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Building Simulations from the Ground Up: Modeling and Theory in Systems Biology

Published online by Cambridge University Press:  01 January 2022

Miles MacLeod  and
Nancy J. Nersessian
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Abstract

In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, we analyze the alternative role and meaning theory has in systems biology expressed as canonical template theories like Biochemical Systems Theory.

Type
Research Article
Information
Philosophy of Science , Volume 80 , Issue 4 , October 2013 , pp. 533 - 556
Copyright
Copyright © The Philosophy of Science Association

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Footnotes

†

We appreciate the support of the US National Science Foundation in conducting this research (DRL097394084). We thank the directors and members of the research labs in our investigation for welcoming us into their labs and granting us numerous interviews. We thank the members of our research group for contributing valuable insights, especially Lisa Osbeck, Sanjay Chandrasekharan, and Wendy Newstetter. We thank Sara Green, two anonymous reviewers, and the editor of the journal for helpful comments and advice.

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