There is a gap in the knowledge of each and every person and there always will be. The gap extends directly from the human condition in a number of ways at least consisting of human nature’s imperfect ability to ascertain, process and retain information.
Other sources of the gap may exist as well, including some which I haven’t mentioned because the knowledge of those limits itself lays in the gap. This gap is ironically demonstrated by the improvement of our knowledge rather than direct observation of the thing of which we are ignorant.
When Louis Pasteur invented pasteurization the resulting efficiency illustrated the fact that a particular gap had existed prior. Some of the brighter minds of the time would have known their limits and said, “We don’t know why milk spoils.” They would not have said, “We don’t yet know about bacteria,” at least with the term ‘bacteria’ meaning anything beyond the unknown cause of milk spoilage. If used in that context perhaps ‘bacteria’ would only mean something milk itself does rather than the name of an external agent. No one would have known prior to the appropriate verification of some theory such as the germ theory.
Theists have often been accused of invoking a God of the Gaps. It is true that our ignorance cannot be used to prove God exists, but it is equally fallacious to conclude that our ignorance discredits God’s existence. There is a related fallacy discussed by Dembski:
“Scientists rightly resist invoking the supernatural in scientific explanations for fear of committing a god-of-the-gaps fallacy (the fallacy of using God as a stop-gap for ignorance). Yet without some restriction on the use of chance, scientists are in danger of committing a logically equivalent fallacy – one we may call the “chance-of-the-gaps fallacy.” Chance, like God, can become a stop-gap for ignorance.”
― William A. Dembski
Certainly the logical progression from I don’t know what the cause is to therefore God exists is fallacious, however indirect reasoning is often misdiagnosed as God of the Gaps reasoning. One form of indirect reasoning would be:
1 A exists.
2 A fits the explanatory pattern of B.
3 Therefore, B may explain A.
If I can demonstrate that B explains A better than B’, or better than competing explanations, B is a justified belief, although not necessarily true. This is not an argument from ignorance, another name for the gap fallacies such as the God of the Gaps argument. See the video below for Dinesh D’souza’s more in-depth and in-context discussion of the misdiagnosis of indirect reasoning as an argument from ignorance:
Indirect reasoning is valid. Even mainstream science is based on indirect reasoning. See the section entitled “Fuel for the Fire” near the bottom of the first page of this article for an example of indirect reasoning being used for mainstream science.
In conclusion all people are necessarily subject to the Great Gap. Ignorance cannot support any form of position or it is not real ignorance, but indirect reasoning doesn’t constitute the real ignorance of the gap and is justified in use.