Abstract
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.
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Notes
Mechanistic explanations "account for the behavior of a system in terms of the functions performed by its parts and the interactions between these parts" by identifying the "parts and their organization, showing how the behavior of the machine is a consequence of the parts and their organization" (Bechtel and Richardson 2010: 17). Functional explanations involve "analyzing a disposition d of a [system] a into a number of other dispositions d1 … dn, had by a or components of a such that programmed manifestations of the di results in or amounts to a manifestation of d," where a programmed manifestation is one that "could be specified in a program or a flow chart" (Cummins 1975: 759). Piccinini and Craver (forthcoming) maintain that functional explanations are incomplete mechanistic explanations by virtue of omitting structural aspects regarding the location, shape, orientation, and organization of a system's components; Bechtel and Richardson, that elements of mechanistic explanations include elements of functional ones (2010: 89–90).
These models are, in turn, the basis for formulating and testing hypotheses about the biological mechanisms that regulate the cell cycle. The diagrams also can be used to summarize published data. Through peer review, these summaries can be considered to be firmly established. However, in most cases the models involve uncertainty, so that the diagrams can be considered to be encodings of hypotheses. In such cases, the mathematical models also encode hypotheses, and computational simulation experiments with the model can be brought into agreement (or disagreement) with experimental data in order to validate the hypotheses through the diagram, in combination with mathematical modeling and computational simulation. Further discussing these issues would take us beyond the scope of this paper.
But see our previous footnote.
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Acknowledgments
We thank Laura Perini, Thomas Millat, Anuradha Chauhan, and Justin Barnard for helpful comments on earlier versions of this paper.
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Jones, N., Wolkenhauer, O. Diagrams as locality aids for explanation and model construction in cell biology. Biol Philos 27, 705–721 (2012). https://doi.org/10.1007/s10539-012-9311-9
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DOI: https://doi.org/10.1007/s10539-012-9311-9