similarities in the expression patterns of homologous genes are sometimes used to argue for the homology of the structures in which those genes are expressed, but the genes might well have existed before the higher level structures came on the scene. As long as genes can change their functions over evolutionary time, this possibility is not easily dismissed. Even complex networks of interacting genes are, as Jarvis and colleagues argue in Chapter 4, capable of becoming involved in the assembly of novel structures. If similar changes in function occur independently in multiple lineages, then the structures would be nonhomologous, even though the underlying genes are homologous. In such cases, one might say that the structures are “deeply homologous” but “superficially nonhomologous,” although this terminology is likely to engender confusion.
Analogous challenges arise in comparative neuroethological studies. One can certainly homologize behaviors, be they swimming in snails or math skills in primates, but those behavioral homologies offer only loose predictions about the homology or nonhomology of the underlying neuronal circuits. If neurons can change their behavioral functions over evolutionary time, then homologous behaviors may involve nonhomologous neurons, and nonhomologous behaviors can involve at least a few homologous neurons. This point has been made before by various authors (Striedter and Northcutt, 1991), but it continues to befuddle the unsuspecting mind. As mentioned earlier, the task of understanding how the tangled bank of molecules, cells, structures, organisms, and behaviors has managed to transform itself in evolutionary time has only just begun. Still, as this volume aims to show, some progress has been made, especially if we compare our current state of knowledge with the knowledge in Darwin’s time.