Ok, you’re welcome to that opinion, but it’s completely at odds with population genetics & neutral theory. Do you know what ‘effectively neutral’ mutations are?
How so? Nowhere does neutral theory state that positive and negative selection don’t exist. Positive and negative selection operate right alongside fixation by neutral drift.
Yes, they are mutations that effectively don’t increase or decrease fitness. What do you think happens when mutations do effectively increase or decrease fitness?
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The vast majority of mutations are deleterious. Nearly every single one that can be tested by any known means. This means that any significant amount of positive genetic changes, if they are happening, must be in that dark corner we can’t (directly) examine. Effectively neutral mutations. This is, in essence, what @glipsnort has been arguing here. Do you disagree with him?
That’s incorrect. They do impact fitness very slightly, but they are not selectable. This means NS is irrelevant to effectively neutral mutations. Mutations having no impact on fitness are called strictly neutral, and they either don’t exist, or are so rare as to be negligible.
This is demonstrably false as PDPrice has already seen a list of known beneficial mutations in humans. Why PDPrice feels the need to continually misrepresent the data is something he really need to explain.
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In the human genome, the vast majority of mutations are neutral. This is why we only see 5 to 10% of the human genome under selective pressure. The other >90% of the genome is accumulating mutations at a rate consistent with neutral drift which means the majority of mutations are neutral.
Your proposal results in a very strange world. Humans have positive adaptations compared to chimps. The reason we are different from chimps is the differences in our genomes. Are you saying there are absolutely no beneficial differences for humans among the differences that separate us from chimps?
Why don’t we wait for @glipsnort to agree with your description of his position.
Hence, they effectively don’t increase or decrease fitness.
If those mutations start leading to the lowered fitness then they are no longer effectively neutral. That’s the part you are missing. You are assuming that the reduction in fitness is linear for each mutation, but there is no evidence to support this claim. In fact, there is evidence that additional mutations become more strongly deleterious as they accumulate which allows selection to remove them.
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That’s not at all what he’s been arguing.
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Correction: effectively (nearly) neutral. Not strictly neutral. There is still a fitness impact from these.
Correction: very slightly deleterious.
Let me answer you first as a modern evolutionist like Dr. Schaffner:
Yes, there are many beneficial differences, but they were built up very gradually from tiny changes that accumulated over time primarily via genetic drift.
Now as myself:
The differences between humans and chimps are not meaningful, because there is no genetic relationship between humans and chimps.
If he chooses to return, I would like him to pick up where our conversation left off. But if I’ve inadvertently misrepresented him, I welcome that correction so we can get it right.
They are called “effectively neutral” because NS is not effective on them. Not because there is no functional fitness impact.
“… it seems unlikely that any mutation is truly neutral in the sense that it has no effect on fitness. All mutations must have some effect, even if that effect is vanishingly small. However,there is a class of mutations that we can term effectively neutral. These are mutations for which Nes is much less than 1, the fate of which is largely determined by random genetic drift. As such, the definition of neutrality is operational rather than functional; it depends on whether natural selection is effective on the mutation in the population or the genomic context in which it segregates, not solely on the effect of the mutation on fitness.”
Eyre-Walker, A., and Keightley P.D., The distribution of fitness effects of new mutations, Nat. Rev. Genet. 8(8):610–8, 2007.
The distribution of fitness effects of new mutations | Nature Reviews Genetics.
Of course they are! Their fitness impact is significant only in aggregation, not individually.
Why did you make two different “corrections” to the same word: “neutral”?
Nearly neutral is correct, you don’t know that they’re mostly very slightly deleterious. That’s what you’re trying to prove, remember?
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Yes, I agree that it cannot be directly proved, but it can certainly be deduced from all that we do know. The burden of proof is on the person claiming that a signficant percentage of effectively neutral mutations are beneficial, when all the evidence from what we can actually directly test shows the opposite tendency, and when simple logic (“it’s easier to break a machine than to improve on it”) would strongly dictate the opposite.
LOL! Humans and chimps are closer to each other genetically than house cats are to tigers. I bet PD has no problems with the cat “kind” being related though.
LOL! There goes PD regurgitating his favorite YEC talking point again. It’s like a go-to security blanket. 
Once their accumulated deleterious effects become significant enough to be selectable, there is pressure to get rid of these mutations. Here’s a toy example.
A population accumulates 10 slightly deleterious mutations. When they had just 9, the accumulated deleterious effect was too small to be effectively selected against. When the 10th occurred, their accumulated effects then became selectable. For a start, there is now selection pressure against this 10th one being fixed in the population. If it does, there is now selection pressure against all 10 mutations (or for beneficials to compensate). If one of these mutations gets “corrected”, this genotype will be selected for. Now the population is back at 9 very slightly deleterious mutations, and there is no selection against them any more. This same process keeps happening as deleterious mutations occur in individuals. This is the certain amount of genetic load that is maintained in all populations, unless other factors interfere.
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That only works if you assume the entire genome is a “machine”, which isn’t supported by evidence. The opposite is supported - that most of the genome lacks a sequence-specific function that could be “broken” by mutations.
Selection pressure cannot see any individual effectively neutral mutation.
No, there isn’t. That 10th mutation is still just as much effectively neutral as all the other ones. You cannot simply turn off mutations. Mutations always keep happening, and there is always a limit beyond which NS is unable to see the mutation. NS is not omniscient or omnipotent.
It’s a nice idea, as far is it goes, but it bears no resemblance to genetic reality.
No, it can’t. You’re deducing it from the idea that all genomes were perfect some 6000 years ago, which you believe, but which isn’t true.
NO. The burden of proof for your claim that the vast majority of nearly neutral mutations are deleterious is on you.
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No. There’s no need to debate what fraction is functional: the human body is a machine regardless. And somewhere in the genome, there’s the information needed to code for that machine. And thus, our principle applies. It’s always easier to break a machine than it is to improve upon it.
But the genotype is a single inheritable unit (in simple terms, of course complicated by recombination). If person X is fitter than person Y because person Y carries an additional mutation, that means person Y is selected against, relative to person X. This means the addition mutation is selected against.
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If 90% of the human genome is non-functional, then that 90% can’t be “broken”, rendering your analogy inapplicable to the vast majority of mutations.
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But the combination of the 10th with the previous 9 isn’t. If creatures with all 10 get selected out then the 10th doesn’t get fixed.
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I think we all agree that most mutations that are not nearly neutral are detrimental, the question is what is the average fitness effect of those mutations that are nearly neutral. Take the threshold fitness effect for selection and divide by the mean fitness effect of nearly neutral mutations per generation and you get the number of generations between selectable adaptive mutations required for equilibrium. Fill in the blanks and show your work.