Philosophy can shed light on mathematical modeling and the juxtaposition of modeling and empirical data. This paper explores three philosophical traditions of the structure of scientific theory—Syntactic, Semantic, and Pragmatic—to show that each illuminates mathematical modeling. The Pragmatic View identifies four critical functions of mathematical modeling: (1) unification of both models and data, (2) model fitting to data, (3) mechanism identification accounting for observation, and (4) prediction of future observations. Such facets are explored using a recent exchange between two groups (...) of mathematical modelers in plant biology. Scientific debate can arise from different modeling philosophies. (shrink)

There are at least twelve major virtues of good theories: evidential accuracy, causal adequacy, explanatory depth, internal consistency, internal coherence, universal coherence, beauty, simplicity, unification, durability, fruitfulness, and applicability. These virtues are best classified into four classes: evidential, coherential, aesthetic, and diachronic. Each virtue class contains at least three virtues that sequentially follow a repeating pattern of progressive disclosure and expansion. Systematizing the theoretical virtues in this manner clarifies each virtue and suggests how they might have a coordinated and cumulative (...) role in theory formation and evaluation across the disciplines—with allowance for discipline specific modification. An informal and flexible logic of theory choice is in the making here. Evidential accuracy, according to my systematization, is not a largely isolated trait of good theories, as some have made it out to be. Rather, it bears multifaceted relationships, constituting significant epistemic entanglements, with other theoretical virtues. (shrink)