methodological indifference

I’m beginning to wonder if so-called ‘methodological naturalism’ ought to be critiqued on purely philosophical grounds (i.e. not as a sneaky pre-apologetic move).

It seems that many people (against the evidence) are under the impression that ‘science’ supports naturalism (All-is-Nature) more than it supports theism (Nature caused and sustained by Supernature).  But if our scientific observations are to be truly objective, then we must admit that when we look at any particular thing or set of things (or any particular process or set of processes) in what we call the world, we do not find accompanying labels or name-tags that tell us “Made by YHWH” or “Purely Natural: No God Required”.  One must go beyond the evidence (though not leaving it behind!) to make such statements.  The theist knows she is doing this, though she will rightfully claim that she has followed reason in doing so.  The naturalist, however, seems to not often admit that they ‘go beyond the evidence’ to their Naturalism.  Why is this?  Do they think the world screams “not made by any God at all”?  If so, why?

I (in all my lack of importance for both science and the philosophy of science) propose a new term: methodological indifference!