Does neutral evolution explain the genetic differences between humans and chimpanzees

First of all, no one has claimed there were no beneficial mutations. The evidence for the existance beneficial mutations seems pretty clear.

Second, you keep coming back to “… different reproductive fitnesses as demonstrated by the 20,000 times differences in population size.” when the difference in fitness due to intelligence is more quality than quantity. This has been pointed out several times and you haven’t seemed to notice. There is a new thread discussing just this topic that might interest you:

Your most recent argument requires knowledge of just what those beneficial mutations are, and indeed the entire evolutionary sample space since the MRCA to do probability calculations. This is definitely far afield from your original claim.

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