I. Definitions and Presuppositions
Before I start critiquing the propositions, I want to set forth very brief and minimal descriptions of the way I define the important terms used in this paper - this will set forth in plain sight most of the core presuppositions upon which the points I make in this paper depends.
First, I take methodological naturalism to be the practice of adhering to the kind of methodology a metaphysical naturalist devoted to fulfilling the aims of science would adhere to. Methodological supernaturalism, correspondingly, is the practice of adhering to the kind of methodology a metaphysical supernaturalist devoted to fulfilling the aims of science would adhere to. Astute readers will note that these two categories are not altogether mutually exclusive - a point which will resurface later on in the paper.
Second, I take science to be an enterprise that endeavors (1) to uncover as many phenomena present in the universe as possible, and (2) to provide for those phenomena explanations that correspond with what really exists "out there." It should be clear from this that this paper presupposes a scientific realist interpretation of the goals of science, which I will not attempt to argue for here. I will leave it to others to determine how other interpretations of the objectives of science might affect the arguments I make (my suspicion, however, is that they will not have a significant effect).
Third, I take the supernatural to designate the standard things like gods, fairies, ghosts, necromancy, divination, and so forth, all of which are united by the fact that they exploit materials or processes the basis of which extends or derives from beyond the physical universe. It is worth noting that the word "supernatural" is not, contra Strahler, analytically the same thing as "beyond the domain of science" - to equate the two, one must show that anything that exploits or results from transcendent materials or processes is beyond the domain of science, which is not a simple matter of definition.
II. Can Methodological Naturalism Say Anything About the Supernatural?
Proposition 1 expresses the standard view of the scientific community that methodological naturalism renders science and the supernatural entirely isolated from one another. Science presumably can say nothing at all about the supernatural, whether positive or negative. Even if supernatural forces are constantly at play around us, methodological naturalism would presumably forbid scientists from ever acknowledging them. In this section, I will argue that this view is false - trivially in that methodological naturalism can falsify supernatural hypotheses, and not so trivially in that methodological naturalism can also confirm supernatural hypotheses.
At this point, it would be a good idea to try to explicate the nature of methodological naturalism a little more thoroughly. I have claimed that methodological naturalism is the practice of adhering to the kind of methodology a metaphysical naturalist would employ if he wanted to fulfill the basic aims of science. Recall also that I take the basic aims of science to be the uncovering of phenomena in the universe, and the attempt to provide for those phenomena explanations that correspond to the way the universe actually is. So how would a metaphysical naturalist try to fulfill these aims? By doing exactly what practing scientists currently do: he would use emprical observation as a means of discovering things about the world, and would attempt to provide plausible naturalistic explanations for the things he observes.
Now at first glance, this may seem to entirely destroy my project - if the methodological naturalist must attempt to provide naturalistic explanations for the things he observes, then doesn't that automatically bar him from even considering the possibility of a supernaturalistic explanation, much less accepting it as the most plausible one? I would argue that, initial appearances to the contrary, methodological naturalism does not rule out any explanation a priori. To see why this is, let us recall that methodological naturalism is defined by the way a metaphysical naturalist trying to advance science would act. I think it is relatively clear that such a person would have to be a fallibilist with respect to even his metaphysical beliefs; remember that he wants to be as sure as he can that his explanations correspond to the way the world really is. Since he does not have all possible data, he cannot be sure that there is not some kind of evidence for the supernatural out there, so he would not want to trap himself in a routine that would ignore even blatant evidence for the supernatural in favor of a less plausible naturalistic hypothesis. The metaphysical naturalist who wishes to fulfill the aims of science cannot rule out the possibility that his metaphysical views may eventually be shown to be wrong - hence, he must be open to some degree to supernatural explanations. However, this degree is likely to be a very slight one, which is what gives methodological naturalism its naturalistic flavor - the methodological naturalist, in acting like a metaphysical naturalist devoted to science, will, while being open to the slight possibility of evidence for the supernatural, consider naturalistic hypotheses on average more parsimonious than supernaturalistic ones, and hence will give them more benefit of doubt. In short, his methodological commitments can tell him to examine all possible naturalistic explanations for a phenomenon first, and can assign higher prima facie probabilities to such explanations on average, but the least plausible naturalistic explanation will tend to have a lower prima facie probability than the most plausible supernaturalistic explanation.
Let me try to illustrate this with a few examples:
Let's imagine that instead of the scientific data we currently have, that we have uncovered the following facts: (1) every stratum of rock contains exactly the same fossils at every level, even in the very lowest strata; no species is represented in the fossil record that is not alive today; and no evidence of intermediates between any two taxa shows up anywhere; (2) radioisotope dating shows that every stratum of rock in the earth, and every piece of rock in the solar system has the same age - namely, about a few thousand years; (3) every species - even anatomically similar ones living in the same region - possesses genetic material composed of radically different chemicals and relying upon vastly different coding systems. This is the kind of scenario scientific creationists probably dream about, and rightfully so - what kind of naturalistic explanation would explain such data as elegantly as a supernatural creation hypothesis? A methodological naturalist faced with such data would, I think, end up having to choose between something along the lines of a supernatural creation hypothesis and the naturalistic hypothesis that the atoms in the universe configured themselves into their current form through a massive thermodynamic fluctuation. In the face of such a dilemma, I don't think a methodological naturalist would have any misgivings about choosing the supernatural explanation. Add to all of this data the sudden appearance of the glowing word "God" in the sky over every populated area, and I think even Strahler would accept a supernatural explanation without fearing that he is destroying science.
This, of course, was a toungue-in-cheek example designed to show the in principle possibility of methodological naturalism confirming a supernatural hypothesis. In reality the universe does not show such blatant, unambiguous signs of creation, which is why scientists currently judge naturalistic explanations to be prima facie more parsimonious on average. But it is not beyond the realm of possibility that this might change - there are still some areas left where supernaturalistic explanations may ultimately turn out to be more plausible than naturalistic ones. I believe cosmology is good example of such a area - currently, our best cosmological theories seem to contain a number of ad hoc constants that are stuck in various places to make a fit with the data. If, after many decades of reasearch, no naturalistic explanation as to why those unlikely constants - providing the exact conditions necessary for a universe with life in it - are there instead of others can be formulated, I believe the idea of supernatural creation will begin to seem more and more plausible as time goes by. This is not to say that I believe this is how things will end in actuality - quite the contrary in fact - but I think I have to conceed the possibility that they might end up that way, and methodological naturalism will not serve as a barrier to it. The same kind of scenarios can be drawn up for other currently troublesome areas of research, such as origin-of-life studies.
Of course, if naturalistic methodology can lead to the confirmation of supernaturalistic hypotheses, it can also lead to the falsification of supernaturalistic hypotheses. In fact, this is what has appened to a number of models offered by scientific creationists. Far from being unfalsifiable, the hypothesis that the earth was created 6,000 years ago by a supernatural entity has been falsified by the discovery of so much data that points to the old age of the earth. Likewise, the notion that a supernatural being directly created every "kind" seperately is given the lie by excellent transitional sequences. This is, I think, trivial, but there seems to be a lot of confusion about it, because scientists often assert that hypotheses like these creation models are unfalsifiable. However, such assertions on their part are themselves a bit confused - I think what scientists mean when they label hypotheses like special creationism unfalsifiable, is to draw attention to the fact that proponents of supernaturalistic hypotheses frequently fail to admit any data that disconfirms their hypotheses, and hence act unscientific themselves. But it is perfectly clear that a large number of hypotheses that appeal to the supernatural make sufficient emprical predictions to be falsified.