Philosophers of science often assume that logically equivalent theories are theoretically equivalent. I argue that two theses, anti-exceptionalism about logic (which says, roughly, that logic is not a priori, that it is revisable, and that it is not special or set apart from other human inquiry) and logical realism (which says, roughly, that differences in logic reflect genuine metaphysical differences in the world), make trouble for both this commitment and the closely related commitment to theories being closed under logical consequence. (...) I provide three arguments. The first two show that anti-exceptionalism about logic provides an epistemic challenge to both the closure and the equivalence claims; the third shows that logical realism provides a metaphysical challenge to both the closure and the equivalence claims. Along the way, I show that there are important methodological upshots for metaphysicians and philosophers of logic. In particular, there are lessons to be drawn about certain conceptions of naturalism as constraining the possibilities for metaphysics and the philosophy of logic. (shrink)