The God of the Gaps: Why God and science are not competing explanations.

Posted on June 11, 2012 By

“The common belief that… the actual relations between religion and science over the last few centuries have been marked by deep and enduring hostility… is not only historically inaccurate, but actually a caricature so grotesque that what needs to be explained is how it could possibly have achieved any degree of respectability.”

–Cambridge University historian of science Colin Russell

“Just because science hasn’t explained something yet doesn’t mean that we should just give up and say, ‘God did it.'”

-A comment made, in various versions, by multiple atheist commenters to this website.


The cartoon above provides a good depiction of how many (perhaps most) atheists perceive God. They perceive him as an explanation for natural phenomena that competes with scientific explanations, and that serves to fill gaps in scientific understanding. But this perception is completely flawed and misguided.

Atheist Dan Barker (Public Relations Director for the Freedom From Religion Foundation) and Christian (philosophy professor) Richard Howe publicly debated God’s existence at the University of Florida in 1997. Barker comments:

“All through human history, we’ve had…questions [such as these:]. What causes thunder? What causes the lightning? I don’t know, there must be a big Thor [Norse God] up there that does it. [audience laughter] But now, now we’ve learned about electricity. Now we don’t need that Thor anymore. We’ve erased that God, right? And as the line moves up, answering more and more questions, the gods disappear. We still have a lot more questions up here and we no longer put a God down here… He’s living in gaps, and the gaps are getting smaller…”

And, among atheists, Barker is certainly not alone. A review of comments made by atheists at this website (or virtually any other website where God’s existence is debated) will quickly reveal that many (perhaps most) atheists consider God and science to be competing explanations for natural phenomena, such as thunder and lightning, or the phenomenon of life. God, according to this atheist view, is only necessary to fill gaps in current scientific understanding….”the God of the gaps.” Eventually science will fill the last of these gaps and then there will be no longer be any need for God whatsoever.

Citing a natural mechanism as an alternative explanation to God is what is known as a “category error” in philosophy.

But when atheists make such arguments, they commit what is known in philosophy as a “category mistake” or a “category error.”

Oxford University mathematician John Lennox provides excellent commentary on this logical fallacy as it relates to the above described atheist reasoning in God’s Undertaker: Has Science Buried God?:

“…In some quarters the very success of science has also led to the idea that, because we can understand the mechanisms of the universe without bringing in God, we can safely conclude that there was no God who designed and created the universe in the first place. However, such reasoning involves a common logical fallacy, which we can illustrate as follows. Take a Ford motor car. It is conceivable that someone from a remote part of the world, who was seeing one for the first time and who knew nothing about modern engineering, might imagine that there is a god (Mr. Ford) inside the engine, making it go. He might further imagine that when the engine ran sweetly it was because Mr. Ford inside the engine liked him, and when it refused to go it was because Mr. Ford did not like him. Of course, if he were subsequently to study engineering and take the engine to pieces, he would discover that there is no Mr. Ford inside it. Neither would it take much intelligence for him to see that he did not need to introduce Mr. Ford as an explanation for its working. His grasp of the impersonal principles of internal combustion would be altogether enough to explain how the engine works.”

“So far, so good. But if he then decided that his understanding of the principles of how the engine works made it impossible to believe in the existence of a Mr. Ford who designed the engine in the first place, this would be patently false – in philosophical terminology he would be committing a category mistake. Had there never been a Mr. Ford to design the mechanisms, none would exist for him to understand. 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 its upholder.”

“The basic issue here is that those of a scientistic [not to be confused with “scientific”] turn of mind like [prominent atheists] Atkins and Dawkins fail to distinguish between mechanism and agency. In philosophical terms they make a very elementary category mistake when they argue that, because we understand a mechanism that accounts for a particular phenomenon, there is no agent that designed the mechanism. When Sir Isaac Newton discovered the universal law of gravitation he did not say, ‘I have discovered a mechanism that accounts for planetary motion, therefore there is no agent God who designed it.’ Quite the opposite: precisely because he understood how it worked, he was moved to increased admiration for the God who had designed it that way.”

Lennox’s above comments call attention to a grave oversight that is pervasive in atheist reasoning: Citing a natural mechanism behind a natural phenomenon is NOT equivalent to explaining the ultimate source for that phenomenon. In Lennox’s words, “We should not confuse the mechanisms by which the universe works either with its cause or its upholder.” Put more simply, it is impossible to cite a natural mechanism as the source of the natural world because natural mechanisms are an aspect of the natural world. An aspect of something cannot be cited as the cause for that something.

Citing a natural mechanism behind a natural phenomenon is NOT equivalent to explaining the ultimate source for that phenomenon.

Moreover, Lennox’s above critique calls attention to an even more basic problem prevalent in atheist thought: The persistent confusion of scientific and ontological questions. God is an answer to ontological questions, NOT scientific questions. A little review of terminology is in order. The Oxford Dictionary defines science as “The intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and natural world through observation and experiment.”

Ontology is the branch of philosophy which discusses the nature of being, existence, or reality. And the Oxford Dictionary defines philosophy as “The study of the fundamental nature of knowledge, reality, and existence, especially when considered as an academic discipline.”

Any time a natural mechanism is cited as the cause of a natural phenomenon, a scientific explanation has been proposed….but an ontological explanation for the source of this mechanism has NOT been proposed. These are two separate questions. In simpler terms, science discusses questions of intermediate (or natural) causes, and ontology discusses questions of fundamental (or ultimate) causes.

Science cannot study the premises upon which science is based. Questions that are of a fundamental nature cannot be answered by science.  As an illustration, consider the question of why 2 + 2 = 4. Such a question cannot even be subjected to scientific study because it discusses a FUNDAMENTAL mathematical premise. Will a scientific experiment conducted sometime in the future finally reveal to the world why 2 + 2 = 4? Of course not, because such a fundamental mathematical premise is something which underlies science and is therefore meta-scientific. Scientific inquiry can contribute to ontological reasoning, but it cannot replace ontological reasoning.

For further illustration, consider the following breakdown of the topic of evolution:

Scientific question: What accounts for the diversity of life on Earth?

Proposed scientific answer to the above question: A mechanism known as the random mutation of genes and the natural selection of reproductive offspring is responsible for the diversification of life (Darwinism).

Ontological question: What is the source of this above mentioned mechanism? (Please read Why Evolution Cannot Be Used To Rationalize Atheism and Riddles for Atheists for a more thorough exploration of this topic).

Atheist answer to the above ontological question: ??????????????? (Atheist commenters to this website are encouraged to furnish any answers they wish).

Theist answer to the above ontological question: A conscious and intelligent being, God, is the fundamental ground of reality, and the mechanisms we experience in nature are the product of this being.

As I discuss in my essays titled God Is Real…Why Modern Physics Has Discredited Atheism and The Ultimate Cart Before the Horse (Why Atheism is Illogical), theism holds God to be the fundamental ground of reality, whereas atheism is rooted in the materialist worldview, which holds that inanimate matter is the fundamental ground of reality. Citing inanimate matter as the fundamental ground of reality leaves some very significant unanswered questions. Regarding this point, Albert Einstein wrote (also cited in Riddles for Atheists):

“You find it strange that I consider the comprehensibility of the world (to the extent that we are authorized to speak of such a comprehensibility) as a miracle or as an eternal mystery. Well, a priori, one should expect a chaotic world, which cannot be grasped by the mind in any way… the kind of order created by Newton’s theory of gravitation, for example, is wholly different. Even if man proposes the axioms of the theory, the success of such a project presupposes a high degree of ordering of the objective world, and this could not be expected a priori. That is the ‘miracle’ which is constantly reinforced as our knowledge expands.”

Please note that Einstein says this “miracle” is “constantly reinforced,” rather than diminished, “as our knowledge expands.” If inanimate matter is the fundamental ground of reality, why is the universe comprehensible rather than chaotic, and why is it so ordered, rather than disordered? Citing a natural mechanism or a physical law does NOTHING to answer such questions because three fundamental, ontological questions remain unanswered: 1) Where do natural mechanisms and physical laws come from? 2) If matter is the fundamental ground of reality, how can matter be compelled to do anything, much less follow a physical law (or “regularity” if you prefer)? 3) Why these laws and not laws that allow for chaos and disorder?

The theistic model places consciousness (God’s consciousness) as the fundamental ground of reality, which is much in line with modern physics (as demonstrated in God Is Real…Why Modern Physics Has Discredited Atheism). And if God’s consciousness is the fundamental ground of reality, and our world is a manifestation of this consciousness, it is immediately clear why there is such a “high degree of ordering of the objective world.” But if matter is the fundamental ground of reality (as with atheism) the question of where this ordering comes from is completely unanswered.

Further, NO AMOUNT of “the study of the structure and behavior of the physical and natural world” will ever by itself answer such fundamental questions as why there even exists a physical and natural world, for us to study, in the first place. In his book The Limits of Science, Peter Medwar (an Oxford University immunologist who won the Nobel Prize for Medicine) writes:

“That there is indeed a limit upon science is made very likely by the existence of questions that science cannot answer, and that no conceivable advance of science would empower it to answer…I have in mind such questions as:

How did everything begin?

What are we all here for?”

And David Bentley Hart incisively lays down the distinction between scientific and ontological explanations, as they relate to God, in his book Atheist Delusions:

“Even if theoretical physics should one day discover the most basic laws upon which the fabric of space and time is woven, or evolutionary biology the most elementary phylogenic forms of terrestrial life, or palaeontology an utterly seamless genealogy of every species, still we shall not have thereby drawn one inch nearer to a solution to the mystery of existence.”

“Even the simplest of things, and even the most basic principles, must first of all be, and nothing within the universe of contingent things (nor even the universe itself, even if it were somehow ‘eternal’) can be intelligibly conceived of as the source or explanation of its own being.”

In summary, atheists who argue that scientific explanations are an alternative to God either confuse, or deliberately conflate, science and ontology. We are not dealing with a “God of the Gaps,” but rather, as Lennox puts it, we are dealing with a “God of the whole show.” Atheists frequently try to frame the debate as God vs. science so as to distract attention from the inadequacy, or rather bankruptcy, of their ontological reasoning.

Scientific questions demand scientific answers, and ontological questions demand ontological answers. Therefore, answering such ontological questions as why there is such a “high degree of ordering of the objective world,” and why the world is comprehensible rather than chaotic (as Einstein marvelled at), by saying, “I don’t know, but science may someday figure it out,” simply has no value. Scientific and ontological explanations can and must interact, but science cannot by itself produce an ontological explanation because the scientific method cannot examine fundamental presuppositions that underlie science. Extra-scientific, and therefore philosophical/religious reasoning is a necessary part of the explanatory equation*.


*Please read I Believe in Science! Why Do I Need Religion?! for a further exploration of the necessity for extra-scientific, and therefore philosophical/religious reasoning.

  1. Anon says:

    Atheists may try to assert that we shouldn’t try to make things up to try to understand why we’re here or give our lives meaning. However, doesn’t this just mean that you give life the meaning of no meaning? Is anyone in accordance or am I talking nonsense?

    • C.S. Lewis put it best: “If the whole universe has no meaning, we should never have found out that it has no meaning: just as, if there were no light in the universe and therefore no creatures with eyes, we should never know it was dark. Dark would be without meaning.”

      There would be no such human concept as meaning if the universe had no meaning.

  2. RATIONAL DUDE says:

    Something occurred to me, and it seems to be a good contribution to the above discussion –too late by now, but hopefully it will be useful in another post? My primary aim in commenting is being useful.

    What I realized is that if atheism is true, a paradoxical conclusion is derived. The Postmodernists would still be wrong (facts would still exist), but Nietzsche (who denied the existence of truth) would be right.
    Truth only exists if we meet these two conditions: Firstly, there must be such a thing as a fact. What size are Sherlock Holmes’ shoes? There isn’t any fact to the matter. No possible answer could be given, as none of them would be true. None of them would be false either. This involves the second condition, which is Language can describe reality.
    For atheism to be the correct position, facts about God must exist. Namely, His non-existence. However, atheism gives us no assurance that language can describe reality. In fact, the concept of a meaningless universe precludes it, as language cannot describe a meaningless universe.

    The only thing that bothers me about this conclusion is how it could be turned on its head. I may have given the atheist invincible armor, so they can waive away any argument for God’s existence that rears its head.
    An irrational universe would not be expected to give evidence exclusively for the truth about its nature; maybe the universe really IS only six thousand years old? In an irrational universe, we would not be able to know.
    The comfort in this, however, is that it forces the atheist off his high-horse, as he is no longer the purveyor of rationality. Plus, the fact that he could communicate such a proposition indicates that it is false anyway.

  3. radaractive says:

    I immediately linked this page on my blog and intend to “advertise” the blog tonight on mine. The world is starving for more critical thinkers who are able to express themselves well to others. The world is full of people who do not THINK!!! It is frustrating to attempt to present evidence to the brainwashed masses, those who refuse to so much as audit their own worldview, let alone any aspect of what they have been taught to mindlessly repeat to their teachers in what passes for science classes in public schools.


  4. […] claims atheists make about science “explaining” things without the need for God. As I note in The God of the Gaps: Why God and Science Are Not Competing Explanations, atheists commit what is known in philosophy as a category error any time they declare that science […]

  5. Robert L Clark says:

    By far one of the best articles I have ever read on this subject and I have read many.

    Accessible to all levels and succinct well don .. book marking permanently as a reference.

    Thank you for taking time out of your life to write this.

  6. radar says:

    Fantastic article!!! Linked and posted and recommended around my circle…Since it was believers in the logical Creator God that founded the sciences in the first place, it is both ironic and foolish that so-called scientists deny the existence of God and promote a fatally flawed hypothesis as fact instead.

    Perhaps you will consider making a post in honor of Question Evolution Day on or around Darwin’s birthday?

  7. Hi Scott. Would you agree also then that scientific or natural reasoning can’t be used to parse religious claims? IOW, there is no logical way to determine if Hinduism, Christianity, or Santeria is ‘true’? I frankly think most atheists would be happy as clams to maintain a line between the natural and measurable and the religious. The problem for both sides is when ‘truth’ – which, as you state here, cannot be determined by rational means – is interjected as somehow binding.

    And do you recognize that science *has* moved the bar? Questions there were once ontological and mysterious have indeed been explained by use of the scientific method. We now understand that the earth doesn’t rest on anyone’s shoulders precisely because of rational investigation apart from religious dictum.

    I think the question is much more messy that you describe.

    • Scott Youngren says:


      The crucial role that Christianity played in the foundation of modern science is powerful evidence in support of the Christian worldview. Science historian Ronald Numbers writes:

      “Generations of historians and sociologists have discovered many ways in which Christians, Christian beliefs, and Christian institutions played crucial roles in fashioning the tenets, methods, and institutions of what in time became modern science. They found that some forms of Christianity provided the motivation to study nature systematically; sociologist Robert Merton, for example, argued seventy years ago that Puritan belief and practice spurred seventeenth-century century Englishmen to embrace science. Scholars still debate what Merton got right and what he got wrong, and in the intervening years they have drawn a far more detailed portrait of the varied nature of the religious impetus to study nature.”

      “Although they disagree about nuances, today almost all historians agree that Christianity (Catholicism as well as Protestantism) moved many early-modern intellectuals to study nature systematically. Historians have also found that notions borrowed from Christian belief found their ways into scientific discourse, with glorious results; the very notion that nature is lawful, some scholars argue, was borrowed from Christian theology.”

      Nancy Pearcey elaborates on how the Christian worldview was necessary for the rise of science in The Soul of Science:

      Science “demands some kind of unique soil in which to flourish.” Deprived of that soil, it is “as capable of decay and death as any other human activity, such as a religion or a system of government.”’

      What is that unique soil? [Science writer Lauren] Eiseley identifies it, somewhat reluctantly, as the Christian faith. “In one of those strange permutations of which history yields occasional rare examples,” he says, “it is the Christian world which finally gave birth in a clear, articulate fashion to the experimental method of science itself.“

      Eiseley is not alone in observing that the Christian faith in many ways inspired the birth of modern science. Science historians have developed a renewed respect for the Middle Ages, including a renewed respect for the Christian worldview culturally and intellectually dominant during that period. Today a wide range of scholars recognize that Christianity provided both intellectual presuppositions and moral sanction for the development of modern science.

      Science is the study of nature, and the possibility of science depends upon one’s attitude toward nature. Biblical religion gave to Western culture several of its fundamental assumptions about the natural world.

      To begin with, the Bible teaches that nature is real. If this seems too obvious to mention, recall that many belief systems regard nature as unreal. Various forms of pantheism and idealism teach that finite, particular things are merely “appearances” of the One, the Absolute, the Infinite. Individuality and separateness are illusions. Hinduism, for instance, teaches that the everyday world of material objects is maya, illusion. It is doubtful whether a philosophy that so denigrates the material world would be capable of inspiring the careful attention

      Science rests not only on metaphysical convictions but also on convictions about value. A society must be persuaded that nature is of great value, and hence an object worthy of study. The ancient Greeks lacked this conviction. The ancient world often equated the material world with evil and disorder; hence, it denigrated anything to do with material rial things. Manual labor was relegated to slaves, while philosophers sought a life of leisure in order to pursue the “higher things.” Many historians believe this is one reason the Greeks did not develop an empirical science, which requires practical, hands-on observation and experimentation.

      In Biblical teaching, nature is good, but it is not a god. It is merely a creature. The Bible stands firmly against any deification of the creation. Pagan religions are typically animistic or pantheistic, treating the natural world either as the abode of the divine or as an emanation of God’s own essence.

      Dutch historian of science R. Hooykaas describes this as the “de-deification” deification” of nature.” Natural phenomena-sun, moon, forests, rivers-are no longer seen as the locus of deity, no longer objects of religious awe and reverence. They are creations of God, placed in the world to serve His purposes and contribute to human welfare.

      The de-deification of nature was a crucial precondition for science. As long as nature commands religious worship, dissecting her is judged impious. As long as the world is charged with divine beings and powers, the only appropriate response is to supplicate them or ward them off. In the words of seventeenth-century chemist Robert Boyle, the tendency to regard nature as sacred “has been a discouraging impediment” to science. Science is not merely a method of inquiry; it begins with an intellectual stance vis-a-vis the natural world. As Cox writes, “however highly developed a culture’s powers of observation, however refined its equipment for measuring, no real scientific breakthrough is possible until man can face the natural world unafraid.” The monotheism of the Bible exorcised the gods of nature, freeing humanity to enjoy and investigate it without fear. When the world was no longer an object of worship, then-and only then-could it become an object of study.

      Biochemist Melvin Calvin, winner of the 1961 Nobel Prize in Chemistry for his discovery of the Calvin cycle, agrees with this concept. He writes:

      “As I try to discern the origin of that conviction, I seem to find it in a basic notion . . . enunciated first in the Western world by the ancient Hebrews: namely, that the universe is governed by a single God, and is not the product of the whims of many gods, each governing his own province according to his own laws. This monotheistic view seems to be the historical foundation for modern science.”

      William Lane Craig writes:

      Christianity furnishes the conceptual framework in which science can flourish. Science is not something that is natural to mankind. As science writer Loren Eiseley has emphasized, science is “an invented cultural institution” which requires a “unique soil” in order to flourish. Although glimmerings of science appeared among the ancient Greeks and Chinese, modern science is the child of European civilization. Why is this so? It is due to the unique contribution of the Christian faith to Western culture. As Eiseley states, “it is the Christian world which finally gave birth in a clear, articulate fashion to the experimental method of science itself.” In contrast to pantheistic or animistic religions, Christianity does not view the world as divine or as indwelt by spirits, but rather as the natural product of a transcendent Creator who designed and brought it into being. Thus, the world is a rational place which is open to exploration and discovery.

      Furthermore, the whole scientific enterprise is based on certain assumptions which cannot be proved scientifically, but which are guaranteed by the Christian world view; for example: the laws of logic, the orderly nature of the external world, the reliability of our cognitive faculties in knowing the world, and the objectivity of the moral values used in science. I want to emphasize that science could not even exist without these assumptions, and yet these assumptions cannot be proved scientifically. They are philosophical assumptions which, interestingly, are part and parcel of a Christian world view. Thus, religion is relevant to science in that it can furnish a conceptual framework in which science can exist. More than that, the Christian religion historically did furnish the conceptual framework in which modern science was born and nurtured.

      Physicist Paul Davies, the winner of the 2001 Kelvin Medal issued by the Institute of Physics and the winner of the 2002 Faraday Prize, discusses how the Judeo-Christian concept of natural law (instituted by a Lawgiver) is crucial for science:

      “People take it for granted that the physical world is both ordered and intelligible. The underlying order in nature-the laws of physics-are simply accepted as given, as brute facts. Nobody asks where they came from; at least they do not do so in polite company. However, even the most atheistic scientist accepts as an act of faith that the universe is not absurd, that there is a rational basis to physical existence manifested as law-like order in nature that is at least partly comprehensible to us. So science can proceed only if the scientist adopts an essentially theological worldview.”

      The famed English mathematician Alfred North Whitehead discusses how modern science arose as a result of Christian theology in the middle ages:

      “I do not think, however, that I have even yet brought out the greatest contribution of medievalism to the formation of the scientific movement. I mean the inexpungable belief that every detailed occurrence can be correlated with its antecedents in a perfectly definite manner, exemplifying general principles (causality). Without this belief the incredible labours of scientists would be without hope. It is this instinctive conviction, vividly poised before the imagination, which is the motive power of research: — that there is a secret, a secret which can be unveiled. How has this conviction been so vividly implanted on the European mind?

      “When we compare this tone of thought in Europe with the attitude of other civilizations when left to themselves, there seems but one source for its origin. It must come from the medieval insistence on the rationality of God, conceived as with the personal energy of Jehovah and with the rationality of a Greek philosopher. Every detail was supervised and ordered: the search into nature could only result in the vindication of the faith in rationality. Remember that I am not talking of the explicit beliefs of a few individuals. What I mean is the impress on the European mind arising from the unquestioned faith of centuries. By this I mean the instinctive tone of thought and not a mere creed of words.

      “In Asia, the conceptions of God were of a being who was either too arbitrary or too impersonal for such ideas to have much effect on instinctive habits of mind. Any definite occurrence might be due to the fiat of an irrational despot, or might issue from some impersonal, inscrutable origin of things. There was not the same confidence as in the intelligible rationality of a personal being. I am not arguing that the European trust in the scrutability of nature was logically justified even by its own theology. My only point is to understand how it arose. My explanation is that the faith in the possibility of science, generated antecedently to the development of modern scientific theory, is an unconscious derivative of medieval theology.”

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