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The Big Problems with Naturalism

When skeptics, agnostics, and atheists oppose theists, Christians, and, specifically, Catholics, they frequently do so from the perspective of philosophical naturalism. This article will challenge the rational credibility of naturalism.

Naturalism has historical roots in early Pre-Socratic Greek philosophers: Thales, Anaximander, and Anaxagoras. These thinkers are sometimes called “naïve materialists,” because they espouse a purely material world—without explicitly rejecting a spiritual one. Later, Leucippus and Democritus elaborated “atomism,” the claim that all reality is composed solely of atoms and the void. But a “detour” into dualistic worldviews then took place through thinkers such as Plato and Aristotle, the Neo-Platonists, the Scholastics (including St. Thomas Aquinas), and early modern philosophers, such as Descartes. Naturalism re-emerged by the time of Baron d’Holbach (eighteenth century) whose work has been called “the culmination of French materialism and atheism,” as epitomized in his book, The System of Nature.

Nineteenth century atheistic materialism has largely been replaced today by “metaphysical naturalism,” which affirms a purely natural world, largely based on natural science, while clearly rejecting God and other spiritual entities.

There is also “methodological naturalism,” which describes natural science’s default expectation that all events are the result of physical forces or entities. While methodological naturalism operates in much the same manner as metaphysical naturalism, it makes no ontological commitments as to whether physical reality is all that exists, or not.

Metaphysical Naturalism's Assumptions

Naturalism, a science-based take on reality, makes many related claims, including: (1) there is an objective extramental universe shared by all rational observers, (2) the universe is governed by uniform natural laws that make it orderly and comprehensible, (3) such orderly reality can be discovered through scientific observation and experimentation, (4) nature is in principle rationally intelligible, (5)  mental entities, such as theories, mathematics, ethical values, and so forth, reduce to, or emerge from, neural activities in the brain, (6) the universe itself is its own ultimate explanation of its existence and operations, (7) nature operates as a blind force acting according to fixed laws with no purpose, (8) complex things, such as minds and living organisms, are composed of simpler constituents that are reducible to ultimate particles obeying physical laws, (9) reason itself is the product of an undersigned process with no intrinsic relation to truth (yet, naturalism is claimed to be true), (10) all things are either physical in nature, or else, depend upon or emerge from physical entities. (Of course, emergentism violates the principle of causality by assuming that you can get being from non-being.)

While the first four of these claims are necessary premises of natural science, the remainder consists of ontological philosophical claims about the world, which—although they talk about the same physical entities that science deals with—do not, as purely philosophical assertions, derive any authority from natural science. Much more importantly, naturalism itself derives most of its seeming authority from natural science. The problem is that, while natural science need not justify its own assumed premises – since no science demonstrates its own starting points, any philosophy, such as naturalism, relying on natural science must itself justify those same scientific assumptions, or else, that philosophy itself relies on mere assumptions.

This means that all of the above claims are either mere assumption, or else, require philosophical demonstrations which are not directly attempted by naturalists. Rather, the last six of the above claims are simply ontological assertions hiding behind a façade of scientific verbiage. They rely on the philosophy of naturalism, which presents them as just-so stories that defy disproof, but for which naturalism itself offers no direct scientific demonstration that is independent of philosophical assumptions.

These just-so stories appear scientific, but hide their naturalistic assumptions. For example, claims of (1) abiogenesis (which assumes that life can arise unaided from non-life), (2) nature without purpose, (3) mental entities reducing to the brain, (4) complex structures arising from fundamental particles, (5) reason coming from an undersigned process, and (6) the universe explaining its own existence – all these claims rely on the blatantly philosophical assumptions that (1) everything is merely physical and (2) no non-material intellectual agent exists to produce these observable effects. Hence, naturalism argues, if these higher effects occur, blind material nature must have somehow produced them. Logical, if and only if, you beg the question by assuming that naturalism is true in the first place! So, too, is the assumption that all things are physical or physically dependent.

Of the first four claims, it is true that science presupposes them – and properly so, since that is simply the scientific method, which, as science, but not philosophy, is perfectly valid. Yet, the necessary scientific assumptions that (1) an extramental universe exists that (2) is governed by natural laws, which (3) can be discovered and understood by reason through (4) using observation and experimentation – while perfectly proper to natural science – are nonetheless clearly not facts that the scientific method itself can prove. Rather, these assertions are the undemonstrated intellectual foundations upon which the methodology of natural science rests. These are, in fact, philosophical assumptions.

Finally, while natural science necessarily operates on the principle that an extramental world really exists and we can directly observe it, this principle – when combined with naturalism’s physicalist assumption, plunges naturalism into an epistemological quagmire from which it cannot be rescued – as will be demonstrated now in detail.

Naturalism's Version of Extramental Realism

Naturalism assumes extramental realism, which is the philosophical claim that a real physical world exists independently of our consciousness of it. And yet, its own materialist account of sense perception logically implies the conclusion that all we really know are the internal states of our brains. Because the entire process of perception is assumed to entail exclusively material/physical components, this leads to the “causal theory of perception,” which means, for example, that sight entails light coming from an external object, hitting the retina in the eye, being conveyed as nerve impulses by the optic nerve to the occipital part of the brain, where, it is naturally assumed, vision actually takes place.

From this logical sequence follows the absurd, but necessary, inference that what is known is no longer the actual external object, but simply some “neural pattern” internal to the brain.

This latter inference would appear to make natural science merely a description of the internal rules that govern brain states, and yet, the existence of a real external world is presupposed in order to derive the very physical model whereby is inferred that all we really know is internal brain states!

Naturalism assumes a principle of causality, since no realist account of the extramental world can be given unless we presuppose, gratuitously, that external events somehow impact our sensory faculties so as to give an essentially accurate account of the external physical world. And yet, naturalists are inherently wary of metaphysical principles, especially causality.

Most importantly, to know that the external object somehow properly corresponds to the internal image we must know directly both the image and the external object itself – for purposes of comparison, which contradicts the inference that all we directly know is the internal image.

Naturalism must also presume the validity of extramental physical laws and mechanisms in order to derive the biological description of the way the senses physically function so as to infer that what we really know is changes inside the brain, instead of extramental objects directly themselves, such as the tree outside my window.

All this entails an ongoing ambivalent epistemology, wherein the naturalist cannot decide whether he really knows the tree outside his window, or merely an image of it inside his head. If he follows the physiological/optical pathway from the external tree to the inside of his brain, he must deny direct knowledge of the tree, and thus, of the whole external world. But if he does not directly know the external world, how then does he develop the scientific model that leads him to deny his immediate knowledge of the external world?

Implicit in the previous assumption is the problem of how does the naturalist even know that the external world exists at all – assuming we never actually have direct knowledge of it and all our scientific knowledge appears merely to be studying the relationships of neural patterns inside the brain?

If naturalism is actually based on so many assumptions, why do naturalists so firmly believe in its essential truth, or at least, that it is the only rational, sane way to approach reality – complete with immense confidence that nothing spiritual or metaphysical exists? The standard defense is that science has proven itself, and thus, indirectly, the value of a naturalistic perspective—because science works. It predicts experimental results which actually happen. And it makes phenomenal progress in understanding the extramental world. Conversely, they point out, religion and philosophy make no empirically verifiable predictions – at least none that skepticism cannot challenge.

Still, we don’t know if natural science actually works unless we can verify that the external world actually mirrors the claims of scientific progress. But naturalism merely assumes the existence of that world. As I have demonstrated elsewhere, naturalism’s inherently physicalist ontology necessarily leads to a subjectivist epistemology. Unless the naturalist assumes the world is extramental, all his “proofs for naturalism” cannot be known to apply to anything except the inner consistency of his own brain patterns – that “brain,” which he can only know to exist itself by assuming that  the external world exists.

This is circular reasoning in the extreme.

Is There a Better Alternative?

All truth claims require substantiating reasons. Proof requires evidence—some prior, more certain fact or facts from which a claim is deduced in valid logical form. If someone gives no reasons for his claims, no one will believe him – and rightly so.

Surprising to many, Aristotle defined the original meaning of “science.” He insisted that, if you really know what you are talking about, that means that you know something is true, you know why it is true, and you know why it cannot be otherwise.1 This fulfills the Greek meaning of “epistêmê” as absolutely certain knowledge. In Latin derivation, we call it “science,” from the word, “scire,” meaning “to know.” From this comes “scientia”—in English, “science.” Not experimental science, but science as meaning objectively sure knowledge. Aristotle defined science as “certain knowledge through causes.” (Remember that experimental science itself ultimately turns out to be based on certain assumptions!)

The reasoning process through which one comes to a “scientific” Aristotelian conclusion is called the “scientific syllogism,” which epitomizes “certain knowledge through causes.” The “causes” are the premises, which are prior and better known than the conclusion, and from which, assuming a logically valid inference, the conclusion necessarily follows – since the knowledge of the premises, combined with a valid deduction, causes our certitude of the truth of the conclusion.2

But then, how do we know the truth of the prior premises? What if they need to be proven as well? Well, if they need proving, then we must prove them by the same logical process, that is, by finding certain prior premises from which these premises needing proof are validly derived.

The “Assumed vs. Proven Pseudo-Dilemma”

A seeming dilemma now appears. Either prior premises are themselves proven, or else, they are merely assumed. Could one regress to infinity in the taking of prior premises? Aristotle rightly says, “No.” In the practical order, since reasoning takes some time, if you had to go to infinity in establishing prior premises, the mind could never traverse the infinite time it would take to reach a conclusion!

Thus, we must come finally to premises that are not themselves proven – which, then, it would appear, “proves” they must be assumed. Does Aristotle thus wind up mired in assumptions—just like the naturalist?

Not at all. Rather, insists Aristotle, what this logic actually demonstrates is that, since one cannot go to infinity in the taking of prior premises, we must come to first premises which – though they are not proven—neither are they merely assumed. They must, somehow, be immediately evident—evident in themselves.

Now a truth can be made evident by prior premises, as shown above. But it can also be “evident in itself,” that is, if it is somehow immediately evident. There are two ways in which a statement can be evident in itself: (1) if it is immediately evident to the senses, or (2), if it is a self-evident, metaphysical universal first principle of being.

But, didn’t Descartes prove that the starting point of all knowledge is just ideas or images in the mind? Isn’t that all we first know in sensation? Descartes did say just that when he posited his “Cogito.” Cogito, ergo sum. I think, therefore, I am. For Descartes, “thought,” as an internal, subjective experience, is the first object of cognition. But what he missed is that extramental reality is just as immediately evident as thought itself. In fact, it is logically prior to thought, since the thought or idea or image is but a secondary reflection of the object as externally encountered.3

If I open my door and see a man-eating tiger about to pounce upon me, I have no doubt about its given immediacy as an extramental object. It is only when I close the door and then recall an image of the tiger that I can doubt the reality of the tiger itself. But, curiously, I cannot doubt having an image or idea of the tiger when I am actually experiencing it as an intramental object. Should I reopen the door, the tiger’s extramental reality would again be undeniably evident.4

The perfectly licit and proper methodology of natural science begins by admitting that extramentally observed things are real. But while science observes solely physical reality, it does not logically follow from this that only physical things can exist – as naturalism gratuitously claims.

A correct description of cognition shows that we have the immediate knowledge of external reality that both natural science and philosophy require. Doubtless, this is the basis for the naturalist’s instinctive certitude that an external universe of physical objects is real.

The naturalist’s problem is that his own gratuitously-assumed physicalism leads him to the absurd inference that all he really knows are images inside his brain – a conclusion that contradicts his own initial direct experience!

Metaphysical First Principles of Being

But, what about metaphysical first principles of being? How do we know that they are true, self-evident, and universally applicable?

From the first time the human intellect encounters any reality whatever in sensation, it forms a concept of being.5 This concept is universal since it applies to all being, not just some restricted form of it. The mind immediately predicates being of itself and forms the self-evident principle of identity: being is being. Equally immediately self-evident is the negation: non-being is not being. From these, with equal certitude, is formed the principle of non-contradiction: being cannot both be and not be (at the same time and in the same respect).

The principle of non-contradiction is so evident that no one can ever deny it without rendering his own utterance or thought utterly incoherent. While there are other self-evident first principles, it suffices to focus solely on this most evident universal first principle, since all naturalists must use it in every thought and every statement, but none can adequately explain where it comes from within the schema of naturalism.

Some naturalists may claim that the non-contradiction principle is merely a rule of logic. But, even the mere positing of a logical rule presupposes the principle itself, since the intelligibility of any rule would be vitiated if its contradictory could simultaneously be affirmed. The principle is simply “there,” and every honest intellect is forced to affirm it in the very act of understanding it. Naturalism lacks the epistemic tools to defend the principle; Thomism discovers it comfortably within its metaphysics of being, as I have shown elsewhere.

Moreover, unlike other universals, the concept of being applies to all possible beings, since while there can be beings that are not, say, trees, there can never be an actual tree that is not a being. Thus, while our knowledge of chickens holds good for all possible chickens, there might be a being that is not a chicken – resulting in our knowledge of chicken-ness not applying to it. But there can never be a being that is not a being, and thus, our concept of being applies to all possible beings. Hence, the principle of being, known as “non-contradiction,” applies to all possible beings and is truly transcendental.

The philosophy of naturalism rests ultimately on certain gratuitous assumptions, whereas, Aristotelian-Thomistic sciences are grounded on premises which are known with immediate certitude, by being either (1) immediately-given knowledge of extramental objects, or (2) self-evident first principles of existential metaphysics.

Given its evident epistemological inconsistency and ungrounded assumptions, does not naturalism itself merit skepticism?


  1. Aristotle, Posterior Analytics , I, ch. 2 (71b 8-15).
  2. Ibid., (71b 18-32).
  3. Brother Benignus Gerrity, Nature, Knowledge, and God (Milwaukee: Bruce Publishing Company, 1947), 300-305.
  4. Ibid., 304-305.
  5. Ibid., 360.
Dr. Dennis Bonnette

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Dr. Dennis Bonnette retired as a Full Professor of Philosophy in 2003 from Niagara University in Lewiston, New York. He taught philosophy there for thirty-six years and served as Chairman of the Philosophy Department from 1992 to 2002. He lives in Youngstown, New York, with his wife, Lois. They have seven adult children and twenty-five grandchildren. He received his doctorate in philosophy from the University of Notre Dame in 1970. Dr. Bonnette taught philosophy at the college level for 40 years, and is now teaching free courses at the Aquinas School of Philosophy in Lewiston, New York. He is the author of two books, Aquinas' Proofs for God's Existence (The Hague: Martinus-Nijhoff, 1972) and Origin of the Human Species (Ave Maria, FL: Sapientia Press, third edition, 2014), and many scholarly articles.

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