In philosophy, there is a system of thought called philosophical naturalism—the belief that nothing exists beyond the natural (physical realm). There is another philosophical conjecture which sounds similar but is not entailed by philosophical naturalism, and that is methodological naturalism. Science, as it is done today and has been since at least the Enlightenment, assumes methodological naturalism, which is simply the practice of explaining the natural world only through natural causes. In other words, methodological naturalism does not invoke anything supernatural to explain the natural. On the one hand, Christians are typically partly accepting of methodological naturalism, as it is a reaction against the polytheistic and pagan beliefs that natural phenomena are the result of actions of the gods. It is ludicrous, in today’s world, to believe that a storm wreaking havoc on a ship at sea is the result of Poseidon’s anger. But, on the other hand, many Christians are wary of methodological naturalism because they think it implies that one cannot explain things in the natural world as the handiwork of God.
I take issue with that claim—that methodological naturalism precludes explanation of any natural phenomena as the handiwork of God.
First, there are multiple types of causation: material causation and final causation, to name two. Material causation is the material explanation of an event, that is, that which explicates everything there is to be said about the matter and its interactions. Final causation is the purpose or goal which explains the event. So if the event was me baking cookies, you might ask, “What’s that you’ve got there?” I might say, “I’ve got two dozen inch-in-diameter portions of dough being heated at 400 degress Fahrenheit.” Now, that wouldn’t be the whole material cause, but it touches on it, and says nothing about the Final cause. Alternatively, to answer the question, I could just say, “I’m baking some cookies to eat. Want one?” This explanation says nothing (or at least, not much) about the materials or their interactions; it’s referring to my purpose in the action.
Likewise, in any other area of scientific inquiry, we might say there is a teleological explanation which involves God and yet also a material explanation which doesn’t. We might go for a hike and happen upon a cascading waterfall, pausing to marvel at its beauty and enchantment. We may even see God’s handiwork in this waterfall, as it reminds us that God has created the universe with such a grand capacity for beauty and the human mind or spirit with a faculty to recognize and appreciate this beauty. But that does not preclude a purely materialistic explanation of the waterfall. Neither, actually, does it preclude a purely natural explanation of what it means for humans to be attracted to beauty.
One can look at the eyeball and marvel at its complexity, also marveling at the processes which produced that eye and ultimately whatever or whoever put those processes in motion. That does not mean there isn’t a purely natural explanation of the eye and where it came from.
Another, more specific, way of applying this idea is to assert that a final cause might sometimes be the efficient cause of a material cause. An efficient cause is that which causes a change in motion to start or stop. If I grabbed the sheet of cookies out of the oven, the quickest and most obvious way of describing this is precisely that: I grabbed the sheet of cookies out of the oven. It takes much more work to describe that event in terms of material causality (“the neurons in my brain sent a signal to my hand…”) or final causality (“the cookies smelled great and I couldn’t resist anymore”). Take a religious worshipper’s spiritual experience while in worship. Some think that simply because we can explain the neurology of a worshipper’s brain, and what typically happens in the brain before or during a perceived spiritual experience, we can discount the act of worship as a purely physical reaction to stimuli—that there is nothing supernatural going on at all. That is a philosophically naturalistic claim, but it’s not necessary to hold this view to accept the neurological evidence. It may be the case that the neurological data is simply showing what is happening in the brain during a genuinely spiritual experience. Perhaps, in the case, the final cause is that God wishes to communicate or encourage or present himself to the worshipper, and this leads to the efficient cause that God moves or acts in the person’s mental state to bring about the material cause—certain neurons firing and chemicals being produced in the brain.
So perhaps we could explain events in the natural world as being ultimately caused by God (in a final causality way), or even immediately caused by God (in a final or efficient causality way), but since God is not material, and since God created the universe with certain set physical laws which we can observe, there is a way in which we can explain all material events without invoking God. That is, since matter and material systems behave according to set laws, we can assume that any given material event is understandable according to these laws.
This, of course, does not include miracles, which might be defined as acts of God which, in some cases, have no purely materialistic explanation. But miracles, by their definition, are exceptions, not the rule. Methodological naturalism would assert that, if one were to come across an anomaly in the natural world, it would be more rational to assume there is a material explanation for it than that it is a miracle.
Why accept methodological naturalism? Why not say that sometimes the best scientific explanation for a natural event is that it’s a miracle—that God did it? (This would assume that it is within the realm of science to make such assertions as “God did it,” thus denying methodological naturalism.) The primary problem with this approach is that it halts scientific inquiry and indeed supposes that there cannot be a natural cause for the event. It is a form of argument from ignorance in that it asserts its truth on the basis that no other contradictory explanation has been proven in its place. Notice, it does not assert that no other contradictory explanation can be given in its place, for that would be a much stronger—and more difficult to prove—statement. (Note that any natural explanation would constitute a contradictory explanation in this case, as the miracle assertion is that, since God did it, there is no natural explanation.) If it did propose that it would be impossible for a contradictory (natural) explanation to be proven, it would have to show why. But it’s difficult to show how a natural event could not possibly have a natural explanation. And, moreover, if no other explanation could possibly be true, then the claim is not falsifiable, because there has to be some explanation for every event. If no claim is being made, however, to the impossibility of other explanations, then it is indeed a sort of appeal to ignorance: since no other hypothesis has been proven, the “God hypothesis” must be true.
A more solid foundation for miracle claims would be through theology or philosophy. If, at its core, your miracle claim is through theology or philosophy, it may have scientific (material) implications, and it might not. Say you looked into the sky and saw a cloud forming the shape of a cross, and you concluded that God was using this to remind you of Himself. The claim that God is using the cross-shaped cloud to remind you of Himself is theological. To go on to say that God intervened in nature to create this cloud, thus precluding any natural explanation for the formation of the cloud, is not necessary to the theological message received from it.