Why Methodological Naturalism Is Dumb
Certainly it makes sense for scientists to focus on secondary causes [i.e. not God]… [s]uch scientific investigation is legitimate.
But methodological naturalism means more. It says that scientists are supposed to assume the uniformity of natural law and that they exclude “supernatural” or “preternatural” influences. This kind of recipe has coherent meaning if we already know what is “natural.” We have to know (1) what the laws are (thereby specifying what is in accord with “nature”), (2) that there are no exceptions, and (3) that everything in principle is determined by law.
But we know none of these things.
—Vern Poythress, Chance and the Sovereignty of God (Crossway, 2014), p. 129.