[Besides entering my busiest time of year work-wise, I'm teaching one class at the Kilns and another two classes on the internet. What suffers is my time to write new blog posts. So the following is taken from a discussion thread in my internet class, in which I clarify what I take to be the issue with the God-of-the-gaps charge.]
I guess I have a slightly different take on the God-of-the-gaps issue. As I see it, this is not so much something of which Christians generally (and much less practicing scientists who are Christians) are really guilty. Rather, it is an illegitimate charge made against Christians by naturalists. And when naturalists raise this charge, they are generally guilty of several logical fallacies...
1) They are guilty of creating a straw man. While there may be some who easily claim "because God did it" too early in the search for explanations, this is an extreme position and not the one taken by the vast majority of Christians engaged in scientific discussion. When one addresses only the absurd, extreme articulations of his opponents (setting up a straw man that is easily knocked down) instead of addressing the thoughtful, difficult objections made by more moderate opponents, one is being academically disingenuous and logically fallacious.
2) They are guilty of the ad futurum fallacy. (I actually wanted to make up my own name for a fallacy, the "log-in-your-own-eye fallacy," but will stick with a well-recognized name.) But what I mean is that the naturalist is equally guilty (moreso, actually) of engaging in naturalism-of-the-gaps. The claim is that while we don't currently know the natural explanation, give us 75 years and we will. This is a faulty appeal to the future. In good reasoning, one is expected to find the best explanation for all the currently available evidence, rather than appeal to hypothetical future evidence.
3) More fundamentally, the naturalist is guilty of equivocation, wrongly using two significantly different definitions of the 'gaps' being addressed.
The naturalist likes to identify epistemological gaps (gaps of knowledge), and show that historically such gaps have closed. But the more interesting gaps--and those raised by the old-Earth creationist and the proponent of Intelligent Design--are ontological gaps (gaps of existence or being). The naturalist serves his own cause by conflating these two definitions or by ignoring this crucial distinction.
We could discuss (for example) the gap between the existence of a universe and the non-existence of a universe, or the gap between the Edicarean life forms and those of the Cambrian. These are fundamentally gaps of being, not merely gaps in our knowledge. And while the actual gaps involved are unchanging, the epistemological gaps (as we better understand the breadth and suddenness of the Cambrian explosion) are getting larger, not smaller. Perhaps the best example is that of the origin of life. The gap between non-living chemistry and the simplest life is now understood to be much larger than any evolutionary naturalist ever conceived.
So, it is rather uninteresting to note that we ought not be guilty of appealing to the supernatural prematurely, when there is still every indication that a natural (process) explanation will be found (for whatever phenomenon is being studied). But when we are studying origins* questions (rather than process questions), there is every reason to use abductive reasoning, and explanations that involve a supernatural being can reasonably be offered in such cases. This is especially true since only a theistic worldview logically grounds the assumptions that make science worthwhile (as discussed in another thread).
* Failure to differentiate between empirical (process) research and historical (origins) research also serves the scientific naturalist's cause. Whether this represents mere imprecision/naivete or disingenuity on their part I'm never quite sure.