The natural is, as Lib said, the universe and everything in it (not just the material but the waves/particles and forces, indeed the spacetime itself - that’s why “materialism” is a little old fashioned compared to my preferred term of physicalism). The universe and everything in it is an entity in an Ockham’s Razor sense.
Now, can the supernatural affect the natural? Let us suppose that it can. It is still the case that all we can observe of the supernatural is the effect is has on the natural. And so the question is Is there any phenomenon which can only be explained by reference to a supernatural cause? Of course, the God of the Gap is largely denied even by believers in the supernatural, and has unfortunately developed into something of a perjorative. I, a physicalist through and through, think that there are gaps in natural explanations in which reasonable people could place God if they so wished. Here are what I consider the “5 current gaps”:
[ul][li]The universe itself. Where did the Big Bang come from? How d’you get something from nothing? What was there before? The natural answer is that all of these questions are a bit skew whiff. Relativity says that the universe is space and time. You can’t have before all of time or next to all of space. You can’t have a time of -1 second because the universe can’t be -1 metre wide. The different states of the universe are the different times, and no cosmologist I know of proposes a state of absolute nothingness. In short, science says that the universe has always existed. There was no creation or nothing-to-something transition, we need only explain its nature, its history, hence the title “A brief history … of time”.[/li]Now, of course there are still gaps. Exciting gaps, in fact. We might live in the 3 dimensional region of the universe: the gravity in regions of two or less is too weak for life, it’s too strong in the four or more dimensional regions, maybe we’re Goldilocks and the three dimensions, just right. Maybe there are other states which could be said to be “before the big bang”, but we might never observe any evidence for them so those explanations might forever be, if you like, protoscientific rather than properly scientific. But the gap seems to be shrinking and changing shape all the time literally year on year, so much so that it seems just like Newton’s 1690’s or Darwin’s 1890’s. Yes there is a gap there, but let’s just see what it looks like in 20 years time. The explanation isn’t full and satisfactory now cos it’s only half baked.
[li]The very first life from non-life: Abiogenesis. Evolution is fine from DNA and single cells onwards, but did it need a divine spark in the first place? Well, there’s a whole new scientific field called astrobiology which looks for basic biological molecules in space. Then there’s what seems to be plausible mechanisms by which those molecules form structures on Earth such as enclosed surfaces like a balloon in which proteins can link up to eventually form RNA and then DNA. Again, is this so big a gap that science will never fill it? If anything, God would probably just be giving a lucky nudge to some process which wasn’t all that unlikely anyway, but again, let’s see, let’s try and do it in the lab, let’s look on other planets (and try not to crash this time), this uncertainty is exciting: how dull to live when it had all been worked out![/li][li]Consciousness: Could we really be said to be a kind of biological computer which processes sensory information and stores it in different kinds of memory, labelled with language and accompanied by some kind of chemical emotion output? Does that really explain this incredible feeling of being me? Well, it explains one hell of a lot. Cognitive science, psychology and neuroscience have decades of experimental results which are predicted and accounted for pretty well by this Computational Theory of Mind. Again there are gaps but again, they’re shrinking all the time and new facts are changing their shape such that God looks like quite an odd piece to put there.[/li][li]The paranormal: Has anything “supernatural” ever happened ever? That’s the million dollar question. Literally. Randi wants a testable demonstration - if I said that my supernatural ability was calling a coin toss correctly 50.00001% of the time he’d tell me to get stuffed, and rightly so. He’s looking for an ability, not something hidden in statistical noise. Nor is he looking for things like unexplained astronomical measurements or paths in a particle accelerator. We know the limits of Relativity Theory - James Randi’s looking for something that would turn Einstein upside down. Of course, nobody’s won the million. Nobody’s even got past the preliminary tests. If there is a gap here, it’s a funny kind of gap which appears and disappears so randomly and inconsistently that we have to ask whether it’s really there at all? [/li][li]Finally, related to the previous two: What about personal, subjective experience of God? Intense epiphanies or near-death experiences or even just personal conviction of a higher significance? Surely here is a gap which science will never fill? Even here, there is natural Polyfilla of a sort. The way the brain works is that parts of the temporal lobes, near your ears, judge the significance of sensory input. Now, what happens when these modules in the temporal lobes go a bit haywire? Temporal lobe epileptics show huge bursts of activity in those modules during a seizure, and they often say they get a strong feeling of divinity or cosmic significance from it. Could it be that there is a natural neuropsychological explanation for those deeply personal experiences? We all have to judge significance somehow, and we all occasionally have little glitches in our significance judgements. They’re called deja vu. Maybe not even this gap will stay open for ever.[/ul][/li]
But even if there is a scientific explanation for everything, even if the gaps all do eventually get filled, that still doesn’t disprove the existence of the metaphysical or supernatural. Even Ockham’s Razor is only a guiding principle, and respected thinkers like Leibniz and Kant even proposed their own anti-razor (“The variety of beings should not rashly be diminished.”)
If proposing supernatural entities exercises your significance-judging modules and thus causes your words and actions to be judged by my modules as “kind” and “good”, that’s surely all that really matters?