The God of the Gaps Fallacy
The fallacy of the "God of the gaps" underlies many arguments for the existence of God. It is one of the oldest and most common mistakes among religious believers.
Essentially, those who use the "God of the gaps" argue that gaps in human knowledge are evidence of God's existence. We cannot explain something, therefore this must be supporting evidence for God.
Human ignorance was the original basis for the development of religion, so it makes sense that appeals to ignorance should figure prominently in the justification for belief in God.
God of the Gaps
Since every question must have an answer, adherents of the "God of the gaps" fallacy point to unanswerable questions as questions that only a God could answer. Questions about the stars and planets, how animals reproduce, why there is a drought this year, what causes the tides, and so on, are answerable by science, reason and other human tools. But what about questions that we can't seem to answer? God or the supernatural is the only explanation available.
The fact that there are limitations to our knowledge indicates that there is something bigger out there, some kind of larger intelligence at work in the universe. It is that entity that fills in the gaps. This is the basis for believing in God.
The problem is, just because one believes that God is the only answer doesn't mean it's true. There may be other answers they are unaware of, or unwilling to accept. Many seemingly mysterious or "unanswerable" questions actually have been answered through science and naturalism.
God of the Gaps and Morality
For example, many religious people ask "Why do we have a moral instinct?" This seems like a good potential reason to believe in God because the answer is not immediately obvious. (Of course, the answer to almost any significant question is never immediately obvious.) So religious believers conclude that, since there is no material or scientific explanation for human morality, God must have done it. They believe that God created humans with a very specific kind of moral temperament.
But the fact is, there is a scientific explanation for morality. Over time, people that felt a sense of belonging and commitment to their fellow community members, and sought to help them more than harm them, survived and prospered. Communities populated by backstabbing, untrustworthy and self-centered people prospered much less. In times of crisis, they would not be able to hold together and overcome. And in times of prosperity, the self-centered tendencies of the population would quickly diminish any surpluses.
So, over many years of population growth, the qualities and traditions of people that were nicer to each other--in other words, people who were more "moral"--became more common. As a result, almost all human beings today have a strong moral instinct. Communities of moral people have a clear and distinct advantage over communities of immoral people.
God of the Gaps and Creationism
Another example of "God of the gaps" is in arguments for creationism to be taught alongside evolution in schools, or to "teach the controversy." The thrust of this argument is that since evolution is not one hundred percent certain, another competing theory for the development of life (namely, creationism) should be taught alongside it. The gaps and shortcomings in the theory of evolution are used as justification for teaching a God-based theory of the development of life, or at least mentioning it.
Creationism and its current popularization "intelligent design" are unscientific, and do not belong in a scientific discussion regardless of the shortcomings of any theory. Nobody argues that our ignorance of the human brain justifies teaching students that magical sprites and spirits might be at work inside our heads.
But aside from that, the fact is that the theory of evolution has gotten stronger every decade since its inception. Arguments that creationists made 100 years ago against evolution have now been answered or resolved, and creationists must continually fabricate new controversies and/or focus on ever-narrower and insignificant shortcomings. Every year more information and more evidence is attained by scientists around the world, further supporting and substantiating the theory of evolution. The gaps continue to close, and the God of creationism becomes smaller.
Problems with the God of Gaps
Assuming that there is an actual gap in human knowledge on some topic, this still does not constitute proof or evidence for the existence of a God. The fact that we do not understand something or are not aware of something does not mean that God exists, any more than it means that Zeus, Apollo, mermaids, unicorns, hobbits or any other possible creature exists.
The gap in knowledge may be fillable by a naturalistic or reason-based explanation that has not been discovered yet. Examples might be some kind of physical force, a chemical reaction, a mistake in our understanding, a lie, an unrecorded historical event, or even intelligent extraterrestrial aliens.
And, assuming supernatural explanations are possible, the gap may be fillable by some kind of supernatural entity other than God--angels, ancestor spirits, a universal life energy, the Force, nature gods, or anything else imaginable. There are countless explanations that must be overcome before God becomes a viable option for explaining a mystery.
"We are to find God in what we know, not in what we don't know."
The Gaps in God
The fallacy of the God of the gaps has been used for thousands of years. Of course, in earlier times the gaps in human knowledge were very different, and much larger. People did not understand things that today are easily explainable by a schoolchild. These gaps diminished over the centuries with new knowledge, and God has become smaller as a result.
Today, there is scarcely a single question that God is needed to answer. Even more esoteric questions like "why are we here" or "what is the purpose of life" are considered by more and more people to be answerable without appeals to God. Secular philosophies and belief systems have become more popular and more viable.
Moreover, even among spiritual or religious individuals, who might be interested in a God-based explanation, God is used less and less. These individuals are turning to different kinds of supernatural or spiritual explanations, whether polytheistic, pagan, or pantheistic in nature. Many hold supernatural beliefs that ignore the concept of "god" altogether and opt instead for a universal "life force" of some kind.
The concept of a God of the gaps, seemingly helpful to traditional theism, has ultimately sowed the seeds of God's destruction.