I’ve noticed that many nonbelievers (and even believers) misunderstand what constitutes a “God of the gaps” argument. They tend to think one is guilty of a God of the gaps argument if they offer God as an explanation for some X rather than some natural phenomenon. The problem with this definition is that it presumes the only valid explanation is a naturalistic explanation. God is ruled out as a valid explanation for anything a priori, so anyone who offers God as an explanation for X is thought to do so merely because they are ignorant of the proper naturalistic explanation. This begs the question in favor of naturalism and against theism. One could only conclude that every effect has a naturalistic explanation, and that God is not a valid explanation, if one has first demonstrated that God does not exist. So long as it is even possible that God exists, then it is possible that God may be the cause of X, and thus explain X.
What makes an argument a God of the gaps type of argument is when God is invoked to explain X simply because we do not know what else can explain X. In other words, God is used to plug a gap in our knowledge of naturalistic explanations: “I don’t know how to explain X, so God must have done X.” This is not at all the same as arguing that God is the best explanation of X, based on what we know regarding X and the explanatory options available to us. Here, God is being invoked to explain what we know, not what we don’t know.
A good example of this is the origin of life (Parts 1, 2, 3, 4, 5, and 6). We have plenty of knowledge about how life works, the minimum requirements for life, and the productive capacity of naturalistic and intelligent processes. We know the basis of life is biological information encoded in DNA. Even the simplest forms of life require massive amounts of biological information. We also know that unguided naturalistic processes are incapable of generating information. The only type of cause known to produce information is an intelligent agent. The best explanation for the origin of life, then, is an intelligent agent that transcends biological life (God). God is not being offered to plug up a gap in our knowledge, but as the best explanation for what we know to be true about life.
Ironically, it is the naturalist who is usually guilty of invoking a gaps-type argument. Rather than invoking God for what he cannot explain, he invokes nature. We don’t know what can explain the origin of biological information? No problem! Nature did it…somehow. We don’t know how to explain the origin of material reality? No problem! Nature must have done it…somehow. Naturalists are so committed to the notion that natural causes, and only natural causes exist, that even when we have exhausted every natural cause and found them all wanting, they remain committed to the belief that there must be a natural cause. This is a “nature of the gaps” argument in which nature is invoked to plug gaps in our knowledge.
So the next time someone accuses you of making a God of the gaps argument, explain the difference between invoking God to explain what we do not know/understand and invoking God as the best explanation of what we do know/understand. God is the best explanation for the origin of the material world, the origin of life, morality, the laws of logic, free will, etc. We invoke God to explain these phenomena, not because we are unaware of possible naturalistic explanations, and not just because we have found all naturalistic explanations wanting, but because the existence of God best explains these features of reality.