On Homology and the Ontological Relationship of Parts

Recent literature suggests that a phylogenetic orientation may lead to unique perspectives on homology. An analysis of absence of avian hind limb flexors is used to explore this perspective. This approach suggests that synapomorphy is not equivalent to homology but rather that synapomorphies are hypotheses of homology (otherwise phylogenetic analysis is tautological). Homologies should be viewed as relationships among historical individuals, and we can only discover interorganismic homologies by phylogenetic analysis. Intraorganismic homologies, however, must be studied by other methods, primarily ontogenetic ones. Viewing homologies as (1) genetically and developmentally individualized entities or (2) sets of historical individuals may not always be particularly helpful from an operational perspective, but this is irrelevant because homologies are real entities that must be discovered, yet the process by which they are sought, as in all science, is one that does not yield truths, only hypotheses.