Current discussions of the concept of homology center on metaphysical and epistemological issues: what are homologs, and how can they be discovered? Homology is the relation of common ancestry shared by homologs. Homologs are the "same" parts of two or more organisms under every variation of form or function that are shared due to inheritance from a common ancestor. Homology is the key to phylogeny reconstruction, because the hierarchy of homologs/ homologies is isomorphic with the phylogenetic hierarchy of taxa. Consequently, the discussion of homologs as evolving entities shares many parallels with the discussion of species evolution. Homologs are conceptualized as tokens of natural kinds that engage in causal processes of ontogeny, phylogeny, and physiology. Operational criteria for the discovery of homology are the topological relations (connectivity) shared by homologs. These operational criteria are (at least to some degree) grounded in ontogeny, where developmental modules may share the relation of homology. In that sense, the operational criteria for the discovery of homology are aligned with the structure of the causal processes in which the homologs qua tokens of natural kinds engage. The discussion of concepts of partial homology and the complementarity of static (taxic, hierarchical) versus dynamic (developmental, transformational) approaches to homology reveals empirical as well as a semantic components.
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