One way of distinguishing supernaturalism and varying shades of naturalism is to consider them as providing different solutions to the “problem” of our lack of complete knowledge of the world. It is evident that we lack complete knowledge of the physical world, that is to say of “nature”. Why?
The supernaturalist says incomplete knowledge is inevitable because nature has its ultimate source in something which is beyond nature and (more importantly) beyond human knowability. This “beyond” is something immaterial (non-physical) and because of this it is something that lies outside the possibility of empirical knowledge. (There are different versions of supernaturalism which correspond to different claims about the “beyond.”)
Naturalism has to provide an alternate explanation for our lack of complete knowledge of the world, and there are different flavors of naturalism depending on the explanation given. I’ll touch on a few here.
1) Complete knowledge is possible, we just haven’t gotten there yet. This is the position taken by Bertrand Russell in Has Man a Future? Someday, scientists will know everything there is to know about the world – in a few hundred (or thousand) years, our knowledge will be complete. Advocates of naturalism who take this view today are often quick to accuse theists of a “God of the Gaps” fallacy. Sure, there is a lot we don’t know—yet. Give us time.
2) Complete knowledge is possible in theory, but not in practice. This version of naturalism maintains that although there are no theoretical limits to complete empirical knowledge of the world, there are practical limits that will prevent us from ever achieving the goal. Among other things, this means there will always appear to be room for a “God of the Gaps”.
3) Complete knowledge is impossible in both theory and practice. This is because knowing is an inventive process which in principle can be carried on ad infinitum. It is not a process of mining “facts” already embedded in the physical world because, quite simply, that’s not where facts exist (facts are sensations, aspects of animal/human consciousness). We don’t discover knowledge but invent it, and then winnow out what is most useful (i.e. “true”) by adopting point of view invariance (which provides objectivity) and by testing using the scientific method (which provides reliability). The world does not contain facts—we do.
This last version of naturalism maintains a view of knowledge that is far removed from that employed by supernaturalism. As a consequence, it can be difficult for people in one camp to understand the reasoning of those in the other. We live in different worldviews, if not in different worlds.
Supernaturalism assumes that the physical world is inherently knowable in itself, but that human knowledge will always be incomplete because there’s more to the story than just the physical world. My preferred version of naturalism assumes the opposite—that the physical world is inherently unknowable in that sense because it contains no mental substrate—no blueprint. But importantly, this is not so much a claim about the nature of the physical world as it is a claim about the nature of knowing.
Humans evolved with a capability to invent factual knowledge about anything we can detect and distinguish, and in that sense we absolutely do know the world. However, the physical world is other to that knowledge, precisely because knowledge is a simulacrum. The facts we know are experiences in consciousness, and like all aspects of consciousness they are nothing other than sensations we have. The physical world (exclusive of organisms) contains no sensations according to the natural worldview, and therefore contains no facts, no knowledge, no blueprint.
When we know the world, we do not know its nature. We know (at best) a useful model of its nature – thus our knowledge will always be incomplete. This is a consequence of the nature of knowledge—it evolved to be useful. But it is also a consequence of the inherent mismatch between knowledge and the natural world. Whatever the nature of the physical world is, it is not the same as the nature of knowledge, otherwise there would be no such mismatch.
The supernatural worldview paints an entirely different picture of these matters, so much so that it is a colossal struggle to explain the underlying concepts of a natural worldview to theists. Even among like-minded advocates of naturalism there is a great amount of confusion. This can be chalked up, I think, to the fact that we are all struggling to abandon the inapplicable terminology of supernaturalism—struggling even to recognize that it is now inapplicable—so that we may completely enter a natural worldview.
It is that different.