Summary of problems with claim:
Similarities in developmental pathways are one of several criteria scientists use for "homology." Presenting it as the sole criterion is incorrect.
As noted elsewhere, the authors of Explore Evolution first create a "strawman" in generating their "Case For". Specifically, for anatomical homology, the authors draw the following conclusion: two different animals can be said to have "homologous structures because they were built by homologous genes" through "developmental pathways" that are homologous (p. 41). To add support to their conclusion, the authors quote two "neo-Darwinian biologists" Alfred Romer and Thomas Parsons who believed "[T]he identity between homologues is based upon the identity or similarity of the developmental properties [and] hereditary units, the genes" (EE, p. 41). The source cited is a textbook originally published in 1949, with the latest edition published in 1977. Biologists understanding of genes and development has advanced dramatically in the past 30 years, and it is irresponsible of the authors to rest their discussion on such an outdated source.
Closer examination of the "Case For" reveals many problems with assuming the above conclusion. Darwin did not know about genes and developmental pathways. Darwin s theory of common descent and thoughts regarding homologous structures make no predictions about what we expect to find at the developmental and genetic level. Numerous evolutionary biologists have addressed this assumption. Wagner (1988) stated that there is no simple congruence between anatomical characters and genotypes and hypothesized that only those features of the developmental system that cause a restriction in the possible phenotypic consequences of genetic variation (i.e., developmental constraints) are important. Even de Beer (1951), quoted by the EE authors as a critic of anatomical homology, believed that "the homology of phenotypes does not imply the similarity of genotypes".
Certainly, similarity in developmental control can be helpful in establishing structures as homologous (similar in structure and position as the result of common ancestry). Development, however, is far more complex than the EE authors would have their readers believe.
Developmental plasticity plays a major role in our modern understanding of biology and evolution. Processes such as the change in timing or location of developmental events may lead to changes in size and shape, and may alter the relationship between a developmental pathway and morphology without altering homologous relationships. In general, variations in the expression of a gene (late versus early, prolonged versus brief, constant vs. intermittent, spatially contiguous vs. discrete locales) can influence developmental and phenotypic outcomes.
Mindell and Meyer (2001) point out that reticulate (lateral) evolution and the dissociation among traits at different hierarchies (e.g. genes, morphology, development) can result in genes having complicated histories. Orthology, paralogy, and xenology all describe similarities between genes that arise from processes of organismal lineage splitting, gene duplication, and horizontal transfer of genetic material, respectively. The dissociation of traits can result in the co-option of genes for different functions. For instance, Mindell and Meyer (2001) hypothesize a dissociation has occurred between the developmental mechanisms and the digit primordia in the avian hand. In theropods, developmental mechanisms acted on primordia 1-3, whereas the same mechanisms act on primordia 2-4 in birds. Mindell and Meyer (2001) argue this might explain why the digits do not appear to be phylogenetically homologous in theropod dinosaurs and birds, in conflict with many other characters that suggest they are sister taxa.
The issue is not whether homologous structures exist, but why developmental and genetic processes inadequately account for homology. The authors of Explore Evolution want you to believe that the lack of correspondence between some phenotypic structures hypothesized to be homologous and genetic\developmental pathways underlying these structures is evidence against common ancestry. Recent scientific research in evolutionary developmental biology (evo-devo) is providing data in support of other, more parsimonious, and even wondrous, explanations, as well as proposals of new terms such as homocracy, to describe organs/structures which are organized through the expression of identical patterning genes. Hence, many homologous structures are in all probability homocratic, whereas only a small number of homocratic structures are homologous. And while intuitively one might expect that the historical continuity of morphological characters should be underpinned by the continuity of the genes that govern the development of these characters, Wagner (2007) points out that things are not that simple. Instead, regulatory networks of co-adapted transcription factor genes may be more important in orchestrating the development of homologous characters.
In a major work synthesizing developmental biology and its effects on evolution, Mary Jane West-Eberhard lists various major criteria which have been used to propose homologous relationships. These include "similarity in position and structural detail"; "presence of connecting intermediates or transitional forms, including in ontogeny [development]"; "similarity in development, taken to mean shared developmental pathways, shared developmental constraints, or evoked by the same stimuli"; "lack of conjunction, or lack of coexistence in a single organism"; or "genetic similarity" (M. J. West-Eberhard, 2003, Developmental Plasticity and Evolutionary Biology, Oxford University Press:Oxford, p. 489 of 794, references and quotation marks omitted).
Any of these criteria can be applied in a given situation, depending on the information available and the interests of the researcher. West-Eberhard observes:
As pointed out by Donoghue (1992) "The choice of a [specialized] definition is, at least in part, a means of forcing other scientists to pay closer attention to whatever one thinks is most important" (p. 174). It also invites endless argument over what the "correct" definition should be. The choice of criteria is partly a pragmatic matter. The most powerful procedure is to recognize that there are numerous criteria, and given the difficulty of tracing homologies, as many as possible should be used.Mary Jane West-Eberhard (2003) Developmental Plasticity and Evolutionary Biology, Oxford University Press:Oxford, p. 489 of 794, and quote from Donoghue (1992), "Homology" in Keywords in Evolutionary Biology, E. F. Keller and E. A. Lloyd (eds.). Harvard University Press: Cambridge, MA, pp. 170-179.
These criteria are the ground for initially proposing homology, but are not the final step. The scientific process rests on repeated inquiry and testing, using new lines of evidence to test the evolutionary history of a lineage, and to understand the detailed history of a particular structure. Developmental pathways are one line of evidence examined, but are not the only basis for identifying homology, nor for testing a hypothesis of homology. Explore Evolution fails here by misleading students about the way scientists assess homology and by misrepresenting the scientific method of proposing and testing hypotheses.