In relatively recent years, quite a number of diverse case studies concerning the use of visual displays—such as graphs, diagrams, tables, pictures, drawings, etc.—in both the physical and biological sciences have been offered in the literature of the history and philosophy of science —see, e.g., Miller 1984; Lynch and Woolgar 1990; Baigrie 1996; Pauwels 2006. These case studies have shown that visual representations fulfill important functions in both the theoretical and experimental practices of science, thereby emphasizing the non-verbal dimension of (...) scientific inquiry that had been neglected by the traditional language-based conception of science, which takes the production, justification and... (shrink)

Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically their role in biological reasoning. The diagrams we discuss are, in practice, integral and indispensible elements of reasoning from experimental data about the cell division cycle to mathematical models of the cycle’s molecular mechanisms. In accordance with prior analyses, the diagrams provide functional explanations of the cell cycle and (...) facilitate the construction of mathematical models of the cell cycle. But, extending beyond those analyses, we show how diagrams facilitate the construction of mathematical models, and we argue that the diagrams permit nomological explanations of the cell cycle. We further argue that what makes diagrams integral and indispensible for explanation and model construction is their nature as locality aids: they group together information that is to be used together in a way that sentential representations do not. (shrink)

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. (shrink)