What Counts as "Natural?"

My apologies for the delay in posting, and the rather rambling post.

Jeffrey replied, to my previous post:

Well, if I wanted to play Designer's Advocate for the moment I might say, "In the case of geology, we begin with a well-attested natural principle (the half-lives of certain isotopes) and the conclusion proceeds directly from that principle; in the case of evolution, we begin with a set of brute facts (e.g. certain organisms have certain genes disabled in identical places) and conclusion proceeds from an assumption that these resemblances are a product of common descent rather than design."

In propria persona I'd probably re-reply by saying something like "every scientific theory begins with the assumption that patterns come from natural causes rather than unaccountable, supernatural interventions." Anything you would add?

The only thing I can think of to add is that any cause that could be investigated -- any cause that exhibited discoverable regularities, so that one could test hypotheses about it -- would be, from the standpoint of methodological naturalism, a "natural" cause.  If telepathy, or precognition, or other "psychic" powers could be consistently demonstrated, with their regular abilities and limitations discovered, they would be "natural" even if scientists were, for the moment, at a loss to explain how they worked.  If a testable theory of the Designer's motives, methods, and/or design philosophy could predict the distribution of similarities and differences among living things better than common ancestry could, intelligent design would be not only a real theory, but a "naturalistic" one (if cosmologists can have an "inflation force," why couldn't biologists have a "design force?").

Interestingly, Cornelius Hunter's latest post to his blog tries to raise the obverse of  Jeffrey's question:

The Dover opinion makes the circular assertion that phenomena are natural and so therefore ought to be explained by naturalistic causes. Of course natural phenomena ought to be explained by naturalistic causes, but how do we know if a phenomenon is natural? How do we know that human consciousness arose by strictly natural causes? We don’t, of course.

"Is it natural" and "did it arise from natural causes" are not quite the same question; human consciousness is obviously "natural" by virtue of existing in this world and exhibiting regular, discoverable properties.  It seems to me at least logically possible that the cause of consciousness does not have these properties.  On the other hand, if it doesn't, then what possible means of investigation could uncover facts about the cause, beyond the fact that we start with: we don't (or at least don't fully) understand it?

Hunter concedes that  his version of the Designer is supernatural (no space alien intelligent designers for him!), but it's not clear whether his "supernatural" Designer has to be "God:"

Evolutionists say that any theory that includes supernatural causation is religious. I think this is self-serving. If the empirical evidence points to supernatural causation, then I don't think that conclusion is religious.

This is in the context of an argument that any insistence that God (or a Designer) would almost certainly not design in certain ways (e.g. identically-disabled GULO pseudogenes in separately designed and created primate species) represents an illicit introduction of theology into science.  Now it seems to me that, first, if it's legitimate to introduce God as a scientific explanation, it must be legitimate to include reasoning about God's possible motives.   If the Designer need not be God, conversely, then arguments about his motives is not theological (and if the Designer must be God but introducing Him as an explanation isn't religious, then, again, discussion of the attributes He could reasonably possess isn't religious either).  But certainly humans have a rich history of speculation about and belief in supernatural entities that aren't "God."

But I stand by my earlier assertion: if such entities don't have discoverable, regular, testable properties (at least, behaving in a regular way with observable results), then how is empirical evidence supposed to point to them?  Hunter, it's pretty clear, assumes that if a "supernatural" cause fits in a gap in our knowledge, then we're justified in inferring that the "supernatural" cause is what really occupies the gap.   Actually, he goes further than that: if a "supernatural" cause would do the same job as a known natural cause, it's a purely metaphysical, theological prejudice that prefers the natural to the supernatural explanation.  The first position would have led us, a couple of centuries ago, to attribute lightning not to poorly-understood electrical forces, but to supernatural wrath.  The second would lead us to do so today.