I am about to make a point here that I thought of on my own. By that I mean have not yet found specific reference in my reading to the ideas below. But I do not really suppose these are original ideas, though. No doubt serious thinkers have covered this ground in a much more sophisticated way. For all I know my thinking may be quite flawed. So, if anyone can point me to sources that deal with this, I would be grateful.
I assume, for purposes of this discussion, that there is a real universe out there.
According to naturalism, we humans (and all animals) are biological, chemical, what-have-you organisms. There is no ghost in the machine. Moreover, the universe is material. Science stripped of any supernatural claims explains it all. Or at least, it is futile to speculate about or believe in anything that is inherently untestable or inexplicable by naturalistic or scientific means.
If that is so (and I suspect that part of it may be), then there is no reason to suppose that either human sensory perception, or human reason (our biological computing power, one might say) are unlimited vis á vis the universe out there. It would be quite a metaphysical leap to insist that our empirical and reasoning capabilities are unlimited in relation to all phenomena in the universe.
So what? Well, unless I have made an error in reasoning, this means that there may well be phenomena that we could experience, but never make sense of in scientific terms. And, if our sensory apparatus are limited, there may even be actual phenomena that we cannot detect. One response to my claim is, I think, probably related to positivism. Roughly “if we cannot experience it, test it or explain it, it is nonsense”. That’s wrong, at least as regards things we may be unable to explain.
By analogy, what I mean is this. Consider the flatworm. It seems fair to say that the flatworm comes equipped with sensory abilities, and with a brain, that are quite radically different from those of humans. Its nervous and sensory apparatus allow it to deal with certain things. As I recall, if it bumps into an obstacle it (eventually) learns to go around the obstacle. But surely it cannot perceive or meaningfully process all phenomena. I imagine that if we played Beethoven’s Fifth loud enough in the vicinity of a flatworm, the flatworm might, you know, disintegrate. Which I suppose the flatworm would actually experience, if only briefly. But the flatworm probably cannot tell what key the symphony is in. So, the flatworm is affected by the sound of the symphony, but cannot “make sense” of it. And so on.
So, from a naturalistic point of view, maybe we are in the same boat as the flatworm. Perhaps it is quite possible that things happen in the universe that our sensory apparatus cannot record, and to the extent our senses can detect such phenomena, they may be beyond the reach of our brains to understand.
Now, my argument here is a classic case of turning a point of view back on itself. But it does not reveal a paradox. In other words, this argument does not force one to abandon naturalism. What it does (if it is not completely wrong) is to throw into question the boundary between “natural” and “supernatural”. That is, while this implies the possible existence of non-lawful and inexplicable phenomena in the universe, it obviates the need to attribute such phenomena to a Big Bearded Man in the sky. So “miracles” might occur, but they may be nothing more than phenomena beyond the reach of either or both of human perception and human reason. (Of course, my reasoning does not prove that miracles are not the result of divine intervention.)
Maybe science, empiricism, and human reason have limits that we don’t usually like to admit.
None of this is to say that scientists, or anyone else, should be quick to say “that’s a miracle, that’s beyond science”. As I recall (without being able to put my finger on the citation) Popper suggested that science must make a methodological commitment to explaining the universe in terms of comprehensible (to humans) lawful behaviour, even though this may not be entirely justified by evidence or logic. And this is quite a different commitment than the claim that “if it’s not scientific it’s not happening”.