As a slight diversion from my three part critique of David Bentley Hart’s The Experience of God: Being, Consciousness, Bliss I’d like to make a more general point about philosophical materialism and methodological naturalism and why pace Hart they are not logically absurd positions.
There are good evolutionary reasons why this purely materialist point of view is the quotidian default. At the scales in which biological life can evolve the underlying nature of things is invisible and insensible. Even at bacterial dimensions the interactions with the environment are on a molecular or, at the least, atomic level as far as its sensory capabilities are concerned and millennia of evolution has equipped us and all life to perceive reality reliably but within boundaries that are relevant to natural selection. It is in this trivial sense that Alvin Plantinga is correct to say that evolution limits our cognitive abilities although not, I suggest, to the extent that we cannot make rational sense of the material world.
It is only when we try to investigate the universe systematically that the philosophical issues become paramount. When considering what extra sensory causes lie behind the physical effects we experience the only logical course open to us is to assume that the principles of cause and effect, one material object upon another, continue to obtain even when we cannot directly observe them. To suppose otherwise offers no fruitful line of enquiry because once you allow for the answer to be in some way magical it would be impossible to design an experiment or predict an observation that would disprove it. Methodological naturalism is therefore the only coherent philosophy under which science can proceed even if the ultimate reality, whatever is holding up the last detectable turtle, is something immaterial.
Part of the problem that non-materialists (of whatever stripe) seem to have with methodological naturalism as a scientific presupposition is based, I believe, on a misunderstanding of what science claims to know. In most situations science is not claiming possession of absolute factual truths about the universe but rather a collection of well tested theories that are both explanatory and predictive of what we can expect to observe either by our evolved senses or the machinery we have invented to enhance those senses. These are conceptual models that if applied via material reality produce reliable outcomes, nothing more; they say zip about what may be the underlying cause of everything. In fact when methodological naturalism is defined it is as a working assumption, not an absolute truth, the overriding idea being that regardless of whether or not supernatural forces operate at some fundamental level the material observations would appear identical. In this scenario supernaturalism is a null hypothesis that eventually science could, in principle, falsify to everyone’s satisfaction making metaphysical naturalism (which does claim, strongly, that there are no supernatural phenomena) the most likely situation. Personally, I suspect that however far science is capable of reaching it will still be turtles all the way down for all practical purposes simply because any cause that we can ever detect or postulate must be interacting physically with some other material system we have either observed or conceived.
Even if the sophisticated theologians or the Deepak Chopras of this world are correct and the turtles swim in something divine or pantheistic it still makes no sense for us to explore the universe from any other perspective than materialism despite alleged logical inconsistencies with its metaphysics. You cannot arrive at a coherent consensus description of reality by appealing to a sensus divinatis that if it exists at all is not universally reliable and no amount of meditation or naval gazing will solve the proximal mysteries of existence even if, for some, they seem to point the way to ultimate ones: for now, and probably forever, materialism rules.
"Religion is a hypothesis about the world: the hypothesis that things are the way they are, at least in part, because of supernatural entities or forces acting on the natural world. And there's no good reason to treat it any differently from any other hypothesis. Which includes pointing out its flaws and inconsistencies, asking its adherents to back it up with solid evidence, making jokes about it when it's just being silly, offering arguments and evidence for our own competing hypotheses...and trying to persuade people out of it if we think it's mistaken. It's persuasion. It's the marketplace of ideas. Why should religion get a free ride"