Via PZ Myers, comes a long and recommendable argument by Sean Carroll on the philosophy of science and how scientific understanding of the world thus far precludes any room for miracles (thus making the religion and science incompatible). Excerpted from the much longer article with interesting things on the philosophy of science which I recommend reading in full, here is his ending discussion of the possibility of the thesis that there are supernatural causes passing into science as a plausible explanation:
Could science, through its strategy of judging hypotheses on the basis of comparison with empirical data, ever move beyond naturalism to conclude that some sort of supernatural influence was a necessary feature of explaining what happens in the world? Sure; why not? If supernatural phenomena really did exist, and really did influence things that happened in the world, science would do its best to figure that out.
It’s true that, given the current state of data and scientific theorizing, the vast preponderance of evidence comes down in favor of understanding the world on purely natural terms. But that’s not to say that the situation could not, at least in principle, change. Science adapts to reality, however it presents itself. At the dawn of the 20th century, it would have been hard to find a more firmly accepted pillar of physics than the principle of determinism: the future can, in principle, be predicted from the present state. The experiments that led us to invent quantum mechanics changed all that. Moving from a theory in which the present uniquely determines the future to one where predictions are necessarily probabilistic in nature is an incredible seismic shift in our deep picture of reality. But science made the switch with impressive rapidity, because that’s what the data demanded. Some stubborn folk tried to recover determinism at a deeper level by inventing more clever theories — which is exactly what they should have done. But (to make a complicated story simple) they didn’t succeed, and scientists learned to deal.
It’s not hard to imagine a similar hypothetical scenario playing itself out for the case of supernatural influences. Scientists do experiments that reveal anomalies that can’t be explained by current theories. (These could be subtle things at a microscopic level, or relatively blatant manifestations of angels with wings and flaming swords.) They struggle to come up with new theories that fit the data within the reigning naturalist paradigm, but they don’t succeed. Eventually, they agree that the most compelling and economical theory is one with two parts: a natural part, based on unyielding rules, with a certain well-defined range of applicability, and a supernatural one, for which no rules can be found.
Of course, that phase of understanding might be a temporary one, depending on the future progress of theory and experiment. That’s perfectly okay; scientific understanding is necessarily tentative. In the mid-19th century, before belief in atoms had caught on among physicists, the laws of thermodynamics were thought to be separate, autonomous rules, in addition to the crisp Newtonian laws governing particles. Eventually, through Maxwell and Boltzmann and the other pioneers of kinetic theory, we learned better, and figured out how thermodynamic behavior could be subsumed into the Newtonian paradigm through statistical mechanics. One of the nice things about science is that it’s hard to predict its future course. Likewise, the need for a supernatural component in the best scientific understanding of the universe might evaporate — or it might not. Science doesn’t assume things from the start; it tries to deal with reality as it presents itself, however that may be.
This is where talk of “methodological naturalism” goes astray. Paul Kurtz defines it as the idea that “all hypotheses and events are to be explained and tested by reference to natural causes and events.” That “explained and tested” is an innocent-looking mistake. Science tests things empirically, which is to say by reference to observable events; but it doesn’t have to explain things as by reference to natural causes and events. Science explains what it sees the best way it can — why would it do otherwise? The important thing is to account for the data in the simplest and most useful way possible.
There’s no obstacle in principle to imagining that the normal progress of science could one day conclude that the invocation of a supernatural component was the best way of understanding the universe. Indeed, this scenario is basically the hope of most proponents of Intelligent Design. The point is not that this couldn’t possibly happen — it’s that it hasn’t happened in our actual world. In the real world, by far the most compelling theoretical framework consistent with the data is one in which everything that happens is perfectly accounted for by natural phenomena. No virgin human births, no coming back after being dead for three days, no afterlife in Heaven, no supernatural tinkering with the course of evolution. You can define “religion” however you like, but you can’t deny the power of science to reach far-reaching conclusions about how reality works.