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.

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.

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.

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.

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;

The Origins of Species

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.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.

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.

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.

Transitional Fossils

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 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. 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.

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.    

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.

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.

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'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 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 WikiCommons

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:

• Kevin Padian's testimony on whale evolution in Kitzmiller v. Dover
• The whale evolution pages of researchers Hans Thewissen and Philip Gingerich
• The Origin of Whales and the Power of Independent Evidence
• PBS Whale Evolution video

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. 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.

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. 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.

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 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" 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.

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.

Faculty members of the University of San Francisco Biology Department)

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.

CSC Fellows

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.

Interview with Paul K. Chien, The Real Issue, March/April 1997

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:

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.

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.

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 relationships

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) 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

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.

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.

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]

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

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.

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 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.

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.

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.

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.

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.

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:

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

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.

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.

Alan Gishlick (2001) Icons of Evolution? Why Much of What Jonathan Wells Writes about Evolution is Wrong, National Center for Science Education: Oakland, CA. 64 p.

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.

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.

Homology 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.

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?

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:

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.

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. 3.5

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):675-680

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, 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.

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. 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.

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).

Do Different Genes Mean Different Phylogenetic Trees?

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 14:177-178

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)

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.

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.

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; 2:49-58

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.

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.

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

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.

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

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.

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.

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.

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 HaeckelIllustrations 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

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 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.