“What if we could keep in mind that methodological naturalism is merely methodological, and so refrain from confusing it with philosophical naturalism? …Surely the more central methods of science-calculating, measuring, observing- are in some sense religiously and philosophically neutral. After all, we all-believer and unbeliever alike- see that heavy objects fall and that we need to divide both sides of the equation by the same thing…
This suggestion is appealing. Nevertheless, the very act of doing science- of expecting to understand nature at all- depends on whether God exists or not.
…The real point is that the very practice of science can only be explained, or only makes sense, if nature is rational. To put it differently, the practice of science implies that nature is inherently rational.
…And the world, contrary to Stenger’s claim-must be rational in some sense. At the very least, there must be some sort of rational “fit” between the world and our cognitive faculties. If they were wholly different from one another, there would be no reason to think that our methods would give us reliable results. Not just any old universe will allow for science.
The possibility of science-why the methods of science work- will be accounted for in different ways, depending on whether you think God exists. Methodological naturalism alone cannot account for the reliability of our scientific methods.
But maybe scientists like Stenger can practice science without worrying about why their practice is successful. That is, maybe that can still do science according to methodological naturalism. And so methodological naturalism may still be a fine practical rule.
But Plantinga points out ways in which our beliefs about God affect our actual scientific theories, how they affect what goes on inside science. There are, he says, ways in which scientists fail to follow methodological naturalism in practice…Plantinga points out that when scientists declare that humans and other organisms are merely accidents, they aren’t making a scientific declaration but a philosophical or theological one (at least if we think of scientists as having to adhere to methodological naturalism). They’re making inferences that follow from scientific findings plus theological or philosophical premises. And typically one of theses premises is, “God doesn’t exist.”
Notice therefore that not everything scientists include in their theories conforms to methodological naturalism. Science cares whether or not God exists- even if some scientists do not. God makes a difference.”
(Stokes, A Shot of Faith to the Head, 133-36)