Anatomical Homology

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

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

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

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

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

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

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

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

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

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

Major flaws:

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

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

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

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

Defining "homology"

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

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

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

Homology and similarity

Summary of problems:

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

Full discussion:

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

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

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

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

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

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

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

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

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

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

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

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

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

Homologous structures, genes, and developmental pathways

Summary of problems with claim:

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

Full discussion:

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

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

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

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

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

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

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

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

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

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

Circular definitions

Summary of problems:

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

Full discussion:

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

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

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

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

Wells writes:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Convergence

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

Common function vs. common ancestry

Summary of problems:

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

Full discussion:

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

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

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

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

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

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

Vertebrate limbs

Summary of problems:

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

Full discussion:

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

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

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

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

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

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

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

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

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

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

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

Similarity of shape vs. similarity of form

Summary of problems:

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

Full discussion:

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

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

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

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

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

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

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

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

Convergence vs. natural selection

Summary of problems:

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

Full discussion:

Explore Evolution says the following about convergence:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Convergence and common descent

Summary of problems with claim:

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

Full discussion:

Explore Evolution claims:

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

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

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

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

Development

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

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

Primer

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Homology via different genes or developmental pathways

Summary of problems with claim:

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

Full discussion:

Explore Evolution claims:

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

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

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

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

In brief:

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

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

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

Non-homology via homologous genes

Summary of problems with claim:

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

Full discussion:

Explore Evolution presents this example:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Misquoting

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

Brian Goodwin

Summary of problems:

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

Full discussion:

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

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

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

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

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

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

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

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

David Wake

Summary of problems with claim:

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

Full discussion:

From Exploring Evolution:

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

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

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

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

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

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

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

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

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

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