Conclusions

Homology is one of two perennially discussed topics in comparative biology— the other is species. The two discussions show many parallels, as indicated previously: proper names versus general names, individuals versus classes, sets, or kinds. To turn homologs into individuals and anatomical (or molecular) terms into proper names (Grant and Kluge 2004) is patterned on the argument that species are individuals (e.g. Hull 1999). This latter argument has received a lot of attention from evolutionary biologists, who largely missed an important part of its theoretical foundation. In his defense of the argument from a philosophical point of view, Hull (1976 p 179, n. 4) drew attention to the semantic behavior of species names in evolutionary theory, which in his analysis corresponds to the semantic behavior of proper names as "rigid designators'' (Kripke 2002). Such behavior of proper names is tied to a specific theory of reference for proper names, i.e., the "historical,'' "causal,'' or "direct'' theory of reference (Hull 1976 p 179, n. 4; see also Hull 1988). These are all rather technical issues that need not be reviewed here; there is also no need to deliver a verdict on the ontological status of species here. The important point is that authors who want to use—in an evolutionary context—the "names'' that refer to "the same organ in different animals under every variety of form and function'' as proper names will need to worry about those technicalities but have not done so far.

In the present context, homology is conceptualized in terms of natural kind term semantics, and the names associated with natural kinds can be general names or singular terms (Soames 2002). Kripke (2002) himself already expanded his theories to also apply to natural kind terms, such as "tiger'', "water,'' or "gold,'' but as noted by Devitt and Sterelny (1999), the use of such terms — at least in the case of biological natural kinds — at some level involves some descriptive account (for Kripke 2002, a descriptive account may help to fix reference, but does not determine reference, of proper names or natural kind terms). This means that the use of names (associated with natural kind terms) to refer to "the same organ in different animals under every variety of form and function'' must be tied to a conditional phrase that specifies the hierarchical level at which the use of that name gains some cash value in terms of marking out monophyletic groups. This in turn means that phylogeny reconstruction cannot be a matter of mere exten-sionality and ostension (Kluge 2003a, b; Grant and Kluge 2004), but requires a conceptual, i.e., a theoretical framework. There is no immediate access to objective reality, but this only means that careful phylogenetic analysis will require at least an attempt to causally ground hypotheses of homology, proximally in criteria of topology and connectivity, ultimately in the theories of inheritance, development, and evolution.

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