Edited on 15-Feb-20
While some theistic arguments are “God of the gaps” arguments, many, including those defended by Christian philosophers, are not “God of the gaps” arguments. Before accusing a theist of trotting out another “God-of-the-gaps” argument, atheists should first verify that the argument actually is a “God-of-the-gaps” argument.
Here is the basic structure of a “God-of-the-gaps” argument:

1. Some odd or puzzling thing, E, occurs or exists.
2. Science is unable to offer a plausible, God-free explanation for E.
3. Therefore, God is the best explanation for E.
4. Therefore, God exists.

There are many, well-known problems with such arguments. I’ve written on this topic elsewhere, so I won’t repeat those points here. Instead, I want to sketch how a theistic argument can avoid appealing to a gap in scientific knowledge. Here is the structure of an F-inductive argument from consciousness:
Let E=consciousness exists; N=naturalism; T=theism; B=background information; Pr(|H|)=the intrinsic probability of H; and Pr(x|y)=the epistemic probability of x conditional upon y

1. E is known to be true, i.e., Pr(E) is close to 1.
2. N is not intrinsically much more probable than T, i.e., Pr(|N|) is not much greater than Pr(|T|).
3. Pr(E| T & B) > Pr(E | N & B).
4. Therefore, other evidence held equal, N is probably false, i.e., Pr(T | B & E) > 0.5.

Whatever problems may exist with that argument, being a “God of the gaps” argument isn’t one of them. The present inability of science to explain consciousness plays no role whatsoever in the argument. What’s doing the work in the argument is the fact that theism, as a version of supernaturalism, entails that consciousness exists, whereas naturalism has no such entailment.

Allow me to explain. “Naturalism” is really just short-hand for “source physicalism,” which says that the physical world exists and, if the mental world exists, the physical explains why the mental exists (or, to allow for eliminative materialists, appears to exist). “Supernaturalism” is really just short-hand for “source idealism,” which says that a mental world exists and, if a physical world exists, the mental explains why the physical exists (or, to allow for eliminative idealists, appears to exist). “Theism” is a specific version of supernaturalism; it says that the mental being or entity which explains why the physical exists is a perfect supernatural person.

N.B. While theism does not entail human consciousness exists, theism does entail consciousness exists because theism entails that God exists and God is conscious, by definition. In contrast, naturalism is compatible with the non-existence of consciousness. So the existence of human consciousness, while not entailed by theism, isn’t surprising on theism in the way it is on naturalism. In that sense, human consciousness is evidence favoring theism over naturalism.

Objections to the Argument

Objection to (1): “We have no idea what ‘consciousness’, ‘mental,’ and ‘physical’ mean. Science can’t explain some E if the E is poorly defined.”

Reply: By a “mental world,” I mean the existence of a private, subjective world. By a “physical world,” I mean the existence of a public, objective world. By “consciousness,” I mean sentience.

Objection to (2): “But intrinsic probabilities don’t appeal to the propositions included in our background knowledge, and so ignore prior probabilities.”

Reply: As we say in computer science, that’s a feature, not a bug. Intrinsic probabilities come before prior probabilities. As the name implies, intrinsic probabilities are probabilities determined solely by the intrinsic properties of a proposition. Draper has argued (convincingly, in my opinion) that intrinsic probabilities are determined by scope, modesty, and nothing else. In contrast, prior probabilities are determined by the propositions in our background knowledge, such as “A physical universe exists,” “The universe is life-permitting,” “So much of the physical world is intelligible without appeal to supernatural agency,” and so forth.

Objection to (3): “The claim that Pr(E | T & B) > Pr(E | N & B) is unfounded because generic or mere theism doesn’t contain enough information to predict or demystify E. One would have to appeal to a specific kind of theism to justify something like (3), but a more specific kind of theism would have a lower intrinsic probability than mere theism.”

Reply: This is false for the reason explained above. While theism does not entail human consciousness exists, theism does entail consciousness exists because theism entails that God exists and God is conscious, by definition. In contrast, naturalism is compatible with the non-existence of consciousness. So the existence of human consciousness, while not entailed by theism, isn’t surprising on theism in the way it is on naturalism. In that sense, human consciousness is evidence favoring theism over naturalism.

Objection to (4): “But consciousness depends upon a physical brain. That’s more probable on naturalism than on theism.”

Reply: Correct. We know much more about the mental than the fact that it exists. We also know that it is dependent upon the brain, a fact which is much more likely on naturalism than on theism. So, once the evidence about consciousness is fully stated, it’s clear that there is also evidence favoring naturalism over theism. That fact, however, does nothing to refute this argument, which contains an “other evidence held equal” clause in its conclusion.

Objection to (4): “But the naturalistic evidence of mind-brain dependence outweighs the theistic evidence from consciousness.”

Reply: I am not aware of anyone having offered a successful argument for that claim. It’s not clear to me how such an argument could be adequately defended.

Objection to (4): “But the history of science contains numerous examples of naturalistic explanations replacing supernatural ones and no examples of supernatural explanations replacing naturalistic ones. That gives us reason to expect that science will eventually explain consciousness without God.”

Reply: I agree that gives us some reason to expect that science will eventually explain consciousness without appealing to God. That doesn’t change the fact, pointed out by (3), that the content of “naturalism,” as I have defined it, gives us no antecedent reason to expect consciousness to exist if naturalism is true, whereas “theism,” as I have defined it, does give us an antecedent reason to expect consciousness. This promissory naturalistic ‘atheodicy’ has no logical relevance to the argument anyway.

Objection to (4): “But (4) must be false because theism is false.”

Reply: That would follow only if one assumes that there can never be true evidence for a false proposition, but why assume that? There can be circumstantial evidence that a defendant is innocent of murder, while at the same time there could be other evidence for the defendant’s guilt, such as DNA evidence, which completely outweighs the circumstantial evidence. Similarly, a theist might say, “Suffering, imperfection, poor design, and mind-brain dependence are evidence against God’s existence, but that evidence is completely outweighed by the evidence from the finite age of the universe, the life-permitting conditions of the universe, human consciousness, etc.” Similarly, even if one believes (as I do) that it’s extremely improbable that God exists, one can consistently allow that consciousness is evidence–even strong evidence–favoring theism over naturalism, while simultaneously believing that other evidence outweighs the theistic evidence. People in general need to stop taking a binary, “all-or-nothing” approach to evidence.