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).