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

Hi all,

I have just published another blog post on this issue at the Nature Ecology and Evolution Community here:

https://natureecoevocommunity.nature.com/users/24561-richard-buggs/posts/32171-adam-and-eve-lessons-learned

best wishes
Richard

2 Likes

Dear @DennisVenema

I am very grateful to you for your response to my original email and blog about the possibility of a bottleneck in the human lineage, and for the discussion that we have had in blogs and on this forum. Your work has helpfully highlighted an area of misunderstanding of current science that is probably shared by many, and it has been extremely informative to all of us to debate this issue and establish what current genomics does and does not show about past human population sizes. All of us have learned a great deal from this.

It is clear to me, as someone who has followed this debate closely and participated in it, that you (like me) now understand the field a lot better than you did before 2017. When you wrote Adam and the Genome you clearly believed that genomic evidence – from the case of the Tasmanian devils, from PSMC analyses, from the Tenesa et al study of linkage disequilibrium, and from allele counts – meant that it was almost impossible that humans had ever passed though a bottleneck of two since diverging from chimpanzees. You left your readers in no doubt about this.

In contrast, your more recent contributions on this forum show that you have now realised that the evidence that you cited in Adam and the Genome does not support this claim. You now realise that the studies you cite did not test a single-generation bottleneck of two. Your new understanding is clear to me as someone who has followed the discussion on this forum in detail, and weighed up what you have said and what you have not said, and what you have implied. Please do correct me if I have misunderstood you and I am drawing a wrong conclusion, as I have had to “read between the lines” in places to come to the conclusion that you realise that every one of these lines of evidence does not support the claim.

Assuming that I have understood you correctly, I think it is my responsibility to encourage you to make a clear public statement correcting what is erroneous in Adam and the Genome. I do this on behalf of readers of Adam and the Genome who will not have the time to read through the the debate on this forum (which is now much longer than chapter 3 of your book), but who are honestly seeking to understand what current science says and does not say about human population history. Not only will this be of service to your readers, but your reputation as reliable communicator of science will be enhanced by such a statement.

Yours sincerely,
Richard

3 Likes

@DennisVenema

I support what Richard has said. It is clear that when you wrote Adam and the Genome you were taking the published literature at its word, most of which said our population at the time of our split from chimps had an effective population size of 10,000. This seemed solid, as a number of different analyses yielded similar numbers. However, you made an extreme claim when you said that the certainity we could not have come from a bottleneck of two was as certain as heliocentricity.

Why this went wrong should be a lesson to all scientists: it is dangerous to extrapolate or over-interpret data, to go beyond what has been explicitly tested. No one had explicitly tested a bottleneck of two; it was the received knowledge that of course we couldn’t have come from two. Evolutionary theory said species were formed by progressive differentiation from an ancestral population. The claim was made that current genetic diversity could not be explained under standard assumptions if the species started from two. And that is true for recent origins. Standard assumptions won’t work for a young origin of two.Therefore it was not even worth examining, most assumed. But that conclusion was wrong, as we have seen.

Richard gave a very good summary at https://natureecoevocommunity.nature.com/users/24561-richard-buggs/posts/32171-adam-and-eve-lessons-learned.

Because the claim that we could not have come from two is wrong, and because that claim impacts the faith of many Christians, with corresponding doctrinal effects, it would be very helpful, even important, to set the record straight. This is not just a matter of a scientific dispute. All we are asking for is a public statement something like this: In a prolonged discussion with my colleagues it has become apparent that the claim that we had to originate from a population of 10,000 was never sufficiently or completely tested. Further analysis has indicated that it is possible that we could have come from a bottleneck of two.

1 Like

Hi Richard,

Thanks for your comments. Sorry I’ve been slow to respond.

I feel like I’ve gone over this before, but perhaps a recap would be in order.

In AatG I defend two claims - (1) that as our species, Homo sapiens (anatomically modern humans or AMHs), comes into being, we do so as a population. This is the “heliocentric” quote.

I also say that (2) the dip to ~10,000 seems to be the lowest our lineage experienced over the last 18 MY, based on the methods applied to date.

Both of these statements remain accurate. Our discussion has led us to agree that a 2-person bottleneck for the lineage leading to present-day humans is not plausible within the last 700,000 years or more. This is well before AMHs appear in the fossil record. So, point (1) stands, even if one might differ over just how “heliocentric” that certainty is.

Point (2) also stands. I’ve learned a bunch from our discussions - and I’m grateful for it! - but nothing we have uncovered provides any positive evidence for a 2-person bottleneck (or even a sub-~10,000 bottleneck) at any point over that timeframe. So, it still would seem that the ~10,000 number was the low point.

What we have established is that a very sudden bottleneck to 2 followed by exponential population growth might escape detection using current methods if it occurred before 700,000 years ago. That is interesting, but it does not change the points I made in the book. It still seems that ~10,000 was the low point based on current methods. In order to say that those methods might have missed the real 2-person bottleneck event, I have asked you (or others) to propose how such an event might have taken place.

Unless I’ve missed it - and I might have - I have not seen you propose any mechanism for a precipitous drop to 2 followed by exponential population growth. I don’t see this as plausible. @Swamidass gave it a go earlier, but that showed the difficulties. It can’t reasonably be genetic isolation of a population, since this is happening in Africa/Eurasia, and there is no way to geographically isolate populations on that landmass (the only way to assure genetic isolation). So, it would have to be an event that (a) kills off all but 2, but then somehow also allows for exponential growth immediately thereafter.

That’s not biologically plausible. At least, not to me, nor to any biologist I’ve discussed it with (except for @Swamidass, perhaps). Perhaps you have a model in mind to explain it that I am missing?

In other words, if what you are proposing is not biologically plausible I don’t see a pressing need to address it.

Now, if I was writing AatG today, I would include a discussion of this conversation, and what we’ve learned from it, to be sure. What I would also do, however, is discuss why I don’t find the “sudden catastrophic bottleneck to 2 followed by explosive exponential growth” hypothesis to be compelling.

Thoughts?

… And now for something completely different:

Another thing that I have been meaning to ask for a long time in this conversation is this. Several years ago, you were widely quoted by the Discovery Institute and other ID sources as claiming that the identity of the human and chimpanzee genomes was around 70. It seems your original article on the subject is no longer online, but here’s how the DI quoted it at length:

Do you still think that humans and chimpanzees are around 70% identical at the DNA level? If so, why? If not, why not? Seeing as this is @glipsnort 's area of expertise, he might also be interested in your thoughts. I’ve been meaning to ask you this for months, and I keep forgetting to do so.

4 Likes

6 posts were merged into an existing topic: Discussion with Richard Buggs about chimp DNA

This claim is not substantiated by evidence. It requires an equivocation between Homo sapiens and “all our ancestors.” This is an example of the ecological fallacy.

The fact of the matter is we know that Homo sapiens dip down (backward time) to zero, so that obviously goes down below 10,000. Your heliocentric claim is transparently false.

You have missed it. That is a caricature of the argument and what is required for a genetic bottleneck. Someday we can press that argument, but its not worth it now.

More importantly, this is not related to your prior claim above, which is clearly not substantiated by evidence, and precisely false.

I confess to not having followed this discussion very closely. I thought around 500,000 years was the agreed limit – what are you basing the 700,000 years on? (Just curious.) Obviously, all of these numbers are somewhat mushy. If you accept the estimated time of 700,000 years for the sapiens/Neanderthal split, then that’s your limit, of course.

Not exactly my area; I was an author of the chimpanzee genome paper, but my contribution was in modeling selection, not in the sequence comparison. On the other hand, I am pretty familiar with the paper, and it’s safe to say that the quoted text is completely wrong. Similar claims have been repeatedly introduced into Wikipedia, where they have have had to be weeded out.

Short summary of the actual comparison:
2700 million base pairs (out of a total of roughly 3100 million bp) of the chimpanzee genome was sequenced well enough to be compared. That is the portion we can say something about. Of that 2700 million, 2400 million could be aligned to the human genome. This portion is the basis for the conclusion that 1.23% of sites in shared DNA differ by a single-base substitution, and that another ~1.5% was unique to each genome. (Based on these numbers the most reasonable single statement of overall similarity is that approximately 97.3% of the human genome is identical to the chimpanzee genome.)

The remaining 300 million base pairs of chimp DNA was sequenced but was not compared. 240 million bp were left out because they aligned to multiple places in the human genome. Much of this (I don’t know exactly how much) was the result of badly assembled chimp DNA, while some may represent genuine duplications in the human lineage. Another 90 million bp didn’t align to human at all; again, most of this was probably garbage of various kinds – badly assembled chimp DNA, parts of the human genome that hadn’t been assembled, etc.

3 Likes

No, we don’t know that. We know that there were once zero Homo sapiens, but that is not the same as saying that Hs “dipped down” to some specified bottleneck size, or to zero. The former is a statement about the characteristic of the population, while the latter is a statement about the population size. Two quite different statements.

I missed it too,

4 Likes

I know. Let’s grab a bear :bear: in Boston at the ASA meeting and hash it out. I’ll buy the first round for you =).

[:blush: Silly @BradKramer adds a :bear:, obviously I meant a :beer: ]

That is just an example of how we know the population genetics data does not tell us how many homo sapiens are around. It all comes down to how we define “homo sapiens”.

Regardless, this is all a red herring any ways (perhaps even intentionally), as there is no good reason to link “human” to Homo sapien. That is an example of eisegesis and concordism. “Human” in theology is not a scientific concept.

1 Like

I try to avoid grabbing bears – the results are always unpredictable and often painful. (Also, there are surprisingly few bears in Boston.)

I’m not currently planning on going to the ASA meeting, other than the science panel, but I’m sure we can arrange something.

1 Like

Other than the Bruins, that is.

4 Likes

You’re correct in your guess - the human / (Neanderthal - Denisovans common ancestor) split at ~ 700KYA. There’s also the fact that that Denisovans genome has some parts that seem to be around 1MY old, but that’s more up for debate.

I just don’t find the sudden bottleneck to two compelling either. For multiple reasons: 1. Hominins have always been pretty widespread so what kind of event can cause a severe bottleneck of two? What kind of natural disaster? Now I guess you could argue the event happened to a local population and that population dipped to two and then they outlived the other populations and didn’t reproduce with them. Which leads me to my second issue
2. If it happened to a local population what in the world could keep them isolated from the other populations? Like I said hominins moved around.
3. It seems the prior probability of a population dipping to two and not going extinct would be very low. And these two individuals would have to be male and female and at the right age to reproduce. A 40 year female and an infant aren’t going to do you much good.
4. I also have theological concerns

It’s an interesting idea but I don’t find it compelling at all.

3 Likes

I’m hoping to meet both of you!

Hi Dennis,

I think that you and @RichardBuggs might be working from different definitions of the problem.

The hypothesis under scrutiny is that all of humanity on the planet today is the genetic (not genealogical) offspring of a single couple. Your view is that this implies that 100% of our genome must be traced back to that couple. So the couple would have to be the exclusive genetic forebears of H Neanderthalis as well, because over 1% of the genome of non-African populations comes from Neanderthals. Since the Neanderthal/H Sapiens split was 700kya, that is the earliest possible date for the single couple.

On the other side, @RichardBuggs seems to believe that the claim of single couple sole genetic ancestry does not imply that 100% of humanity’s DNA must trace back to that couple. He would thus allow hybridization between humanity and non-humanity (Neanderthals, Denisovans), and logically the date could be earlier (500kya).

It seems logically incoherent to claim that humanity is solely descended from a single couple, and also to allow for hybridization with creatures that are not descended from that couple. I note that Hugh Ross stated about 10 years ago that the Bible predicted that there was no hybridization between H Sapiens and Neanderthals; the Bible claimed (in Ross’ view) that 100% of humanity’s genetic code must come from that single couple. So I would accept your definition of the claim, Dennis. (And Ross’ 10 years ago.)

Moreover, if anyone is willing to permit humanity to have less than 100% genetic descent from that couple, then the vastly more sensible solution is @Swamidass’ genealogical Adam and Eve hypothesis, which would easily put the couple in the timeframe of the capabilities we associate with humanity.

Pax Christi,
Chris Falter

2 Likes

@Swamidass (and @DennisVenema ):

Joshua, I think you have made a category error in your thinking here… and this is the post I just made back where your “…Against a Bottleneck of Two?” first appears. And you made it quite some time ago!

I, like @glipsnort, didn’t even notice you doing this so many months ago!

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Continuing the discussion from Heliocentric Certainty Against a Bottleneck of Two?:

@swamidass

This is the kind of distortion that I would have expected from a YEC, not from you.

You appear to be attempting to “divine” a dividing line between Homo Sapiens and NOT-Homo Sapiens… but this has nothing to do with a regression analysis of genetics back through the common ancestry!

Whether there is a “first” Homo Sapien in God’s eye rather than in the view of human operated sciences, (made through evolution rather than through special creation), the first “man” would still be part of a fairly large population!.. say 10,000 or more!

You need to straighten out your description of this key part of your operating scenario… because right now you are mixing apples with oranges…

Hi all, I have been a bit distracted from the bottleneck issue by the human-chimp genome similarity issue that @DennisVenema raised. This has now moved to another thread here: Human Chimp Genome Similarity
I will try to get back to the bottleneck issue soon!
Richard

1 Like

Hi all, this paper, by some of my close colleagues and collaborators, came our yesterday in Nature Evology and Evolution "The ash dieback invasion of Europe was founded by two genetically divergent individuals"

@RichardBuggs

This is a portion of what the article discusses:

You aren’t trying to suggest that the 2.5 million haploid individuals have disappeared from the Earth, are you?

Hi Dennis,
Sorry to take a while to respond. You have quite distracted me by bringing up the human-chimp similarity issue, which is very interesting. I had been wanting to re-visit that issue for some time. But back to bottlenecks…

This is an “argument from personal incredulity” (to borrow a phrase from Richard Dawkins). I am interested that this now appears to be your strongest argument against a bottleneck. I suspect that many people will find argument this less compelling than the “certain” case from population genetics that you appear to make in Adam and the Genome.

As far as I can see, a step-by-step evolutionary pathway for a lineage passing through a bottleneck is clear, and you just have doubts about the selective forces that could drive it. As arguments from personal incredulity go, that is not a very strong one.

I am sorry, but I don’t think this is a complete summary of your claims in Adam and the Genome. You made very specific claims about what the literature was saying, and these have not stood up to scrutiny.

In addition, I think that most readers of Adam and the Genome pp45-65 would conclude that your major claim was that a bottleneck of two in the human lineage is almost impossible on the basis of analyses of current human genetic diversity.

But we have discussed these issues before, and anyone can read your book and make up their own mind, so I won’t belabour the point.

No, as we have discussed, methods applied to date suggest that effective population sizes have not dipped below several thousands, but they do not show that census population sizes have not dipped below that figure.

As I say, I think that most readers of Adam and the Genome pp45-65 would conclude that your major point was that a bottleneck of two in the human lineage over the last 18 million years is almost impossible on the basis of analyses of current human genetic diversity. Your new view is a significant departure from this point.

So have I! Thank you for coming to the table.

May we all be more and more like Chaucer’s Clerk: “And gladly wolde he lerne, and gladly teche.”

Good to hear that. It would be a very different chapter, to be sure.

You would do your readers a service if you wrote a blog to tell them now, as far as you are able, that present day genomic diversity in humans does not preclude a bottleneck in the human lineage between approx 700K and 7myr ago. I think you owe this to them, and to everyone who has taken the time to participate in this discussion.