This is a nice long thread, and much of what I would have put in has been covered by others. I would definitely have brought in Feynman's talk about science as a method to prevent us from fooling ourselves.
Joe writes:
“With me the horrid doubt always arises whether the convictions of man’s mind, which has always been developed from the mind of lower animals, are of any value or at all trustworthy,” wrote Charles Darwin. “Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?”
Note that the above says "a monkey's mind" not a whole society of minds with a tradition of thousands of years of passing knowledge (true and not so true) through symbolic representation outside the genetic inheritance. The extent to which natural selection promotes that ability has yet to be studied.
Joe continues:
Although Darwin admits he wasn’t much of an abstract thinker, he could not shake the “inward conviction” that “the Universe is not the result of chance.” Unlike many who followed after him, he appears to have intuitively understood the paradox of combining naturalism with evolutionary theory: If evolution is a non-teleological process, it undercuts our ability to trust that we can form true beliefs and convictions.
First, what evidence do you have as to Darwin's "inward conviction"? Next, if Darwin's inward conviction were as you say, so what? Remember, he did not publish that and ask for peer review. What Darwin was right or wrong about in his time is not a bound on what we know is true or false, today.
As for the idea that a non-teleological process somehow cannot produce "reliable equipment" again, based on what evidence? Others have approached this above, I will just note that simulations of non-teleological evolution can, and do, produce control systems and nothing in theory prevents reliable equipment from being achieved out of ensembles of such; and evolution does ensembles a plenty.
Continuing with Joe:
To have trustworthy convictions, we have to have properly functioning noetic equipment (i.e., a brain, spinal cord, sensory apparatus, etc., that recognize reality). But can a strictly materialistic, non-teleological, evolutionary process produce such reliable equipment? The philosopher Alvin Plantinga, one of the greatest thinkers of our era, thinks the answer is “no.” Although his argument is too complex and tightly argued to be adequately summarized, the basic outline of his case shows his point to be all but incontrovertible.
No, no, a thousand times no. You do not get to tell us we must accept an explanation that is too complex for you to tell us.
Onward:
Plantinga claims, not that evolution is untrue, but that the truth of evolution is incompatible with the truth of naturalism. “As far as I can see, God certainly could have used Darwinian processes to create the living world and direct it as he wanted to go,” he argues. “Hence evolution as such does not imply that there is no direction in the history of life.”
What does imply that life is not directed, he adds, is not evolutionary theory itself, but the theory of unguided evolution: the idea that “neither God nor any other person has taken a hand in guiding, directing, or orchestrating the course of evolution.” For our purposes, we’ll call this view “evolutionary naturalism.”
No, what we see in the scientific evidence is that there is neither an indication nor a need for direction. It would not be possible to rule out direction that leaves no evidence of its action. We can't show evolution was not directed by Leprechauns or anything else that leaves no evidence.
Back to Joe:
Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties.
Again, this kind of look at evolution is about the maps of the outside world that naturally form in the brains of individuals, and puts no necessary constraints on the development of knowledge that is formed and passed on in culture, especially the culture after the development of the scientific method. As others have said, the scientific method is all about getting reliable knowledge from the work of imperfect humans.
Joe says:
Take Zed, a prehistoric caveman. Zed is the first to cross the line over tohomo sapien (his parents are very proud) and is the first to develop functioning noetic equipment that is the equivalent of our own. His equipment could produce four types of beliefs.
It is very important to understand that there was no "first homo sapien" we only see these changes looking back over long time periods at the characteristics of the study groups. It is like the Sorites question in philosophy of the exact grain of sand that turns a pile into a dune. In the history of human evolution every next generation looked and acted exactly like their parents. The process works over long time periods through the changing distribution of gene frequencies in a breeding population, which is difficult to see happening at any given point.
I am going to skip over the discussion of "Zed" because the issue of the validity of the beliefs of any given individual is not a restriction on the collective knowledge.
Back to Joe:
If, as evolutionary naturalism claims, our noetic equipment might have developed in different ways, then a belief in evolutionary naturalism itself could be any of the four types of belief listed above. What is the likelihood that evolutionary naturalism has produced in us cognitive equipment able to reliably form true beliefs and know that they are true? Extremely low. Even then, we could never truly know that we knew the truth, because we would know our belief might merely be the most advantageous to us.
No, because Zed did not come up with evolutionary naturalism by himself with only himself to talk to.
Finally:
In order to accept the naturalistic evolutionary explanation for the development of our noetic equipment we have to be agnostic about its reliability. All we would really know is that it works for evolutionary purposes, not for the purposes of discerning truth from falsehood. Evolutionary naturalism, it turns out, is a self-defeating argument. If we believe the theory, we have no reason to believe the theory is true.
Yes, without education (i.e. with only the info in the genes we get from evolution) we really need to be skeptical about our own thinking powers. Thankfully, we have education, and the scientific method has provided us with vastly more reliable knowledge that any one person could ever learn. Just as reliable knowledge produces aircraft we trust to get us from coast to coast, the evidence for evolution is reliable and overwhelming. As for direction, there is no indication, so far, of any kind.

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