From Angus Menuge ("Against Methodological Materialism," Waning of Materialism, p 381):
[E]ntirely materialistic science employs gap arguments routinely when explaining unlikely historical events. The most widely accepted explanation of the geologically rapid, widespread extinction of dinosaurs invokes a rare, but fully materialistic event: asteroid impact. Part of the evidence for this event is that none of the processes believed to be going on at the time (including likely diseases - initially a competing hypothesis) are sufficient to account for such a catastrophic extinction. In other words, there is a gap between these processes and the fact of extinction. Asteroid impact was then hypothesized as a possible cause, leading to independent predictions of shocked quartz in the Cretaceous-Tertiary boundary, which were subsequently confirmed. Not only is this gap argument completely materialistic, it is also a good one, because it depends on the confirmation of independently testable predictions that discriminate between the asteroid hypothesis and its competitors.
In fact, historical science of all kinds is filled with gap arguments. There is a gap between the unloaded military antique mounted on a wall and the deceased Colonel Mustard who was somehow killed using the antique, and this gap may be best explained by the intelligent agency of a murderer. There is a horrific numerical gap between the population records for Jews and Slavs before and after the Second World War that is best explained by deliberate genocide. There may be a gap between a student's own creative ability and the spectacular slide show on impressionism he presented, best explained by the artistic skill of impressionist artists. Evolutionary scientists themselves frequently employ gap-arguments, claiming that there must have been intermediary creatures between those whose fossils have actually been discovered, for otherwise there is no suitably gradual explanation of the presumed transitions. In general, a good gap argument is based on a careful assessment of what the normal course of nature is capable of doing, thereby providing evidence of an objective gap in nature, not merely a gap in our knowledge, and this leads to the postulation of some additional factor or agency whose causal powers are known to be capable of filling the gap. Good gap arguments are therefore not arguments from ignorance but arguments from knowledge, both of what nature is normally capable of doing, and of the resources capable of doing more.