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

(Chris Falter) #489

My favorite post ever! Thanks a gazillion for taking the time to explain the analysis so clearly.

(Dennis Venema) #490

Agreed. Thanks, @Swamidass!

(Richard Buggs) #491

Thank you Joshua @swamidass for such a clear explanation. I am very glad to have got to the bottom of where I was misunderstanding the ARGweaver paper. I will have to have a bit of a think now about what this means for the various critiques I was offering before.

(George Brooks) #492

Swami’s posting … link below… is now for the history books:

Posting 481 in Thread 37039 !

(Peaceful Science) #493

Hello all. When I make mistakes, I like to correct them as quick as possible, even if they do not have an impact on my overall point. I try to do so quickly, but please do keep in mind that this is not my real job. I do this on the side to serve everyone that cares about these questions. So, unfortunately, sometimes it takes me a bit longer then I’d prefer.

Fixing the Prior

For a while, I had been saying that the ArgWeaver prior was using a Ne = 10,000, leading to a prior TMR4A of 100 kya. That turns out not to be precisely correct. Instead…

This was pointed out to me in private a couple weeks ago, and since then I have been able to confirm it. So some of my earlier figures (and statements) were not precisely correct. The median of the prior of TMR4A is 123 kya, and the median estimate (the posterior) of TMR4A is 495 kya. You can see the figure below.

So the prior is 123 kya for TMR4A, but the data updates this posterior to 495 kya. Does this change affect any of my key points? Not that I can see. Still I did want to make the correction. I wish I had enough time for this to have retracted it sooner.

About Retractions in Science

One of the counterintuitive things about science is that we respect those who retract their errors quickly. Scientific work is difficult, and we know firsthand that even the best of us make mistakes. Though our instinct is to never admit mistakes, we really reward scientists that admit their mistakes.

As surprising as this may be, I’m not sure BioLogos as an organization is accustomed to this part of scientific culture. It is a very non-intuitive thing. Making a retraction ultimately increases our reputation. I do hope that, given what we are doing here, that some thought will be given to retracting statements that have gone beyond the evidence.

I think, for example, that there is a “Part 3” of @DennisVenema’s response to @RichardBuggs scheduled. It’s curious that it has not yet been published. I’m hopeful that figuring out the right way to do this (and perhaps getting it approved) is why it has been delayed. That would be a very good thing, and a great outcome of this conversation. If that is what happens, eventually, it’s important to remember that the best scientists make retractions, it is one of the ways we recognize honestly, and it’s something worth respecting.

(Dennis Venema) #494

It’s been delayed because I’ve been working with Charles Cole - the person that @RichardBuggs cited regarding PSMC modelling - to use PSMC models to directly test Richard’s hypothesis as best we can. Charles has been busy, I’ve been busy, the modelling wasn’t straightforward, and it’ll be a bit yet before I’ve got it together. I’ll probably invite @Swamidass and @RichardBuggs to look over the data before putting the post up so we can perhaps put our heads together on it. I’m hoping Cole will also join us here for that discussion. It should be interesting. Intuitively, one would think that PSMC modelling should see something if Ne went to 2 - but testing is better than intuition.

I also think we’ve reached a point in the conversation where the evidence is solidly showing to @RichardBuggs 's satisfaction that we can reasonably exclude a bottleneck to 2 in the last 350,000 years - am I correct there, Richard? If so, that pretty much means that we are in agreement. My certainty level in Adam and the Genome was only to 200,000 years ago, though I’ve said that I’m ok pushing that back to 300,000 plus or minus. This is of course excluding interbreeding with Neanderthals and Denisovans. @Swamidass, as I mentioned to you via PM, I’m really talking about ancestors to present-day sub-saharan Africans over this timeframe. Any species definition is going to break down, especially with hybridization going on. Once we include hybridization, we’re back past 500,000 years as far as I can see.

Thanks again for your really nice exposition of the Argweaver paper. Kudos. I don’t know that I’ll actually do anything on LD - I think the argweaver paper more or less covers that territory better. I think the next part will be the PSMC results and we’ll leave it at that.

(Peaceful Science) #495

@DennisVenema I’ll take this as your version of a retraction.

You made two claims, both of which you have backed off of in this post. That is good news, and should be received as such.

Claim 1: Homo sapiens never go to a single couple

  1. Homo sapiens specifically do not dip down to a single couple in 300 kya to the confidence we have in heliocentrism.

But population size estimates are always of Homo sapiens + all of our other ancestors at the time. The finding that our ancestors do not go to a single couple tells us nothing about Homo sapiens specifically, because Homo sapiens are not our only ancestors past about 50 kya.

The Ecological Fallacy.: Homo sapiens go to zero, so why couldn’t they go to two?

Now, as you explain here…

Which seems like a long way of saying that you cannot demonstrate with heliocentric certainty that Homo sapiens never go to a single couple. After all, they go to zero, so they might very well start with a single couple by some definitions.

That is a pretty important concession, as claims of heliocentric certainty really seem to have provoked the whole debate in the first place. It looks like you have backed of that claim, because you cannot defend it.

Claim 2: Our ancestors never go to a single couple after 3 mya.

  1. 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.

That is a bit of a soft pedal too, because at times you have made the claim they never go to a single couple since well before they diverged from chimpanzees. However, now…

That is really excellent that you are doing this. I shows a sensitivity to the question and a desire go engage the data. I think this is a really important effort, and I’ll look forward to seeing the results. Of course, its on my to-do list too, so we’ll see who finishes it first.

However, that study is also an admission that you are going of instinct, not settled scientific work. Given that the TMRCA for humans is about 1.8 million, we just do not expect that anything based on coalescence inference like PSMC or MSMC will be able to detect a couple after 1.8 million, which is clearly before 3 million, and also well after Homo erectus arises: the first “human” as understood by @agauger. Maybe there will be a surprise here, but it seems that this claim too is ending up unsubstantiated.

The fact that new research is being commissioned is a good thing, but it also makes clear that we are at the frontiers of scientific inquiry, not established scientific findings. Clearly, a mistake was make when instincts about this frontier were presented as settled scientific findings.

Retractions are Good

So, of course, it is a good thing that the original claims are being walked back. It would better to acknowledge the mistake more clearly, because I think that @RichardBuggs deserves some credit here. Though it took some help from me to make the case, his instincts on the big points appears to have been borne out. Honestly, it is not what I expected. @RichardBuggs deserves some credit for helping us see this more clearly.

What about Tran-species Variation?

This might seem preemptive, in light of additional data (e.g. HLA haplotypes), to observers. However, there has been substantial behind the scenes conversation that shows that this is not nearly as strong evidence as I first thought. At this point, we may have to just take my word for it. Hopefully, we will get a chance to get into it. Of course, if my assessment (totally unjustified right now) ends up being wrong, its possible that Dennis might gain some ground on claim 2.

(Dennis Venema) #496

I would certainly agree with this. This whole conversation has been very helpful and has increased my understanding of this area, to be sure. Richard’s questions and contributions have been a significant part of that, so credit where credit is due.

I do think Richard is being a bit too skeptical, though. Perhaps he can clarify - he seems to be looking for any possible reason to doubt the evidence - even going back to his final replies to @glipsnort about the allele frequency spectrum. He also seems to be doing the same sort of thing with your discussion of the Argweaver paper - I just don’t see how the Lenski work relates to that at all. I’m all for critical thinking and skepticism, but there comes a point where it looks like a duck and quacks like a duck. I haven’t even yet seen @RichardBuggs say that he’s in agreement with no bottleneck to 2 in the last 300-350KYA - but I might have missed it. Are we in agreement, Richard?

The next thing to consider, in my mind, is how reasonable Richard’s proposed bottleneck is (biologically - not really thinking theology here, but that’s an issue too). A population drop from ~10,000 down to 2 in a single generation followed by exponential population growth - how exactly did this happen? I can’t think of a reasonable biological explanation for this. Our lineage was widely dispersed in Africa at the proposed time of this event - what happened to wipe all of them out but just two? Richard - thoughts?

(Jon) #497

Are there any published studies which say homo sapiens emerged from a single couple rather than emerging from a population? Thus far I have seen no evidence to contradict the statement that “Homo sapiens specifically do not dip down to a single couple in 300 kya to the confidence we have in heliocentrism”. All I’ve seen in response is “Well maybe it happened but it did so in a special way which left absolutely no evidence and is totally undetectable”. That’s just YEC reasoning, like the idea that God did a big “cleanup” after the flood to remove all the evidence of meteors and volcanoes and comets and other silly ideas.

(Peaceful Science) #498

@DennisVenema do you agree with @Jonathan_Burke on this assessment?

If we are so certain that it did not happen, why can no evidence be marshaled in support of the claim?

(Jon) #499

Actually my statement was aimed at your claim, not his. You seem to be the one saying “Well maybe a recent homo sapiens bottleneck did happen but it did so in a special way which left absolutely no evidence and is totally undetectable”. In terms of evidence, all the genetic population studies (including your own), seem to demonstrate repeatedly that there’s no evidence for such a bottleneck even when testing specifically and robustly for such a bottleneck.

Additionally, you keep saying that since the homo sapiens population was zero at one point, it might very well have been a single couple at one point. I don’t understand the reasoning for this.

(Christy Hemphill) #500

I don’t understand this either. If the boundary lines between species are fluid, it is populations that get designated a divergent species, not individuals. Using the language analogy, you could never identify the “first couple who spoke French.” It would be a whole population that would be called French speakers that diverged at some point from the ancestral Latin form that became French over time. The only way I can imagine a population of two homo sapiens is if the rest of the homo sapiens (or whichever species we are talking about) got killed off somehow, not as two special individuals emerging from a population of non-homo sapiens.

(George Brooks) #501

@DennisVenema I believe the YEC position is that God could have arranged for Adam and Eve to have the diversity as if they were the only survivors of a 10,000 population. We could even also assume that God made the pair to genetically emulate the result of surviving a 10 million population, right?

But does this really change things much? Isn’t there a point in the curve where it really doesn’t matter how big the “hypothetical prior population” is? There is only room for a certain number of alleles… so maybe even 10,000 is well past that point in the curve?

(Jon) #502

That is exactly why I find this fixation on the idea that homo sapiens emerged as a single couple so odd. The language analogy is widely used to explain the non-intuitive idea that homo sapiens did not emerge as a single couple. The only reason I can see for insisting on a single couple origin of homo sapiens, is theological; specifically to give the YECs a foot in the door and to imply that they can legitimately oppose evolution.

(George Brooks) #503

Yep… this is what it look like.

But I don’t think 10,000 or 10,000,000,000 is going to change things much.

(Jay Johnson) #504

Exactly. There is the Toba super-eruption during the timeframe of the previously calculated bottlenecks associated with the Out of Africa event. In the case of a bottleneck to two, we are talking about an extinction-level event that would have to wipe out all other hominins except for one breeding couple. Is there anything comparable to Toba that would account for this? Even if one held to the de novo creation of Adam & Eve, we are still talking about all other hominin species suddenly going extinct, and then God presumably “starting over” with A&E. Is there any evidence of such a cataclysmic event?

(Jon) #505

Of course there is, the Genesis flood!

(Andrew M. Wolfe) #506

It’s interesting to think about this, though.

I mean, I agree. But suppose you had a particular shibboleth that was thought to be The Indicator for the French language — say, the use of “oui” versus the use of “òc”, from which we get “Languedoc.” This is the most widely known difference separating French from the Occitan language. (Anyone interested can see the subsection “History of the Modern Term” at the Languedoc Wikipedia link.)


So, from a certain popular perspective, could not the first person to say oui, back when it was still pronounced oïl, be thought of as the “first French speaker”?

Of course, it’s not at all scientific, because [1] there are lots of differences between French and Occitan, [2] the language, and indeed even the specific use of oïl, really did evolve in a speech community, [3] the difference actually started as a difference in saying ‘yes’ between Latin hoc (this) and Latin hoc illud (this [is] it), which then evolved into oïl, and [4] the difference was only recognized in retrospect, by Dante in the 13th century, not precisely when it first happened.

But I wonder if a parallel here could be drawn, particularly if (as @swamidass has been urging) we allow for some fluidity between the biological definition of H. sapiens and the theological definition of Adamic human. Couldn’t one imagine Adamic humanity as the origin of one particular indicator (or cluster of indicators) of what makes us “human”?

Of course, playing the devil’s advocate against myself, I have to ask myself whether such philosophical gymnastics are actually useful or just trifling.

(Peaceful Science) #507

@DennisVenema claimed in his book…

First, this statement was shown to be incorrect by genealogical science. That was want our dust up was last June. Good news too, the PSCF article showing this mistake @DennisVenema made is in press, and BioLogos even endorsed the science behind it as correct. It turns out that we do all descent from individual couples. @DennisVenema Did not clarify that in his book, and this is material to the conversation. This is an unintentional error at best, and intentionally misleading at worst.

Leaving that aside, let’s look at how he clarified what he meant by this block of text. He first clarified that by “human” he means Homo sapien. So its claims here are meant to be understood as…

  1. Homo sapiens specifically do not dip down to a single couple in 300 kya to the confidence we have in heliocentrism.

We came to understand this from asking him to clarify his statements in the book. He agreed that this is what he meant and we moved forward from it. Then it became clear that this is false. Let me give several reasons why.

Dennis No Longer Defends It

First off, it is notable that since January 1, @DennisVenema has no longer defended this claim. That is because, it seems, he has been convinced it is indefensible. Yes, others have leapt to his defense, but notice that he is not offering his agreement.

If he meant something different, of course, he should clarify his earlier statements. If he still has heliocentric certainty that original claim is correct, he can certainly offer evidence. Since Jan 1, however, he has not done this. Rather than trying to defend him, it’s worth asking him to explain his process on this.

In the end, its not terribly clear to observers, but I think this is @DennisVenema’s way of retracting things. I give him credit for backing of his clearly false claim, but its not fair to everyone else if they do not recognize it for what it is. Of course, if I’m misreading this, I welcome @DennisVenema to make the case.

The Claim Relies on a Logical Error

However, it would not be wise to defend that claim. It relies on a clear logical error. Let us grant everyone for a moment that we have high certainty from genetics that…

  1. Our ancestors do not dip down to a single couple in the last 300 kya.

I understand some may dispute this (not sure how), but lets just all concede this point for the purpose of understanding the logical flaw. This finding in population is NOT equivalent to…

  1. Humans do not dip down to a single couple in the last 300 kya.

Moreover, it is NOT equivalent to…

  1. Homo sapiens do not dip down to a single couple in the last 300 kya.

One logical level, #1 can only be offered as support for #2 if “our ancestors” = “human”. If any of our ancestors during this time are not “human,” than #2 does not follow from #1. Even if #2 is true, #1 is not evidence of #2. Likewise, #1 can only be offered as support for #3 if “Homo sapiens” = “our ancestors.” If any of our ancestors during this time are not Homo sapiens, then #3 does not follow from #1. Even if #3 is true, #1 is not evidence of #3.

That is the logical error. We cannot substitute “our ancestors” for “human” or “Homo sapiens” as @DennisVenema does.

It’s Self-Contradictory

If we knew @DennisVenema’s claim with heliocentric certainty, we would not be able to produce multiple counter examples that (1) contradict his statement, and (2) are 100% consistent with the data. Yet that is exactly the case we have. This partly because @DennisVenema himself agrees that:

  1. Our ancestors != human alone. He agrees that our ancestors = humans + others. For this reason, we can imagine several scenarios where the number of “humans” dips down to zero. In fact, Dennis himself subscribes to one of these scenarios. If we think there are ZERO “humans” at 300 kya, it is self-contradictory to claim that “humans” never dip below a few thousand. The two claims are in contradiction with each other, so we know one must be false.

  2. Our ancestors != Homo sapiens alone. He agrees that ancestors = Homo sapiens + others. The same logic applies. If we think there are ZERO Homo sapiens at 300 kya, it is self-contradictory to claim that Homo sapiens never dip below a few thousand. The two claims are in contradiction with each other, so we know one must be false.

We know exactly which one is false too. Its the claim that @DennisVenema makes, which is just not substantiated. We cannot use “our ancestors” and “human” and “Homo sapiens” interchangeably. That was the source of the error.

The reasoning is that self-contradictory positions are false.

What “Really” Happened Is Beside the Point

First off, there are both theological and scientific reasons to wonder if we begin as a single couple. I’m not going to elaborate this, because it will be more fun to let it play out of time. Also, it’s probably worth a publication in its own right, and I do not want to scoop myself. For the curious wanting a hint, you can wonder about “grasshoppers.”

Second, this is all really beside the point. We are not arguing about what really happened, but whether @DennisVenema’s representation of the scientific evidence is accurate. He had heliocentric certainty in a statement cannot be substantiated (whether or not it’s true). It’s a separate question entirely whether this is what really happened or not. @DennisVenema’s conclusion might be ultimately right, but currently his argument for this conclusion has not been sustainable.

Where Confusion Lies

Just because we could never identify who is the first could who spoke French does not mean that French (by some definition) does not begin with a single couple. As is well put…

So we can imagine a context were a specific definition of French could plausibly lead to a “first speaker” of French. Of course, we do not need to specifically identify this first speaker to posit that he or she exists. In fact, if such a person existed, we do not expect to identify him.

To flesh out the analogy, here are several possibilities regarding “humans” (none of which I will defend as normatively correct).

  1. Perhaps “humans” are those with eternal souls, and are defined as such.
  2. Perhaps “humans” are those given the divine appointment to represent God on earth, and are defined as such.
  3. Perhaps “humans” are those with knowledge of God, and are defined as such.
  4. Perhaps “humans” are the genealogical descendents of a specific single couple, and are defined as such.

In all these cases, it is possible that “humans” arise as a single couple. In the third case, it is guaranteed they arise as a single couple. A similar case can be made for the taxonomic category Homo sapiens on biological characteristics or (much easier) on behavior. In the end, it comes down to the fact that we just because thing are blurry from a distance does not mean there was never theological (or taxonomical) distinctions up close. It’s a grand leap to jump from one to the other.

Where We Are Now

Well, like I said about retractions…

However, it does seem that this claim of heliocentric certainty is not sustainable. Case in point, @DennisVenema is no longer making the claim. That is a good thing. Given that he has backed away from it, perhaps it’s a good moment for the rest of us to back away from it too.

(Peaceful Science) #508

@RichardBuggs I think @DennisVenema makes a fair point.

As I understand it, you are rethinking much of this…

As I understand it, you are trying to pressure test any claims being made. I can appreciate that, and am fine with that. At the same time, I think it is important to be honest with the Church about what the evidence appears to show, at least at this point in the conversation.

So I do hope that you can, after contemplation, agree that…