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

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).
[/quote]

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”.

Swamidass,

Was it not a bottleneck to two within 200KYA Dennis was trying to demonstrate was implausible at “heliocentric” levels of certainty? Not 300KYA? I may have missed something here, but I want to make sure we’re not stacking the deck unfairly.

Hi Josh @Swamidass,

Those TMRCA values (in the second paper) are not in years - they are in generations. Multiply them by 25 to get TMRCA in years. That tripped me up at the first as well.

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Dennis, it’d probably be more appropriate to ask this question of you. Which bar were you setting here?

It’s up the thread ^ . “Heliocentrism certain” = humans. 200KYA in the book. I’m ok with stretching that to 300KYA if needed.

That is certainly helpful. Thanks! I did make that mistake. I’d use a generation time of about 15 (at minimum) to 25. So that brings the TMR4C from that table up past 2 mya. Now I see why it helps your case.

However, they are MAX values of samples from a distribution with a very high variance. This is an extreme-value distribution. We need to see the whole distribution. Know any papers with that? Perhaps they can send us their values if we ask them? Perhaps send them an email.

Because of how these numbers are selected, we cannot draw a strong inference from them yet. It is not sound to cherry pick regions with low TMRCA’s, but this study is just cherry picking the ones with high TMRCAs, if it is used this way.

The claim was that Homo sapiens do not dip down to a single couple, and we know this with certainty approaching heliocentrism.

At the time, everyone thought Homo sapiens arose 200 kya, but now there is strong enough evidence that this is no longer the consensus. Some think Homo sapiens arose 300 kya or even as early as 350 kya. If that new finding unsettles Dennis’ claim, then that claim should never have been presented as heliocentrism level certainty. There is no similar sort of evidence we can imagine that would unsettle our view of heliocentrism. The fact that Dennis did not take into account uncertainty in determine the origin date of Homo sapien is part of what is at question here.

To be clear, he certainly is not responsible for excluding evidence published after his book was published. However, that evidence does call into question his heliocentrism certainty, if in fact population bottlenecks between 300 kya and 200 kya are plausible (which we have not yet determined). If that is the case, then part of his certainty rested on false confidence in when humans arise. Of course, if we cannot see plausibility for a bottleneck till say, before, 1 mya, that is not really relevant any ways.

Setting that issue aside, none of the studies I have seen correct for interbreeding. The scientific consensus is that our ancestors never dip to a single couple, not that Homo sapiens never dip to a single couple. It would be really interesting to see the studies that raises Dennis’ confidence so high on this one. He has read the literature more, so he might have seen something I missed.

Just as he corrected me on that TMRCA table, I’d love to have him correct me here too. However, this really does to seem to be a novel claim he is making. I am not even sure I can envision the study that could demonstrate this claim.

That’s what I’d thought ;). Thanks! Is it your sense Richard is disputing an exclusion of a bottleneck within 200KYA then? Or just your upper ranges with less than such a high level of confidence?

The paper is a whole-genome study, and these are the largest TMRCA values that they found. Why is this “cherry picking”? Shouldn’t we be interested in the range of TMRCA values in the genome if we’re interested in the range of estimated TMR4A values?

Put another way: finding more recent TMRCA values is not an issue for Richard. The issue is how far back the range of TMRCA values we see in the genome goes.

I was actually surprised to see some regions with TMRCA values higher than the MHC complex. I expected that to be near the top (and it is) but there are several regions with similar TMRCA values.

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I have no idea. Richard has not clarified what timeframe he is interested in.

We need to see the whole distribution. Just looking at the tail of the distribution does not tell you about the mean or the mode. Using these TMRCA values is like using an estimate well outside the 95% confidence interval (on the high side). We could have just as well used the minimum TMRCA values as valid estimates. Both approaches are not valid for similar (though not identical) reasons.

As you know, the sampling distribution for TMRCAs have very high variance. As I understand it, the signal to noise ratio actually increases as you go farther back. For that reason, looking at extremal values (maxs and mins) is always going to be flat out wrong. We need to see the full distribution, to see if it is unimodal, bimodal, and what the means/modes are. That’s just basic statistics, right?

The good news is that these authors actually have the data we need. I’m going to send them a note asking for data.

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I think that’s my frustration as well. It’d be very helpful for him to do so. He’s been asked by yourself and others. Hopefully when he returns to this thread he will be more forthcoming with his answers to these questions, especially since you’ve held up your end of the bargain in meeting all of his.

In the meantime, what do you think of Swamidass‘ point that humans may have speciated at 300 or even 350KYA? Do you find this relevant? For me, given that distances us so far from behaviorally as well as anatomically modern humans, it doesn’t mean much to me. But I’m curious as to your thoughts and whether Swamidass‘ point means a revision of your claim is warranted.

I’m not quite following you here (maybe I need another cup of coffee). I agree if we’re interested in the TMRCA for the genome as a whole then the whole distribution is important. In this case, we’re interested in the TMRCA value of specific genome regions. Why would the oldest measures be intrinsically less accurate?

Also, we’re looking at TMRCA values in excess of 10 million years in some cases. Are we saying that this isn’t good evidence for a TMR4A > 400KYA?

I’m not making any revisions.

There is immense debate about what “human” and Homo sapiens is. If we are trying to communicate the scientific consensus to the public, to make claims of heliocentrism level certainty, we need to be taking that lack of consensus into account.

The real problem, however, is not with the date of 300 kya vs 200 kya, but in making a claim about Homo sapiens, when population genetics seems only to be making claims about “our ancestors”, our total “lineage”, which includes non-Homo sapiens.

You can try this yourself with a gaussian distribution and python code. If you want, I can even write up a piece of code. Sample numbers from a distribution ten thousand times. Take the maximum of those samples. How close is that to the mean? Not very close. Same problem here.

We cannot really estimate the average height of people by just looking at the heights of people in the NBA. Its just not statistically sound. Same thing here.

One of the things I try to communicate in the book is that delineating “species” is an attempt to draw a line on a gradient. As we learn more and more about our ancestors, it’s going to get harder and harder to draw a line - a point I make in the book. I think we see with the remains at 300KYA exactly that issue - some say they are sapiens, others aren’t so sure. It’s exactly what we would expect.

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We’re not interested in the genome average, though. We’re interested in the range.

“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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