Macromolecular Pluralism

Abstract

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

Biochemical Kinds

“…Standard physico-chemical classification leads us to say that we have one protein, but intuitions about biological function lead us to conclude otherwise. These intuitions come out when Slater (2009) insists that protein kind classifications preserve 'important biochemical facts' about the molecules, something that structural definitions fail to do. Though the chemical facts are presumably explained, many functional (often physiological) ones are not.…”

“…Functional classification, though tempting, will not suffice. Not only are there well-rehearsed difficulties with functional individuation (Slater (2009) rehearses some of these with regard to proteins), the functional flexibility of molecular structures, the multiple realization of biological functions, and the evolutionary contingency of function suggests that function is an accidental property of molecules, not an essential property of any kinds. Instead, I suggest conceiving of biological kinds as historical kinds.…”

“…But philosophers have long-strained to find any such notion. Slater (2009) has already shown how difficult it is to find the function for a given protein molecule. Which of many actions and interactions we take to be the function is a matter of explanatory context.…”

“…On its own, Goodwin's account privileges no particular interpretation. Two other recent papers, by Matt Slater (2009) and Emma Tobin (2010), also call for pragmatic pluralisms but invite metaphysical conclusions along side epistemic ones. Slater and Tobin's descriptions point toward a highly permissive brand of pluralism.…”

Structure, function, and protein taxonomy

“…In their work on biochemical classification, both Slater (2009) and Tobin (2010) focus on proteins. This is a good choice because not only are proteins the workhorses of the cell, but their basic structure is well-understood.…”