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Eugine_Nier comments on [LINK] Loss of local knowledge affecting intellectual trends - Less Wrong
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In that case why is the allele still around at all?
Consider a deck of cards that is randomly shuffled. It must come to some arrangement. Now consider the chance that shufflling another deck gives the same result. That's only 1 / 52! which is around 10^-67. But if someone said that therefore no deck of cards is ever shuffled they'd be wrong. Similarly, consider a protein with 600 base pairs describing it. The chance that a mutation occurs in that specific protein at any given time is pretty small, the chance that the exact same mutation occurs will be much smaller by roughly two orders of magnitude (assuming just singleton substitution errors).
The key is that mutations occur but repeated mutations don't generally occur unless there's something very weird going on like in the case of Huntington's where there's a whole family of bad alleles and there's a biochemical quirk which makes the mutations much more likely.
Pardon me if I'm being obtuse, but wouldn't we expect "a whole family of bad alleles" to be the usual case, since you can break a protein in any number of different ways?
I've heard that some fairly high percentage of hemophilia A and B cases are de novo mutations (a quick Google turned up this). I'm sure it's because hemophilia is pretty lethal and often doesn't get the chance to be inherited, but it's another case where mutation rates do seem to matter.
Yes, hemophilia is an example like Huntington's where there's a family of alleles. And of course, in that case, the allele is extremely lethal, killing a large fraction of males, and killing any female that is homozygous. So the allele has to stay really rare.
In general though for most proteins it is surprisingly difficult to break them. Most mutations will actually be neutral. They will be neutral either because the mutated codon actually codes for the same allele, or codes for a chemically similar allele, or because it is a section of the protein which provides something like structural support, if it mighta ctually have a phenotypical effect that just doesn't matter much either way . Many other mutations might have a negative effect but it won't be the same negative effect or it will be a negligible negative effect.. Moreover, some of the negative effects from mutated proteins aren't because the protein itself is now broken at what it normally does but because the protein now in addition to what it is supposed to do gums something else up or isn't as easily broken down or something like that. Those sorts of things also require specific mutations to occur. So in general, it is very rare for a mutation to get repeated.