Structure, function, and protein taxonomy

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.

Biochemical Kinds

“…The tools and techniques of biochemistry are accordingly built around structure. This is how I interpret Goodwin's (2011) finding that biochemical classification is 'fundamentally' grounded in structure. As Goodwin writes, "one of the enduring goals of biochemistry has been to explain the function of proteins in terms of their structure" (p. 534).…”

“…Microstructural classification is thus supplemented with biological considerations, when appropriate, to correct these irregularities. Thus Goodwin's (2011) concession: though he wishes biochemical classification to be based on physicochemical structure, biological facts must be accommodated, often ad hoc, by augmenting or supplementing structural classifications. He explains, While there is a fundamental, structural way of individuating proteins, there are also supplemental classifications introduced to address various biological interests.…”

“…William Goodwin (2011) recently argued that the practice of protein taxonomy is 'fundamentally' grounded in structural considerations, which are then adjusted ad hoc as dictated by specific phenomena and scientific interests. Call this position 'pragmatic pluralism' about classificatory practice.…”

Where Do You Get Your Protein? Or: Biochemical Realization

“…The question is, does the case of IUPs differ significantly from the type of moonlighting that was deemed unproblematic for the ontological reductionist? Goodwin ([ 2011 ]) answers in the negative, so does Havstad ([ 2018 ]).…”

“…Philosophers of science have recently taken an interest in biochemical kinds, namely, natural kinds at the intersection of chemistry and biology, such as proteins (for example, Slater [2009] ; Tobin [2010] ; Goodwin [2011] ; Bartol [2016] ; Havstad [2018] ). Proteins are macromolecules, which can be studied from both biological and chemical perspectives.…”