Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)

@T_aquaticus, perfect answer.

@Swamidass, it is clear that @DennisVenema has been avoiding the “bugaboo” of “Defining what is a Human” by simply ignoring the categories, and working with a single continuity of “common descent”.

While common descent is a maze of riddles if you are going from “older to newer” populations (because you never know when you are going to end up in a genetic cul de sac).

But if we are going backwards, from “newer to older”, there’s only path to follow, right?

Some might want to entertain the idea that one branch “cross-bred” with another branch… but is that in keeping with the Biblical model of human descent? Yes, there are the Nephilim … but is that how you and @RichardBuggs are going to solve the diversity problem?: “we get around the one mating pair bottleneck” by introducing a few hundred additonal breeding pair where one of the genetic contributors are Nephilim"

Even if we were to allow for that … it doesn’t look like you can get down to a single mating pair, or even a few hundred mating pair in just 6000 years.

Oh, I’m quite sure that bloppobops had a unique origin - right here! I guess if I’ve quoted your post that’s now N=2, and writing out the term once more bumps them to N=3. :slight_smile:

In all seriousness, I won’t be able to contribute much of anything to this thread for the foreseeable future. Merry Christmas, all.

Hi Dennis,

I would love to do this, but my offer of moving on was contingent on us agreeing that it does not provide a suitable citation to support your case in chapter 3 of Adam and the Genome.

Please let me just summarise why this paper does not support your case.

  1. The fact that the authors conclude from their data that there was not an out-of-Africa bottleneck is because they have data from both inside and outside Africa and they can compare the two sets of populations. It is the relative levels of diversity in the two populations that allow them to exclude an out-of-Africa bottleneck. They spell this out clearly even in the abstract (“The comparable p value in non-Africans to that in Africans indicates no severe bottleneck during the evolution of modern non-Africans”) They cannot exclude an earlier bottleneck using their data because they do not have genetic data for a population from which their African populations were derived. To do this they would, I guess, need to use ancient DNA from bones, and they were working before this was technically possible. Therefore you cannot claim that because they exclude an out-of-Africa bottleneck, they also exclude a bottleneck in the lineage leading to the African populations.

  2. The authors estimate a long-term human effective population size of between 8100 and 18800. These estimates are based on present day numbers of segregating sites in the sample sequences, and estimates of mutation rate. This method assumes a fairly constant population size over time. No historical reconstruction of effective population size at different time-points in history is given. Thus this does not exclude a bottleneck.

  3. The authors present a coalescent analysis for this region gave a mean estimate of time to the most recent common ancestor (MRCA) for this region of 1,356,000 years ago; and the 95% confidence interval was between 712,000 and 2,112,000 years ago. This is assuming a constant effective population size of 10,000. Using the approximation of @swamidass that the time to the coalescent of 4 alleles will be a quarter of this time, this means a bottleneck could have occurred between 178000 and 528000 years ago. And these figures do not include an adjustment in the light the point that I have made about rapid population growth after a bottleneck giving further reductions of these dates.

Therefore it seems to me very clear that this paper does not support your case.

I am puzzled as to why you are not willing to concede this rather minor point. After all, looking back over your previous posts in this discussion, your own understanding of the paper and its methods have clearly deepened during the course of our discussions, and your position has shifted somewhat.

You initially seemed to think that Zhao et al (2000) based their conclusions about effective population size on their coalescent analyses.[quote=“DennisVenema, post:87, topic:37039”]
Have a look at Table 5, which shows their data for the distribution of TMRCA values. This is the data and analysis they are basing their conclusions on. Bottlenecks increase the probability of coalescence (this is also how PSMC methods work). We see a distribution of TCMRA values for the alleles in the study. This is basically what a PSMC analysis does sequentially for an entire genome to get a much larger sample size.
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I immediately showed that this was wrong, but you continued to believe this through-out most of our discussion until you finally re-read the paper.

You also thought that the method they used to calculate effective population size did not assume a fairly constant population size over time:

You were wrong on this point, so then you said:[quote=“DennisVenema, post:97, topic:37039”]
I guess I’m asking you to look at the TMRCA data there and think about your hypothesis (a bottleneck to two in the last few hundred thousand years).
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You then appear to have made the mistake of thinking that a bottleneck could only have happened at the TMRCA. This is clear in the quote below, where you date any potential bottleneck at the TMRCA[quote=“DennisVenema, post:102, topic:37039”]
That study identified 75 variants in this region that have a minimum coalescence time of over 700,000 years. The mode is 1.2 million years, and 700,000 is the lower bound of the 95% confidence interval for the combined sample. So, how did all of that variation survive a bottleneck to two? It can’t. So, how did all of that variation arise after a proposed bottleneck to two? Through new mutations. How long would that take? Even with a steady-state population of around 10,000, about 1.2 million years.
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You then made the mistake of suggesting recombination was unlikely to have occured much in a 10,000kb region[quote=“DennisVenema, post:109, topic:37039, full:true”]
Richard - are you aware how closely linked those variants are? They’re at most 10,000 bases apart. Are you seriously suggesting that they passed through a bottleneck en masse in two individuals and then recombined to the forms we see now?
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I think that Joshua’s analysis has shown you to be wrong on this point.

You also suggested that the raw data presented by Zhao et al does not form clusters that could have been derived from four ancestral haplotypes:

By “eye-balling” in Excel and by drawing a haplotype network in Splitstree, I have shown this to be wrong.

You later expressed skepticism that three mutations could occur within a timeframe of a few hundred thousand years[quote=“DennisVenema, post:231, topic:37039”]
I’m still not seeing how you can fit everything you need into the timeframe you’ve allowed yourself. If there is a bottleneck to 2, every haplotype in the Zhao (2000) data set has to come from your four ancestral haplotypes. Why did you decide that three mutations was an acceptable deviation from those types? How do you have time for three mutations, each interspersed with drift?
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However, the coalescent analysis of Zhao et al clearly shows that many cumulative mutations have occurred in this region in such a time-frame.

You also suggested that the low Ne after a bottleneck would reduce the numbers of mutations available[quote=“DennisVenema, post:231, topic:37039”]
Don’t forget that if you lower Ne to get a faster coalescence time, you also lower the number of forward mutation events that are plausible.
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But I argued that if the population revered quickly, this effect would be small, and expansion to an Ne of over 10,000 would quickly allow far more mutations.

Thus, I am struggling to see how you can still think that this paper supports your case.

As we have been discussing the paper, you appear to have changed your position on when in history you believe a bottleneck has been shown to be almost certainly impossible. On page 55 of Adam and the Genome, you wrote:

"It seems our smallest effective population size over the last 18 million years was when we were already human, at around the time our ancestors left Africa…
All methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last 3 million years or more – long before our lineage was even remotely called “human”.

You now seem to be saying in the current discussion that in fact you only think a bottleneck is excluded by the data in the last 200,000 years:[quote=“DennisVenema, post:247, topic:37039”]
A few questions for you - if we take as reasonable your suggestion that Zhao (2000)'s data coalesce to four haplotypes between 300,000 - 1,000,000 years ago, how does that help your case? In Adam and the Genome I consistently discuss humans as a species arising ~200,000 years ago. So, by your calculations, Zhao (2000) supports my case - human variation in this all region of the genome cannot be reasonably explained by a bottleneck to 2 individuals within human history, as I argue in AatG. Am I missing something here?
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Yes, you do discuss humans as a species arising ~200,000 years ago, but you also say that “the human lineage has not dipped below several thousand individuals for the last 3 million years or more – long before our lineage was even remotely called “human””. Thus, it seems to me that a bottleneck between 300,000 and a million years ago would be a direct contradiction of the claim you make on page 55 of Adam and the Genome.

All in all, it seems to me that we have made considerable progress in our discussion of Zhao et al over the past weeks. It has helped us clear up several misunderstandings of the paper and of its methods. It has helped us all to think through how to think about a bottleneck in terms of a coalescent analysis. It also appears to have helped you to change your position expressed in Adam and the Genome – that a bottleneck could not have occurred in the last 18 or 3 million years – to a position that one could not have occurred in the last 200,000 years.

Given all this progress, it baffles me that you are not willing to now concede that Zhao et al does not support you case in Adam and the Genome, and is not therefore an appropriate citation. I honestly don’t think you have much to lose by making this admission. It is not as if you actually cited Zhao et al in your book. It is not mentioned there. Why not just admit that you were mistaken to cite it?

I also will struggle to contribute much to this discussion over the Christmas period. I will be reflecting on it though from time to time. I wish you and all other contributors and readers a very happy Christmas. Thanks for an interesting discussion so far, and helping me to try to answer my questions about bottlenecks.

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Richard, while I think it’s very magnanimous of you to “offer” to review the stronger papers you demanded of Dennis 300 comments in on this thread, all for the meager price of his admitting something you’re demanding of him, I cannot help but notice you remain free of offering your own such admissions of whether the body of evidence compellingly attests to common descent, or if the body of evidence compellingly excludes a bottleneck of two in the human lineage within the past 10,000; 50,000; 100,000; 200,000; etc. years. Obviously basic questions of science highly relevant to this conversation.

I merely point this out as you’re drawing a link between what a scientist is willing to admit to what the evidence does or does not support, and ostensibly their credibility as well as how productive a conversation with them may or may not be. All the while you continue to refuse to admit to what the evidence does or does not support. On topics Dennis and others have repeatedly asked you to address.

I just thought I’d point this out. Since I believe in the golden rule. So please don’t do unto Dennis what you yourself are not prepared to have done to you. Or perhaps more aptly put:

Yet, as only a simple reader on this thread who only captures your interest whenever I elicit information from Dennis you find useful, I breathlessly await your ignoring what I’ve brought to your attention (or lack thereof) while you continue on your merry way of pushing the envelope on what double standards may achieve.

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@RichardBuggs, introduces his charge that @DennisVenema contradicts himself with this reference to page 55 of “Adam and the Genome”:

He then proceeds down a long-winded narrative, where he quotes @DennisVenema on the following:

DennisVenema:
“A few questions for you - if we take as reasonable your suggestion that Zhao (2000)'s data coalesce to four haplotypes between 300,000 - 1,000,000 years ago, how does that help your case? In Adam and the Genome I consistently discuss humans as a species arising ~200,000 years ago. So, by your calculations, Zhao (2000) supports my case - human variation in this all region of the genome cannot be reasonably explained by a bottleneck to 2 individuals within human history, as I argue in AatG. Am I missing something here?”

As we can readily see, Dennis asks the rhetorical question: “if we take as reasonable your suggestion that Zhao’s … data coalesce to four haplotypes between 300,000 [to] 1,000,000 years ago, how does that help your case?”

This is where @RichardBuggs attempts the coup de grace: “… Thus, it seems to me that a bottleneck between 300,000 and a million years ago [aka 1,000,000 years] would be a direct contradiction of the claim you make on page 55.”

Waaaaiiiiiittttttttt a minute here … You are quoting Dennis as contradicting himself by using his sentence “… if we take as reasonable your suggestion that Zhao (2000)'s data coalesce to four haplotypes between 300,000 - 1,000,000 years ago, how does that help your case?”

I think everyone in the room should nonchalantly check the continued presence of their wallets in their back pockets or in their purses. I think we’re watching one of those classic movie plots in real time … where wallets go missing and and someone almost always gets an ice pick in the throat…

The heliocentric quote, which I thought was the object of your concern, is about humans (Homo sapiens). When I’m speaking about our lineage leading up to humans at 200KYA I use “lineage” or similar.

The other two quotes remain valid. Does “it seems” sound like I’m saying this is as certain as heliocentrism? That would be quite the understatement. That is a summary statement of all the lines of evidence in the literature to date that do not provide support for a bottleneck below ~10,000 at any time in the last 18MY (which remains the case).

"All methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last 3 million years or more – long before our lineage was even remotely called “human”.

This quote also remains valid. There are no studies in the literature that support a lower bottleneck, and several that support large Ne values over this timeframe (PSMC and LD studies, for example). If there were (perhaps if I had missed one somewhere?) I’m sure you would point it out if you were aware of it.

So: “heliocentric certain”: humans. Pretty darn certain: lineage leading to humans over the last several hundred thousand years (say back to ~500,000 years ago). Confident but not as definitive: lineage over the last few million years. Survey of literature to date: no evidence of a bottleneck greater than thousands anywhere, regardless of time.

You suggest that perhaps the data in Zhao could go back to 4 haplotypes in 178,000 years. How certain are you about that value? You have to (a) pick the very lowest value within the 95% CI and then (b) assume that 1/4 of that is reasonable in this case. One quarter of the mean value is 339,000 years ago, which pretty much any scientist on the planet would say is more accurate than cherry-picking the lowest value. The upper bound (528,000 years ago) is just as probable as the lower bound. I could pick that value with the same confidence which which you pick the lowest one.

If that’s what counts as a “win” that’s a pretty thin “win”, don’t you think?

Ok, so that we can move this conversation forward to the stronger data: I agree that Zhao (2000) does not support the case I make in Adam and the Genome, in that it might be statistically possible to have the variation in their dataset come from 4 haplotypes less than 200,000 years ago.

Done and dusted. Shall we move on?

Are you ever going to answer my questions about common ancestry and what you think are reasonable speciation times? They are directly relevant to determining mutation rates.

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I am still wondering exactly who out there thinks its important to their faith that there’s a bottleneck of two in the homo sapiens lineage somewhere in the last 500,000 years, where this bottleneck is part of a lineage which includes common descent and homo sapiens evolving from pre-homo sapiens ancestors. Who are these people?

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I actually think there could be quite a few such people.

What I don’t understand is who it is that thinks it’s so important to pin Dennis into admitting fault in his published work. I would expect people are more interested in using this amazing meeting of the minds to discuss the actual science at hand. But what do I know?

This is speculation - so it’s worth what you paid for it - but I think the people most interested in this idea are people who reject common ancestry to begin with. There is already a move to make H. erectus “fully human” and ignore all the problems with that approach. In the big new anti-TE book this is clearly the strategy: they state that the cranial capacity of erectus falls within the sapiens range, and selectively quote the literature to make it sound like erectus is just like us. There is also no mention of the difficulties with such an approach.

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I’d agree. It seems Richard has purposefully evaded any acknowledgement that he sees humans sharing common ancestry, any acknowledgment that humans speciated some hundreds of thousands of years ago, and any acknowledgment that a bottleneck to two within any timeframe that exceeds young earth boundaries, whether 10K, 50K, 100K, 200K, etc. years is implausible.

If this is a truth finding mission Richard is engaged in, he’s done an excellent job avoiding stating what he thinks is scientifically true on these highly relevant issues. All for ostensibly the purpose of sowing doubt that perhaps if Dennis is wrong about a greater than 500,000 year timeframe on his bottleneck, maybe he’s also wrong on a bottleneck of less than 500,000 years including maybe only 6,000 years. A conclusion he may not state but would be more than happy to have his readers infer. And of course in such a model other hominids are just considered other humans and descendants of Adam.

This is what I suspect may be going on. Given Richard’s evasiveness on answering these very basic questions of biological science.

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That’s what I think, and that’s where the bait and switch comes in. These people want a literal “Adam and Eve”. I believe in a literal Adam and Eve, but they want all humans to have descended from this Adam and Eve, and it seems to me that they’re going to be told “Science cannot rule out an Adam and Eve who were the ancestors of all humans”, while quietly leaving out the part about no such bottleneck being found within the history of actual homo sapiens, and the fact that all models which might even allow for such a bottleneck are still predicated on common ancestry of humans from pre-human ancestors.

There are quite a few such people. Just yesterday a theologian commented to me on how he saw this conversation progressing. Right now, many are asking:

  1. Who is empathetic to the questions in the Church?
  2. Are those empathetic to their questions treated with respect?
  3. What are the certainty, limits, and extents of these findings?
  4. Who can we trust to be honest with us about the scientific evidence?

So yes, this is an immensely important conversation. @RichardBuggs, even if he is ultimately wrong, is coming off pretty good. Whatever one’s disagreement is with him, he is empathetic to the questions in the Church. That counts for a lot.

It is also surprising the resistance to #3, as that is a fundamental question in scientific work. Scientists are always questioning the mainstream consensus this way. This is not a rejection science, but how it proceeds. Clarity here has real value.

Other than the standard challenges with the “antiquity” of humans, what exactly are the difficulties with such an approach? And is this approach even really new?

Claiming that Homo erectus = “human” is a fairly standard claim in creationist circles. I’ve been reading AiG, for example, and was just given a copy of Contested Bones to review, which follows this age old pattern. Ironically, most scientists actually agree with them now. There was a major shift in thought on this over the last several years (decades?). This is why, for example, that Homo Erectus is considered “human” in the Natural History Museum. At the very least, we have to acknowledge that there is not yet consensus on the degree to which Homo erectus was “human.”

Moreover, their may never been consensus.I think the challenge everyone faces is in drawing a line somewhere in the distant past. There is no clear dividing point, so there is disagreement and consensus is ellusive.

And Richard could clear up all that confusion by answering a few basic scientific questions Dennis and others have requested of him. Let us hope he has it within him to do so.

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Yes, it’s common in the YEC literature, but they have all of this variation arising in less than 10,000 years, so they’ve got bigger problems that they are not dealing with.

It’s a relatively new approach in the OEC literature. RTB, for example, would strongly disagree with erectus as human.

The basic issues are that cranial capacity in erectus is quite different from sapiens, and behaviourally erectus lacks things we consider definitive of sapiens. Add to that the challenges of squaring the Genesis context with 2MYA.

And then there’s the challenge of carving a line between erectus and earlier hominins. If erectus is fully human, then the “gap” between “humans” and australopithecines and habilis gets that much smaller. Which doesn’t stop @agauger from trying - a big section in the TE book is devoted to trying to draw a firm line between erectus and other hominins.

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I couldn’t agree more. But it seems to me that there is a particular fervor here not primarily to determine “certainty, limits, and extents” but more than anything to force Dennis’s hand to recant something in his published work.

That’s right; the Tim Kellers and Henri Blochers of the world (who wrote In the Beginning) are keen on preserving a literal first couple who fell from grace, even if common descent has to be maintained. At least this modicum of literalness helps, for some, to preserve a certain fidelity to Pauline (Pauline/Augustinian) theology. We can agree or disagree and debate that, but this is how some will see it. And we do well to respect that.

Lastly, a general comment…

May I request that you divide participants here into “specialists” and “non-specialists” rather than “scientists” and “non-scientists”? Otherwise one gets the distinct impression that non-geneticist scientists are second-class citizens around here.

But in general, I agree: my comments (among others’) are not particularly helpful here. Let me add that while I’ve not said it, I honestly do respect and greatly appreciate the work that all the primary participants here — you, Steve, Dennis & Richard — are donating to this discussion. It is vitally important to the Church, and we (I) would do well to step aside and let it take its course with as little interference as possible, rather like a good golf tournament with its silent crowds. :slight_smile:

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But none of those questions are actually what I am referring to. So I am still looking for the people described in my questions. Remember, my question only includes Christians who accept evolution, obviously. It excludes the vast majority of people who don’t accept evolution, because they could not possibly accept an “Adam and Eve” who were not homo sapiens, or who were the descendants of non-homo sapiens ancestors. It also excludes anyone who doesn’t accept the earth could be over 10,000 years old. So who really are the people to whom Dr Buggs is referring?

But he has not shown the least empathy for, or even interest in, the exceptionally polite questions put to him right here, on this forum, by people who want to know the theological implications of his proposal. That also counts for a lot, but in a rather different way.

Right… @Swamidass, his role as Champion Apologist is certainly assured.

But on the other side, I think it’s pretty clear that he is also coming across as a bully.

Certainly not someone who refuses to say what they think the scientific evidence does or does not support, for apologetic reasons presumably. Those people I do not trust to give an honest picture of the evidence. Nor should anyone. Though let their arguments proceed forward fairly all the same.

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Here’s another two papers for @RichardBuggs’s reading list. I was chasing another rabbit trail and came across these, and thought they were relevant to the conversation.

First one is here (PDF). This one looks at polymorphisms that were present in the common ancestral population of humans and chimpanzees and which do not coalesce in either lineage. This means that both humans and chimpanzees (and in one case in their data set gorillas) have the same variants. The TMRCA values for these would thus be over ~4MYA (the lower bound of the human-chimp divergence). This would put an estimate of TMR4A at around 1MYA (or higher). Note: some of their examples are called into question by the next paper, but others are supported.

The next one references the one above, and also does a genome-wide scan for regions with limited and elevated TMRCA values. They identify several regions with TMRCA scores that predate the human-chimp divergence (including some identified in the above paper). Some of the TMRCA values are above 8 million years, which would place our estimate of TMR4A at around 2 MYA or more.

Just in case Richard, Josh and I needed more reading material… and @RichardBuggs, we really do need to know if you accept common ancestry if we’re going to profitably discuss these two papers.

Dennis,

Very interesting papers. I’ve read the first one already, but not the second. However, I am not sure how they help your case. As I understand it, you are trying to demonstrate…

  1. Homo sapiens specifically do not dip down to a single couple in 300 kya to the confidence we have in heliocentrism.
  2. Our ancestors as a whole do not dip down to a single couple between 300 kya and 3 mya with very high confidence, but maybe not as high.

As you put it…

As I understand it, the first claim appears to be novel, and I cannot find it in the literature anywhere. It would be help to see a paper that estimates population size of Homo sapiens specifically. I have not been able to find one. Have you?

The second one is only supported by the Ayala paper on MHCs, which is strong evidence in my view. The vast majority of studies are not even looking at population structure past 2 mya. So I am not sure how you get to high confidence at 2 mya to 3 mya.

As I read the papers you , the first paper…

This paper does not give a TMRCA > 4 mya for more than 4 alleles at any locus. They find 125 non MHC regions with ancestral variation, However, at none of these locations is there more than two or three haplotype clades shared by chimp and human. You can see some of them below; Figure 3…

The second paper is really an important paper, and I am glad you raised it. However, I am not sure how it helps your case. Table 2 and 3 give the TMRCAs the calculate in their method, which is notable for doing a much better job with recombination that most analysis:

This tables show the MAXIMUM estimates for TMRCA across the whole genome. Taking recombination into account, therefore, seems to REDUCED the estimates for TMRCA from 2 mya (as in your last study) to at most 600 kya. That measurement, however, appears to be an outlier. More consistently, we see TMRCA’s around 400 kya. [An error was made here. The TMRCA is by generation, not year. See my response below.]

Using our estimate that TMR4A approximately equals TMRCA / 4, that allows for a bottleneck after 100 kya (or 150 kya if want to use largest coalescence). This is consistent with TMRCAs from Y-chromosomes and mitochondria, and undermines your last paper too. I trust the TMRCAs here more than the 2 mya MRCA from the prior paper (which used a simplified analysis), because this is across the whole genome and uses a much more sophisticated method for detecting recombination. [An error was made here. The TMRCA is by generation, not year. See my response below.]

Now, it is possible when more data is used (rather than just the 69 genomes here) that a higher bound is placed. This is all strong evidence for common descent too. I am not sure, however, what this shows about your two claims. If anything, these two papers appear to undermine claim #1 and limit the amount of data we can expect to find for #2. [An error was made here. The TMRCA is by generation, not year. See my response below.]

Can you clarify how these papers help you?


Also, it seems odd to remind us all that absence of evidence is not evidence of absence.

[quote=“DennisVenema, post:308, topic:37039”]the literature to date that do not provide support for a bottleneck below ~10,000 at any time in the last 18MY (which remains the case).
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This quote is helpful and accurate…

If someone were to assert that there is an elephant on the quad, then the failure to observe an elephant there would be good reason to think that there is no elephant there. But if someone were to assert that there is a flea on the quad, then one’s failure to observe it there would not constitute good evidence that there is no flea on the quad. The salient difference between these two cases is that in the one, but not the other, we should expect to see some evidence of the entity if in fact it existed.
— J.P. Moreland and W.L. Craig,

I’m not sure we expect to see any evidence against a brief bottleneck in the very distant past (before TMRCA4). We do find the strongest evidence in transpecies variation of MHC, but that is remarkable. As far as I know, that is the strongest evidence there is (and I have always pointed to it).

However, appealing to lack of evidence is only meaningful if we expect to see evidence. It certainly does not get us to “heliocentrism level certainty”.

“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6

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