If interesting, I have discussed the topic of methodological naturalism at length elsewhere. I have noticed that there are two slightly different aspects that need to be careful he clarified to make sure that people are not talking past each other. Otherwise, there seems to be some unintentional equivocation that happens in the discussions.
Specifically, the term “natural” can mean to somewhat different things in these discussions… it can mean:
A. “Natural” as opposed to “supernatural”
-or-
B. “Natural”, as opposed to “fabricated”, I.e., as opposed to having been constructed by intelligent purpose.
So, Consider your cell phone: do we call that a “natural phenomenon”? In sense “A” yes, of course, absolutely. There is nothing supernatural about it. It is made of atoms and molecules, and is as much a part of this natural order of things as a tree or an asteroid.
But in sense “B”, no, a cell phone is not a “naturally” occurring object. Apples occur naturally, fish, rain, solar radiation, very small rocks, these are all “natural” objects. A cell phone, by contrast, is an artificial, or designed, or “man-made” object. In that sense, it is not part of “nature”
What happens in these discussions, someone says that science, following methodological naturalism, says “science must only study what is part of nature.” And if we mean nature in sense “A”, i entirely agree. We can’t see angels in telescopes, we can’t examine miraculous forces in a Particle accelerator, etc. and thus science has no business, in itself, in saying “God did this.”
But the determination that something is or isn’t “natural” in sense “B” is very much part of science. As I’ve written in these pages before, archaeology, forensics, computer science, cryptology, and SETI are all predicated on the fact that science, as science, can and should in fact distinguish between “naturally occurring” phenomena and that which has occurred by design. So long as the scientist makes no theological determinations in his paper, and in his scientific paper he limits himself to saying no further than “X is naturally occurring” or “X does not occur naturally, but it exhibits the hallmarks of design,” then this absolutely is within the realm of science.
If interesting, I discussed at length (and even added pictures!) here…