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The god-of-the-gaps fallacy is an argument commonly used to belittle faith. It is predicated on the notion that as our knowledge of the natural sciences increases, fewer supernaturally motivated conclusions about our universe will be necessary. In other words, God is only a placeholder explanation for phenomena until researchers discover the actual cause.

For example, modern man is well aware that lighting and thunder has nothing to do with angry deities; Instead, it is understood that it is actually an arc of electricity in the atmosphere. In the same way, modern man is also rightly skeptical of the conclusion that illness results from the anger of malevolent “spirits”. Research has revealed the causes to be known bacteria, viruses, cancers, and other related things.

In the past, because god-of-the-gaps was utilized to explain what could not be understood, some theorize that there is a coming time when the “god” of the gaps will explain nothing. In other words, science will explain all of man’s questions. Not only is this conclusion misguided but actually is utilizing the same logic it is attempting to decry.

Positive Arguments

The classical arguments for the existence of God (ontological, axiological, cosmological, teleological) are not negative arguments. They are not responses to unexplained phenomenon. Rather they are responses to what is known about the world.

Creation paiting on Sistine ChapelFor example, because we know all things which begin to exist need a cause, it is impossible for anything that began to exist to be self-caused; It follows then that everything from human consciousness to the universe would need a cause. Further, in all cases where something is caused, the producer of the cause must have certain features which enable it to be the cause the observed effect.

In the case of the universe, for example, such features must include: intelligence, consciousness, intentionality, and sufficient power. Thus, because of what we do know about the world, and how cause and effect works, the existence of God is not a lowest common denominator god-of-the-gaps response. Instead, is the best possible response to the data we have at hand.

Even if one argues that the existence of the universe is not restrained to the laws of causality, as some theoretical physicists do, believing that the universe is an anomaly of the “quantum vacuum” is still highly problematic. If as a recent paper from Japan asserts, the universe is indeed the result of such a rare occurrence as a the expansion of a quantum vacuum bubble, then one would have no justification for believing that such causation would be reasonably possible; Possibility does not necessitate reality. On the other hand, if one assumes it is possible, as the Japanese paper asserts, then why do we only see one universe? An even better question is: Why only universes?

Big Bang TimelineOf course, if one wanted to be honest and go the route of saying that the universe is an anomaly of which we have only mathematical models, with little actual physical evidence, then that same person has just argued that we have no reason to believe the philosophical conclusions they create based on such a model. In reality, the only reason atheists argue that the universe doesn’t need a cause is personal volition. Many argue this way because they personally, but not intellectually, prefer to believe in a religion which allows them to do as they wish. They do not like where alternative conclusions take them.

The god-of-the-gaps fallacy occurs when one goes from what he does not know to god (or some supernatural phenomenon). The apologist is not following that line of argumentation. Instead, he is going from what he does know (e.g. causality) to God. Basing conclusions on what is known and logical could hardly be considered the a god-of-the-gaps fallacy.

In an ironic twist, if one defends the belief that science will one day answer all of men’s questions, that one should use the belief in science to fill in the “gaps”, he is actually making the same argument … merely with a different conclusion. Scientific methodology and mathematical models become “gods-in-the-gap”.

Conclusion

While the theist is charged with arguing from what is unknown to God, the skeptic is going from what is scientifically unknown (i.e. the answers to man’s problems and questions) to no God; The justification or evidence is the same for both scenarios. Thus if a skeptic convinces someone that they are refuting a god-of-the-gaps fallacy, they may also refuting their own argument. Usually, they are making a straw man argument, because it does not accurately portray the evidence, the conclusion, or the methodology of the Christian.

Source.

I agree. However as the article stated: "In an ironic twist, if one defends the belief that science will one day answer all of men’s questions, that one should use the belief in science to fill in the “gaps”, he is actually making the same argument … merely with a different conclusion. Scientific methodology and mathematical models become “gods-in-the-gap”.

God is the God of everything. He is the God of miraculous one time events, that are not something we can prove by testing, and He is the God of repeated, testable natural events. It is when we are trying to limit Him to one or the other, that we are in danger of misunderstanding His nature.

A belief in a being who can operate unbound by the laws of nature is not a belief in magic either. This is an issue of the existence of God, and the nature of God - not an issue of whether the miracles mentioned in the Bible are really magic. That what we can observe always turns out to be testable models, doesn't mean that we are in possession of all the knowledge we need to make a definite statement saying all things have predicable models, and are able to be tested with the scientific method.

But you can test what God revealed of Himself through His creation and through revelation, yet God is so great that you can't understand everything there is to know about Him. If we were able to I would say that our concept of God then was man-made. There are things that are revealed and we have the ability to understand, and then there are things that are beyond our ability to comprehend, that are veiled. These are not contradictions, but show a God who knows His audience and who's existence is not limited to mankind's imagination.

Romans 1:20 tells us, "Since the creation of the world God's invisible qualities – his eternal power and divine nature – have been clearly seen, being understood from what has been made, so that men are without excuse."

Romans 11:33
Oh, the depth of the riches of the wisdom and knowledge of God! How unsearchable his judgments, and his paths beyond tracing out!

Ecclesiastes 3:11
He has made everything beautiful in its time. He has also set eternity in the human heart; yet no one can fathom what God has done from beginning to end.

Psalm 147:5
Great is our Lord and mighty in power;
his understanding has no limit.

1 Corinthians 13:12
For now we see only a reflection as in a mirror; then we shall see face to face. Now I know in part; then I shall know fully, even as I am fully known.

To address a major point to begin, I would refrain from using Scripture in apologetics of any kind unless it goes to back a point for which you've already demonstrated convincing and testable evidence for. What the non-believer could point out from the verses you chose to quote here is, "Wow! You have an omnipotent god, whose qualities are so innumerable that we can't even understand them; yet he can't even manage to write a single book that is universally agreed upon, contains blatant inaccuracies, morally reprehensible commands, and had to be bound into a single volume by committee? I would think that such a powerful God could present a message that was discernibly his own, and set apart from any other that claims a similar source. What makes your holy book right and the Qu'ran wrong?" So I would stay away from that particular tactic. It's not very productive, and certainly not convincing to anyone who doesn't already accept the Bible as inerrant and divine.

Now, here are two definitions of the word MAGIC from the Merriam-Webster Online Dictionary. The first is "a power that allows people to do impossible things by saying special words or performing special actions" and another is "the use of means believed to have supernatural power over natural forces." So please don't assert that Christianity is not a religion chock full of magic. To say otherwise is dishonest. To say that God is responsible for any phenomenon simply because we do not as of yet understand its mechanics is exactly the same thing as saying, "we don't know, therefore magic."

"That what we can observe always turns out to be testable models, doesn't mean that we are in possession of all the knowledge we need to make a definite statement saying all things have predicable models, and are able to be tested with the scientific method."
It does always turn out to be a testable model though, and we have no evidence to suggest that there is any other possible explanation. The supernatural being cannot even be posited as an option until there is evidence to back a supernatural being of any kind to begin with, deity or otherwise. Saying that we don't have all the knowledge to make a determination about everything, does not mean we have the authority to thrust forth a baseless explanation grounded in religion. To suggest that God is the cause, then using the cause to suggest the existence of God is circular logic, and another fallacy. Though this is exactly what happens when you say we can prove God because there is creation (though most would suggest that you would have to demonstrate the creation aspect first if you were having a legitimate apologetics conversation).

Evidence for God's existence much be established before he can be allowed to explain as much as a shift in the breeze.