People often have a presumption of naturalism when it comes to debates over God and Christianity. That is to say, in a discussion over whether or not God exists, it is often assumed naturalism is true unless or until God is shown to exist. This assumption is faulty, and this article will show why.
First, one must understand exactly why the presumption of naturalism is held (from a naturalist’s perspective). The idea is that naturalism just describes the physical world and how it works. In that case, supernaturalism is just naturalism plus God. In this way, supernaturalism (and its positing of God) is shown to be gratuitous (or unnecessary).
Second, one must understand the problem with this presumption. Claiming naturalism is just descriptive of the way the world works assumes that naturalism can account for everything. This requires an argument, not a presumption. Certainly, if naturalism is true, then supernaturalism becomes wholly unnecessary (and even false!). But it simply will not do to offer a position that is not argued for on a definitional basis. There must be a reason to claim naturalism.
Next, the presumption of naturalism assumes that it makes sense to say naturalism explains how it is that the world works. “Now wait a minute,” an objector may interject, “that’s part of the definition!” This is not quite true. Naturalism describes the physical world, but it does not account for why it is that the physical world acts the way it does. Why do the physical laws act the way they do? Metaphysical naturalism can speculate (these laws are brute facts, or they are logically necessary, or some other such thing), but again, without argument, why suppose this explanation is adequate? In any case, without argument, it cannot be shown that God as an explanation is gratuitous.
In fact, it is precisely because of this idea of the ultimate explanation of the physical universe and how/why it works the way it does that one cannot simply presume his position is correct without argument. What if it is the case that naturalism cannot plausibly account for the metaphysics of the universe, but God can? We cannot know from merely presuming our respective positions to be correct. That, on the contrary, takes sophisticated argument.
Naturalism cannot be presumed without argument any more than God can be presumed without argument. If that is the case, it cannot be shown that God is gratuitous without argument. If the explanation of the universe is not some kind of God, then we cannot take it for granted that we do know that explanation. Anyone in that epistemic situation must be open to all of the options–even if that includes believing in God, after all.
 In fact, it may be argued that a flip-flop in presumption may be assumed, where the believer in God enjoys a kind of internal justification or warrant for her belief in God. This would be a significant advantage over naturalism, but is tangential to this discussion. See William Alston, Perceiving God.
See this post published originally at Possible Worlds.