Abstract: After describing the difference between methodological and metaphysical naturalism, I distinguish three theistic positions – creationism, deism, and the view that evolutionary theory is true but incomplete because God‟s interventions in nature sometimes supplement the causes that the theory describes. I argue that evolutionary theory is compatible with the third of these positions as well as with the second. I do so by clarifying what biologists mean by saying that mutations are undirected. I then consider three defenses of methodological naturalism ─ that science, by definition, is an enterprise in which claims about supernatural deities are excluded, that claims about the supernatural are untestable, and that including such claims in scientific theories would bring science to a stop. After criticizing these arguments, I provide a more modest defense of methodological naturalism. “ … any confusion between the ideas suggested by science and science itself must be carefully avoided. ” – Jacques Monod, Chance and Necessity, p. xiii.