There will always be unknowns in science. Many theists see these unknowns as reasons for believing in God. The argument usually goes something like this: "We don't understand how the universe got here, therefore God must have created it." (This is today's version of the argument, years ago it was "We don't understand thunder, therefore the thunder god must have done it.") But is saying "God did it" really an explanation? No, it isn't. An explanation is a description of something we don't currently understand in terms that we do understand. Theists will usually admit that they don't understand their god, saying things like "God works in mysterious ways". Well if we don't understand how God does something, then "God did it" is just about meaningless. We will never have all the answers, but postulating an infinite god and pretending that this provides the answers is just irrational. It is much better to have the intellectual integrity to simply admit that we don't yet know.

A fairly common example of the god of the gaps fallacy is the argument that since we don't understand where the dimensionless constants in the equations of physics come from, and since carbon based life could not have evolved if some of the parameters varied by a small amount, a god must have chosen the parameters to produce human life. In addition to being an example of the god of the gaps fallacy, this argument is wrong for several other reasons. For example, it assumes that the dimensionless parameters are fundamentally arbitrary. In other words, it assumes that the parameters cannot be predicted with a more fundamental theory. But in string theory, all dimensionless parameters are expected to be predictable (see Internet Physics Resources). Several other problems with the argument are discussed in Cosmythology and Is God in the Details?.