Frank claims that the elephant weighs more than 1 ton.
Thomas claims the elephant weighs 5 tons.
Can they both be right?
It seems to me that the meaning of āthe 18 million year old dateā has gotten lost, which in turn is leading to some accusations that are not entirely warranted. As far as I can tell when reading the relevant paper cited in the āoriginalā Biologos piece, the 18 million year figure comes from this paragraph in the paper:
Speciation times and ancestral population sizes
In the presence of ILS, the divergence times can be separated from the speciation times. Assuming a substitution rate of 1.0 3 109 per year and a generation time of 20 yr, we find very recent speciation times for human and chimpanzee and for these and the orangutan (see Fig. 1C). The humanāchimpanzee speciation is estimated to be 4.22 Mya (standard error interval [4.20, 4.24]) and the human orangutan speciation to be 10.70 Mya [10.62, 10.78]. The average sequence divergence time of the latter is 18.17 Mya [18.08, 18.28]āa reflection of the large effective population size of 187,000 [185, 189] of the humanāchimpanzeeāorangutan ancestral species. The humanāchimpanzee ancestral population size is 47,000 [46.5, 47.5]. The inferred speciation times are similar across the 21 autosomes analyzed (Fig. 1D).
To the extent that the article at Biologos was just making a statement about (relatively large) effective population sizes as long as 18 million years ago, they seem to be correct. I donāt believe this has much bearing on other studies that focus on the more recent past, and I donāt believe this issue detracts in any way from @glipsnortās Biologos piece.
I agree. The issue is that many scientists, including the one who wrote that article, feel very differently about this than you @art. Keep in mind that there is a book still promoted heavily by the website on which @glipsnort published his article that includes this as evidence against @glipsnort, alongside other lines of evidence too.
It should be very easy for @glipsnort to dispatch with this set of arguments. It is not okay for him to just ignore them though. It is puzzling that he is not willing to explain his position.
As for @John_Harshman ās evidence, it is more complicated. That is harder to dispatch. @glipsnort certainly has to engage with him. The way I and WLC address this line of evidence is not entirely available to @glipsnort .
FWIW, I donāt think my claims contradict his article. I think heās saying that the data he assesses preclude a bottleneck of 2 after 500ka but do not address one before 500ka. His conclusion seems not to be that such a bottleneck is possible, only that his data donāt make it impossible. And Iām saying that phylogenetic data do address, and eliminate, the possibility of an older bottleneck.
So I agree with @T_aquaticus here.
Again, I donāt see this as disagreement. At least not on my part; Venema may be different.
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If you are correct, doesnāt the transpecies variation evidence it preclude the possibility of a bottleneck of 2 at 500,000? Iām pretty sure it does.
If Iām correct, you have to change this assessment.
The power of the trans species data you propound is that, if successful, it precludes a bottleneck any time within the last 6 million years.
So it seems you do disagree with his conclusion, but havenāt yet realized it.
Though you also chimed in quickly earlier to direct to this evidence too. So I think you do know that this contradicts his position 
.
You appear to be trying to start a fight where there is none, and that puzzles me. Yes, the cross-species polymorphism precludes any bottleneck of two at any time during at least the past 6 million years and I suspect at any time in the last 40 million. But nobody here is arguing in favor of a bottleneck of two either. There is nothing to change unless you stretch the interpretations of various things people have said beyond their sensible meanings.
I think you are misinterpreting his conclusion by adopting the least charitable possible understanding. This is far from peaceful. Usually you bend over backwards to find accord, and now you are bending over, in what direction is unclear, to find conflict. Very strange.
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No fights here. You appropriate raised this evidence. I want to see his response to it. I think neglecting to address this evdince is a significant omission.
When I discuss a 500,000 ya bottleneck, you always raise this objection with me. I have responded in depth to you, and actually do not make claims as strong as @glipsnort. This is no different.
He, however, is making a stronger claim than me. So his response is more important. This is no more a fight than when you raise this evidence against claims I make. I am grateful to you for this, as your resistance has greatly improved my argument.
If I misunderstood his conclusion, I invite @glipsnort to clarify.
Usually you are emphasizing the need to address the transspecies data. I agree. Iām not the only one subject to that criticism. Iāve modified my claims as a result of your pushback. In fact, I agree that he needs to address that data.
I fail to understand. @glipsnort is not proposing a bottleneck of two. So why should he have to confront evidence against something he doesnāt claim? Nor is phylogenetic inference the concern of population geneticists, and the evidence from population genetics was the subject of that article. I remain mystified by your belligerence on my behalf.
I donāt even think you have weakened the case, which depends not at all on Ayalaās focus, on strictly human alleles, and I think you have misunderstood the paper on convergence.
Then there was no bottleneck of two.
Iām pretty sure that without interbreeding between Adamās and Eveās lineages they would have no descendants. Perhaps there are a few words missing there? And of course thatās what āsole-genetic progenitorā actually means to people who value language.
There is no argument. You are trying to create one.
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I just mean scientifically. If you are unwilling to explain the evidence here, perhaps I will.
Agreed. WLC does not require a bottleck of two. He is not working from within @glipsnort 's paradigm.
I am always careful to clarify that the transspecies data might rule out a bottleneck of two, putting a minimum bottleneck of limit of 10 to 20 at worst. Thatās why @glipsnort 's claims are far stronger than any I have made.
@glipsnort is making a far stronger claim than am I, and he is certainly qualified to do so. I want to see him justify this claim.
Sure. You do not agree with my case. But Iāve already addressed that a different way. This is a more acute problem for @glipsnort 's claims about a bottleneck of 2.
No belligerence.
I understand him to be claiming to summarizing all the genetic evidence pertinent to a single couple bottleneck. He presents several lines of evidence, but leaves out the lines of evidence that several scientists claim rules out single couple bottleneck. That is a substantial omission.
Perhaps he has worded his claims so as to not claim that āthere is no evidence against a bottleneck of 2 before 500,000.ā That loophole would not be sufficient. No discussion of the genetic evidence pertaining to a single couple bottleneck is complete without addressing trans-species variation. He has not addressed this evidence.
You yourself point this out. You were not belligerent. You were just point out a key omission. I agree with your point and am making sure it is not lost. Thatās it.
He is claiming to present the genetic evidence pertinent to a single couple bottleneck. Thatās why the trans species data is important.
Of course, he is welcome to clarify exactly what he is and isnāt saying.
What??
That isnāt @glipsnortās paradigm. I truly do not know whatās going on here.
Perhaps you could quote the claim in question from the article, because Iām not sure what claim you mean.
???
I donāt think he makes any such claim. Heās summarizing all the population genetic evidence, as is appropriate for a population geneticist. Are you familiar with the cliche āLetās you and him fightā?
I wasnāt. I was in fact responding to you, asking for information.
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That is very true. WLC is not insisting there must be a bottleneck of 2, nor am I.
He is claiming to present the critical genetic evidence pertinent to a bottleneck of two. His take away from this evidence is that we can rule out a bottleneck more recent than 500,000 years ago, but more ancient than this the evidence is equivocal.
We addressed it like so:
You correctly point out that, then, WLC does not require a bottleneck of 2. That is exactly right. That is why this evidence is not relevant to his position.
If that is the case, he is more than welcome to explain. I am sure there are brief ways to deal with this. Iāve had to deal with extremely aggressive critics from all sides. In fact, you have pushed back harder on me. This is just collegial pushback. Iām sure he can handle it.
See here:
I responded ānoā because that was not one of Venemaās arguments. It is an argument you have taught me a great deal about. That is why I named you going forward.
You certainly are not pressing him half as hard as you have pressed me. I am certainly not pressing him nearly as hard as you have pressed me.
Nor is @glipsnort. Seriously, whatās going on here?
Please quote, for a start.
No, it was @glipsnort I was talking about.
Nobody said it was, to my knowledge.
Thatās because I donāt think there is any disagreement. I think you are misunderstanding the scope of his conclusions.
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@John_Harshman I see you confusion. At this point letās put the back and forth on hold. The only reason I raised this matter publicly is because @glipsnort insisted I do so. My preference was to stay out of this, but he was very insistent.
So letās hold off the back and forth, and wait till he responds. From there, I am sure there will be much more clarity. Thatās a far better approach than attempting to read his mind or word parsing.
As I said in the beginning, I didnāt want to be in a public back and forth. He insisted. So let him answer.
Dr. Schaffner never said that his assessment supported a bottleneck of 2 farther back than 500,000 years ago. He simply said that the data in his assessment couldnāt answer that question. I donāt see why that would require a reassessment.
Again, Schaffner was pointing to a single data set that he believed conclusively ruled out a 2 person bottleneck 10,000 years ago. That was the entire aim of the article. Never was Schaffner trying to accurately determine just how far back the evidence could take us.
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How does one entertain even the idea of a bottleneck of two when clearly there was a lot of admixture between many species of hominids for millions of years?
If thatās his response, Iād love to hear it from and and take from there.
Thatās what he wrote in his article. I donāt understand why he would need to repeat it.
Later in the article:
And farther on:
Everywhere in the article it is contrasting 10,000 years and 500,000 years, and what the evidence indicates about the human population at those time points. Nowhere does the paper attempt to put a hard upper limit on how far we can go back and rule out a 2 person bottleneck.
I canāt know what is going on in your head, but I suspect there are some past conflicts that are causing you to read too much into the article. I would suggest rereading the article with a bit more charity.
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Happy to hear this from him. If that is the case, I have follow up questions.