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

Yes. But my assessment of his sensitivity has been tempered by his practice of consistently ignoring various simple, easily answered, questions from those he is supposedly most concerned about assisting. Several people (including myself), have put very basic questions to him, the answers to which would help us assess the relevance of this complex scientific discussion, to our beliefs or those of others who feel affected by the subject. Those questions have been phrased consistently respectfully and graciously, with full acknowledgment of his time constraints.

However, those questions have been ignored. Note that this is not even a case of Dr Buggs responding to these questions with “I understand your concern and note your questions, but regret I cannot address them within my current time constraints”, it is a question of him completely ignoring them and not acknowledging them in any way at all. Perhaps now you have asked a couple of these same questions, he may feel more inclined to answer them, but at this point it really does look like his main concern is “taking down” Dennis in the name of ID and the Discovery Institute, rather than actually addressing the personal concerns of rank and file Christians.

No one has attempted to dismiss or ignore his question on the basis of its source, or claim that it is invalid on the basis of its source. The point being made is that his question has not arisen on a scientific basis; it has not arisen from a need to find a scientific solution to a scientific problem. It is an apologetic argument which has arisen on a theological basis, and this needs to be both acknowledged and stated explicitly. When someone’s interpretation of the science is affected by their theological constraints, it is important to identify this and examine how it affects their interpretation of the science. When this is swept under the carpet, and discussion of it is discouraged, red flags should fly.

He has also made the claim that there have been no scientific bottleneck studies which have ruled out a bottleneck of only two people. I believe Dennis has already shown that this is simply not true, and has listed a number of them. If Dr Buggs had mentioned these other studies and explained why he thought they didn’t support the conclusions of their authors, that would have been fine, but instead he has given the impression that they don’t even exist. My surprise at this claim of his was matched only by my surprise that Dennis was able to show easily that they do exist.

There is nothing wrong with Dr Buggs challenging Dennis over Dennis’ representation of the science. However, I don’t think Dr Buggs has been accurate in his representation of the science, and it is clear to me that he really does believe it is about the science, not simply Dennis’ representation of it.

I don’t think that Dennis has conceded this, or that Dennis has overstated the science. I am still wondering why Dr Buggs has not contacted Zhao et a, if he is so concerned that their analysis of the data is wrong.

I think this wrongly suggests that Dennis is acknowledging some kind of failure on his part which weakens his case.

You are missing my point here.

That is actually a defense of @DennisVenema.

It is NORMAL to quote historical and easier to understand references when engaging the public on established science. Dennis did nothing wrong here. The fact that he used weaker references ends up strengthening the case, because there is so much data out there that makes it clearer that our ancestors do not dip down to a single couple (at least within the last several 100,000 years).

Btw, I think the strongest evidence against a bottleneck in the last 6 million years is trans-species variation, which does not even appear to be on the “menu,” as it were. Trans-species does not have the same horizon problems as does allele frequency spectrums and LD estimates. Nor is it subject to as much uncertainty from population structure (though interbreeding can explain it away too).

To me, that seems to be exactly right. The fact that Zhao 2000 does not make the case with the strongest data is not really a big problem. There is so much more data. Even if a single couple bottleneck at 500,000 years ago, provisionally, can fit Zhao 2000, does not mean the same will work for all the rest of the data. I want to see how far we can go.

It is not really expected to give the best references in a book like Adam and the Genome. The field is huge. There is just so many papers out there, I doubt any of us have read absolutely all the relevant studies. None of the conclusions Dennis presented are disputed in mainstream science either. So he is not so much “making the case” but explaining what others have found. The evidential standards are just much much lower for that type of activity. He did not thing wrong by quoting a selection of papers.

Taking him to task on that is really beside the point. That is why I think we should move past a referendum on @DennisVenema. He has already basically admitted his references are not the best evidence. There is no reason, also, to think his references should include all the relevant evidence, because there is so much here, and historic papers actually make sense in this context.


[taking my own advice and removing a distracting post]

I know it was, which is why I objected to the word “admission”, since that doesn’t seem congruous with the point you’re making.

Yes, which is why I think that “admission” is not the best word to use in this context. It makes it sound like Dennis was caught out in some way, when in actual fact his point was the opposite.

@DennisVenema,

Absolutely! Your mileage may vary!

If we are going to make any progress with the @Swamidass scenario, we have to put Adam at the 6000 year mark… at the very least. And even there, there are problems…

Thanks for sharing this Steve, that is very good of you, given your many other commitments.

Hi @Swamidass thank you for contributing some substantial and substantive posts to this discussion in the past few days. Sorry that I have not acknowledged your presence here sooner. Because my time available for this discussion is very limited, I have had to prioritise responding to Dennis as he has invested more in this discussion than anyone else. I have therefore been making a lot of the use of the website function that allows me to only see Dennis’s posts, so many of the other posts I have not even read, let alone had time to engage with (though I would like to have done, were there not so many demands on my time). However, your posts have now come to my attention and I will just make a few comments. I will try to restrict myself to your points most narrowly focused on the points I have raised, as I don’t have time to comment on everything you have said. Many of your comments and observations I agree with, and I appreciate the peaceable nature of your contributions, and your occupation of the middle ground between Dennis and myself.

Hear, hear!

This is exactly my point. Thank you for stating it so concisely. To my mind, the way ahead would be to write a programme that computes the TMR4A for each haplotype block of the human genome, and work out a reasonable time frame using data from all blocks. Until that has been done, I do not think we can say that the bottleneck hypothesis has been rigorously tested.

I am glad that you agree with my back-of-the-envelope calculations, and my conclusions from that. I am interested that when you add in recombination you get a potentially shorter time to a primordial pair. I would also be glad to hear what you think of the rest of my post, where I suggest that if the population continued to expand from a single couple up to 7 billion individuals, then the time to a primordial pair could be lower than 500,000 years. All in all, it seems to me that the jury is still out on a minimum bound for a bottleneck.

I agree that more rigorous treatment is desirable. However eyeballing the data can be a useful heuristic in illustrating a point and deciding what ideas to follow up. The clustering that I did of the Zhao et al (2000) sequences shows that one can reasonably place them into clusters, and that not every possible combination of the variants are found in that data. If you prefer, here is a haplotype network for the whole Zhao et al (2000) dataset:

Looking at this - “eyeballing” again! - there are clear clusters with fairly recent common ancestors.

Agreed. So not every haplotype block in the human population today would have its TMR4A at the bottleneck (if one occurred) - some would have them at a more recent date, due to earlier loss of ancestral haplotypes. Just looking at such blocks in isolation would give a misleadingly young age for a bottleneck.

I think we are planning to come on to linkage disequilibrium in this discussion, one we come to the Tenesa et al paper.[quote=“Swamidass, post:254, topic:37039”]
Is this conversation assuming common descent?
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Absolutely[quote=“Swamidass, post:260, topic:37039”]
Btw, I think the strongest evidence against a bottleneck in the last 6 million years is trans-species variation,
[/quote]
I agree. I am assuming we would come to this in detail at some point.[quote=“Swamidass, post:260, topic:37039”]
None of the conclusions Dennis presented are disputed in mainstream science either. So he is not so much “making the case” but explaining what others have found. The evidential standards are just much much lower for that type of activity. He did not thing wrong by quoting a selection of papers.
[/quote]
Here I disagree with you, sorry! Most mainstream papers have not tested the bottleneck hypothesis. As you have said, the “Time to Most Recent 4 Alleles (TMR4A)… is not a standard computed number in genetics”. To test a bottleneck of two hypothesis, this is what is needed. There is quite a lot of interpretation going on by Dennis. Take the Zhao et al paper: Dennis is not making a point that the authors are making. This is to a greater or lesser extent the same for the other papers he cites in Adam and the Genome, as I have shown in my blog. Also, and this is just a minor point, the Zhao et al paper was not cited in Adam and the Genome: Dennis has cited it in this discussion to back up a passage which has no citations in Adam and the Genome. I would also note that thus far, no mainstream scientist has disputed my blog which has been read by many scientists.

Thanks again for your input. The time I can give to this discussion today is up. It is 10pm my time and I need to wake my baby son to have his final feed for the day!

I don’t see this. Dennis is making the point that there’s no evidence for a two person bottleneck in any of the studies he has cited. I don’t think that’s a matter of interpretation. Your only argument is this.

None of the studies above set out to explicitly test the hypothesis that humans could have passed through a single-couple bottleneck.

But you haven’t demonstrated that this hypothesis needs to be tested in a special way which hasn’t already been tested by previous studies. The fact is that previous studies have consistently arrived at the conclusion that a bottleneck of only a very small number of people is just not credible.

Here’s one.

Genetic variation at most loci examined in human populations indicates that the (effective) population size has been approximately 10(4) (i.e., 10,000) for the past 1 Myr and that individuals have been genetically united rather tightly. Also suggested is that the population size has never dropped to a few individuals, even in a single generation. These impose important requirements for the hypotheses for the origin of modern humans: a relatively large population size and frequent migration if populations were geographically subdivided. Any hypothesis that assumes a small number of founding individuals throughout the late Pleistocene can be rejected.

Here’s another.

There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained.

Note that this paper states specifically that there’s no evidence for “an exponential expansion out of a bottlenecked founding population”, which is precisely the model you are proposing. So this study has tested this specific aspect of your hypothesis.

This study likewise specifically denies the severe bottleneck of your hypothesis.

On the other hand our results also deny the hypothesis that there was a severe hourglass contraction in the number of our ancestors in the late middle and upper Pleistocene. If humans were descended from some small group of survivors of a catastrophic loss of population, then the distribution of ascertained Alu polymorphisms would show a pre-ponderance of high frequency insertions (unpublished simulation results). Instead the suggestion is that our ancestors were not part of a world network of gene flow among archaic human populations but were instead effectively a separate species with effective size of 10,000-20,000 throughout the Pleistocene.

This study also specifically tested the hypothesis of a very small bottleneck.

Moreover, the ancient genetic history of humans indicates no severe bottleneck during the evolution of humans in the last half million years; otherwise, much of the ancient genetic history would have been lost during a severe bottleneck

All of these studies are clearly testing exactly what you claim has never been tested. They say there’s no evidence for a bottleneck down to a small handful of people, and no evidence for an exponential population expansion after such a severe bottleneck. This is not a matter of Dennis’ interpretation, this is what the studies state explicitly. If you want to claim these studies are inadequate, you have to address their contents and explain their deficiencies.

I don’t see how this is relevant. Have you attempted to submit this for peer review?

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Did I let my mainstream scientist card expire again? I knew I was forgetting something… :slight_smile:

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This “heckling” from the sidelines by amateurs detracts from an otherwise interesting discussion. As I read it, @RichardBuggs is questioning the certainty expressed by @DennisVenema (that pop gen modelling is as certain as the earth going around the sun), and he is showing that such modelling includes assumptions that may not be testable.

In any event, the notion of two individuals as “starting” human population, instead of a large number, is only relevant to the biblical account, if we discard virtually all meaning in the account in Genesis - I do not think pop gen modelling can do that.

Yes. Everyone genuflect and remain silent. The scientists are speaking.

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Hi Dennis,

I am glad to see that you have taken another look at the Zhao et al (2000) paper now and are willing to say this:

So I think (correct me if I am misunderstanding you here) we agree that the authors are not explicitly supporting your case. If you are happy with the comments that I and @swamidass have made on the coalescent analysis at the end of the Zhao et al (2000) paper, suggesting that the data is compatible with a bottleneck in the human lineage, then I am very happy to move on. Please could you tell me which paper you would like me to read next?

I think that to pick up where we were before, it would be helpful if the paper you choose explicitly supports this passage in Adam and the Genome:

“One simple way is to select a few genes and measure how many alleles of that gene are present in present-day humans. Now that the Human Genome Project has been completed and we have sequenced the DNA of thousands of humans, this sort of study can be done simply using a computer. Taking into account the human mutation rate, and the mathematical probability of new mutations spreading in a population or being lost, these methods indicate an ancestral population size for humans right around that 10,000 figure. In fact, to generate the number of alleles we see in the present day from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal.”

But if you prefer to leave that statement behind now, I would be happy to move onto another method of analysis. If you could tell me which paper you would like me to read next, I will be very happy to give it a close read. I think all of us will be happy to move on to a fresh paper! Thanks again for all the time you are putting into this discussion - I know that all of us have many pressures on our time.

Richard,

I’m encouraged to see you moving on to Dennis’ stronger evidence, and am glad to see my dialogue with him was useful to you in that regard. I do believe there is an outstanding question from Dennis for you to address. Since I know you’re focusing your efforts in responding to him rather than other readers, I’m confident we’ll see a reply from you very shortly on this:

Since most of the papers in this field use other primates to calibrate mutation rates in specific genome areas, it would be helpful if Richard would answer this straightforward question now before proceeding.

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Just so my position is not overstated.

In this region alone, not taking LD into account, the number of variants seems consistent with a bottleneck of our ancestors (I would not use the term “human”) at or before 500,000 years ago. It is possible a more careful analysis will show problems, especially if LD is taken into acoount, but we should not mistake TMRCA in a single autosomal region for a limit on bottleneck time. TMRCA also is not an estimate effective population size.

As long as we are here, the data figure of the region clusters shows that samples are clustering strongly with population, which strongly undercuts the notion that any observable clusters correlate with alleles from a primordial couple, which we would expect to be randomly distributed in geography at this point. This does not necessarily mean it does not fit an ancient bottleneck but it does show another view of the data might weaken the case

In the end it doesn’t matter so much because, as Dennis has repeated, the evidence from other sources are much clearer.

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I agree.

And as such, this paper supports the conclusion I state in Adam and the Genome. If one was to squeeze this variation into the last 200,000 years (or even 300,000 years), one would have to increase the mutation rate to do so.

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Yep. Where alleles are found in the present day is also important. If everything tracks back to 2 ancestors at 500,000 years ago, why are patterns of alleles in the places they are? Why did some haplotype blocks end up outside Africa only? Why are others only found in Africa?

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I hope these are only rhetorical questions at this point, otherwise we’re never moving on from this paper :wink:

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He has said he is at least assuming it for this discussion, see post 264:

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Christy,

In the same sense Richard was not willing to accept Dennis moving on “ad argumentum” from the Zhao et al (2000) paper but wanted something more real, I think Dennis is also asking for Richard’s actual take on common ancestry. I can think of no legitimate scientific reason to refuse to answer this question. Can you? If Richard does not accept what is universally considered established scientific fact within genetics, it would be informative to the discussion. For instance, he may be more inclined to treat things such as mutation rates as assumptions rather than conclusions. Which may color his intuitions on how much freedom he has to play with the parameters to get to a bottleneck of two. I also believe given all the transparency he’s demanded of Dennis, he owes him an answer.

Not a scientific reason, no. But lots of people commenting here have relationships with various organizations and institutions with certain a-scientific commitments, and so I understand and sympathize with a reticence to be completely upfront with one’s personal beliefs and convictions on points that are considered political or controversial in those arenas. People have lost their jobs over things they have said on BioLogos. It should be enough to clarify what the terms of the discussion are.

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