A common defense of the materialist approach to science is to say that positing the supernatural as an explanation for any aspect of nature commits the error known as God-of-the-gaps—plugging divine agency into current gaps in scientific knowledge. The argument typically goes as follows: As man’s understanding of nature has grown, the space left for theistic explanations has been steadily shrinking. The areas presently unexplained—the deficiencies in scientific knowledge—are the spots where religious people tend to insert God rather than recognize a need for continued scientific exploration. The materialist may point to the various failed gaps arguments made throughout the history of science in an effort to show that rationality is gradually winning out over superstition—the category into which they place theological beliefs.
Admittedly, some theists have indeed made God-of-the-gaps claims that progress in the sciences eventually overturned. One example would be the now-discarded belief that God created every single variety of every single plant and animal species from scratch in an instantaneous act of supernatural creation. We now understand that there is a natural, observable explanation: Varieties of species arise through the spread and preservation of genetic mutations in populations of living organisms. Invoking God’s direct agency to account for variations among species turned out to be a mistake.
Even so, the God-of-the-gaps label is often misused; it is not uncommon for materialists to unfairly apply it to philosophical conclusions that are based upon the existing evidence, not missing scientific information. For example, suggesting that a designing intelligence is responsible for the elegant mathematical order of the cosmos or the exquisite complexity of life is not a gaps argument; it is a philosophical conclusion drawn from mounds of data, not a lack thereof. In addition, there remain deep mysteries about the origin and character of nature which suggest positive reasons to suspect that a Mind was somehow involved (though not necessarily by way of miraculous intervention into the natural order). These situations are markedly different from gaps arguments because they involve an inference to the best explanation based upon the actual observations. This type of logical reasoning (known as abductive reasoning) is typical in science as well as detective work; though it does not yield certainty, it is quite useful in establishing the plausibility of a working hypothesis. Nevertheless, this is not to say that science should not continue to work toward closing holes in its account of nature, only that philosophical inferences about a designing Mind may very well be reasonable in light of the data and are by no means a hindrance to any further scientific research.
At the end of the day, even where scientific explanations of natural phenomena are relatively complete, the likelihood of a Maker is in no way diminished. This is not a zero-sum game. Theists fully recognize that God works through primary (direct) causation as well as secondary methods of causation, such as the laws and mechanisms he has built into nature. This understanding of divine agency in creation goes back at least as far as St. Augustine (354 – 430), who explained in his commentary on Genesis that God created the world with intrinsic potentialities that are realized over time through processes of growth and development. Whether something in the natural world is the product of primary or secondary causation, it is no less a product of the mind of the Maker.
As John Lennox puts it, insightful believers have no interest in a God of the gaps; they’re arguing for the “God of the whole show”: the God over what science has established, what it hasn’t yet but might in the future, and everything that is, arguably, well outside its sphere of inquiry—the big why questions of cosmic existence, the rationality of nature, and the explanation for science itself.