 Identifying and coding characters is certainly a biological problem, but it is a philosophical one as well. On what basis can we judge that one character is homologous to another? Debates on this extend back to the very beginning of contemporary biology, e.g., Richard Owen’s influential pre-Darwinian notion of homologue to Ernst Haeckel working to develop accounts of homology in the context of Darwinian evolution. In the mid-twentieth century, the pheneticists argued that character identification must be “theory-free” and advocated using raw similarity as a guide to identifying homology (Sokal &amp; Sneath 1963; Sneath &amp; Sokal 1973). There are well known philosophical and biological problems with trying to use similarity in this way (e.g., Goodman 1972), many of which were raised as objections to strict pheneticism during the Systematics Wars (e.g., Mayr 1965b; Neff 1986; Rieppel &amp; Kearney 2002 though see Lewens 2012 for a recent defense of pheneticism in a contemporary context).