Abstract
This paper considers two recent arguments that structure should not be regarded as the fundamental individuating property of proteins. By clarifying both what it might mean for certain properties to play a fundamental role in a classification scheme and the extent to which structure plays such a role in protein classification, I argue that both arguments are unsound. Because of its robustness, its importance in laboratory practice, and its explanatory centrality, primary structure should be regarded as the fundamental distinguishing characteristic of protein taxonomy.
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Notes
Throughout this paper, for simplicity of expression, I will used the terms ‘biochemistry’ and ‘biochemist’ to refer to all of those disciplines, and their corresponding scientists, that investigate the structure and function of proteins.
Though most of Slater’s paper is explicitly about whether we should be monists or pluralists about protein classification, it is also clear that issues of essentialism are central to his thinking. He dismisses the significance of biologists’ talk about protein structure because this talk does not occur “in the context of describing a protein’s essence” (Slater 2009, p. 854); further he challenges the monist to explain why a certain description characterizes “what it is to be a certain kind of protein” (Slater 2009, p. 855).
As suggested by a referee, biologists may well characterize two structurally distinct polypeptides as both being instances of “hemoglobin,” in which case these distinct polypeptides are treated, in some sense, as the same protein. Surface discourse of this type could be regarded as smoothly reconcilable with more fundamental distinctions in the background by simply thinking of “hemoglobin” as the name for a class of proteins, the membership conditions for which include both structural and functional elements (which might vary according to investigative context). This may not be how biologists actually talk, but they might, without any obvious “cost” to the practice. Indeed, if it ever became important to explain why not all hemoglobin behaves the same (why there are several distinct spots on your gel, for instance) it would be natural to refine the use of “hemoglobin” in this way.
If this were enough, then by parity of reasoning the surface discourse of chemists (which Slater seems to accept as a scientific practice which can be interpreted monistically) would also be sufficient to recommend pluralism about chemical classification. As I will discuss in more detail later on, chemists frequently individuate chemicals in ways that are both finer and courser than their chemical structure; however, there can be no doubt (at least from the point of view of the practice) that chemical structure is the fundamental way of individuating chemical species.
Stereochemistry refers to the relative three-dimensional arrangement of atoms in space. For example, though the left and right hands have the same “connectivity”, they differ in their relative three-dimensional arrangement. Similarly, though any two carbon atoms bonded to the same four distinct groups will have the same ‘chemical connectivity’, there are two distinct ways of arranging these groups around the carbon atom; these molecules differ in their stereochemistry.
See Goodwin (2010) for a characterization of the goals and development of structural organic chemistry.
For a more detailed discussion, in a philosophical context, of this subfield of organic chemistry (called “conformational analysis”) see Goodwin (2009).
Slater, too, seems to endorse some such conception of the explanatory role of fundamental classificatory properties. He explains, in the process of rejecting structural monisms, that “[t]his stance presumes, of course, that the individuation of proteins will to a certain extent represent important biochemical facts about them” (Slater 2009, p. 853). Further, he argues against a monism based on primary structure because, “[a]n amino acid sequence alone has no direct link with a protein’s ultimate biological role” (Slater 2009, p. 852). The plausibility of these positions depends on what is meant by a ‘direct link’ and ‘representing important biological facts.’
To attempt to put this in the more formal terms that Tobin favors, one might say that a classification, K, is compatible with microstructuralism so long as the capacities and/or dispositions in virtue of which something is a K are held to be consequences of its microstructure. So classification into functional groups is compatible with microstructuralism because chemicals are held to have their various reactive capacities and dispositions in virtue of their molecular structure. Similarly, the distinction of various conformations is compatible with microstructuralism because the space of conformations, and thus the potential of being in any particular conformation, depends on molecular structure.
Only roughly, though. Some functional proteins include bonds to metal ions, others include disulfide bridges, etc.
After all, it is structure that is supposed to explain function, not the other way around.
Tobin also claims: “Clearly, because the primary structures of some moonlighting proteins are intrinsically disordered, then the structural arrangement of the microstructural parts is insufficient to classify any protein as a member of a macromolecular kind” (Tobin 2010, pp. 52–53). The italicized portion (the italics are mine) makes it seem as if Tobin thinks that IUPs have no fixed primary structure, and this is why they undermine microstructuralism. If this is the argument, then it is based on a misunderstanding of IUPs.
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Goodwin, W. Structure, function, and protein taxonomy. Biol Philos 26, 533–545 (2011). https://doi.org/10.1007/s10539-011-9252-8
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DOI: https://doi.org/10.1007/s10539-011-9252-8