How do you know it has that capacity?
You claimed that if naturalism were true, and chemical events gave the brain the capacity to make judgments, then naturalism was self-refuting; I said no, if naturalism is true, and chemical events gave the brain the capacity to make judgments, it would
not be self-refuting. It makes no sense at all for you to respond, "how do you know that naturalism is true, and that chemical events give the brain the capacity to make judgments"!
You are assuming what you are trying to prove again.
But I'm not trying to prove the truth of naturalism, I'm only trying to show that your particular criticism of it is wrong.
The weighing of evidence would require the brain to operate according to the laws of logic, but if it is just physical brain states then it is only operating according to the laws of physics. While there is some minor overlap between the two, overall they are two very different things.
When you say that the brain "operates according to the laws of physics," you presumably mean certain physical activities (in accordance with physical laws) cause the brain to enter certain physical states; and that's a reasonable summary of what the naturalist would say. So when you say that in weighing evidence, the brain "operates according to the laws of logic," do you mean "logical activities (in accordance with logical laws) cause the brain to weigh evidence and reach conclusions"? That wouldn't be what a naturalist would say, because "logic" in itself isn't something which can cause anything to happen, certainly not in the naturalistic view of things.
Perhaps a better summary of the naturalist position is that certain physical activities (in accordance with physical laws) cause the brain to enter certain physical states; that those physical states cause sentient states; and that those sentient states include such things as weighing evidence. In other words, sentience is an emergent property of physical brain states. And it may be the case that an emergent property operates according to laws which are not present in the stuff that causes those properties to emerge. Moving water acts according to laws of fluid dynamics; but there is no fluidity, let alone laws of fluid dynamics, in hydrogen atoms and oxygen atoms.
Now it may well be that you just find the naturalist position about the mind being an emergent property of brain chemistry entirely implausible; you wouldn't be alone in thinking so. But even if it were an implausible position, that wouldn't make it a
self-contradictory position. "Brain states cause sentient states; sentient states allow us to pretty reliably weigh evidence and make decisions" is not a self-evidently inconsistent claim. It really makes no more sense to say "if naturalism is true, there's no such thing as weighing evidence, there's just brain chemistry" than it does to say "if physics is right, there's no such thing as water in motion, there's just molecules."
Do you agree or disagree with this: "If there is a chain of causes, in which an underlying cause gives rise to a more immediate cause, the immediate cause does not thereby become irrelevant or gratuitous."