If thinking is only chemistry, then the thought that thinking is only chemistry is also only chemistry.
Philosophical naturalism is the claim that the physical world is all there is. No God, no soul, no spirit. Matter and energy, physics and chemistry, and nothing standing behind them. It presents itself as the hard-headed, scientific view, the position of people who have grown up and put away myths. It is worth taking seriously, and worth stating fairly, because it is the default faith of the modern West.
But naturalism has a problem it cannot solve, and the problem is not out at the edges. It is at the very center, in the act of making the argument at all. Naturalism cannot account for the reasoning it uses to argue for naturalism. It saws off the branch it is sitting on.
The Argument From Reason
Follow the logic slowly, because it is decisive. If naturalism is true, then every thought in your head is the end product of purely physical causes: neurons firing, chemicals crossing gaps, electrical signals obeying the laws of physics. Nothing more. Your belief that two plus two equals four is, at bottom, a brain state produced by prior brain states, which were produced by physics, all the way down.
Now ask the question that undoes the whole system: why would a process like that ever be trusted to produce true beliefs? Physical causes do not aim at truth. A chemical reaction is not right or wrong; it just happens. If your conclusions are simply whatever your neurochemistry cranked out, they are neither reasonable nor unreasonable. They are just what the atoms did. Reasoning requires that one thought lead to another because it is true, not merely because it was pushed there by blind causes.
C. S. Lewis put the knife in cleanly: if the whole universe has no meaning, we should never have found out that it has no meaning, because the very act of “finding out” would itself be meaningless. A thought that is only the byproduct of irrational forces gives you no reason to believe it is correct, including the thought that naturalism is correct. The naturalist has to use reason to reach naturalism, but naturalism, if true, is exactly the theory that guts reason of its authority.
Survival Is Not Truth
The usual escape is evolution. Natural selection, the naturalist says, tuned our brains to be reliable, because false beliefs get you killed and true ones keep you alive. But look closely and the escape does not hold. Selection cannot see beliefs. It can only see behavior. It rewards whatever keeps an organism breeding, whether the belief attached to that behavior is true or wildly false.
A caveman who runs from the tiger because he loves to sprint and thinks the tiger is a playmate survives just as well as the one who runs because he correctly believes the tiger will eat him. Behavior is selected; truth is optional. So evolution plus naturalism gives you a brain fitted for survival, with no guarantee whatsoever that it is fitted for truth. And if you cannot trust your mind for truth, you cannot trust the argument that led you to naturalism. The escape hatch opens onto the same cliff.
This is not a god-of-the-gaps move, filling a hole in current science with God. It is the opposite. It is pointing out that naturalism destroys the very tool science depends on. You cannot do science without trusting that the mind can grasp truth. Naturalism removes the ground for that trust.
Where Reason Actually Comes From
The Christian answer is not a dodge. It is a foundation. Reason is trustworthy because it is not an accident. It is the gift of a rational God to creatures made in His image.
“In the beginning was the Word, and the Word was with God, and the Word was God… All things came into being through Him, and apart from Him nothing came into being that has come into being.”
John 1:1, 3 (NASB1995)The word John chose is Logos. It means word, reason, the rational principle behind all things. John is saying the universe did not begin with mindless matter but with Mind, with Reason Himself, and that everything that exists came through Him. That is why the world is intelligible and why your intelligence can grasp it. Rational minds can know a rational universe because both came from the same rational God.
“Then God said, Let Us make man in Our image, according to Our likeness.”
Genesis 1:26 (NASB1995)You reason because you bear the image of the One who is Reason. Your thoughts can track truth because they were designed to, by a Designer who is Himself the source of truth. That is a foundation naturalism can never provide, because it starts with the mindless and tries to explain the mind, and the accounting never balances.
The Same Crack Runs Through Morality
What is true of logic is true of morality. If we are only rearranged chemistry, then “you ought not torture children” is not a fact about the world; it is a feeling your species evolved, no more binding than a preference for salt. Yet no one actually lives that way. Everyone treats cruelty as really wrong, not just personally distasteful. That universal conviction points beyond the molecules to a Lawgiver, the same God who grounds reason grounds right and wrong.
“For since the creation of the world His invisible attributes, His eternal power and divine nature, have been clearly seen, being understood through what has been made, so that they are without excuse.”
Romans 1:20 (NASB1995)Come, Let Us Reason
Here is the quiet irony. Every time a skeptic reasons carefully toward a conclusion, insists you follow the evidence, and demands you be logical, he is borrowing from a Christian universe to attack it. He is standing on the reliability of reason while denying the only foundation that makes reason reliable. The unbeliever who prizes logic is closer to the truth than he knows, because logic itself is a signpost pointing back to the God who is its author.
And that God does not despise the mind. He invites it.
“Come now, and let us reason together, says the LORD, Though your sins are as scarlet, they will be as white as snow.”
Isaiah 1:18 (NASB1995)Naturalism ends the conversation by making the reasoner an accident. The gospel opens it, and then goes further than logic ever could. The God who gave you a mind to know Him also gave His Son to cleanse you. Come and reason. And when reason has led you as far as it can, you will find a Person standing at the end of it, with hands held out and sins washed white.
Teaching the Word. Watching the Times.
— SmithForChrist