No, it's not. Don't be alarmed: nobody is claiming that dark matter is supernatural. That's just the provocative title of a blog post by Chris Schoen, asking whether science can address "supernatural" phenomena. I think it can, all terms properly defined. This is an old question, which has come up again in a discussion that includes Russell Blackford, Jerry Coyne, John Pieret, and Massimo Pigliucci. (There is some actual discussion in between the name-calling.) Part of the impetus for the discussion is this new paper by Maarten Boudry, Stefaan Blancke, Johan Braeckman for Foundations of Science. There are two issues standing in the way of a utopian ideal of universal agreement: what we mean by "supernatural," and how science works. (Are you surprised?) There is no one perfect definition of "supernatural," but it's at least worth trying to define it before passing judgment. Here's Chris Schoen, commenting on Boudry et. al:

Nowhere do the authors of the paper define just what supernaturalism is supposed to mean. The word is commonly used to indicate that which is not subject to "natural" law, that which is intrinsically concealed from our view, which is not orderly and regular, or otherwise not amenable to observation and quantification.

Very sympathetic to the first sentence. But the second one makes matters worse rather than better. It's a list of four things: a) not subject to natural law, b) intrinsically concealed from our view, c) not orderly and regular, and d) not amenable to observation and quantification. These are very different things, and it's far from clear that the best starting point is to group them together. In particular, b) and d) point to the difficulty in observing the supernatural, while a) and c) point to its lawless character. These properties seem quite independent to me. Rather that declare once and for all what the best definition of "supernatural" is, we can try to distinguish between at least three possibilities:

The silent: things that have absolutely no effect on anything that happens in the world. The hidden: things that affect the world only indirectly, without being immediately observable themselves. The lawless: things that affect the world in ways that are observable (directly or otherwise), but not subject to the regularities of natural law.

There may be some difficulty involved in figuring out which category something fits, but once we've done so it shouldn't be so hard to agree on how to deal with it. If something is in the first category, having absolutely no effect on anything that happens in the world, I would suggest that the right strategy is simply to ignore it. Concepts like that are not scientifically meaningful. But they're not really meaningful on any other level, either. To say that something has absolutely no effect on how the world works is an extremely strong characterization, one that removes the concept from the realm of interestingness. But there aren't many such concepts. Say you believe in an omnipotent and perfect God, one whose perfection involves being timeless and not intervening in the world. Do you also think that there could be a universe exactly like ours, except that this God does not exist? If so, I can't see any way in which the idea is meaningful. But if not, then your idea of God does affect the world -- it allows it to exist. In that case, it's really in the next category. That would be things that affect the world, but only indirectly. This is where the dark matter comparison comes in, which I don't think is especially helpful. Here's Schoen again:

We presume that dark matter --if it exists--is lawful and not in the least bit capricious. In other words, it is--if it exists--a "natural" phenomena. But we can presently make absolutely no statements about it whatsoever, except through the effect it (putatively) has on ordinary matter. Whatever it is made of, and however it interacts with the rest of the material world is purely speculative, an untestable hypothesis (given our present knowledge). Our failure to confirm it with science is not unnerving.

I would have thought that this line of reasoning supports the contention that unobservable things do fall unproblematically within the purview of science, but Chris seems to be concluding the opposite, unless I'm misunderstanding. There's no question that dark matter is part of science. It's a hypothetical substance that obeys rules, from which we can make predictions that can be tested, and so on. Something doesn't have to be directly observable to be part of science -- it only has to have definite and testable implications for things that are observable. (Quarks are just the most obvious example.) Dark matter is unambiguously amenable to scientific investigation, and if some purportedly supernatural concept has similar implications for observations we do make, it would be subject to science just as well. It's the final category, things that don't obey natural laws, where we really have to think carefully about how science works. Let's imagine that there really were some sort of miraculous component to existence, some influence that directly affected the world we observe without being subject to rigid laws of behavior. How would science deal with that? The right way to answer this question is to ask how actual scientists would deal with that, rather than decide ahead of time what is and is not "science" and then apply this definition to some new phenomenon. If life on Earth included regular visits from angels, or miraculous cures as the result of prayer, scientists would certainly try to understand it using the best ideas they could come up with. To be sure, their initial ideas would involve perfectly "natural" explanations of the traditional scientific type. And if the examples of purported supernatural activity were sufficiently rare and poorly documented (as they are in the real world), the scientists would provisionally conclude that there was insufficient reason to abandon the laws of nature. What we think of as lawful, "natural" explanations are certainly simpler -- they involve fewer metaphysical categories, and better-behaved ones at that -- and correspondingly preferred, all things being equal, to supernatural ones. But that doesn't mean that the evidence could never, in principle, be sufficient to overcome this preference. Theory choice in science is typically a matter of competing comprehensive pictures, not dealing with phenomena on a case-by-case basis. There is a presumption in favor of simple explanation; but there is also a presumption in favor of fitting the data. In the real world, there is data favoring the claim that Jesus rose from the dead: it takes the form of the written descriptions in the New Testament. Most scientists judge that this data is simply unreliable or mistaken, because it's easier to imagine that non-eyewitness-testimony in two-thousand-year-old documents is inaccurate that to imagine that there was a dramatic violation of the laws of physics and biology. But if this kind of thing happened all the time, the situation would be dramatically different; the burden on the "unreliable data" explanation would become harder and harder to bear, until the preference would be in favor of a theory where people really did rise from the dead. There is a perfectly good question of whether science could ever conclude that the best explanation was one that involved fundamentally lawless behavior. The data in favor of such a conclusion would have to be extremely compelling, for the reasons previously stated, but I don't see why it couldn't happen. Science is very pragmatic, as the origin of quantum mechanics vividly demonstrates. Over the course of a couple decades, physicists (as a community) were willing to give up on extremely cherished ideas of the clockwork predictability inherent in the Newtonian universe, and agree on the probabilistic nature of quantum mechanics. That's what fit the data. Similarly, if the best explanation scientists could come up with for some set of observations necessarily involved a lawless supernatural component, that's what they would do. There would inevitably be some latter-day curmudgeonly Einstein figure who refused to believe that God ignored the rules of his own game of dice, but the debate would hinge on what provided the best explanation, not a priori claims about what is and is not science. One might offer the objection that, in this view of science, we might end up getting things wrong. What if there truly are lawless supernatural actions in the world, but they appear only very rarely? In that case science would conclude (as it does) that they're most likely not supernatural at all, but simply examples of unreliable data. How can we guard against that error? We can't, with complete confidence. There are many ways we could be wrong -- we could be being taunted by a powerful and mischievous demon, or we and our memories could have randomly fluctuated into existence from thermal equilibrium, etc. Science tries to come up with the best explanations based on things we observe, and that strategy has great empirical success, but it's not absolutely guaranteed. It's just the best we can do.