“According to methodological naturalism, scientists may not refer to God in their scientific theories. Any description or explanation must be naturalistic.
Methodological naturalism is methodological for the obvious reasons: it’s a limitation on the method of science, on what science is allowed to do, on what it can look for…But, says methodological naturalism, the method must be naturalistic- science may refer only to natural events and entities. Scientists may not explain natural phenomena with anything outside nature-with anything supernatural.
Of course, methodological naturalism isn’t say that there is no supernatural realm; that’s the position of philosophical naturalism- plain old naturalism. The kinder, gentler methodological version just says that scientists- while wearing their scientist hats- should behave as if plain old naturalism is true. Scientists should pretend there’s no supernatural realm. They should pretend they’re atheists.
“it (methodological naturalism) lulls people into believing in philosophical naturalism. Although we might say that scientists are merely following Newton in this methodological naturalism, many scientists haven’t followed him far enough. They haven’t emulated Newton’s clear understanding that science doesn’t encompass all of reality. Instead, many scientists have shrunk their notion of reality to fit science’s limited reach. If it ain’t science, it ain’t real.
We might call this scientific provincialism, and it has become orthodoxy among secular scientists. Its cause, however, is a confusion of methodological naturalism with philosophical naturalism (with some wishful thinking thrown in). No wonder scientific provincialists think science has shown there’s no God: by definition there is nothing outside nature.
…Yet science itself never claims its domain exhausts reality. Such a proclamation would be an extra-scientific claim, something that, by definition, science isn’t fit to determine in the first place. It’s one thing to mandate the methods of science; it is quite another to say that science is all we need to understand reality. Therefore, scientists who have made this claim have left science far behind.
And so science itself- if we limit it by methodological naturalism, turning it into what we might call naturalistic science- has never shown that there’s no supernatural realm. How could it possibily do that? It has explicitly said that only the natural is within its ken, and so, by its own admission, science could never show there’s no God. Furthermore, even the more meager claim that science has never found evidence for God (whether or not he exists) isn’t newsworthy.”
(Stokes, A Shot of Faith to the Head, 128-129)