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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.
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."
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.
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.
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.
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).