This dissertation presents an account of the practice of modeling in science in which scientists' perceptual and bodily interactions with external representations take center stage. I argue that modeling is primarily a practice of constructing, manipulating, and analyzing external representations in service of cognitive and epistemic aims of research, and show that this account better captures important aspects of the practice of modeling than accounts currently popular in philosophy of science.
Philosophical accounts of the practice of modeling classify models according to the categories of abstract and concrete entities developed in metaphysics. I argue that this type of account obscures the practice of modeling. In particular, using the analysis of the Lotka-Volterra model as an example, I argue that understanding mathematical models as abstract entities---non-spatiotemporally located, imperceptible entities---obscures the fact that the analysis of the Lotka-Volterra model relies primarily on visual perception of external representations, especially hand- or computer-generated graphs. Instead, I suggest that we apply the concepts of internal and external representations, developed in cognitive science, to models, including mathematical models.
I then present two case studies that illustrate different aspects of modeling, understood as a practice of constructing, manipulating, and analyzing external representations. First, using Sewall Wright's long-term research on isolation by distance, I articulate the relationship between the uses of a model, the particular aims of research, and the criteria of success relevant to a given use of the model. I argue that uses of the same model can shift over the course of scientists' research in response to shifts in aim and that criteria of success for one use of a model can be different from those for another use of the same model. Second, I argue that in successful scientific research, a scientist uses a model according to the methodological principles of realism and instrumentalism despite the tension that they create among the scientist's uses of the model over time. This thesis is supported by a detailed analysis of successful scientific research done by Seymour Benzer in the 1950s and 60s
