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? 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.