Roffé, Ariel. Dynamic Homology and Circularity in Cladistic Analysis. Biology and Philosophy. (forthcoming).
In this article, I examine the issue of the alleged circularity in the determination of homologies within cladistic analysis. More specifically, I focus on the claims made by the proponents of the dynamic homology approach, regarding the distinction (sometimes made in the literature) between primary and secondary homology. This distinction is sometimes invoked to dissolve the circularity issue, by upholding that characters in a cladistic data matrix have to be only primarily homologous, and thus can be determined independently of phylogenetic hypotheses, by using the classical Owenian criteria (for morphological characters) or via multiple sequence alignment (for sequence data). However, since in the dynamic approach, sequence data can be analyzed without being pre-aligned, proponents have claimed that the distinction between primary and secondary homology has no place within cladistics. I will argue that this is not the case, since cladistic practice within the dynamic framework does presuppose primary homology statements at a higher level.
Keywords: Homology, Circularity, Cladistics, Dynamic Homology, Multiple Sequence Alignment, Direct Optimization