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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.