I. Introduction. Philosophical discussions of models and modeling in the biological sciences have exploded in the last few decades. Given that there are three-dimensional models of DNA in molecular genetics, individual-based computer simulations in population ecology, statistical models in paleontology, diffusion models in population genetics, and remnant models in taxonomy, we clearly should have a philosophical account of such models and their relation to the world. In this essay, I provide a critical survey of the accounts of models provided by philosophers of science and philosophers of biology including models as analogies, relational structures, partially independent representations, and material objects. However, there is much, much more work to be done.
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Steven French (2011). Shifting to Structures in Physics and Biology: A Prophylactic for Promiscuous Realism. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 42 (2):164-173.

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