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.

Many other flaws are built on that ancestral error. The book uses an example from differences in the developmental pathways in insect species 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.

Additionally, 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.

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.

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. That error is also on display when EE presents the erroneous creationist canard of claiming that homology is circular. The supposed circularity is simply a reflection of the authors' inaccurate presentation of the concept they are writing about.

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 Evolution further belies the book's claim to be inquiry-based. Its erroneous treatment of homology belies any claim that it accurately explores evolution.