I have been working through Barbara Forrest's essay "Methodological Naturalism and Philosophical Naturalism: Clarifying the Connections." In this she argues on the one hand that there is a difference between methodological naturalism and philosophical (or metaphysical naturalism). However, the supernatural, if it is real, is not knowable by humans in any systematic, intelligent fashion. Therefore, we must proceed naturalistically if we are to get to know the world around us at all, and this gives us a powerful reason to accept naturalism metaphysically, while leaving open the bare logical possibility that naturalism is false.
The tricky part, however, is getting an account of naturalism that doesn't simply presuppose a conception of the natural. Natural, you know, just whatever ain't supernatural. And you know what supernatural is, right? It's anything having to do with God, that they talk about in church and stuff.
She starts of with a quote from Kurtz:
First, naturalism is committed to a methodological principle within the context of scientific inquiry; i.e., all hypotheses and events are to be explained and tested by reference to natural causes and events. To introduce a supernatural or transcendental cause within science is to depart from naturalistic explanations. On this ground, to invoke an intelligent designer or creator is inadmissible....
There is a second meaning of naturalism, which is as a generalized description of the universe. According to the naturalists, nature is best accounted for by reference to material principles, i.e., by mass and energy and physical-chemical properties as encountered in diverse contexts of inquiry. This is a non-reductive naturalism, for although nature is physical-chemical at root, we need to deal with natural processes on various levels of observation and complexity: electrons and molecules, cells and organisms, flowers and trees, psychological cognition and perception, social institutions, and culture....
OK let's work with these definitions for a minute. The first of these definitions assumes that we know what a natural cause is. Surely, we say, God must be supernatural. But must he? If you are enunciating a principle of methodological naturalism, then it is incumbent on you to tell me what it is about the theistic God that would make him not a part of nature. If nature is what is, and there is a mentally driven what is and a non-mentally driven what is, have we really excluded anything?
The other requires that naturalism maintain that the world is at root physical. Whatever is real either is physical or supervenes on the physical. But now we have to define what "physical" means, and here we have the same difficulties as we find for defining "natural."
My dissertation advisor once said that a scientific theory could possibly quantify over God, in which case it would make God physical. But surely, in defining the physical, or the natural, God is precisely the very sort of being you are trying to exclude. Can we define methodological naturalism in any kind of systematic way, such that advocates of intelligent design can't just embrace the principle?