Immanuel Kant noted that there are three primary forms of argument for the existence of god: cosmological, teleological, and ontological. Cosmological arguments are based on our general experience of existence, or the nature of causality to be more precise. Teleological arguments are based on our experience of the universe, specifically the appearance of "design" in nature. Ontological arguments use abstract experience of concepts to make an a priori case for god's existence.
Today it occurred to me that all of these arguments fall under god-of-the-gaps reasoning. The cosmological argument designates god as its "first cause." The teleological argument assumes that god is behind the appearance of complexity and order in the universe. The ontological argument attempts to define god into existence by imagining the greatest possible being. In none of these do we find a clear and sufficient explanation for why god is involved. It's as if god is simply tacked on because the theist can't imagine any other possibility.
British biologist and geneticist J.B.S. Haldane said, "My own suspicion is that the universe is not only queerer than we suppose, but queerer than we can suppose." Intuition once led us to believe that the world is flat, that the sun orbits the earth, that heavier objects always fall to the ground before lighter ones, and other 'common sense' musings that have now been undermined by scientific study. Even if we ignore all the additional flaws in the three argument forms, there is no justification for applying the god label to the first cause, the appearance of design, or the greatest conceivable being.
The god-of-the-gaps fallacy is a fallacy because it does simply tack on god to whatever the believer can't make sense of (or whatever they think only an explanation of god can make sense of). In the past, we have made this mistake by attributing lightning to the gods, putting god's realm above the clouds, and crediting god with the creation of the human species. It stands very likely that what these arguments put forward in the name of god may be explained by some as yet unknown natural phenomena. Or they may never be explained. But nonetheless, a gap in understanding does not make any old answer as good as the next.
It's interesting to me to reflect on how common this god-of-the-gaps reasoning is among theists. Our tendency to plug god into the unknown may show just where the concept of god originates from. In our desire to understand and find comfort in the chaos, we created an explanation in our own image. Is it not ironic that some of us still continue to use distinctly human traits, like reason, to attempt a justification for the reality of our 'pet theory'?