This fallacy occurs when someone argues that because natural causes can't explain a phenomenon P, that therefore P must be the result of supernatural causes. In other words, it's alleged that the guilty party is unnecessarily filling the gap in our knowledge with a supernatural entity, i.e. God.
People often accuse Intelligent Design (ID) theorists of committing this fallacy, but that's a mistake as philosopher Stephen Meyer explains in an article at PJ Media.
Meyer explained that "god of the gaps" arguments fail to convince because they are arguments from ignorance. Such arguments "occur when evidence against a proposition is offered as the sole grounds for accepting an alternative position."In other words, ID does not commit the god of the gaps fallacy because ID is not based on what we don't know about information but rather upon what we do know. There's good reason for supposing that information-rich systems can be generated de novo by intelligent agents and cannot be produced by random processes and forces.
For instance: Evolution cannot explain this part of life, ergo there must be a designer.
Intelligent design does not work like this, the author argued. "Proponents of intelligent design infer design because we know that intelligent agents can and do produce specified information-rich systems," Meyer wrote. "Indeed, we have positive, experience-based knowledge of an alternative cause sufficient to have produced the effect in question — and that cause is intelligence or mind."
Put differently, we have no experience of blind, undirected processes producing complex information like computer programs or libraries full of books, so we're at a loss as to how to explain how such processes could have produced the even more complex information that runs a living cell.
We do, however, have daily experience of such information systems being produced by intelligent agents, therefore it's not fallacious to hypothesize that the very complex information contained on DNA sequences and the information which choreographs the functions that occur within the cell are themselves a result of intelligent agency.
Thus, so far from commiting the god of the gaps fallacy positing intelligent agency is an example of a perfectly ordinary process in science called inference to the best explanation.
Here's a two and a half minute video of Stephen Meyer explaining why ID is innocent of the fallacy of which it's often accused: