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


(Jon Garvey) #383

Yes - one can use considerable expertise and ingenuity to argue whether the population genetics model supports a particular contention or not. That’s the nature of this thread.

But the question of whether the model itself is adequately valid over such timescales, given its known limitations and the state of flux of theories of large-scale evolution, is a significant one.

“All models are wrong - some are useful”. But their utility is only measurable by the ability to validate them by independent observation under the situation for which they are being used - in this case the origin of humanity defined, at least, as our species or even across hominin species by some protagonists. That’s very different from studying the evolution of Y-chromosomes in the living population.

In this case, validation would seem to require counting fossils that are as rare as hens’ teeth - in the absence of physical evidence, the population genetics model seems to validate itself in a circular manner.


(Chris Falter) #384

AFAIK, it’s basically the same thing, but on a longer time scale and across more of the genome than typical Y-chromosome studies.

Perhaps one of our biologist friends like @Swamidass, @glipsnort, @DennisVenema or @RichardBuggs would be able to shed more light.


(GJDS) #385

Perhaps you would elaborate; what predictions can any model make on what seems to be current data used to set up the model itself?


(Chris Falter) #386

Good question, George. Assuming I have understood this thread, the data being predicted/compared with current state and the data used in rate calculations are not the same. The predictions/observations of current state focus on the distribution of genomic features, whereas the assumptions of rates of change are based on known history.


(GJDS) #387

Hi Chris,

Validation of models, as I have practiced (and is commonly understood) requires a result from the model to be similar to an observation/measurement of a system independent of the model data base. Within this I have a difficult time noting such validation of the models discussed here. Since a major point is the size and time of a bottleneck, for example, validation would be considered by using physical data of a real bottleneck. There may be other ways, and if you can identify them I would be interested to know.

This is not a question on the technicalities of the modelling proceure.


(Dr. S Joshua Swamidass) #388

Thanks for the invitation.

This is not accurate. They are estimating the average population size in a sliding window (that is quite large). They are not estimating the minimum. Just the average. The really interesting question is whether or not there is a way to determine the minimum.

Population size estimate studies, to be clear, are not testing for a brief bottleneck followed by an exponential expansion. The only paper I know that did this is the Ayala paper on MHC (http://www.pnas.org/content/91/15/6787.abstract) from 1994. Eventually we will get around to it, but this is the only published study I know that actually tests the idea. That was 25 years ago though, so the follow up studies are going to be interesting to look at.

The point that @RichardBuggs is making is that the power of population studies past about 500 kya to detect brief bottlenecks are not well studied. The fact that they do not find them, therefore, cannot be taken as evidence they do not exist. At least not yet. This is a question about detectability and statistical power.

We are not speaking theologically at all. This is about the science.

I imagine those that take this position might take it not for Genesis, but because of Paul’s statements in Acts, Romans, and I Cor. I suspect New Testament theology drives this more than Genesis hermeneutics. Whatever the case, the impact on theology should be sorted out later. Perhaps we start a thread for that?

I’m not sure I understand the question. For one, I agree that that TMRCA > 1mya are legitimate signal of ancestry, for DNA. We are not talking about segments of DNA though, but a couple with four genome copies between them both. Its an equivocation to place them at an autosomal TMRCA. Right?

Well, for one, I am an academic! =)

Also, we were brought here by the claim that “Homo sapiens” never dip below a few thousand. Though, we all know, they eventually go to zero in the past. How can we know then that they do not stop at 2 on the way to zero? Yes, this is all about definitions. No scientific study goes here, because there is not enough traction to get clarity here. Which is why heliocentric certainty is not likely.

As I understand it (and it seems was confirmed by others, there are two claims at question here.

That’s right. I’d say this higher confidence than the Y-chromosomal studies too.

That is exactly what these studies do. There is real quality work here.

If you read the papers, you will see that quite a bit of validation is going on. There is really good work being done by scientists here. It is a mistake to dismiss it this way. There is a great deal of independent validation. Often they find that specific parameters do not affect the results much (e.g. mutation rate and generation time), except to scale the time. That leaves the debate on exact dates open (and does expand the confidence intervals), but it does not invalidate the whole effort.

The question here is actually far more interesting on a scientific level. We are getting into understanding exactly what these approaches can and cannot tell us.


(Dr. S Joshua Swamidass) #389

If this is what @DennisVenema means by his first claim, I’m not sure its defensible:

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

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?


Regarding the second claim, things are more interesting.

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.

I had some fun spelunking the data. @RichardBuggs suggested…

I took him up on the challenge and computed it across the whole genome.

That puts a fair estimate of the TMR4A at 430 kya. I’d estimate that there is about 20% error one way or another, at least. That, could, perhaps be even extended down to 340 kya, when some think first Homo sapiens arise (though I would not bank on it). It would certainly work for the common ancestors of Neanderthals, Denisovans and Homo sapiens.

I explain the details here. https://discourse.peacefulscience.org/t/heliocentric-certainty-against-a-bottleneck-of-two/ And @DennisVenema, the authors of the ArgWeaver paper were really helpful. So kudos to you for sending me that way. The linked discourse is pretty long.

The exact path here is fairly technical, and I wanted to document it so that others could replicate these results. There is a lot in that thread, so this might be a helpful guide:

Claims of Heliocentric Certainty. What are the scientific claims in question?

TMRCA or Time to Most Recent 4 Alleles? TMR4A (not TMRCA) puts the bounds on a couple bottleneck.

Estimate with Median or Max? The statistically sound approach is the median.

TMR4A from Genome-Wide TMRCA. An initial estimate of TMR4A, which we improve on later.

The ArgWeaver Genome Wide Phylogenies 424 GB of data with genome-wide answers.

Genome-Wide TMR4A. A better estimate of TMR4A, based on the ArgWeaver data.

The last two may be most interesting if you have time to take a look. So have fun, I’ll look forward to seeing the conversation continue. I’ve been learning a lot.

Not All the Evidence

To be clear, we have still yet to deal with the stronger evidence, such as Ayalas work where the bottleneck hypothesis was tested, and he put a minimum bound on bottlenecks.


(Tim) #390

Josh,

In your part (1) above, focusing on taxonomically classified homo sapiens narrowly rather than our hominid ancestors to modern day homo sapiens (obviously so very close genetically to interbreed), you would not even require an “Adam & Eve,” but merely an Adam or Eve in proximity to our other genetically compatible ancestors. A bottleneck of one if you will, a bit of a silly proposition that exposes the arbitrariness of such an endeavor.

In your part (2), should I take this as an affirmation of agreement with Steve’s claim below…extending this even further to 300KYA, which I believe echos Dennis’ framing of this issue as well?


(Steve Schaffner) #391

To be more precise, they’re estimating the effective population size in time windows. The effective population size may or may not correspond well to the actual population size.[quote=“Swamidass, post:388, topic:37039”]
The point that @RichardBuggs is making is that population studies past about 500 kya are not powered to detect brief bottlenecks.
[/quote]
I would say rather that their power to detect brief bottlenecks has not been well explored. [quote=“Swamidass, post:388, topic:37039”]
Also, we were brought here by the claim that “Homo sapiens” never dip below a few thousand.
[/quote]
You may have been, but I certainly wasn’t brought here by that question. I think that question (even as you hashed it out with Dennis) is subject to multiple interpretations that lead to very different answers, and different people seem to be assuming different things about what question is actually being asked or answered. Here are at least some of the possible questions we might be addressing:

  1. Could our ancestors have passed through a bottleneck of size two within some time frame? This is one possible interpretation of asking whether Homo sapiens could have passed through such a bottleneck, since “we” are Homo sapiens and Homo sapiens is us. It is a question that may be of scientific, theological and broad human interest.

If the time frame is the last 500,000 years, it is a question whose answer is unambiguously “no”, thanks to the ancestry many of us have in Neanderthals and Denisovans.

  1. Can we answer question (1) based only on genetic variation data from the current human population (i.e. ignoring Neanderthals). This is effectively the question that is addressed by looking at haplotypes and coalescent methods (e.g. PSMC).

  2. Did the African branch of our ancestry go through the same kind of tight bottleneck? In practice, this is the same question as (2), but with datasets restricted to individuals of African ancestry. It is the question I was actually addressing in my simulations (mostly because I wasn’t even thinking about Neanderthals). Both (2) and (3) are of technical interest to population geneticists, and might be of broader interest as well.

  3. Did organisms that we would classify as Homo sapiens ever go through a tight bottleneck? This addresses not just modern H. sapiens, many of whom have Neanderthal ancestry, but also H. sapiens population prior to ~75,000 years ago, who (probably) didn’t. As I have previously pointed out, this is a very different question from (1). I view it as essentially unanswerable and nearly meaningless. Classification as H. sapiens as you look back in time is largely arbitrary and subjective. More importantly, there could well have been interbreeding within Africa between groups that we would classify as H. sapiens and group that we would not, but we have no way of ascertaining whether or when such events happened. Looking at modern genetic variation, therefore, cannot answer this question.


(Dr. S Joshua Swamidass) #392

Agreed.

Agreed. Edited the original text.

I agree with you that the terms are ambiguous. However, they were clarified. Dennis clarified that he mean Homo sapiens specifically and NOT Neanderthals, and pegged his claim on the time at which Homo sapiens arise. I’m sure he was mistaken, bit that is what he claimed.

I thought Neanderthals and Denisovans and Homo sapiens could share common ancestry at 500 kya, or even earlier. Did I miss something there?

That is how I understand the question as normally posed. Restricting it to Homo sapiens specifically seemed novel.

Exactly my point. Which is why I was genuinely surprised to see @DennisVenema make the claim. I did not realize that this is what he mean when he was making his heliocentric certainty claim.

Though, I’m not sure this is meaningless. Some may find this meaningful.


(Tim) #393

Then we may as well drop the “bottleneck” language pretending to have found some way to preserve genetic diversity in a founding original pair. We could just as easily say at some point that a lone homo sapien survivor, not even a mating couple, bred with a population of genetically compatible ancestors of ours. Those ancestors themselves could of course posses a mosaic of various proportions of Neanderthal, Denisovan, Homo Sapien, etc. DNA. Just as we do today. So in what scenario does this even remotely mean anything theologically?


(Lynn Munter) #394

You are ignoring an important point. What he was clarifying was the statement “we evolved as a population,” and he was indicating that by “we” he meant humans, Homo sapiens. He engaged in this clarification strictly to limit the time scales he was referring to, as can be seen in most of the quotes above.

What you are arguing is that since he clarified he meant Homo sapiens, the statement no longer has the meaning “we:”

I think when a statement is clarified, you keep “we” and add “humans” and “Homo sapiens;” I don’t see the justification for leaning all of our weight on “Homo sapiens” and jettisoning the other two to make your point.

I don’t think you are deliberately misinterpreting here. The conversation was long, involved and complex. Statements were made without the original text being quoted for reference. The conversation has continued quite some time additionally without anyone pinpointing the error, which always makes it difficult. However, at the end of the day, I do not think you have enough basis to say @DennisVenema made a mistake.


(Dr. S Joshua Swamidass) #395

Exactly as i understood too, which is why it is an error. Restricted to the time scale in question (300 or 200 kya to present) we do not know if Homo sapiens dip to a single couple. That is why the claim seems to be in error. I that is not what Dennis meant, then his statements specifically excluding neanderthal’s don’t make any sense.

Of course if Dennis meant something else, he should speak up. I’m happy to be corrected by him, as i myself have been corrected by him in the past. Though that would make the string of statements he made about his definition of “human” incoherent. Eg how do we explicitly exclude Neanderthals and then mean Homo sapiens exclusively when discussing a “human” bottleneck? Especially when pop genetics only talks about ancestral bottlenecks, not homo sapien bottlenecks?

My honest opinion is that he, in good faith, misstated the science. That is common. I do the same and quickly correct myself; i’ve even done so more than once on this thread. Identifying and correcting errors is a good thing, right?

[quote=“Lynn_Munter, post:394, topic:37039”]
I don’t think you are deliberately misinterpreting here.
[/quote]Thanks also for clarifying that. This is just a well intentioned and good faith pushback. I’m sure @DennisVenema will clarify shortly.


(Mark Moore) #396

The bible does not really teach that Adam is the sole progenitor of the human race. Gen. 2:1 says that “hosts” were created in heaven and on earth, and the word for host means an army. The instructions to mankind in chapter one sound martial, and nothing like the interactions with Adam and Eve in chapter 2.

The Christ-centered model of early Genesis explains Adam’s naming of Eve very elegantly. It was a funny thing for him to do because she had actually just gotten them both “killed”. But just prior to him calling her the “Mother of All the Living” we understand that the LORD God gave them a talk about “the seed” that would crush the serpent’s head. IOW, they were told that Christ would be born of a woman, and in Christ men can beat the curse and live eternally. So this passage makes perfect sense- if Genesis is viewed through the lens of Christ.


(Dr. S Joshua Swamidass) #397

Thoughtful response at the DI:

https://evolutionnews.org/2018/01/on-prejudiced-models-and-human-origins/


(George Brooks) #398

@Swamidass

Somehow I think the author is twisting things a little too tightly …

"Having said that, I think Swamidass’s new work further illustrates the difficulty of answering far-out questions using mainstream methods. The tool used, ARGweaver, is fantastic in that it combines an enormous amount of real genetic information to model the past genetic history of humans. For this reason it gives the impression of being truly objective, and so when I first read it, I thought he had proved that there could be no bottleneck earlier than 300,000 years."

"However, a little digging into how ARGweaver works reveals that it too assumes a constant population, and uses this assumption to assign probabilities to ancestry trees. Therefore, again, it is not clear if it is really appropriate for asking questions about Adam and Eve. The particular reason why it is a problem is a bit technical: coalescence (branching but backwards in time) happens much more slowly in a large population. In a large population, the last few coalescents could take thousands of generations. But what if you have a small number of generations, drawing to a smaller and smaller population and terminating in a single couple? All the lineages will coalesce (down to at most four as explained above) but at a faster rate."

I think we beat this one to death long ago!


(Jon) #399

They aren’t thoughtful comments, it’s just the usual apologetic spin.

  • Science is based on assumptions
  • Assumptions may nor may not be true
  • We can’t trust what scientists say because of these assumptions
  • You have proved that it’s possible all humanity derived from a single couple

(Dr. S Joshua Swamidass) #400

Its a bit more complex in this case. I think they misunderstood how argweaver works. I’ll explain later. I can’t say if they will publicly acknowledge it, but I can show what the misunderstanding was.

That is what this data shows. It is not consistent with a bottleneck before 300 kya.

This is not exactly correct. Rather, there is a weak prior placed on the coalescence times, that pulls the TMRCA and TMR4A estimates more recent (not more ancient) than would best fit the data. Once again, I’ll explain later in detail.

At this point, before I add anything more substantial, I’m curious the response from @RichardBuggs and @DennisVenema and @glipsnort.


(Jay Johnson) #401

Aren’t you talking about a bottleneck of two? There are numerous studies that show bottlenecks in the human population associated with the “Out of Africa” event. I think it’s confusing to keep saying “no bottleneck” when what you really mean is “no bottleneck to two individuals,” unless you are arguing that you have disproved all previous papers on the subject.


(Richard Buggs) #402

Hi all, I hope you had a good Christmas and New Year. Sorry it has taken me a while to come back online since the break: I was away at a population genetics conference, and then have come back to a lot of urgent tasks, and a stack of marking. I have just taken the time to read through the posts that have been made since I last posted in this discussion, and I am delighted with the progress that has been made, and impressed with the time and effort that Joshua and Dennis in particular have been putting into this while I have been away.

As I come back into the discussion, I would like to reiterate (in response to some posts above) that I am assuming that we share common ancestry with apes and that chimpanzees are our closest living relatives from whom we diverged at least 6 million years ago. I am also assuming that no miracles have occurred in our past. I am also assuming that the earth revolves around the sun (sorry for wrongly saying “rotates” at one point, @glipsnort). I thought that I had been clear on these assumptions, and that it was obvious that much of what I am saying would not make sense if it were otherwise.

I would also reiterate that I do not come into this discussion with any assumption about whether or not there has been a bottleneck of two in the human lineage since the split from chimpanzees. I just come in asking the question of whether or not this hypothesis has been tested. I am not taking a position about the possible timing of such a bottleneck if there were one. If anyone is frustrated that I am not taking a position on these matters, I apologise, but I simply have not explored this issue and the relevant evidence enough to feel able to take a position. This is why I am engaging in this discussion. I am here to learn and to weigh the evidence. I hope that at some point in the future I will know enough to be able to take a position, or to be able to conclude that we simply can’t know for sure from the current evidence.

I see that some references have been made to other blogs that claim that I am taking a stronger position on these issues. Such blogs are mistaken. I tried to correct the author of one such blog a few weeks ago, and asked for it to be changed, but my request was not granted.

I am very glad that @DennisVenema now agrees with me that Zhao et al (2000) does not support the case he makes in Adam and the Genome and I would assure Dennis that I do not view this as “win” for me. I have never seen this discussion in terms of a competition. Indeed, the fact that Dennis is willing to make this admission in the light of evidence and explanation has won him respect as a scientist, in my eyes. I am glad that we examined this paper, and Dennis’ earlier claims about it, in such detail, as it helped us all to think more clearly about the nature of evidence that could be used to test a bottleneck hypothesis. In particular, it has led on to the very interesting work by @swamidass in TMR4As.

I have learned a lot by reading the posts by @swamidass on TMR4As, and the comments about his analyses by @DennisVenema @glipsnort and others. Joshua has brought a great deal of expertise and time to this discussion and I am very grateful for that. This is highly interesting and informative. I think this is getting close to a test of the bottleneck hypothesis. I am still taking in some of the details of what Joshua has done and may have more comments in due course. I do think that the coalescent models used in a test of the bottleneck hypothesis would need to include the effective population size decreasing down to two as we go back in time. I realise that this would be a lot of work, but I do think that this would be necessary. Do correct me if I am missing something, Joshua. I am grateful for the many excellent points that you have made over the past few weeks.