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