In studying the natural sciences, people are in agreement that those things which are directly observable or inferentially derived from the available evidence are truly real. Now, attempts to point to God as an explanation for the evidence is often what skeptics call the God of the Gaps fallacy. It works like this: a theist says that human knowledge, when using empirical science, reaches a point of mystery and the unknown. He or she might say, “We cannot explain the origin of the universe with science, so God must have created us.” On this line of thinking, there is a ‘gap’ in our knowledge, and ‘God’ fills in the gap which then provides closure to the mystery of cosmic origins. But then, a skeptic replies that when enough new information is gained, the gap in our knowledge closes, and ‘poof’—there goes the whole ‘God’ hypothesis. The whole idea of God as Creator went away as the gap closed!
The God of the Gaps fallacy is different from both abduction (inference to the best explanation) and Leibniz’s principle of sufficient reason (while the PSR is explanatory in nature—much like the God of the Gaps fallacy, it uses the principle of causality in order to deny an infinite regress of explanations for why things exist. This is not the same as trying to ‘close a gap’ of knowledge with ‘God’). God of the Gaps arguments depend upon a lack of knowledge in order to sustain the belief that God exists. As long as one affirms theism because of one’s inability to explain some feature of reality, the skeptic can simply posit that science will soon provide an answer for the unexplained feature in the not-too-distant future. This is not the way a theist should make his or her case to a skeptic.
Instead, abduction affirms that given the evidence at hand, theism is the better explanation for what we observe, compared to chance or necessity. It has been stated that chance is not a thing that has power to do anything. In addition, chance is ruled out by measuring probabilities, and necessity is ruled out by simple reason. Consider the universe: as we have mentioned, there are several conditions necessary for the emergence of any complex life forms to arise in the universe. A low-entropy universe is necessary for the emergence, development, and complexity of life forms (a high entropy universe would run out of energy and not allow for the development of complex life forms). Therefore, the probability is far too low for the universe to have arisen by random chance. Roger Penrose, a world-class mathematician of Oxford, has calculated that the odds of low-entropy states existing by chance alone are 10^10^123 to one.
Is the universe necessarily the way it is? Could it have been different? Of course! Is there any reason or amount of evidence which suggests that the universe is necessarily fine-tuned for life? No, it isn’t necessary that the universe is the way it is, or even that it is in the first place. This leaves us with the only alternative: design. Chance, necessity, or design; it is the latter that provides the best explanation given the evidence we have. So far so good. But, what if new evidence were to come about? Wouldn’t that provide the opportunity to return to chance, and thus make abduction no different than the God of the Gaps fallacy? Not at all. This is because God of the Gaps arguments punt to the notion of God’s existence based upon a lack of knowledge. Contrariwise, an inference to the best explanation relies on what is known: the scientific data shows that the universe is finely-tuned, and how such meticulous fine-tuning could not happen by chance or necessity. So, no, inference to the best explanation is not a God of the Gaps fallacy, and it is a viable way to understand evidence.
As stated earlier, empirical science has its limits. The National Academies of Sciences, Engineering, and Medicine (NASEM) reveals the modern sentiment regarding the relationship between ‘science and religion’:
Because science is limited to explaining the natural world by means of natural processes, it cannot use supernatural causation in its explanations. Similarly, science is precluded from making statements about supernatural forces because these are outside its provenance. Science has increased our knowledge because of this insistence on the search for natural causes.
As the NASEM states, there are epistemic limitations of science in terms of its explanatory power: supernatural explanations are not allowed, and this is because the province of science is limited to the sphere of the empirical. The method that is defined here is followed by most people in the academic world. The NASEM doctrine is reminiscent of the non-overlapping magisteria (NOMA) of paleontologist Stephen J. Gould (1941-2002). NOMA states that there are two domains—science and religion, and each domain has its own, unique area of authority. The domain science tells us how the starry heaven go, and the domain of religion tells us how to go to the starry heavens.
Rather than adopting the epistemology of NOMA however, we prefer to say that there are degrees of knowledge, rather than separate domains, as the NASEM states. For empirical science, as seen from the section on Thomas’ 2nd Way, leads us to discussing whether the objects of empirical study have natures or essences, along with principles of causality when investigating things like efficient causes. When we start asking questions like that—and they are inevitable—then we enter into the realm of philosophy more broadly, and metaphysics in particular. (Metaphysics then leads us to discussing the question of the existence of God. So, empirical science leads us to God, although it leads us through degrees and up the ladder of abstract thought from sensible objects e.g. apples, humans, and dogs, to the nature and essence of these things, culminating in the divine Being who is Pure Act and whose essence is his existence).
From the NASEM doctrine, there tends to be a sneaky commitment—once again—to quasi scientism. By this, we understand NASEM to be saying that public, objective knowledge is found in science, while private, subjective knowledge is found in religion. Scientism is epistemological, saying only (empirical) science gives us the truth about the world. As we have seen, scientism holds to metaphysical commitments as well. In his review of Carl Sagan’s The Demon Haunted World, zoologist and biologist Richard C. Lewontin explains how scientists have their own biases, along with prior commitments to the philosophy of materialism (the metaphysical idea that only matter exists):
We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated.
Notice that Lewontin is arguing that no matter where the evidence leads, the goal of science is to give naturalistic or materialistic answers. But Lewontin is confusing methodological naturalism with metaphysical naturalism. Methodological naturalism is a position that says science should seek only natural explanations and that attempts to find supernatural causes are ipso facto, not science. In contrast, metaphysical naturalism starts with the presupposition that all that exists is nature. Presupposing that all that exists is nature and then using methodological naturalism to prove this presupposition, is arguing in a circle.
Scientism, then, is at fault for arguing in a circle due to its pre-commitment to metaphysical naturalism. As a helpful guide, C. John Collins offers some useful definitions regarding the difference between natural and supernatural:
Natural: God made the universe from nothing and endowed the things that exist with “natural properties”; he preserves those properties, and he also confirms their interactions in a web of cause-and-effect relations.
Supernatural: God is also free to “inject” special operations of his power into this web at any time, e.g., by adding objects, directly causing events, enabling an agent to do what its own natural properties would never have made it capable of, and by imposing organization, according to his purposes.
Even though some people see a crucial distinction between the natural and supernatural, the Bible affirms that God is sovereign over creation, and thus the natural and supernatural are conjoined. Christian philosopher Alvin Plantinga writes, “according to [serious theism], God is already and always intimately acting in nature, which depends from moment to moment for its existence upon immediate divine activity; there isn’t and couldn’t be any such thing as his ‘intervening’ in nature.” Since, within theism, God is sustaining the world, God’s actions in the world through miracles, say, are not understood as rank interventions done by an otherwise passive deity, but as the extra-normal activity of a personal God who is interested in showing his goodness and mercy to human beings, even as he sustains them in their being moment by moment.
Skeptics retort against the notion of divine activity by saying that the universe needs no explanation at all, so all this talk about defining science, and the relationship between the natural and supernatural is moot, because the universe is simply a ‘brute fact.’ This was the view of the logical positivists Rudolf Carnap and Bertrand Russell in the early 20th century. Logical positivism was the extension of David Hume’s empiricism, and thinkers like Carnap and Russell asserted that only empirical science gives the truth about the world. Scientism is really just logical positivism in new garb. All the same, while the ‘brute fact’ response seems to be a simpler explanation for the reason why the universe exists, in the end, it shows the emptiness of the materialist worldview. All worldviews should possess adequate explanatory power, and saying the universe is a ‘brute fact’ dismisses the question with a wave of the hand.
To wrap things up: empirical science is generally restricted to questions about the cause and effect relationships among features of the natural world. The assumption of scientism is that an understanding of these leads to the conclusion that the Ultimate is known, and that the Ultimate is not God, but simply the brute fact of the universe. To the contrary, mathematician and philosopher John Lennox reminds us that we can investigate a Ford motor car and see how the impersonal principles of internal combustion cause the engine to work. However, just because we can’t see Mr. Ford directly, it doesn’t mean there is no Mr. Ford who designed the mechanisms of the motor car. How does this illustration apply to God and the universe? Lennox explains:
It is likewise a category mistake to suppose that our understanding of the impersonal principles according to which the universe works makes it either unnecessary or impossible to believe in the existence of a personal Creator who designed, made, and upholds the universe. In other words, we should not confuse the mechanisms by which the universe works either with its cause or upholder.
 Roger Penrose, The Road to Reality (New York: Alfred A. Knopf, 2005), pp. 762–765.
 “Teaching About Evolution and the Nature of Science,” Available at The National Academies of Sciences, Engineering, Medicine (1998), accessed October 14th, 2017, https://www.nap.edu/read/5787/chapter/11.
 Richard C. Lewontin, “Billions and Billions of Demons,” Available at http://www.nybooks.com/articles/1997/01/09/billions-and-billions-of-demons/, accessed May 17th, 2017.
 C.J. Collins, The God of Miracles: An Exegetical Examination of God’s Action in the World (Wheaton: Crossway, 2010), Kindle Locations, 1374 of 2742.
 Alvin Plantinga, “Methodological Naturalism? Part 2,” Available at http://www.arn.org/docs/odesign/od182/methnat182.htm, accessed July 19th, 2017.
 Explanatory power is the ability of a hypothesis or theory to effectively explain the subject matter it pertains to.
 John Lennox, God’s Undertaker: Has Science Buried God? (Grand Rapids: Kegel Publishing, 2011), 44.