: an evolutionary perspective. Fort Worth, Harcourt College Publishers. online sourceLiem's Hearts: This diagram shows a side view of the organisms, with the head facing left and heart and lungs to the right. The highly derived patterns of birds and mammals were formed by loss or specialization of the various arches. The order of events leading to each lineage has been reconstructed in some detail. As the caption says, "One of the hallmarks in comparative anatomy is the discovery and broadly based explanation of the evolutionary pattern of the heart and great vessels of vertebrates. It still has profound and pervasive implications in comparative biology."

From pp. 620-621 of: Liem, Karel F. and Walker, Warren F. (2001). Functional anatomy of the vertebrates: an evolutionary perspective. Fort Worth, Harcourt College Publishers. online source

The shift from three chambers to four chambers is not as large a leap as it might seem. The ventricles of the mammalian heart are separated by a thin muscular septum (wall) which grows out of the muscular sides of the heart. There is a similar septum in the reptilian and amphibian hearts, and as the figure above or even the figure in Explore Evolution illustrates, the transition from three chambers to four would not be at all problematic for the organism. The septum would grow longer, until it entirely separates the two sides. This change prevents oxygenated blood returning from the lungs from mixing with oxygen-depleted blood from the body. In species with slower metabolisms, or which (like amphibians) can exchange gases through their skin, the separation of oxygen-rich and oxygen-depleted blood is less critical, while in species with higher metabolic requirements, there is more intense selection acting on variations which improved oxygen flow to the body. Species with lower metabolisms can go for long periods without breathing, and in those settings, can restrict flow to the lungs, and use the full power of the heart to circulate the blood through the body. For those species, a three chambered heart allows needed flexibility. Mammals with high metabolic requirements cannot go as long without breathing, so there is no need to limit blood flow through the lungs in the same way.

Explore Evolution offers no explanation of why the aortic arch could not have evolved independently of those changes within the heart. Luckily, scientists are not as incurious as the authors of Explore Evolution, and have actually conducted research to better understand the evolution of the aortic arch and other blood vessels. In Functional Anatomy of the Vertebrates, Liem et al. explain:

One of the hallmarks in comparative anatomy is the discovery and broadly based explanation of the evolutionary pattern of the heart and great vessels of vertebrates. It still has profound and pervasive implications in comparative biology.
Karel F. Liem, et al. (2001) Functional Anatomy of the Vertebrates, Harcourt College Publishers:Fort Worth, p. 620
Evolution Aortic Arches: In this depiction, the viewer is facing the chest (ventral side) of the organism.  The birds and mammals are actually very similar to reptiles in their fundamental pattern, except that they have lost the left or right systemic arch, respectively. From: Figure 12-19, p. 461 of: Kardong, Kenneth V. (2006). Vertebrates: comparative anatomy, function, evolution. Boston, McGraw-Hill Higher Education.Evolution Aortic Arches: In this depiction, the viewer is facing the chest (ventral side) of the organism. The birds and mammals are actually very similar to reptiles in their fundamental pattern, except that they have lost the left or right systemic arch, respectively. From: Figure 12-19, p. 461 of: Kardong, Kenneth V. (2006). Vertebrates: comparative anatomy, function, evolution. Boston, McGraw-Hill Higher Education. Aortic Arches: This diagram "zooms in" to show just the fate of the aortic arches in amphibians, reptiles, birds, and mammals.  The diagram clearly indicates (unlike the diagram in Explore Evolution) that the only fundamental topology change between reptiles and mammals is that mammals have lost the right systemic arch.  From Figure 12-20, p. 462 of: Kardong, Kenneth V. (2006). Vertebrates: comparative anatomy, function, evolution. Boston, McGraw-Hill Higher Education.Aortic Arches: This diagram "zooms in" to show just the fate of the aortic arches in amphibians, reptiles, birds, and mammals. The diagram clearly indicates (unlike the diagram in Explore Evolution) that the only fundamental topology change between reptiles and mammals is that mammals have lost the right systemic arch. From Figure 12-20, p. 462 of: Kardong, Kenneth V. (2006). Vertebrates: comparative anatomy, function, evolution. Boston, McGraw-Hill Higher Education.

An understanding of the details of this evolutionary process require more anatomical background than is appropriate for a high school class, let alone this review, which leaves one wondering why Explore Evolution raises the matter. The contrast between the confusion expressed by Explore Evolution and the detailed explanation offered by professionals in the field is a strong sign that Explore Evolution is not drawing its evidence from the biological literature, and is not interested in encouraging students to undertake genuine inquiry.

In fact, the basis for their claims about the aortic arches is most likely to be Michael Denton's Evolution: A Theory In Crisis (1985, Adler & Adler Publishers: Chevy Chase, MD), which spends several pages arguing the implausibility of evolutionary explanations of heart and aortic arch anatomy. Denton was instrumental in inspiring the intelligent design creationist movement, and Evolution: A Theory in Crisis was cited in Of Pandas and People, the intelligent design textbook ruled too religious for science classrooms as Explore Evolution was being written.

While scientists continue to research the evolution of the heart, producing and testing hypotheses, creationists continued to emphasize whatever uncertainty they could find. An intelligent design creationist group claims the evolution of the heart as an unsolvable problem Until 2005, the group hosting that claim "require[d] that club leaders be Christians," and their discussion of the issue reveals that their claims about the heart are not scientifically grounded. Even while acknowledging that "the 4 chamber mammalian heart probably isn't irreducibly complex" (as Explore Evolution intimates), they express certainty that "it might still be the result of intelligent design and not evolution, and irreducible complexity doesn't have to exist in all instances for it to exist in some." This is not critical thinking, and is not inquiry-based learning.

This argument, like its antecedents in the openly creationist literature, is a religious attack on evolution, not a scientifically grounded investigation. Explore Evolution argues that we know nothing unless we know everything. That attitude is both scientifically and pedagogically inappropriate. The evolutionary process leading to the forms of modern mammalian, reptilian, crocodilian and amphibian hearts remains a subject of research. Students interested in that ongoing research need a solid understanding of evolution, anatomy, physiology, and developmental biology, but more importantly, they need to understand how scientists know what they know, how scientific inquiry works. Explore Evolution will teach students none of this.

Crocodilian Hearts

Crocodilian hearts

Summary of problems:

We gain insight into heart evolution by looking across multiple animal groups. The crocodile heart demonstrates that evolutionary processes are not linear (with distinct steps from 2 to 3 to 4 chambers), but are branching processes, which produces a range of final results from a common ancestral condition. This is exactly the evolutionary prediction. Explore Evolution confuses matters by claiming this transition was difficult, reinforcing a common misconception about evolution. Crocodiles independently evolved a 4-chambered heart, demonstrating how easy that transition was, not (as Explore Evolution claims) how difficult it was.

Full discussion:

Different kinds of 4-chambered hearts: The lineage leading to crocodiles evolved a four-chambered heart along a different pathway than mammals, keeping both systemic arches. From Figure 9-5, p. 112 of: Farrell, A. P. (1997). "Evolution of cardiovascular systems: Insights into ontogeny". Development of cardiovascular systems: molecules to organisms. Burggren, W. W. and Keller, B. B., Eds. Cambridge, UK ; New York, NY, USA, Cambridge University Press: 101-113.Different kinds of 4-chambered hearts: The lineage leading to crocodiles evolved a four-chambered heart along a different pathway than mammals, keeping both systemic arches.

From Figure 9-5, p. 112 of: Farrell, A. P. (1997). "Evolution of cardiovascular systems: Insights into ontogeny". Development of cardiovascular systems: molecules to organisms. Burggren, W. W. and Keller, B. B., Eds. Cambridge, UK ; New York, NY, USA, Cambridge University Press: 101-113.

The sidebar ["A Heart-to-Heart Connection?"] distinguishing crocodilian hearts from mammalian hearts is a Straw Man fallacy. Biologists do not claim that the crocodilian heart is ancestral to the mammalian heart, nor that the crocodilian heart's four chambers are the same as the mammalian heart's four chambers. For instance, Liem and Walker (2001) explain "Superficially, the mammalian heart resembles those of birds and crocodiles, but the interventricular septum evolved independently and develops embryonically in a slightly different way, so it is not homologous to the interventricular septum of these vertebrates" (Liem, Karel F. and Walker, Warren F. 2001. Functional anatomy of the vertebrates: an evolutionary perspective. Fort Worth, Harcourt College Publishers).

As illustrated in the first figure above (compare hearts C and D of "A detailed view of the heart and aortic arches"), the crocodilian heart is a slight modification of the ancestral reptilian state. So is the mammalian heart, and the bird heart. The bird heart is similar to the crocodilian heart, as Liem and Walker explain: "the ancestors of birds had a heart and pattern of aortic arches similar to that of crocodiles. Because birds evolved endothermy and lungs that are continuously ventilated, shunts bypassing the lungs--as found in crocodiles--would have had no adaptive value. Equal volumes of blood are sent to the lungs and body at all times, which appears to have been simply the result of the loss of the left systemic arch." This hierarchical pattern of similarities is exactly what would be expected from an evolutionary process.

No one portrays the crocodilian heart as an ancestral form of the mammalian heart (or at least Explore Evolution offers no example of anyone making that claim). Either the authors of Explore Evolution are not familiar with the scientific literature on this topic or they are ignoring these studies in their campaign to raise doubts about evolutionary biology.

Lungs

Bird lungs operate quite differently from mammalian lungs, a fact which Explore Evolution treats as mysterious. In fact, ongoing research by paleontologists, anatomists, and other biologists has rendered this diversity of forms readily explicable. As in so much else of the book, interesting biology is ignored in preference for obscurantism and a lesson that students should learn that certain things cannot be known scientifically.

Birds evolved from a group of dinosaurs, and understanding the anatomy of dinosaurs is an important step in understanding bird lungs. Unfortunately, Explore Evolution offers no background in modern paleontological knowledge about dinosaur lungs or the relationship of dinosaurs to birds. A hands-on exercise for students is suggested, but it offers no meaningful insight into the models of lung evolution proposed by any scientists. The views of scientists who are in the fringes of paleontology are presented uncritically, with no comparable (let alone proportionate) coverage of the views of the overwhelming majority of scientists. This chapter misinforms students about how science works, how lungs work, and, as always, how evolution works.

Parabronchi

Summary of problems:

There are detailed, testable models of the evolution of dual-opening parabronchi in bird lungs from single-opening alveoli found in the reptilian ancestors of birds. Explore Evolution asks a number of questions about this transition, but then fails to offer students any means to answer any of them, or to discuss how a student or scientist might go about finding answers to these questions.

Full discussion:

Explore Evolution asks its readers:

What would the intermediate forms between the single openings (in-and-out) reptilian lung and a dual opening (flow through) avian lung look like? How would it happen in small yet advantageous steps? Can there even be a transition between a single-opening and a dual-opening system? How would the balloon-like alveoli transform into the tube-like parabronchi? How would the lung maintain function? Would the lung transformation happen before or after the development of air sacs? Would it be before or after the four stage breathing cycle?
EE, p. 137
Lungs of various amniotes, mapped onto the phylogeny of the respective organisms: Mammals are very distant from birds and neither the mammalian diaphragm nor the alveolar lung is thought to be an ancestral character for the lineage leading to birds.  The crocodile hepatic-piston method of ventilating the lungs (muscles pulling the liver backwards and thereby expanding the chest cavity) is not homologous to the mammalian diaphragm, and neither basal reptiles nor birds have diaphragms, so it is incorrect to claim that it is "almost certain" that dinosaurs had diaphragms.  Perforations (holes) between lung chambers, however, are shared by birds and crocodiles, and thought to be ancestral, so the alleged "topological" problem in producing the bird flow-through lung is imaginary. Sauropods are known to have air sacs from fossil evidence, so air sacs were attached to the lungs of the dinosaurian ancestors of birds for tens of millions of years before theropod dinosaurs and then birds arose.    Phylogeny diagram by Nick Matzke.  Lungs modified from Figure 1, p. 152 of: Perry, Steven F. (1992). "Gas exchange strategies in reptiles and the origin of the avian lung". <cite>Physiological Adaptations in Vertebrates</cite>. Wood, S. C., Weber, R. E., Hargens, A. R. and Millard, R. W., Eds. New York, Marcel Dekker: 149–167.Lungs of various amniotes, mapped onto the phylogeny of the respective organisms: Mammals are very distant from birds and neither the mammalian diaphragm nor the alveolar lung is thought to be an ancestral character for the lineage leading to birds. The crocodile hepatic-piston method of ventilating the lungs (muscles pulling the liver backwards and thereby expanding the chest cavity) is not homologous to the mammalian diaphragm, and neither basal reptiles nor birds have diaphragms, so it is incorrect to claim that it is "almost certain" that dinosaurs had diaphragms. Perforations (holes) between lung chambers, however, are shared by birds and crocodiles, and thought to be ancestral, so the alleged "topological" problem in producing the bird flow-through lung is imaginary. Sauropods are known to have air sacs from fossil evidence, so air sacs were attached to the lungs of the dinosaurian ancestors of birds for tens of millions of years before theropod dinosaurs and then birds arose.

Phylogeny diagram by Nick Matzke. Lungs modified from Figure 1, p. 152 of: Perry, Steven F. (1992). "Gas exchange strategies in reptiles and the origin of the avian lung". Physiological Adaptations in Vertebrates. Wood, S. C., Weber, R. E., Hargens, A. R. and Millard, R. W., Eds. New York, Marcel Dekker: 149–167.
Perry's (1992) model for the origin of bird lungs: Perry's (1992) model for the origin of bird lungs, showing the relationship to the crocodilian lung.  Archosaur and theropod lungs are hypothetical constructs.  Extinct groups are marked with a "+", and perforations between chambers are marked with "*."  Perry proposes that these perforations play a crucial role in the stepwise evolution of the avian parabronchi, as indicated in the detail sketches of theropod and avian-grade lungs.  CrC and CaC are cranial [forward part of the trunk] and caudal [rearward part of the trunk] chambers, which are connected with the respective regions of the intrapulmonary bronchus.  MvB and MdB are avian medioventral bronchi and mediodorsal bronchi, which are proposed to evolve from CrC and CaC, respectively, as indicated by small arrows. From Figure 6, p. 161 of: Perry, Steven F. (1992). "Gas exchange strategies in reptiles and the origin of the avian lung". <cite>Physiological Adaptations in Vertebrates</cite>. Wood, S. C., Weber, R. E., Hargens, A. R. and Millard, R. W., Eds. New York, Marcel Dekker: 149–167.Perry's (1992) model for the origin of bird lungs: Perry's (1992) model for the origin of bird lungs, showing the relationship to the crocodilian lung. Archosaur and theropod lungs are hypothetical constructs. Extinct groups are marked with a "+", and perforations between chambers are marked with "*." Perry proposes that these perforations play a crucial role in the stepwise evolution of the avian parabronchi, as indicated in the detail sketches of theropod and avian-grade lungs. CrC and CaC are cranial [forward part of the trunk] and caudal [rearward part of the trunk] chambers, which are connected with the respective regions of the intrapulmonary bronchus. MvB and MdB are avian medioventral bronchi and mediodorsal bronchi, which are proposed to evolve from CrC and CaC, respectively, as indicated by small arrows. From Figure 6, p. 161 of: Perry, Steven F. (1992). "Gas exchange strategies in reptiles and the origin of the avian lung". Physiological Adaptations in Vertebrates. Wood, S. C., Weber, R. E., Hargens, A. R. and Millard, R. W., Eds. New York, Marcel Dekker: 149–167.

Having asked its audience of high school biology students these detailed questions about evolutionary biology, EE changes topics, without even suggesting the ways that someone might investigate those questions. These students are unlikely to know anything about the anatomy of bird or reptilian lungs, and little if anything about the anatomy of mammalian lungs. They have no experience forming or testing hypotheses about the evolution of anatomical structures, and Explore Evolution offers no references which might fill in that background. The average teacher is likely to be as stymied by these questions as the students. The authors of Explore Evolution seem to be little better informed, and are apparently comfortable leaving students and teachers with no guidance about how to answer the questions posed by the book.

Fortunately, scientists are not so incurious. The figure above demonstrates one set of hypotheses about the evolution of lungs and their anatomy. By considering not just two sets of lungs, but the full spectrum of variation in lung morphology, scientists can reconstruct the likely evolutionary pathways, and evaluate whether those intermediates might be functional.

Scientists like Steven Perry have proposed detailed models of the evolution of the internal lung morphology, models which answer many of the questions Explore Evolution asks. An inquiry-based textbook might describe this model and invite students to develop ways to test it against new data. Instead, Explore Evolution ignores actual research in order to preserve their creationist argument.

Bird diaphragms

Summary of problems:

The claim that air sacs in evolving birds would put a hole in the a diaphragm and lead to a nonfunctional, fatal intermediate, is based on selective quoting of a single sentence from a scientific publication from 1997; the conclusions in that publication are more complicated than one might guess from reading that single out-of-context sentence. Furthermore, Explore Evolution ignores more recent findings that have overturned the idea that the dinosaur ancestors of birds even had diaphragms to damage.

Full discussion:

On p. 137 of Explore Evolution, the authors argue that the radical transformation of the lung from reptilian to avian seems improbable. Part of the argument goes like this.
Finally, what happens to the diaphragm? The reptiles thought to be the ancestors of birds almost certainly had a diaphragm breathing system (footnote 8). According to many evolutionary biologists, changing from a diaphragm lung system to a flow-through lung would require changing and increasing the musculature of the reptile's chest. At the same time, the diaphragm would need to gradually go away. This poses a fundamental problem. Evolutionary biologist John Ruben points out that the earliest stages of this transformation would have required a hole or hernia in the reptile's diaphragm. This would have immediately compromised the entire system and led to certain death for any animal unfortunate enough to possess this non-functioning intermediate structure.
Explore Evolution, p. 137.

Footnote 8 refers to Ruben et al. (1997), Science 278:1268-1269 (actually 1267-1270), and quotes from the article.

8. "Therapod dinosaurs like modern crocodiles, probably possessed a bellows-like septate lung, and that lung was probably ventilated … by a hepatic-piston diaphragm."
John A. Ruben, Terry D. Jones, Nicholas R. Geist, W. Jaap Hillenius, (1997) "Lung structure and ventilation in theropod dinosaurs and early birds," Science 278:1268-1269. Explore Evolution, p. 140, note 8, quoting Ruben, et al. 1997.

Note that "Therapod" is a misspelling of "theropod." Also, the correct page numbers for the article are pages 1267-1270. The authors of Explore Evolution managed to cram about five typos into their short quote of Ruben, et al., so for the sake of correctness, as well as including the ellipsed text and the rest of the sentence, here is the exact quote from the original Science article, which might be enough to trigger a question in the mind of a student in a truly inquiry-based activity.

These observations, combined with the occurrence among theropods of a distinct, relatively vertical, crocodile-like, highly elongate pubis (Figs. 4 and 5), as well as well-developed gastralia, provide evidence that theropod dinosaurs, like modern crocodiles, probably possessed a bellows-like septate lung and that the lung was probably ventilated, at least in part, by a hepatic-piston diaphragm that was powered by diaphragmatic muscles that extended between the pubic bones and liver.

The authors of Explore Evolution have miscast the conclusions. Ruben, et al. are basically arguing that the theropod dinosaurs are not the earliest ancestors of birds. This position was highly unpopular in the scientific community in 1997, and is extremely unpopular now — the number of holdouts against the idea that birds are descended from theropod dinosaurs can be counted on one hand. In the 1997 Science paper, Ruben, et al. argued that there is a logical problem with an intermediate form between purported ancestors (theropod dinosaurs, which allegedly possessed hepatic-piston diaphragms) and modern birds. But they also argued that theropod lung physiology was not consistent with endothermy [warm-bloodedness], a character that might be important in creatures (like birds and their ancestors) which are capable of flight. Here is the meat of Ruben, et al.'s conclusion section:

Recently, conventional wisdom has held that birds are direct descendants of theropod dinosaurs. However, the apparently steadfast maintenance of hepatic-piston diaphragmatic lung ventilation in theropods throughout the Mesozoic poses fundamental problems for such a relationship. The earliest stages in the derivation of the avian abdominal air sac system from a diaphragm-ventilating ancestor would have necessitated selection for a diaphragmatic hernia in taxa transitional between theropods and birds. Such a debilitating condition would have immediately compromised the entire pulmonary ventilatory apparatus and seems unlikely to have been of any selective advantage.

In other words, Ruben, et al. are not saying that this poses an insurmountable obstacle for any theory that postulates evolution of the bird lung. They are merely saying that this logic, as well as the arguments against endothermy in putative ancestors, argues against the specific theropod-bird ancestral connection. Birds (with their unique lungs and high oxygen requirements) must, by this logic, be descended from other ancestors. And even that conclusion generated almost immediate controversy. In November of 1998 three critiques of this paper, along with a rebuttal by Ruben, et al., appeared in Science (281(5373):45-48). Interestingly, these focused primarily on the conclusions about endothermy, rather than on the idiosyncratic diaphragm anatomy issue highlighted by the authors of Explore Evolution. Evidence has continued to accumulate against Ruben, et al.'s claim that theropod dinosaurs had diaphragms (see below).

Finally, since 1997 many spectacular fossils (both of birds and dinosaurs thought to be ancestral to birds) have been discovered, but none of these more recent findings are discussed in Explore Evolution, even though many of them (e.g. O'Connor & Claessens, 2005. Nature 436 (7048): 253-256) provide evidence that further argues against the conclusions of the 1997 paper of Ruben, et al.

Dinosaur diaphragms

Summary of problems:

The dinosaur ancestors of birds probably did not have diaphragms. The one researcher cited to oppose this view also rejects the evidence that birds evolved from dinosaurs; his views on both topics have been widely refuted.

Full discussion:

Paleontologist Matt Wedel explains:

Non-avian dinosaurs did not necessarily have the same pulmonary anatomy as crocodilians or extant birds. As hypotheses of pulmonary anatomy in dinosaurs, "croc lungs" versus "bird lungs" is a false dichotomy. It is more informative to identify the derived features that non-avian dinosaurs share with their extant relatives, and to determine the hierarchical distribution of these characters in archosaurian phylogeny.
Wedel, Matt (2007) Postcranial pneumaticity in dinosaurs and the origin of the avian lung, Ph.D. dissertation, University of California, Berkeley, p. 112.

That is exactly the approach that evolutionary biologists and textbooks about evolutionary biology take in addressing the evolution of organisms and particular parts of organisms. An inquiry-based textbook could include exercises allowing students to undertake the same process of investigation. Explore Evolution does not use this comparative approach, and discourages students from further investigation in areas of ongoing biological research, or even areas where the research has already been conducted.

By comparing fossils of dinosaurs to modern birds, it is possible for paleontologists to produce and test hypotheses about the evolution of the dinosaur lung. Wedel describes his approach:

Instead of focusing on particular [traits] that are either not present in all birds (large sternum, uncinate processes of the ribs) or not clearly necessary for air sac ventilation (ossified rather than cartilaginous sternal ribs), it may be more productive to identify the skeletal movements that take place during avian respiration and the effects of these movements on the shape and volume of the thoracic cage, and then to ask whether the skeletons of non-avian dinosaurs were able to produce similar movements.
Wedel (2007), p. 119

He concludes that "the respiratory movements in non-avian dinosaurs would have had a similar effect on the volume of the thorax as those of extant birds. … there is no basis for inferring that non-avian dinosaurs could not have ventilated an air sac system, based simply on the absence of some avian features" (pp. 120-121).

Wedel's analysis of the fossils shows that a functional intermediate could have existed without the need for the full suite of avian (bird-like) adaptations. Those adaptations may improve the efficiency of bird breathing, but their absence would not be fatal, despite Explore Evolution's claims. Explore Evolution misrepresents evolution as a linear path from reptilian anatomy to avian anatomy, and considers it problematic if a straight line cannot be drawn from ancestral to modern conditions. This is not how evolution works.

As to the particular issue of a diaphragm in the common ancestor of birds and dinosaurs, paleontologists are skeptical. The paleontological evidence used by Ruben to support the claim that the ancestors of dinosaurs had a diaphragm is weak at best. He takes the coloration of rock within a fossil to reflect the location of the liver in the living organism, and then suggests that a liver in that position requires the sort of diaphragmatic breathing found in crocodiles. Even if he were correct that the color in the rock originated in the liver, and if that liver hadn't shifted as the organism decayed, it would still not support his final claim, since living birds have livers in exactly the same position, and do not have diaphragms (see discussion in Wedel, 2007, p. 128).

While crocodilians do breath using a diaphragm, many reptiles do not use a diaphragm, and neither do the amphibians which are ancestral to reptiles, mammals, dinosaurs and birds. By examining the full range of paleontological evidence, scientists can reconstruct probable anatomies not seen in modern species, but which would provide the sort of functional intermediates which evolutionary theory predicts should exist. By contrast, Explore Evolution and the sources it cites take an "approach to inferring soft tissue anatomy, function, behavior and physiology [which] tends to force extinct animals into the reduced spectrum of animals available to us today, without considering substantial evidence of mosaic change in related extinct forms. It lacks an evolutionary component, produces only conundrums, and explains very little" (Kevin Padian and John R. Horner. 2002. "Typology versus transformation in the origin of birds," Trends in Ecology and Evolution, 17(3):120-124).

Transitional Forms

The precise meaning of an evolutionary transition can confuse students. As NCSE's Louise Mead notes: "A common misconception of evolutionary biology is that it involves a search for 'missing links' in the history of life. Relying on this misconception, antievolutionists present the supposed absence of transitional forms from the fossil record as evidence against evolution." This is the precise strategy employed throughout Explore Evolution.

In this chapter, Explore Evolution obscures the scientific knowledge behind certain significant transitions in the history of mammals, birds, and reptiles. Rather than presenting students with a clear background on the underlying biology, and the fossil evidence we have in hand, the chapter presents every instance of ambiguity or uncertainty in our knowledge as an insurmountable problem for evolution, and indeed for science. Along the way, the book makes trivial errors regarding the biology of mammalian and reptile reproduction, obscures fascinating and well-established science about the evolution of lactation and live-birth in mammals, and how fossilized bones can tell us about the soft tissues of ancient animals.

Intermediates between modern forms

Summary of problems:

Modern species and fossil evidence all give us insight into evolutionary history, and of the sequence of evolutionary changes leading from the common ancestors of modern species to the modern forms.

Full discussion:

Explore Evolution is flatly wrong to tell students "all we can say for sure is that the internal organs of living reptiles, living birds, and living mammals are very different from one another" (p. 139). We can say a good deal more than that, and it is irresponsible to so grossly misinform students. To justify the claim that there is not "much fossil evidence of the internal organs of any 'intermediates,'" they cite a 30 year old paper which provides no empirical justification of its claim. Even if the argument were true 30 years ago, it is decisively not true now.

The claim that "all we can say" is that various living species "are very different from one another" is laughably wrong. It is equivalent to saying that we know nothing about a classroom of students except that all people are different from one another. Everyone certainly differs, and it is definitional that all species are different. But science does not stop with a simple statement that differences exist. What differences (and what similarities) exist? What are the patterns of similarity and difference?

Biologists ask those sorts of questions, and evolution provides a framework for suggesting testable hypotheses to answer them. The variation among living species helps to show what anatomical structures can persist, and what forms might have existed as intermediate stages in the evolution of other living forms. The evolutionary branching process gives us testable hypotheses also about the connections between structures, so that we can make testable predictions about parts of a fossilized organism which weren't preserved. In that way, fossils can tell us much more than just what came first. They allow us to test predictions about what life was like millions of years ago, and how different modern forms came to be.

Few other parts of Explore Evolution are so clear in their contradiction of the book's stated aim of "inquiry-based learning." This passage actively discourages inquiry into the connections between living things, their fossil ancestors, and the processes influencing the evolution of life today and in the past.

Fossils of live birth

Summary of problems with claim:

Fossils are not the only evidence that mammals have a common ancestor with reptiles, and living transitional forms exist illustrating the evolution of the organ systems they cite as examples.

Full discussion:

Explore Evolution acknowledges the evidence of fossilized forms transitional between reptiles and mammals, but asserts that:

critics say that the superficial resemblance between skeletons is not all there is to the story. Transforming a reptile into a mammal would involve more than simply changing some bones along the way. It would also involve major changes in organs and organ systems. … Transforming the reproductive system, for example, is not just a question of changing where the eggs grow. It also requires the development of completely new organs like the placenta and mammary glands.
EE, pp. 129-130

This argument repeats a claim by creationist Duane Gish (Evolution? The Fossils Say No!, 1972) and, more recently, the "godfather of intelligent design," Phillip E. Johnson:

We may concede Gould's narrow point [about transitional fossils for the mammalian skull], but his more general claim that the mammal-reptile transition is thereby established is another matter. Creatures have existed with skull bone structure intermediate between that of reptiles and mammals, and so the transition with respect to this feature is possible. On the other hand, there are many important features by which mammals differ from reptiles besides the jaw and ear bones, including the all-important reproductive systems.
Phillip E. Johnson (1991) Darwin On Trial. Regnery Gateway, Washington, D.C.

It is particularly noteworthy that the authors of Explore Evolution did not even bother correcting the erroneous terminology used by Johnson. Modern evolutionary biologists have found that modern mammals and modern reptiles share a common ancestor, and that ancestral group of organisms is referred to as the amniotes (a reference to a set of membranes found in the eggs of all members of this group, but not in the eggs of amphibians or fish). Johnson's reference to the ancestors of mammals as "reptiles" reflected the accepted usage of his time, but EE's usage of the same term 16 years later does not reflect current scientific thinking. The claim that no transitional forms exist for the mammalian reproductive system was not accurate in 1991, and is even less accurate now.

While fossils can provide only incomplete information about the form of soft tissue, fossils are not the only evidence available in examining the evolution of such organ systems. If those systems could evolve through a series of viable intermediate steps, we might expect that at least some exemplars of transitional forms would persist today.

In the cases of placentas and lactation, examples of transitional forms are not difficult to find. Most mammals, for instance, have distinct nipples which the young use to drink milk. Like all mammals, monotremes produce a form of milk. They do not, however, have nipples. Instead, young monotremes suck milk either from fur on the mother's belly, or from lobules in a pouch as with echidnas. The glands which produce milk are morphologically and developmentally very similar to the glands which produce sweat and oil on the skin.

Studies of the anatomy, development and molecular sequences of mammary glands have given scientists clear insights into the evolution of lactation. Mammary glands are similar in many ways to sweat glands and to the glands which produce oil on our skin. One major component of milk — alpha-lactalbumin — is chemically very similar to an immune protein — lysozyme — found in many species. Support for the idea that the gene for this protein was duplicated and then evolved into a nutrient in milk comes from the observation that some monotremes have "a protein which is a structural and functional intermediate between that of lysozyme and alpha-lactalbumin" (V. Hayssen and D. Blackburn, 1985. "alpha-Lactalbumin and the Origins of Lactation." Evolution, 39(5):1147--1149). This observation suggests that lactation originated as a means to prevent unhatched eggs from becoming infected, a testable hypothesis confirmed by various studies. Other authors have suggested that the mammary glands originated as glands which helped prevent eggs from dehydrating, and that the immune aspects of the mammary glands evolved subsequently. For recent reviews, see Vorbach, C., M. R. Capecchi, and J. M. Penninger (2006) "Evolution of the mammary gland from the innate immune system?" BioEssays 28(6):606–616, Oftedahl, Olav (2002) "The Origin of Lactation as a Water Source for Parchment-Shelled Eggs," and "The Mammary Gland and Its Origin During Synapsid Evolution," Journal of Mammary Gland Biology and Neoplasia, Vol. 7, No. 3, pp. 225-266, and Blackburn, D. G., V. Hayssen, and C. J. Murphy (1989) "The origin of lactation and the evolution of milk: A review with new hypotheses." Mammal Review, 19:1–26.

The transition from eggs to live birth (vivipary) can also be traced using evidence from living species. Amphibians and fish lay eggs which require that they be in water to allow oxygen exchange and to prevent the egg from dehydrating. The hard eggs laid by birds and reptiles contain a number of additional membrane layers which allow gas exchange without excessive loss of water; layers shared by mammalian eggs. This innovation allowed the ancestors of mammals, birds and reptiles to move away from the water.

A few mammals still lay eggs. This group, called monotremes, do not supply their eggs with enough yolk to develop fully inside the egg. The embryos hatch from the egg at an early stage in development and suckle from the mother until they are fully developed. In the platypus, they suck milk from a patch of skin through the hairs growing on it. Young echidnas suckle from lobules containing milk glands; a precursor to the nipples found in other groups of mammals.

This system of external gestation is also found in marsupials. The marsupial mother gives birth to live young very early in development, before all the cranial nerves are complete, before the heart is fully developed, and before the lungs have a complete blood supply. These offspring then crawl to a nipple, where they attach themselves and develop until the stage at which they can survive independently.

Instead of the egg and yolk produced by monotremes, marsupials supply food and oxygen to their gestating offspring through a form of placenta. The marsupial placenta is a modified yolk sac, similar to the one produced by monotremes and reptiles, and derived from the yolk found in amphibian eggs. In marsupials, when this yolk sac contacts the wall of the uterus, the uterine wall secretes a nutritive liquid, which the modified yolk sac absorbs. In general, the diffusion from maternal blood supply to the embryo is much less efficient than is found in truly placental mammals. This system is similar to that found in some viviparous reptiles, which secrete a liquid from the walls of the uterus which is absorbed by the developing embryos.

In two families of bandicoots (marsupials), a different arrangement exists, essentially the same as that found in placental mammals like humans, known as eutherians. In this form, the yolk sac does not have direct contact with the uterine wall, but the fetal blood stream and the maternal blood stream pass close to one another. This allows more efficient flow of nutrients and gases through diffusion. In eutherians, hairlike extensions from the placenta increase the surface area, further improving flow of nutrients.

It is not clear why marsupials have such brief internal gestations, rather than carrying offspring internally until they are more fully developed. One important hypothesis suggests that the maternal immune system may attack the fetus after it reaches a certain stage of development, blocking the flow of nutrients and requiring the mother to expel the embryo before it is fully formed. Eutherian mammals have developed a range of adaptations in the placenta which help prevent the maternal immune system from detecting the foreign antigens produced by the fetus.

Thus, we can observe various transitional forms related to the placenta and lactation in living mammals, and can trace their descent from common ancestors using fossils. We can trace a similar evolution in snakes and lizards. Viviparity has evolved over 100 times in reptiles, mostly through eggs simply being held internally with small amounts of water and nutrients passing through the shell. At least 4 of those lineages have evolved a placenta capable of more significant nutrient transfer. (Recently reviewed in Blackburn, D. G., 2006. "Squamate Reptiles as Model Organisms for the Evolution of Viviparity," Herpetological Monographs 20:131–146)

Researchers Michael B. Thompson and Brian K. Speake explain:

Within the Squamata [lizards and snakes], significant placentotrophy [feeding of offspring through the placenta] has evolved only in the lizard family Scincidae [skinks], and within this family there is a range of modes of nutrient provision from lecithotrophy [nutrition via an isolated yolk] through to placentotrophy, with several lineages showing intermediate conditions. Not surprisingly, therefore, skinks have been the major focus for research into the evolution of complex placentae.
Thompson M. B., B. K. Speake (2006) "A review of the evolution of viviparity in lizards: structure, function and physiology of the placenta." Journal of Comparative Physiology. 176:170–189.

Also unsurprisingly, Explore Evolution ignores that research, pretending that the evolution of a placenta occurred only once, and that no evidence exists to explain how it evolved. The reality is far different. The evolution of the placenta is an area under active research, not just within mammals, but within the herpetological community, with several conferences dedicated to new research in the field in the last few years (see, for instance, Volume 20, Issue 6 of Herpetological Monographs, 2006.

Understanding the likely evolutionary trajectory which led to live birth and lactation, we can even detect evidence of these phenomena in fossils. Dr. Olav T. Oftedal argues that the epipubic bones found in marsupials and monotremes probably evolved to support developing young in an external pouch. While the pouch and mammary glands on which those young would have suckled do not fossilize, the epipubic bones do, and can be found in some of the earliest ancestors of mammals (Olav T. Oftedal, 2002. "The Mammary Gland and Its Origin During Synapsid Evolution," Journal of Mammary Gland Biology and Neoplasia, 7(3):225-252). Oftedal also argues that the shift from continuous replacement of teeth (seen in many reptiles) to a single replacement (as seen in most mammals), reflects a physiological constraint which could only be overcome through lactation. Fossils show the shift in tooth replacement occurring around the same time as the emergence of epipubic bones.

A truly inquiry-based textbook might take this and other evidence and invite students to consider what evidence might allow them to test various hypotheses about the evolution of lactation, placentas, and other mammalian traits. Doing so would encourage students to think scientifically, proposing hypotheses and experiments to test them. Instead, Explore Evolution ignores important lines of evidence and instructs the student to give up when biology gets complicated.

Mammal eggs and reptile placentas

Summary of problems:

There are mammals that lay eggs. There are reptiles that have a rudimentary placenta. A May, 2007 errata from the authors corrects only one of the four major errors in these two sentences.

Full discussion:

This is one of the most baffling claims in the entire textbook. Here is the original text from EE:
Reptiles and mammals reproduce very differently. Most reptiles lay eggs, while mammals carry fertilized eggs internally in a placenta and bear live young.
EE, p. 129

An errata sheet, dated May, 2007, came with the first releases of EE. It made a correction to this statement (correction in bold).

Reptiles and mammals reproduce very differently. Most reptiles lay eggs, while mammals carry fertilized eggs internally, which they nourish through a placenta, and bear live young.
EE, errata sheet of May 2007

These two sentences in EE, and the botched correction, provide perhaps the clearest evidence of the distance between the authors of this book and mainstream science, basic biological knowledge, and science pedagogy.

This correction addressed only one of the many things wrong with this statement. Indeed, the uterus (not the placenta) is the organ in which mammals carry their fertilized eggs; the placenta is the source of nourishment for these internally carried young in most mammals. It is gratifying to note that this basic biological fact is now correct in the textbook, but it is actually quite puzzling that such an error could have escaped the attention of even the most cursory reviewer.

Three other errors, however, remain uncorrected. The sentences (1) ignore other reproductive modes of mammals, (2) downplay the rich diversity in reptilian reproduction, and (3) imply the nonexistence of intermediate reproductive modalities.

The marsupial mammals have a rudimentary and short-lived placenta which is, in most marsupials, structurally and functionally different from the typical eutherian placenta. Placental nourishment of marsupial young is negligible compared to nourishment from the milk obtained in the pouch. Furthermore, there are mammals which lay eggs and have no placenta. These creatures, the monotremes, share with other mammals the characteristics of fur and the ability to lactate, but they lay eggs with leathery shells, which the females then incubate in a pouch.

Some reptiles (e.g. garter snakes) are viviparous and develop a rudimentary placenta (see Stewart, JR, American Zoologist 1992 32(2):303-312, "Placental Structure and Nutritional Provision to Embryos in Predominantly Lecithotrophic Viviparous Reptiles" for a not-so-recent discussion of these facts).

It is also quite telling that these variations on reproductive physiology in both reptiles and mammals are more evidence that there are identifiable transitions in form and function among living organisms. In fact the placenta, in all of its variants, is functionally and structurally derived from membranes found in eggs; the transition between reptiles and mammals becomes obvious when all of the data are considered. A "lack of transitional forms", as noted elsewhere in this review, is a standard creationist canard, but in this book transitional forms are lacking only because the authors choose to ignore them.

In fact, the living mammals illustrate a clear transition from egg-laying through various transitional stages along the way to live birth as seen in humans. In monotremes, which consist of the platypus and spiny anteaters called echidnas, the reproductive system is, as James Vaughan explains in his textbook Mammalogy, "a mix, including primitive features shared with amniotes and unique specializations." Monotreme eggs are structurally more similar to reptile and bird eggs than to eggs of other mammals, and have texture similar to reptile eggs as well. Monotremes, like reptiles, have a structure called a cloaca, in which the reproductive, urinary and digestive tracts all exit through a single opening, rather than through two, a trait shared with birds, reptiles and marsupials, but not with the rest of the mammals. It is a small step from laying these sorts of eggs to the marsupial system of briefly holding the developing embryo internally and nursing the partially developed embryo externally, then successively modifying the placental interface between fetus and mother until we see the sort of live birth found in humans, other eutherian mammals, and even a few transitional marsupials.

This sequence illustrates several important errors in Explore Evolution. Clearly, EE badly misrepresents mammalian reproduction. More fundamental, and more widespread, is its tendency to treat a large taxonomic group of species as if they are all practically identical. Species do differ one from another, and in important ways. Those differences are essential to evolutionary processes, and understanding such variation is vital to a student's understanding of evolution. By teaching students that it is acceptable to treat mammals or reptiles or other groups as if all members of the group were interchangeable does students a disservice and misinforms them about the range of adaptations which exist in the natural world, and how the variation among living things reveals evolutionary processes. Only by obscuring legitimate science can Explore Evolution create the false impression that there are unbridgeable gaps between major taxonomic groups; gaps which bolster their preconceptions against common descent.

These three errors — and the original eggs-in-placenta error — could have been avoided if the authors consulted a standard college-level introductory textbook, or if they were familiar with basic biological literature, or even if they had used used basic resources like Wikipedia, Google, or even a smart 5th grader.

Dissent in Science

This final chapter of Explore Evolution makes grandiose, and ultimately untrue, claims about how the process of science works and how the scientific community deals with dissenting views. The errors in this chapter begin with the title. While claiming to discuss dissent within science, it actually centers on a debate between science and nonscience. In muddying the straightforward distinction between the science of evolution and the pseudoscience of creationism, Explore Evolution misleads students not only about evolution, but about how scientific inquiry proceeds. In service of this last effort to confuse students, the authors repeat their misrepresentations of Malcolm Gordon's views, and obfuscate the true nature of an ongoing discussion about the shape of the universal tree of life. In attempting to defend themselves against charges of misrepresenting and misquoting scientists (a section not necessary in most science textbooks), the authors draw an inaccurate analogy between science and courtroom testimony, and them misstate how courtrooms actually work, not to mention accepted standards of scientific discourse.

p. 142: "an evolutionary biologist … disagree[s] with Universal Common Descent."

The example offered in fact argues that there is a single tree of life, which may have multiple roots. As discussed in other chapter critiques, Explore Evolution misrepresents ongoing research into the shape of the early tree of life in order to advance a scientifically baseless creationist claim.

p. 142: "Michael Behe, a … biochemist who is a … critic of the power of the mutation/selection argument"

Behe has resurrected long-discredited creationist arguments and uses his academic credentials to give them a gloss of scientific respectability. Behe is one of the few anti-evolution activists to accept common descent of all life, including humans, but states that a definition of science which would admit his anti-evolution views would also treat astrology as science.

p. 142: "'the creationists' vs. 'the evolutionists,' a familiar and predictable storyline"

Treating creationism as a form of "dissent in science" is inaccurate. Creationism rejects basic scientific principles in pursuit of a religious agenda. Since it is not a scientific enterprise, it does not belong in science class. Just because something is "familiar and predictable" doesn't mean it is wrong, and trivializing this important distinction misinforms students on a basic level.

p. 143: "dissenters are accused of 'misquotation' or 'misrepresentation.' But is this really true?"

Even within this chapter, scientist Malcolm Gordon's words are taken out of context and twisted to misrepresent his views on evolution. This book is filled with such errors, and the defense offered is scant and irrelevant to the charges. Even in court, a witnesses words may not be used without an opportunity for cross-examination and clarification, precisely because the context of a statement does indeed matter.

p. 143: "Practicing science should be about … using all the evidence … whatever its source"

Scientific evidence must possess certain qualities. Other scientists must be able to make the same measurements, and compare their own experiences of the data with other authors. Some valid forms of knowledge do not fit these criteria, including religious beliefs, hunches, intuition, and aesthetic feelings.

p. 143: "By now, we hope you can see that real science as it's actually practiced can be a very lively subject."

Science as it is practiced is indeed a very lively subject, filled with active debates. Explore Evolution manages to avoid or misrepresent the debates actually going on within evolutionary biology while dredging up long-discredited pseudo-scientific attacks.

Major Flaws:

Nature of Science: Dismissing the distinction between scientific understanding of evolution and the religious commitment to creationism as "a familiar and predictable storyline" ignores the important scientific and practical reasons why that distinction matters. Students deserve better than to have the basic definition of science muddled in order to advance the religious agenda of the authors of Explore Evolution. Just because the distinction is familiar and predictable doesn't make it wrong. It does not serve students to muddy the waters regarding how scientists evaluate evidence. Explore Evolution cracks the door to unscientific evidence being raised in science class, misleading students and harming their broader science education as well as their understanding of evolution.

Standards of scientific discourse: Explore Evolution attempts to create an analogy between scientific debate and a courtroom cross-examination. This misrepresents the way scientific debates are settled, as well as misstating the way courtrooms operate. For instance, courts limit the sorts of evidence a jury considers, and requires that witnesses be cross-examined so that biases and misinterpretations can be resolved. Hearsay is inadmissible, but Explore Evolution relies more on quotations from scientists than on the actual data they've obtained. That those quotations are often stripped of important context and misquoted or misrepresented is only one of many errors in the treatment of scientific discourse. In dismissing these accusations, the book again does students a disservice.

Polyphyly and Malcolm Gordon: Explore Evolution claims the scientific community has two fundamentally different views of common descent, the single tree of life (monophyletic) and the orchard of life (polyphyletic). This claim distorts the meaning of a polyphyletic group. Explore Evolution then implies that because there are evolutionists, such as Malcolm Gordon, who question the monophyletic origins of life and of tetrapods, they must also "disagree with universal common descent," and must therefore support the creationist orchard view of life. This is false.

Malcolm Gordon

Malcolm Gordon disbelieves universal common ancestry, and another scientist, Michael Behe, accepts it

Summary of problems:

The claim is being presented as if it indicates the presence of some deep problem within standard evolutionary theory. There is no such problem. The extent of monophyly is a technical issue within evolutionary theory on which there is continuing work and debate. That an intelligent design proponent may accept complete monophyly (although Behe's field of expertise lies elsewhere) while an evolutionary biologist may question it for the very early stages of life (in what he explicitly calls "A Speculative Essay" — see Gordon [1999]) is irrelevant to the question whether descent with modification through natural mechanisms produced the organisms we see on Earth.

Full discussion:

Explore Evolution claims the scientific community has two fundamentally different views of common descent, the single tree of life (monophyletic) and the orchard of life (polyphyletic). This claim distorts the meaning of a polyphyletic group. Explore Evolution then implies that because there are evolutionists, such as Malcolm Gordon, who question the monophyletic origins of life and of tetrapods, they must also "disagree with universal common descent" and therefore support the orchard view of life.

From Explore Evolution:

Scientists who think that history of life is best represented by a single branching tree have what is called a monophyletic view ("mono" means one or single). Scientists who have a polyphyletic view ("poly" means many) think the history of life looks more like an orchard of separate trees.

As part of this tree discussion, we have to make an important distinction between the terms common descent and Universal Common Descent. You may think that these terms mean the same thing. They don’t. As we've just seen, it's possible to think that some organisms share a common ancestor without thinking that all organisms are descended from a single common ancestor.
EE, p10
The Neocreationist orchard: "Figure:4 A polyphyletic (orchard) view: branching within major groups, but no connections between them." EE, p. 10.The Neocreationist orchard: "Figure:4 A polyphyletic (orchard) view: branching within major groups, but no connections between them." EE, p. 10.

Explore Evolution is silent upon whether this orchard of life is composed of 3 trees or a 3 million trees, nor does Explore Evolution offer students any means by which they could make that distinction.

As discussed earlier in the critique of the Explore Evolution's Introduction, this view of polyphyletic trees is fully embraced by creationists. Indeed, there is a small group of Creation-scientists, baraminologists, who hope to find out how many trees, "created kinds" are in their orchard of life.

Taxonomy for baraminologists (biologists/paleontologists/zoologists who study the original created kinds) is one of detecting continuity and discontinuity. While the secular tree of life is essentially monophyletic (having one root), creationists view the tree of life as being polyphyletic (having multiple roots — each root being a created kind, or "baramin"). Thus, we have continuity between created kinds and offspring, and discontinuity between separate created kinds.

This creationist view of polyphyletic group contrasts with its usage in evolutionary biology. According the textbook Evolution (2007) by Barton and colleagues.

It is frequently useful to refer to groups by how they relate to each other on a phylogenetic tree (Figs. 5.3 and 5.4). The simplest grouping is that of a monophyletic group, or clade, which consists of an ancestor and all of its descendants…. In other situations, species are treated as a group because of some shared biological features, even though they do not share a common ancestor to the exclusion of other species. Such a collection of species is a polyphyletic group (derived from many (poly) ancestors; Fig. 5.3) Examples include gliding mammals (made up of species related to both fox and squirrels), gram-negative bacteria (see Fig. 6.2) and algae (see p. 198).
Barton et al., (2007) Evolution, p. 111

Phylogenetic Trees: In each panel, the phylogenetic group is depicted by a green shaded circle.  A) Monophyletic group.  A species (C and D) share a common ancestor (E) not shared by any other  species.  (B) Paraphyletic group.  All species in the group share a common ancestor (F), but some species (D) have been excluded from the group.  (C) Polyphyletic group.  A grouping of lineages each more closely related to other species not in the group than they are two each other. From Barton et al., (2007) <cite>Evolution</cite>, p. 111.Phylogenetic Trees: In each panel, the phylogenetic group is depicted by a green shaded circle. A) Monophyletic group. A species (C and D) share a common ancestor (E) not shared by any other species. (B) Paraphyletic group. All species in the group share a common ancestor (F), but some species (D) have been excluded from the group. (C) Polyphyletic group. A grouping of lineages each more closely related to other species not in the group than they are two each other.

From Barton et al., (2007) Evolution, p. 111.

















To suggest that at least some mainstream evolutionary biologists accept the orchard view, Explore Evolution "quotes" Malcom Gordon, a paleontologist at UCLA who studies fish evolution.

Statement A

"The phenomenom of a monophyletic [single] origin of the universal tree of life probably did not occur. … At the macro-scale life appears to have had many origins."… Statement A was made by Malcolm Gordon, an evolutionary biologist at UCLA … Would you have guessed that an evolutionary biologist would disagree with Universal Common Descent?
EE, p. 142

Would you have guessed that Malcolm Gordon is being misrepresented by Explore Evolution?

The universal tree of life probably had many roots.
M. Gordon et al., (1999) "The Concept of Monophyly: A Speculative Essay," Biology and Philosophy, p. 331

An example of such a tree is shown below.

Modern tree of life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5.  Note that distances are not necessarily to scale in this image.  This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor.  They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.Modern tree of life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5. Note that distances are not necessarily to scale in this image. This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor. They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.

This view of the tree of life with a reticulated network of roots replaces the concept of the last universal common ancestor (LUCA) with the concept of a community of common ancestors who are related to one another via genetic exchanges. Although the reticulated tree of life began as a controversial idea, it is now fully embraced as a plausible evolutionary scenario.

As Barton and colleagues explain in their textbook Evolution (2007):

DNA can be passed from one evolutionary lineage to another, by a process known as lateral gene transfer. … For our purposes, what is important is that lateral gene transfer creates chimeric organisms- organisms in which different parts of the genomes have different histories. … It therefore follows that there cannot be single "Tree of Life". That is, a single tree cannot accurately represent the evolution of life. It may be better to represent species evolution as a reticulated network (eg. Fig 5.23B) with interconnecting branches.
Barton et al., (2007) Evolution, p. 131-132

Scientists can be skeptical about a single universal common ancestor and accept universal common ancestry.

Creationism Versus Science

"'[C]reationists versus evolutionists' [is] a familiar and predictable storyline" that ignores the fascinating details of this scientific debate

Summary of problems with claim:

The proper description would be "creationism versus science" because creationism--whether it be old-fashioned Young Earth creationism or its Intelligent Design descendant--is simply not science. There is no scientific debate about the correctness of evolution, and there can be no scientific debate about ID until the ID creationists produce some science.

Full discussion:

So we end up with the "the creationists" versus the "evolutionists," a familiar and predictable storyline that, sadly, rolls over most of the fascinating (and relevant!) details about what individual scientists may actually think. Would you have guessed that an evolutionary biologist would disagree with Universal Common Descent?
Explore Evolution, p. 142

It is not simply creationists versus evolutionists that is at issue. More accurately, it is creationists, including young earth-creationists, old earth creationists and intelligent design creationists versus modern science. All of these forms of creationism deny a fundamental ground rule of modern science – that science searches for natural explanations for natural phenomena.

The blatant mischaracterization of Malcolm Gordon's views on common ancestry neatly highlights an often used strategy of creationists: In the absence of scientific support, argue by misrepresenting fragments of text.

Misquoting

Are critics of evolution misquoting or quoting out-of-context

Summary of problems:

Scores of scientists have publicly denounced the Discovery Institute for misrepresenting their views by selectively quoting snippets out of context. The Discovery Institute goes farther than quoting scientists out of context; they manipulate quotes in such a way to make the words of these scientists seem to support creationism, much to the chagrin of the cited scientists.

Full discussion:

Another problem arises, when dissenting scientists quote the work of their colleagues, many of whom question certain aspects of neo-Darwinism, or parts of the case for it, while still happily calling themselves "evolutionary biologists" or :neo-Darwinists" … Often, in such cases, dissenters are accused of "misquotation" or "misrepresentation." But is this really true?
Explore Evolution, p. 142-143

Apparently so. Explore Evolution misrepresents Malcolm Gordon's view of the tree of life by claiming that he "would disagree with Universal Common Descent." As discussed earlier, Malcolm Gordon's argument is not with universal common descent, but whether all life descended from a single common ancestor. Explore Evolution achieved the misrepresentation by misquotation, omitting a key sentence, shown in bold below, that explained Gordon’s view.

At the macro-scale life appears to have had many origins. The base of the universal tree of life appears not to have been a single root, but was instead a network of inextricably intertwined multiple branches deriving from many, perhaps 100 or more, genetic sources (Pennisi 1998b).
M. Gordon et al., (1999) "The Concept of Monophyly: A Speculative Essay," Biology and Philosophy, p. 335

Expert Witnesses

Think of them like witnesses at a trial who have to tell the truth on specifics even if this disagrees with their overall view

Summary of problems:

This is exactly what biologists have always been doing. Moreover, witnesses at a trial get to respond to how their words are being (mis)interpreted by a lawyer. Lawyers can object if one tries to put words into witnesses' mouths. The judge and jury get to hear both sides. What follows is that no claim from the Discovery Institute should ever be trusted without an explicit response from any scientist that they (mis)quote or (mis)interpret.

Full discussion:

Any claim that scientists have not been presenting the full empirical evidence about evolution is blatantly false. Whenever there has been any plausible evidence that suggests problems with the received view of evolution, scientists have been excited to investigate them (Sarkar 2007, Chapter 10). In the 1960s scientists were excited about the proposal that most evolutionary changes at the molecular level were "neutral" and not selected for. In the 1980s scientists debated the possibility that evolution consists of small bursts of change followed by long periods of stasis (what Stephen Jay Gould and Niles Eldredge called "punctuated equilibrium"). In the 1990s biologists debated whether bacterial mutations were "directional," that is, more likely to occur in conditions favorable to them than in those that were not.

The overall view of evolution has so far barely been modified to respond to all these challenges and eighty years of new data. Our confidence in the correctness of the models that comprise the theory of evolution is exactly because of the "specifics" of the evidence.

Additionally, there is a strong disanalogy between scientific reasoning and legal reasoning in the Anglo-American context. Though there are plenty of scientific disputes, the scientific method is not in principle adversarial with each side arguing its case to the detriment of the other. Rather, scientific research is investigative and all honest workers have to consider all the evidence. This is exactly what creationists do not practice even when they claim to be concerned with the "specifics."

Debates

Science is about debate

Summary of problems:

Scientists sometimes debate issues. However, no scientists with educational backgrounds in evolution debate the tenets of standard evolutionary biology. No geographers debate whether the world is flat or spherical; no astronomers debate whether or not the Apollo missions went to the moon. Cranks will always be among us; some people even question plate tectonics or Einstein's theory of general relativity (McCausland 1999). However, the presence of a few cranks arguing does not mean there exists a genuine debate among real scientists.

Full discussion:

The authors of Explore Evolution present their anti-evolutionary arguments to students as if they were part of vigorous, ongoing scientific debate about evolution. This debate does not exist in the peer-reviewed scientific literature or at scientific conferences. Even Paul Nelson, an author of Explore Evolution, acknowledges that their anti-evolutionary arguments have failed to persuade the scientific community. During a conference in 2004, titled Intelligent Design and the Future of Science, and hosted at Biola University (formerly the Bible Institute of Los Angeles), Nelson warned:
The current intelligent design debate has been going on for well over a decade, and I think the panelists and probably many of you will agree, it’s locked in a kind of holding pattern. This is not the first time tonight that you heard about molecular machines. Most of you, I think, a healthy percentage of this audience finds that evidence compelling … Yet the scientific community itself is unpersuaded. They’re unpersuaded. And they have two major criticisms of intelligent design and these are intimately related to one another. The first one is that there is no independent evidence for the cause, namely the designer. We don’t have any direct observational access to whatever being built that bacterial motor, if that bacterial motor was in fact designed and built by an intelligence. So, that’s the first one, there’s no independent evidence of the designer and there are no novel results and findings stemming from intelligent design independent of its criticisms of evolution.

Disagreement

Scientists often disagree about how to interpret evidence

Summary of problems with claim:

This claim is true, and this is exactly why the status of standard evolutionary theory is so secure. Scientist are inherently skeptical and actively challenge both new and old ideas. Evolution is a strong theory because it has withstood these challenges.

Full discussion:

Scientists disagree about the extent to which molecular evidence shows that natural selection has been the most important factor in evolutionary history. They disagree about the degree and importance of deviations from monophyly in early evolution. But they agree that descent with modification through natural mechanism is the only explanation of the unity and diversity of life on Earth.

Given, as the authors of Explore Evolution say, that scientists often disagree about how to interpret evidence, the absence of any credible scientific disagreement on the evidence for evolution shows how well-confirmed that theory is. Scientists do disagree about how to interpret evidence--and evolutionary theory has withstood this scrutiny.

References

References

McCausland, I. 1999. “Anomalies in the History of Relativity.” Journal of Scientific Exploration 13: 271 -290.

Sarkar, S. 2007. Doubting Darwin? Creationist Designs on Evolution . Malden, MA: Blackwell Publishing.

Nature of Science

In discussing dissent in science, Explore Evolution continues to misrepresent the nature of science itself. Science is treated as a courtroom trial with scientists serving as "expert witnesses" and students acting as juries, selecting their preferred outcome from several debating advocates. The "Case for"/"Case against" structure of the book is held out as an example of how science works and should work, with disagreeing voices presented without a context of experimentation and hypothesis testing.

Science certainly can be adversarial, but there are rarely only two sides to scientitific disagreements, and no participant in the scientific process should act like a jury – silent and disconnected. Scientific inquiry requires active participation: forming hypotheses, gathering data to test those hypotheses, modifying the hypothesis to reflect new evidence, and discussing (not debating) the meaning of results. Debate implies two fixed sides, with one absolutely right and the other absolutely wrong. Scientific discourse relies on the willingness of all involved to adjust their views as new evidence becomes available. Explore Evolution, by misrepresenting the scientific process, the views of practicing scientists, and the knowledge gained by scientific practice, shows no such willingness.

Is this how science works?

Summary of problems:

Science is about the pursuit of reliable knowledge that offers cogent explanations and testable predictions. Explore Evolution cannot show how real science works, because to do so would expose itself as a slick exercise in manufactured controversy.

Full discussion:

From Explore Evolution:

Practicing science should be about making a vigorous effort to make true statements about the natural world, using all the evidence we have gathered, whatever its source, wherever it leads.
Explore Evolution, p. 143

Scientists rely on evidence which is disprovable and testable. Sometimes that requires setting aside evidence like intuitions, gut feelings, or religious texts.

How does Paul Nelson, an author of Explore Evolution, foresee "using all the evidence" to make "true statements about the natural world"? Through the inclusion of religious scripture, and through intuition and gut feelings:

Within the past decade, the ID community has matured around the insights of UC Berkeley professor Phillip Johnson, whose central insight is that science must be free to seek the truth, wherever it lies. … The possibility of design, therefore, cannot be excluded from science. Under the canopy of design as an empirical possibility, however, any number of particular theories may also be possible, including traditional creationism. Both scientific and scriptural evidence will have to decide the competition between these theories.
P. Nelson (2002) "Life in the Big Tent: Traditional Creationism and the Intelligent Design Community," Christian Research Journal 24,4

Elsewhere, he acknowledged that intelligent design creationism relies on non-scientific standards of evidence:

We don't have … a theory right now, and that's a problem. Without a theory, it's very hard to know where to direct your research focus. Right now, we've got a bag of powerful intuitions, and a handful of notions … but, as yet, no general theory of biological design.
Paul Nelson, quoted in "The Measure of Design," interview with Jed Macosko, Phillip Johnson, William Dembski, Paul A. Nelson, et al., Touchstone July/August, 2004, p. 64-65

This is the spirit animating Explore Evolution, a desire to elevate intuition and faith above science within the science classroom.

Critique Summary

Problems throughout Explore Evolution

  • Social controversy is misidentified as scientific dispute.
  • Basic terminology is misdefined.
  • Scientists are misrepresented.
  • Pedagogical principles are misunderstood.
  • The book's creationist agenda is misleadingly obscured.
  • Research papers are miscited.
  • Government policies are cited inaccurately.
  • Scientists are quoted out of context in a manner that grossly misrepresents their views.

Anatomical Homology

  • Fails to define "homology" (correctly).
  • Fails to explain how modern evolutionary biologists actually use the concept
  • Ignores the fact that the term "homology" has been superseded by clearer concepts.

Molecular Machines

  • repeats erroneous statements and discredited claims about the bacterial flagellum
  • ignores scientific research that has disproven its claims
  • makes claims central to the "intelligent design" movement while avoiding the term "intelligent design"