My point is that there is no evidence that chemical reactions can produce rational conclusions.
No, the point you were making, up until now, was that
even if chemical reactions caused correct or reasonable conclusions, we couldn't trust those conclusions because their cause was chemical and not logical. That's the point I've been disputing.
No, what I mean is that laws of logic are not cause and effect relations like the laws of physics.
Agreed. (In fact, that's exactly what I just said.) What you seem to believe, however, is that a naturalistic account of how human beings weigh evidence must
implicitly assume that at some point the laws of chemistry hand over control of the reasoning process to the laws of logic. (Or, as you put it, "The weighing of evidence would require the brain to operate according to the laws of logic.") But that is not the case. The naturalistic account is that physical activities cause brain activities, which cause mental activities; and that among those mental activities (at least for humans) were desires to know the right answers to things, consideration of how best to reach the right conclusion, and (sometimes) knowledge of what are considered the best kinds of rules for doing that; and that because of natural selection, our brains (and therefore our minds) have gotten pretty good at this, though obviously far from perfect.
At no point in this account does the naturalist need to assume any causal role for the laws of logic. And if this account is true, there is no self-undermining going on, no basis for saying you couldn't trust such a process to produce rational conclusions.
Even emergent properties are bound by the physical and therefore only a cause and effect relation.
I don't know what you mean by "only a cause and effect relation" in this context, or how that meets my objection. If naturalism is true, then physical events have a cause and effect relation with mental events like considering and weighing, and those mental events have a cause and effect relation with the conclusions we draw based on the weighing of evidence. Do you dispute this? If so, why?
Naturalism itself is not self contradictory but arguing for it with evidence and logic is. Physics is a cause and effect process, Premises and conclusions are a logical relation of inference. So while naturalism may theoretically be true, it makes no sense to argue for it because your conclusion is just based on the ratio of chemicals in our brains and not on rationally inferred conclusions.
The claim is that chemicals cause brain states, brain states cause mental states like considering, weighing and concluding, and the conclusions reached as a result of those mental states pretty reliably correspond with sound principles of logic and evidentiary reasoning: that is to say, they result in rationally inferred conclusions. Instead of simply repeating the claim in
bold, could you tell me why this process is either A) impossible or B) could
not result in rationally inferred conclusions?
Could you also answer my question about whether or not you agree that "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"?
Lastly, given that you agree that logical laws don't cause things; and given that you believe (I assume) that people are indeed capable of producing rational conclusions; then what sorts of causes
can produce those rational conclusions, if physical causes cannot? For example, suppose you asserted that the "choices of the spirit," and not chemical reactions, were responsible for the conclusions we drew. It would still be true that "laws of logic are not cause and effect relations like the laws of spiritual choice," so if you have a refutation of philosophical naturalism here, you also have a refutation of philosophical idealism (or basically any "ism", so far as I can tell).