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

Faith & Science Conversation
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I think the burden is on you to support your criticisms with good science, which I don’t think you have done. There is no reason why any author needs to deal with criticisms that lack scientific backing.

Overall, Venema’s comparison of a 2 person bottleneck and Geocentrism is dead on. Both have been equally invalidated by evidence in every scientific sense.[quote=“RichardBuggs, post:197, topic:37039”]
Your book chapter places a burden of evidence very heavily upon yourself, especially as you claim such a high level of certainty about your view.
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That burden has been met. Venema has given at least 3 independent lines of evidence that all support a large historic population for humans over the last 200,000, at a minimum.[quote=“RichardBuggs, post:197, topic:37039”]
I have an inkling that perhaps your very high level of certainty in the case you are making is because you may perhaps be misinterpreting the data at quite a fundamental level, and by digging down to primary data I may be able to identify where you are going wrong - if you are.
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What you are insinuating is that the entire scientific community is misinterpreting the data, and you have yet to bring anything forward which brings those interpretations into question.

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Hi Dennis,

Thanks for being willing to grant me Zhao et al (2000) for the sake of the argument, and for pointing me to other data sets that you think might be harder to explain from a bottleneck of two. However, I would prefer not to be granted Zhao et al (2000) on those terms - I would prefer us to come to a full agreement. I need to know that you are willing to admit that you have been wrong before it is worth us progressing on to other data sets or other papers. If you are not willing to admit you have been wrong, even when there is clear evidence against you, then our discussion is unlikely to make much progress.

I have shown why the two aspects of the Zhao et al (2000) paper that you originally highlighted are not apropos our discussion – and I think that you have accepted my argument on these. More recently, I have sketched out why I think that the Zhao et al (2000) data is explainable from a bottleneck of two within the last few hundred thousand years, taking their own coalescence analysis as a starting point. As you will see from the paper, they used a mutation rate of 1.15x10^(-9). This is an order of magnitude slower than the mutation rate that you have suggested.

I think that what you are ultimately asking me to do in your recent posts is a full coalescence analysis going back to four haplotypes, with a population expansion. I think you are asking me to conduct these on the Zhao et al (2000) data, the Zhao et al (2006) data, and the whole of chromosome 21. I agree with you that this would be interesting to do, and would be a good test for the bottleneck of two hypothesis. Indeed, it would be nice to do this for haplotype blocks over the whole of the human genome, using phased genome sequences for thousands of individuals.

This would be a substantial amount of work, especially as I do not know of an off-the-shelf package that explicitly models coalescence back to two diploid individuals, and includes exponential (or even super-exponential) population growth, with multiple-merger coalescence events allowed. If we could come to an agreement that this would be a good test of the hypothesis (and I would value the view of @glipsnort on this) then we would have made some useful progress in this discussion.

I would just point out the elephant in the room, however: this is that every time you suggest to me a dataset to analyse to test the bottleneck of two hypothesis you are implicitly illustrating the major point of my blog: that this hypothesis still needs testing and has not been explicitly and reliably tested in an already-published analysis.

In my view the most constructive way ahead would be for you to admit that your chapter expresses far to high a degree of certainty on this matter, and cites a great deal of evidence that is actually not testing the hypothesis. Then we could all collaborate on some analyses that really do explicitly test the hypothesis (which would not be a small amount of work) and really start to come up with some answers. I would be happy to contribute to such a collaboration, in the limited time I have available, and would do so with an open mind as to what the outcome would be.

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Projection is a psychological disorder, not a scientific argument.[quote=“RichardBuggs, post:208, topic:37039”]
More recently, I have sketched out why I think that the Zhao et al (2000) data is explainable from a bottleneck of two within the last few hundred thousand years, taking their own coalescence analysis as a starting point.
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You need to explain how ALL of the data fits a bottleneck of two, and that includes the entire genome, not just a tiny snippet of it. Remember, there are MULTIPLE and INDEPENDENT lines of evidence. Focusing on just one makes it appear as if you are ignoring the evidence.[quote=“RichardBuggs, post:208, topic:37039”]
This would be a substantial amount of work, especially as I do not know of an off-the-shelf package that explicitly models coalescence back to two diploid individuals, and includes exponential (or even super-exponential) population growth, with multiple-merger coalescence events allowed. If we could come to an agreement that this would be a good test of the hypothesis (and I would value the view of @glipsnort on this) then we would have made some useful progress in this discussion.
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If there really were a bottleneck of two then the data would have reflected that. The methods used in these papers are up to the task, so I don’t know why you feel like you need to ignore them. Even estimates of a 100 person bottleneck would lend some credence to your arguments, but that isn’t what we see. Instead, the data clearly points to a population that is 4 orders of magnitude larger than the one you are proposing. FOUR ORDERS OF MAGNITUDE.

At what point do you admit you are wrong?[quote=“RichardBuggs, post:208, topic:37039”]
I would just point out the elephant in the room, however: this is that every time you suggest to me a dataset to analyse to test the bottleneck of two hypothesis you are implicitly illustrating the major point of my blog: that this hypothesis still needs testing and has not been explicitly and reliably tested in an already-published analysis.
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It has been tested.[quote=“RichardBuggs, post:208, topic:37039”]
In my view the most constructive way ahead would be for you to admit that your chapter expresses far to high a degree of certainty on this matter, and cites a great deal of evidence that is actually not testing the hypothesis.
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The problem is that your views are not supported by scientific evidence, so why should they be taken seriously?

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@RichardBuggs

1] All science is subject to testing and re-testing. Your insinuation that Dr. Venema’s is especially subject to such testing is not what I would call politie discourse!

2] How do you draw such a conclusion purely on @DennisVenema’s willingness to suggest a dataset for you to see for yourself? It’s exactly what any scientist would do when challenged by someone who appears to be without the fundamental skills to do the analysis himself.

3] If he hadn’t suggested datasets, you would say he was tilting at windmills… and that he is conducting his work all by himself with nobody performing comparative work.

4] I certainly can’t speak for @DennisVenema in terms of confessing - - to your satisfaction !!! - - that his conclusion or conclusions are somehow in error. But how is it that if you are not in a position to conduct these studies yourself that you presume to pressure anyone into admitting error?

Do you engage in this assault on any evolutionist, knowing that if there is ultimately nothing to your assertions, all you have to do is shrug your shoulders and say: “No harm no foul”?

Frankly, I have never seen this kind of approach before. Usually when someone wants to smudge-up someone’s reputation, they do the work necessary to prove that his results are in error. Surely you owe Dr. Venema that much of your effort - - instead of “phoning in” accusations that you could make against anyone - - even if purely on the theoretical possibility that someone may have used incorrect grammar in his conclusions.

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Hi Richard,

I respectfully disagree. The hypothesis has been tested - it’s even explicitly stated as such in some of the papers I’ve provided to you, and that you have not (as of yet) dealt with.

Pointing out other data relevant to the question and asking how this fits with a 2-person bottleneck is not some sort of admission that the hypothesis has not been tested. It’s an attempt to get you to see the difficulties.

I remain confident that my conclusion in the book is sound. I have not seen anything in this discussion that remotely suggests otherwise. There simply is no evidence to support the hypothesis of a bottleneck to 2. There are converging lines of evidence that our species has not dipped below several thousand individuals.

I think this exchange has been a good illustration to non-specialists just how far one has to go to try shoehorn the evidence into a 2-person bottleneck.

In part 3 of my reply to you, I’ll discuss why PSMC modelling could indeed detect a bottleneck to two, even if followed by rapid expansion. Then, Lord willing, we’ll move on to the Tenesa paper on LD. Perhaps you’ll have some additional comments then.

Best,

Dennis

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Richard,

If mandating full agreement between each step of a conversation were necessary between persons of an evolutionary and ID/creationist perspective, discussions would simply not happen. The fact that you are insisting Dennis move from his characterization of the Zhao (2000) paper as moderately but not robustly supportive of his claims to instead weak and not at all supportive of his claims, while holding hostage your even looking at and engaging what he put forward as his strongest backing in the literature till then, is extremely disrespectful of Dennis’ time and effort honoring your requests to produce such citations and frankly unbecoming of someone of your position. Either deal with Dennis’ strongest evidence or don’t. But if you choose the latter after all your repeated demands and chastisements for him to produce it, I suspect you will not be leaving with the respect of most readers here.

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How does a bottleneck of two in a 200,000 time frame change the impossibility of a bottleneck of two in a 6000 year time frame? This is like the climate denialists who think if they can show climate models are wrong by 10 degrees, then we might as well throw out all the research on global warming !

Now that is a good question. Exactly when does the good Prof. Buggs admit his error?

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No he isn’t. He has already pointed out that this hypothesis has already been sufficiently tested more than once. As he has told you explicitly, the reason why he has suggested that you analyze the data yourself, is that you keep insisting that the scientific work done thus far has not tested the hypothesis sufficiently, and it seems the only course of action which will persuade you otherwise is to actually use the data and replicate the tests which others have already carried out.

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It sounds as though you are waiting on a peer-reviewed paper before you decide what the data and statistics can truly show us. But from what Steve is saying, it seems a publication in this area is not likely forthcoming, since it would be insufficiently report-worthy. However, it has been demonstrated rather convincingly here and elsewhere that a bottleneck of 2 at a time of 6 kya is highly improbable. The mathematics is pretty clear about this, but of course, it cannot rule out a miracle of God. At this point, this is most tenable defense of the 2-person bottleneck.

I agree that it may be overstatement to conclude that the degree of confidence we have in this is on par with the degree of confidence we have in a sun-centered solar system. But pointing out that this data has not been through peer review and publication and calling it the “elephant in the room” ignores the elephant sitting in your lap whispering into your ear regarding the extreme improbability of a bottleneck of two at a period 6,000 years ago.

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To be fair to @RichardBuggs don’t forget that from the get-go he’s been open to the idea of a bottleneck much further back than 6KYA.

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Yes, but he hasn’t said how far back. I’d be curious to know how far back he feels the data excludes a bottleneck of two. And how far back a bottleneck of two may mean something to him.

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@cwhenderson,

And the Elephant sitting on @RichardBuggs’ lap is wearing a dress! There’s no way to miss it !

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@tallen_1 (and @DennisVenema):

Sure he has… he wrote it here :

He is willing to go back 200,000 years… but I somehow doubt he’d be willing to write an article that says that …

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Thanks. But his earlier statement to which he refers said low hundreds of thousands of years or lower. I’d like to know what Richard considers the lower bound of what the data can reasonably exclude. The reason I ask this is if Richard is willing to concede we can effectively rule out even by his standards a founding pair within the range of when humans became behaviorally modern, then the relevance of any purported “Adam & Eve” from that time would seem called into question. Or conversely, on the upper bound, if Richard would feel he’d garner a “win” by arguing the plausibility of a founding pair say 300,000 years ago, what theological meaning would this have to him for a species that was not just pre-behaviorally modern but not even anatomically modern as well? I’d like him to clearly state his claims here.

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Thanks for the reminder, Dennis. You have my apologies, @RichardBuggs. I should have been more careful.

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Yes, and that’s why I asked (several times), if he believes the evidence rules out a traditional Adam and Eve pair 6,000 years ago. He has chosen not to answer that, and I am reading that as an apologetic strategy to stay on the side of the YECs and IDers.

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I agree. There’s something very strange about a man brow-beating others to answer every one of his litany of inquiries while refusing to answer legitimate questions himself.

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Well, as Jon has noted, he has not answered Jon’s repeated question about excluding a pair at 6KYA, so it does lead one to wonder why.

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I don’t think he’s brow-beating, I think he’s asking legitimate questions. But I think he’s ignoring a number of the answers, and the fact that he is choosing not to answer certain specific questions is increasingly looking like an apologetic strategy. We have to remember, his entire line of questioning has not been prompted by anything scientific; no scientists have raised this as a legitimate scientific question. The rationale for this line of questioning is entirely theological.

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I think he’s asking legitimate questions as well. But the brow-beating comes in when he doesn’t get the answers he wants in the way he wants them. Look at the latest on his discussion on the Zhao et al. (2000) paper. Dennis has wanted to move on to the stronger studies he provided for some time now, yet Richard continues to press him to admit to something Dennis by all appearances truly has not been convinced of. Until Richard gets not just an answer, but specifically the answer he wants, he’s holding the rest of Dennis’ more robust papers hostage and not allowing the conversation to progress. In my view, this is brow-beating. Yet notice no one is doing this back to him in kind. He’s repeatedly refused to answer questions that don’t suit his agenda yet we continue the dialogue. There is a basic issue of fair play here, and I think Richard is not holding up his end.

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