What is caused by physical means is neither rational nor irrational, true nor untrue except by accident. If it computer produces the result of an equation, and the result is correct, it is not because the computer knows it is correct: it is because it is correct, as it were, by coincidence with the truth, because it has been programmed with principles that it cannot discern as valid or invalid but which it has been programmed by a human being to take (but not know) to be valid. If cannot help produce that result. If the programming is wrong, it will produce the wrong result.
My perception of the truth of a proposition, say, in geometry, of the validity of an inference, of the validity of a rule that underpins inference, for instance the idea that if something is predicated of a group, it can be predicated also of a member of that group, is intuited automatically.
This underpins the whole of one's perception of reality and the whole of the understanding of what a human being is.
If every thought is caused by movements and interactions of atoms in my brain, nothing means anything, nothing exists except those atoms, everything is illusory, there is no logic or reason, there is no truth value to any proposition beyond descriptions of the operation of atoms, I've never loved anything or anyone, there is no right and wrong or good and evil, there are no ideas, there is nothing but subatomic forces and electrons entering into covalent bonds and suchlike. 'Circles are round', as a perceived truth in my mind, may be true, but only by coincidence with the truth, because the atoms in my brain have produced that observation, whilst they might have produced some other proposition that is not true, and I would not know that it is untrue, because there is no faculty of discernment of the truth of propositions. There is only the proposition itself, no discernment.
But note how no human being is able to hold that to be true and live. People either perceive a meaning to life or are upset because there is apparently no meaning, and this idea is offensive. When people truly adopt the idea that we are simply the accidental mechanical products of physics working through evolution, the show is over.
But look at humanity's vote: to live and continue living.
We know fundamentally that we are more than mere automata. That the mind finds itself reflected in the chemistry of the brain, not vice versa. The mind is not a shadow cast by the physical brain.
This is the primary philosophical question that must be solved before any other question can be validly addressed. It is the question of whether there are questions, of whether there is a philosophical case to answer.
And this question, like everything else of real value, is solved by a combination of intuition and inference, both of which rely on the independence of mind from the material. I, for one, and I think Peter Kreeft and C. S. Lewis would agree, hold that we are more than what Bill Wilson called a 'ten-dollar bag of chemicals'.