The Mysticism of Metaphysical Naturalism
Metaphysical naturalism advertises itself as the sober alternative to religion. No superstition. No divine action. No transcendent mind behind the cosmos. Just matter, motion, and the laws that tie them together.
That is the marketing story. The reality is stranger.
Strip away the slogans and you discover that naturalism rests on a set of unprovable commitments that look far more mystical than anything a Christian affirms. Not mystical in the poetic sense. Mystical in the irrational sense: effects without causes, order without origin, reason from non-reason.
Let’s name the pillars.
1. The naturalist begins with an undefined category
“Nature” becomes a catch-all box that can perform any task. The origin of the universe goes in the box. Consciousness goes in the box. Moral value goes in the box. Logical laws go in the box.
The sophisticated naturalist will object: “Natural means causally continuous with physics. Not undefined at all.”
Fair enough. But now state what physics is causally continuous with. At the foundation you find quantum fields, spacetime, mathematical structure, and laws that govern their behavior. Where did those come from? Why do they exist rather than not? Why are they ordered rather than chaotic?
“Causally continuous with physics” explains nothing about the existence or character of physics itself. The box has walls, but no floor.
The naturalist will reply that all worldviews face brute facts at some level. Theism stops at God; naturalism stops at nature. Even trade.
But this misunderstands the theistic claim entirely. God is not a brute terminus, a place where explanation stops and we shrug. God is an infinite font of ontology, epistemology, teleology, and mereology. The investigation doesn’t end at God; it opens into endless depth. Divine simplicity, the identity of essence and existence, the processions of Trinitarian life, the convertibility of being and intelligibility: these are not conversation-stoppers. They are invitations to further inquiry.
Think of the Mandelbrot Set. It is generated from an elegantly simple rule, yet it contains infinite complexity at every level of magnification. You never hit bottom. Every boundary you examine reveals further structure, self-similar but never exactly repeating. The simplicity of the generating principle and the inexhaustibility of what it produces coexist.
Divine simplicity works the same way. God is simple in essence: no composition, no parts, no distinction between what he is and that he is. Yet this simplicity is not poverty. It is the kind of unity that generates endless depth precisely because it isn’t a composite of finite pieces. Explore the divine nature and you find not walls but vistas.
Contrast this with naturalism’s actual stopping points: quantum fields that just exist, laws that just hold, rational order that just happens to obtain. These are like finite shapes. You can trace the edges, but there’s nothing more inside. The boundary is the end. Ask “why are the laws this way?” and you get nothing. Ask “why is reality rationally structured?” and you get a shrug. These are genuine termini. There’s no further structure to explore.
The asymmetry is not that theism has a final answer and naturalism doesn’t. It’s that theism’s ground is infinitely rich while naturalism’s ground is explanatorily barren. One is an invitation to endless science. The other is a sign that says “no further questions.”
That is mysticism.
2. The naturalist cannot ground the normativity of reason
The naturalist trusts his mind even though his worldview says the mind is a cosmic accident. He trusts logic even though he has no account for why logic should bind a material process. He trusts morality even though he claims value is a byproduct of evolutionary convenience.
The standard reply is evolutionary epistemology: “Natural selection explains why we have truth-tracking cognition. Organisms that model reality accurately survive better.”
This response confuses two different questions.
First, survival and truth are not the same target. A cognitive system optimized for reproduction needs beliefs that produce adaptive behavior, not beliefs that are true. False beliefs can be highly adaptive. Paranoia about predators keeps you alive even when no predator is present. Overconfidence in social status helps you secure mates. Evolution selects for reproductive success, not correspondence with reality.
Second, and more fundamentally, the evolutionary account cannot ground the normativity of logic. Logic is not merely a description of how we happen to think. It is a standard for how we ought to think if we want to reason validly. The laws of logic are prescriptive, not descriptive. They hold whether or not any mind grasps them. They held before biological life existed.
When pressed on this point, the naturalist faces a dilemma. He can say logic is “instrumentally binding”: if you want coherent beliefs, use logic; if you don’t care about coherence, logic has no authority over you. But this reduces logic to a tool, no different from a hammer. The person who affirms contradictions isn’t wrong; he’s just pursuing different goals. That’s relativism about reasoning itself.
Or he can say logic is “constitutive of rationality”: to reason at all is to be bound by logical norms. But then he faces the question he cannot answer: why should anyone reason? If reasoning is optional, and those who opt out aren’t making an error but simply “leaving the domain,” then rationality is a club with membership requirements, not an objective standard. Non-members aren’t wrong. They’re just elsewhere.
The sophisticated naturalist will eventually retreat to something like this: “There is no moral obligation to reason. You can be irrational. You’ll just suffer the consequences.” But this is the concession. There’s no obligation to reason. Irrationality is permitted. The only cost is pragmatic. And pragmatic consequences aren’t the same as error. You’ve turned “you ought to reason” into “you’ll find it useful to reason if you want certain outcomes.”
Push harder and the naturalist appeals to “structure.” Logic is the structure of coherent thought. It’s not a thing that needs grounding; it’s just how reasoning works. But what are structures, ontologically? Not physical (the naturalist admits logic is non-empirical). Not mental (he denies psychologism). Not abstract objects floating in Platonic space (he claims parsimony). What’s left? He’s positing necessary, universal, non-physical, non-mental structures that constrain all possible thought, and he cannot say what they are or where they exist.
Here is the irony. Even the naturalist, when speaking carefully about logic, ends up describing reasons as making demands on us. Uninvited demands. Demands we didn’t choose and can’t dismiss. He’ll say that something in us “compels” rationality, that reasons place claims on us “just by being what they are.”
That’s exactly what theism names and grounds. The naturalist has kept the phenomenon while declining the explanation.
He lives on borrowed capital. He uses tools that his worldview cannot provide.
That is mysticism.
3. The naturalist invokes emergence as a miracle word
Emergence is just a polite way of saying that features with no grounding somehow “arise” from lower-level states.
The sophisticated naturalist distinguishes weak emergence from strong emergence. Weak emergence, he says, is just complex behavior arising from simple rules through lawful causal processes. Nothing mysterious. Flocking patterns emerge from individual birds following local rules. Temperature emerges from molecular motion. No magic required.
Grant all of that. Weak emergence poses no problem because the emergent property is reducible in principle to the lower-level description. Temperature just is mean molecular kinetic energy. The “emergence” is epistemic, a matter of which level of description we find useful.
But consciousness, rationality, meaning, normativity, and intentionality are not like temperature. You cannot translate “this argument is valid” into a statement about particle positions and momenta. You cannot reduce “I ought to keep my promise” to a description of neural firing patterns. The content of a thought is not identical to the physical state of the brain that instantiates it.
These require strong emergence: genuinely novel properties that are not reducible to or predictable from the physical base. And strong emergence is precisely the place where naturalism asks you to accept that higher-order features simply pop into existence from lower-level states that do not contain them and cannot explain them.
The naturalist will say: “We don’t yet fully understand how consciousness arises. But every time science has encountered something labeled irreducible, deeper understanding has eventually followed.”
Notice the move. This is faith in future deliverables. “We don’t know, but it must be natural because science has succeeded before.” That’s not an argument. It’s confidence in a research program. And it’s exactly the kind of promissory commitment the naturalist accuses theism of making.
Rising is not explaining. If your worldview demands that rationality, freedom, mathematics, meaning, and consciousness all sprout from mindless matter through some unspecified process, you owe an account of how the miracle happens.
Naturalism cannot give one.
4. The naturalist practices a faith he refuses to acknowledge
When pressed on origins, the naturalist retreats to a single line.
“We do not know yet, but it must be natural.”
Notice the move. The conclusion is fixed before the evidence appears. Ignorance becomes a defense, not a problem.
The naturalist will say this is simply methodological caution, refusing to invoke supernatural explanations prematurely. But methodological naturalism (a research strategy) is not metaphysical naturalism (an ontological claim). The former says, “Let’s see how far natural explanations can take us.” The latter says, “Only natural explanations can possibly be true.”
The metaphysical naturalist has made a faith commitment. He has decided in advance that no evidence could ever count as evidence for a transcendent cause. Not because he has investigated and ruled it out. Because his worldview requires that it be ruled out.
He will claim that metaphysical naturalism is simply “inference to the best explanation” based on centuries of scientific success. But this conflates two things. Methodological success in finding natural causes doesn’t entail that non-natural causes are impossible. That’s an inductive leap that doesn’t follow. If you define “reliable results” as “natural explanations,” you’ve rigged the game.
That is not skepticism. It is faith in an undefined process that must eventually deliver the worldview he prefers.
5. The naturalist smuggles in the very transcendence he denies
Science works because reality is ordered, intelligible, and stable. The universe is mathematically transparent at every level we have probed. Physical laws hold uniformly across space and time. Rational inquiry yields genuine knowledge about the structure of the world.
None of these features come from the naturalist’s ontology. They are preconditions of empirical knowledge. They are what make science possible in the first place.
Here is the problem stated precisely:
The intelligibility of nature is not entailed by physics. Physics presupposes intelligibility. You cannot derive “the universe is rationally ordered” from any set of physical equations, because the equations themselves are expressions of that rational order. The order is the condition for having equations at all.
Therefore intelligibility cannot be explained by physics. It is logically prior to physics.
The naturalist will reply: “The universe has patterns. Mathematics describes them. That’s not transcendence; it’s pattern recognition.”
But this is exactly the question he’s avoiding. Why are there patterns? Why does mathematics describe physics? Why is reality the sort of thing that admits of rational investigation? The naturalist describes the phenomenon and calls the description an explanation. It isn’t.
If naturalism were true, we would have no reason to expect a universe that could be understood. Matter in motion has no inherent tendency toward rational structure. Blind physical processes have no obligation to produce patterns that finite minds can grasp. Yet here we are, in a cosmos that yields its secrets to mathematical analysis at every turn.
Rational order calls for a rational source.
The naturalist treats intelligibility as a brute fact, something that just happens to be the case. But “it just is” is not an explanation. It is a refusal to explain. And when the feature in question is the very condition that makes explanation possible, refusing to explain it is not philosophical modesty. It is a gap in the worldview that cannot be filled from within.
The Christian alternative
The Christian does not retreat into mysticism. He simply follows the logic. Order implies an Orderer.
The Christian worldview provides what naturalism cannot: a ground for the features of reality that make knowledge, science, and rational inquiry possible.
Reason is grounded in a rational Creator. Human minds can grasp truth because they participate, however finitely, in the Logos through whom all things were made. Logic is not an accident of evolution. It reflects the rational structure of reality itself, a structure that exists because it flows from a rational source. The normativity of logic, its binding authority over all thought, is not a brute fact. It is constitutive of being because being itself is grounded in Logos.
Morality is grounded in a moral Lawgiver. The “oughtness” that naturalism cannot derive from “is” has a home in a worldview where value is not a human projection but a feature of ultimate reality. The good is not arbitrary. It is rooted in the character of God.
Consciousness is grounded in a conscious Source. Persons do not emerge from impersonal matter through unspecified processes. Personhood is fundamental to reality, not a late arrival. Mind comes from Mind.
Intelligibility is grounded in the Logos. The universe is mathematically transparent because it was made through Wisdom. The “unreasonable effectiveness of mathematics” that puzzled Wigner is exactly what we should expect if the world is the product of rational design.
Existence itself is grounded in a necessary being. The question “Why is there something rather than nothing?” has an answer: there is a being whose essence is to exist, who depends on nothing outside himself, and from whom all contingent things derive their being.
This is not a retreat from reason into faith. It is the consistent application of reason to its own preconditions. The Christian worldview does not merely accommodate the features naturalism cannot explain. It predicts them.
Conclusion
Naturalism is not the escape from mysticism. It is its modern form.
It offers a closed universe filled with unexplained miracles that must not be called miracles.
A world that just “is.” A mind that just “appears.” A moral law that just “emerges.” A cosmos that just “orders itself.” A logic that binds all thought but belongs to no ontology. A “structure” that exists nowhere and in nothing but somehow constrains everything.
There is a name for that. It is not science. It is metaphysical mysticism wearing a lab coat.
The Christian looks at the same evidence and draws the rational conclusion. A universe of rational order, moral structure, conscious minds, and intelligible laws points to a source that possesses all these features in infinite degree.
Not a gap to be filled by future science. A foundation that makes science possible.
If you would like to discuss or dispute any of these arguments, I welcome the conversation.
James (JD) Longmire
Northrop Grumman Fellow (unaffiliated research)
ORCID: 0009-0009-1383-7698
Correspondence: jdlongmire@outlook.com