Abstract
The initial surprise generated by the discovery of sequence-similar regulatory genes patterning the anterior/posterior axes of flies and mice has passed. Statements regarding the evolutionary implications of comparative developmental genetic data are now commonplace in the literature. However, despite the continued generation of developmental data, and citation of these data in reference to evolutionary issues, it is less than clear that there has been adequate integration of the developmental and evolutionary disciplines. This is most evident in the language and examples chosen by developmental biologists when they turn to evolutionary themes. Here one finds frequent recourse to transcendentalism and typology. Thus, developmental workers seem to still hold Darwinism, with its unseemly aspects of natural selection, and the complexly branched evolutionary tree, at arm's length. Here, we examine some uses of typology and transcendentalism that pass for evolutionary analyses and apply phylogenetic methods to developmental genetic data. In particular, we use character tracing in phylogeny and gene trees of conserved homeobox regulators to examine the homology of hearts and eyes and the "inversion of the dorsoventral axis", topics of current interest in our rapidly increasing understanding of the evolution of metazoan development.