Biology and Philosophy, forthcoming 2007.

I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function (...) to abstract away from variation and pathology to form a canonical description of a class of biological systems. (shrink)

The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization in the (...) context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes. (shrink)

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme (...) of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology. (shrink)

: According to Kuhn, theory choice is not governed by algorithms, but by values, which influence yet do not determine theory choice. Cladistic hypotheses, however, seem to be evaluated relative to a parsimony algorithm, which asserts that the best phylogenetic hypothesis is the one that requires the fewest character changes. While this seems to be an unequivocal evaluative rule, it is not. The application of the parsimony principle is ultimately indeterminate because the choice and individuation of characters that figure in (...) parsimony computations are indeterminate. The cladistic approach is Kuhnian because the application of parsimony depends on persuasion, background, training and tradition. (shrink)

I examine an argument that has recently appeared in the cognitive science literature in favor of thinking that the mind is mostly composed of Fodorian-type cognitive modules; an argument that concludes that a mind that is massively composed of classical cognitive mechanisms that are cognitively modular is more evolvable than a mind that is not cognitively modular, since a cognitive mechanism that is cognitively modular is likely to be biologically modular, and biologically modular characters are more evolvable. I argue that (...) the notion of cognitive modularity needed to make this argument plausible will have to be understood in terms of the biological notion of variational independence, as follows: a cognitive feature is cognitively modular only if few or no other morphological changes are significantly correlated with variations of that feature arising in members of the relevant population as a result of ontogeny. I also argue that most of the connotations contained in a cluster of notions of classical cognitive modularity are, as far as we know, irrelevant to the argument, and that only the presence of selective impairments—also known as cognitive dissociations—can be considered as strong indicators of the type of modularity that genuinely enhances evolvability. (shrink)