John Harshman: Bottlenecks and Trans-Species Variation

I meant the “intro study” we discussed here:

First, off it does appear I ow you a bear…

I need to settle precisely how many trans-species alleles there are in this studies. I haven’t had a chance yet, and will do so soon. I’m expecting you are going to be right @John_Harshman, though I haven’t settled it firsthand yet.

So this how I see the evidence stacking up…

  1. Genome-wide divergence: 500 kya (very strong)
  2. Introgression: 500-700 kya (very strong)
  3. HLA exon diversity: uninterpretable because of balancing selection
  4. HLA introns: uninterpretable because of draft and balancing selection
  5. HLA exon inter-species variation: possibly in 1 case up to 5 alleles in one locus, and could have been convergence.
  6. HLA intron inter-species variation: not currently in literature.

I think that #6 is the most important experiment to do, and I encourage it. Even then, however, it would only be one line of evidence. Still, depending on the strength of the results, I’d call it enough. That analysis has not yet been done. The best number, then, is 700-500 kya, with the common ancestors of Sapiens, Neandertals, and Denisovans.

So, my assessment is that there is strong evidence against a bottleneck more recent than 500 kya. More ancient, the evidence has been overstated in the past (see Ayala and Venema) and it is much less clear. It is possible that further work will rule out Gauger’s preferred sole-genetic progenitor scenario. I welcome work to settle this question for good, but in the mean time we do not know from evidence yet. We have testable hypothesis, and a clear research plan. That is it.

I want to add @John_Harshman that I want to get the science right. This is actually a big reason I even have this forum. I want to resolve all objections by legitimate scientists like yourself. I’m committed to taking all your scientific objections very seriously, by either successfully making my case or changing my position.

Feel free to complain if I don’t get to a legitimate point after a week or so, but please don’t jump to conclusions after less than a day, especially late at night when conversations are ending. That is not a reasonable standard.

Doesn’t any sole-genetic progenitor scenario require a deceptive God who makes it look as though humans are related to other mammals? Or are you (I mean Gauger, really) talking about a 2-person bottleneck in a previously large population?


I believe its a two person bottleneck from a previously large population. One of the big criticisms from @glipsnort was what kind of natural disaster could cause that sort of bottleneck and leave the necessary conditions to repopulate. Then you also have to take into account this two person bottkeneck has to be male and female and able to breed. Why im not fan of this model. A mature male and infant boy arent going to do you much good. If the bottleneck only happened to
A small subset of the total population, what prevented that pair from reconnecting with other populations? What kind of geographical barrier? One thing we know about hominins is that they sure do move around. It’s not even genetics that makes me strongly question that model.


Yes, and one should also consider how unlikely it is for a two-person sample of a population to have maximum genetic variation in, apparently, every single gene. And how unlikely it is for a population to survive a bottleneck that extreme. Of course with enough miracles anything can happen.


That is actually a very significant issue. This is going to be hard to explain to Creationists, but the right number to look at is TMR3A. I’ve done the simulation work on this but haven’t put it out yet. That pushed the date back to about 700 Kya.

I’ll say though that the mosaic loophole is already were people are heading. It seems the Noahic Bottleneck is going to be more important.

Whatever the case, AIG style YEC has no place to hide. RTB will likely have to make some adjustments but might survive if they do. In my view, however, none of this makes any Theological sense. The Genealogical Adam view is far more coherent with everything. I’m only engaging the bottleneck question because people ask about it and I want to be rigorous.

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Remind me what TMR3A is. Does it deal with genes under frequency-dependent selection like MHC etc.? There seem to be a fair number of them.

More important for what? Falsifying YEC? If so, don’t see the point. YECs won’t believe it, and nobody else needs to be told.

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I’ve focused on Time to Most Recent Four Alleles (TMR4A). TMR3A is just Time to Most Recent Three Alleles. This is computed as a genome-wide median. The justification is explained in depth elsewhere: Heliocentric Certainty Against a Bottleneck of Two? - #6 by swamidass.

I do aim to clarify this point eventually. It is going to be a harder explain to creationists, as population genetics is already just so non-intuitive. Still, I’ve wanted to understand this, and will be likely publishing on this soon too. It has has taken a lot of simulation work that I have not yet put in public. In the end, it is not that consequential, because it just pushes back the date from 500 kya to about 700 kya (or so).

There are many types of YEC. I know you don’t believe me. Just trust that I am not crazy, and wonder if I might know my own community better than an atheist. That just possibly might be the case, right? In the end, time will tell. Let me make my case, and let’s see what happens. Certainly let me know of any scientific errors you find. I need this to be above reproach. On what YECs will or won’t do, that is a different question. Let me make my case without having to guard my flank.

Sure, but what case? Case for what, involving Noah? I’m not attacking you. If anything, I’m pointing out unclear parts of what you write, which seems a valuable function. I don’t know what you meant by “the Noahic Bottleneck is going to be more important”.

Oh I am very thankful for your push back @John_Harshman. You have this incisive and informed resistance that is simultaneously constructive. I’m very lucky to have you as a reader right now. I’m not complaining one bit. In fact, thank you for taking the time to hash this out with me.

I’m making a bid for peace for YECs with the Genealogical Adam. I am offering them a trade.

I’ll attack all the bad arguments against their position, but they have to contend with what is left. The Noahic bottleneck my best creativity cannot get around. Moreover, Scripture does not teach it. I have a solution though. They can keep all the theology and hermeneutics they say is so important to them, but they have to lay down arms with mainstream science making space for people outside the Garden, as they already do with Nephilim. That’s the deal I can offer with integrity, The Genealogical Adam.

That is the bid I’m making. Let me agree up front, AIG is not interested. I’m not talking about them. I"m talking about much of their base, who are honestly weary of war. In place of unending conflict, I am offering A Secular-Confessional Society. This is a good deal. It is a good deal for YECs, for scientists, and for atheists. We should all hope they many of them take it.

I understand you may be doubtful this gambit will work. Maybe. We do know one thing for sure already. I am going to get a hearing. So help me make sure the science is bulletproof, and that I do not overstate or understate one single thing. Defend my flank if you want to help us find a way to peace.

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On this I vehemently disagree. There is no way to interpret that story except that all people not on the ark died. Of course the writers were not familiar with a spherical planet, with any lands very far outside the Middle East, and certainly not with any continents other than Asia, Africa, and Europe. Or with any humans living outside those areas. To them, what they knew was the entire world, and not just in a metaphorical sense.

Yes. If there are any YECs whose only concern is the creation of humans, I have not met or heard of them. YECs demand a young creation, not just a young creation of humans. Is your experience really that different from mine?

I bring you not peace, but a sword.

I can accept that disgreement.

You are an atheist, right?

These are my people. Most my family are still YECs. Yes, I am sure that my experience is different than yours.

I’m speaking nationally on this topic. I’m hearing from students and leaders all the time. There is an immense amount of fear of retribution in YEC communities against anyone who does not toe the line. In private, I hear from even some YEC leaders that they are ready for a change. Observing how this is playing out, if we are lucky, it will be a tipping point.

I’ve been invited to speak to large groups of YEC kids (including homeschoolers), and then been invited back. Here is what the leader of one YEC group (anonymous for now) wrote me:

I am (and we are as an organization) very aware of you. In fact, one of our board members attended your debate with Dr. Sanford. I appreciate your call for civility in the debate about origins… and I appreciate that you walk the walk. “By this all men will know that you are My disciples, if you have love for one another.” John 13:35

I’m telling you that there is a side to YEC most people outside the community do not see. I do because it was the world in which I was raised. I know these people. They are my people, even though I am convinced they are horribly wrong on the science.


Does this side have any online presence that one might observe?


The last sentence of the quoted text is salient!

Allowing for a one-time Special Creation is tolerable if there is no attempt to overturn all of physics. But if it takes a long chain of supporting miracles that threaten to overturn Science… it changes the whole point of the scenario.

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Ah, but that’s 5 alleles in Group B only. If you look at the full tree from that paper, it’s necessary for there to be at least 7 alleles predating the human/chimp split at that locus. So you need to invoke convergence at least 3 times.

As I said, I have to look at that more closely and I will. However, this is a far cry from the greater than 20 that Ayala claimed. Also this study does not test for convergence either. When you look at the convergence test, you see that there is an immense amount of convergence, so 3 alleles by convergence is hardly a stretch. This is especially true when you take the Ka/Ks ratio into account. The clock on the synonymous mutations is much much lower than what we would expect if it was not convergence.

It is transpecies variation in one sense, but the evidence from this alone is not strong enough to demonstrate it is caused by shared history rather than shared environmental pressures and convergence.

What do you suppose would happen if you tried an analysis using only the synonymous mutations?

Did you ever get around to that?

Not closely enough to disagree with you with confidence.

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