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


(Dennis Venema) #287

I think we’re pretty much on the same page with this one, yes.

Is this positive evidence for the claim I make in Adam and the Genome? Yes. I can’t see how we can squeeze this variation into 2 people at 200,000 years ago (or even 300,000 years ago, if one was to accept Homo sapiens at this time). Can you, or can @RichardBuggs?


(Tim) #288

Swamidass,

I’m sorry, but we’re going to have to disagree here. I may not be a biologist or geneticist, but I am scientifically literate and for a time belonged to that community (research-oriented doctoral program I ended with my masters some time ago). What a scientist is or is not convinced of within their field is highly relevant to any discussion within it. You’re pretending it isn’t. And that’s just plain wrong.

Richard is wanting to have this exchange with Dennis take on the appearance of two peers openly debating an issue of scientific merit, both presumably with open minds, both presumably capable of convincing or being convinced to change their minds, and both being being upfront and honest about what the evidence does or does not show.

However, if you have one of these parties absolutely refuse to acknowledge what they believe the science does or doesn’t show, and only grant it as an “assumption” for the purposes of debate, then you distance them from that even platform where the capacity to change views and acknowledge good evidence when presented ought reside.

If Richard for personal reasons refuses to acknowledge that, for instance, the genetic evidence clearly shows that a bottleneck to two is implausible within the last 50,000 years, despite himself thinking so, then he’s clearly not going to acknowledge that the evidence points to no such bottleneck within 500,000 years no matter how strong a case Dennis may provide. Or, alternatively if he feels that a bottleneck within 50,000 or even 10,000 years is entirely plausible, then he really ought share that with Dennis so he can appreciate just how far apart they are and adjust his conversation appropriately.

If Richard likewise personally accepts that common descent is well and convincingly attested to by the evidence but cannot acknowledge it for personal reasons, we would then have to wonder if he would feel the same reluctance to acknowledge no bottleneck of two within the human lineage for similar reasons. If Richard personally is not convinced of common descent, then Dennis ought know that as even if he “wins” the argument, since it is partially premised on common descent as a dependency, Richard will leave the conversation believing Dennis won a technical but ultimately meaningless victory since he does not accept that dependency and so his position will remain unchanged.

The question is are we going to have a fair and honest conversation between peers, where both sides may be expected to change their views if required by the evidence that comes out here in the discussion? Or aren’t we?

Again, I do not think one needs a background in biology or genetics to answer that question.


(Peaceful Science) #289

It seems like you are limiting your claims to merely Homo sapiens, is that correct? I thought we were asking about bottlenecks in our distant past going back to the origin of Homo about 2 million years ago. By limiting your claims this way, are you suggesting that you think it is possible for there to have been a single couple bottleneck, say, 2 million years ago?


#290

It might be useful to remind everyone that Dennis Venema originally stated that the chances of there being a 2 person bottleneck in the last 200,000 years is the same as the chances of Geocentrism being true. That is the claim which Buggs is challenging. As @glipsnort has stated many times, if you go back far enough you can posit a 2 person bottleneck at any time and such a bottleneck will be indistinguishable from a large constant population as determined by modern genetic diversity. This is why Dennis limited the time span so that he could define how certain he was of the conclusion.


(Dennis Venema) #291

In the book I make the claim that humans evolve as a population, and I define human as “our species” - Homo sapiens. (That’s not to say that other species might not have had the image of God, and so on.) In the book I place H. sapiens at 200 KYA, as was the consensus at the time. I think the evidence is solid that there is not a bottleneck to 2 in our ancestry for at least the last 500,000 years, but I don’t defend that in the book per se. From there it gets progressively more challenging to make a strong claim, but I think that even 1,000,000 years is reasonable to exclude a bottleneck. 2MYA? By now we’re at the limit of PSMC and other similar modelling approaches.

Now, is there positive evidence for a bottleneck to 2 (or even 20 or 200 or 2000?) at any time in the last 3,000,000 years or more? Nope. At best one could claim that our present-day methods cannot exclude the possibility between 1-3 MYA.

Homo erectus as Adam? I can’t see how this solves anything.


(Peaceful Science) #292

If that is the case, I am confused.

@RichardBuggs seems to have been clear he has been thinking about a bottleneck at around 500 kya. @agauger is thinking of one as early as 2 mya. It does not seem that @RichardBuggs is challenging claims of a bottleneck before 200 kya, but rather that there was not bottleneck in our ancestors ever. If @DennisVenema means to limit his claims to just within the last 200 kya, then perhaps there is not even a disagreement. Perhaps if @DennisVenema clarifies that he only intended the limited claim, we are done here.

Though, trans-species variation does seem to make a bottleneck in the last 6 mya unlikely…but if the goal is merely to show that within the last 200 kya a bottleneck is unlikely, I’m not sure how this all fits in. What exactly is the disagreement about?

So, it sounds like the “as certain as the earth orbits the sun” claim is merely about Homo sapiens (avoiding the term “human” is helpful here) as a taxonomic category and ignoring interbreeding, and only applies to the last 200 kya to 300 kya.

Perhaps @RichardBuggs can clarify, but it seems he agrees with that; the issue is more about the distant past, and non-Homo sapiens, such as Homo erectus. The only evidence that stretches that far back is trans-species variation. In the intermediary zone of 500 kya, it sounds like you still rule out a bottleneck, but with less confidence. Homo erectus arises about 2 mya at the limit of PSMC, I’m not sure we have the same confidence here at all. It seems you think that also.

If that is the case, maybe there is no real disagreement here. At least, I am struggling to find it.

Some people feel it does solve things. It would be worth understanding why. That is for another thread though.

That seems to be the main thing that @RichardBuggs and @agauger have been arguing for. I still think trans-species variation is the fly in the ointment, but I no longer see the disagreement here. What are we debating exactly?


#293

Here is the original statement posted by Richard Buggs:

"A few months ago, I was reading a new book by Dennis Venema and Scot McKnight entitled Adam and the Genome. I was surprised to find a claim within the book that the past effective population size of humans has definitely never dropped below 10,000 individuals and that this is a fact of comparable scientific certainty to heliocentrism."
link

In that book, Venema and McKnight stated that the human population has not dipped below 10,000 individuals over the last 200,000 years, and that the confidence they had in that conclusion was equal to their confidence in the accuracy of Heliocentrism. By disagreeing with Venema and McKnight, Buggs is disagreeing with that time frame.

It’s a bit like someone saying that a 2 minute mile is nearly impossible for a human, and then changing the argument to a 400 m race and claiming a 2 minute time is completely possible. You can’t change the time frame and still be criticizing the same conclusion.


(Chris Falter) #294

@DennisVenema, @RichardBuggs , @Swamidass

I appreciate the in-depth discussion you are having here. As a tyro in the domain of biology I am only able to listen and learn. However, I do have a pretty good understanding of statistical methods, so I would like to ask that you all quantify the certainty of your assertions. If you could say, for example, that a particular study indicates <5% probability of MRCA < 300kya, and some other study indicates <2% probability of MRCA <300kya, the I would conclude the probability of MRCA <300kya is 0.001, assuming the data in the 2 studies are IID.

In addition, the consistency of today’s genome with a population of just 2 individuals at a certain point in the past does not mean the scientific community believes that was the actual population at that time, correct? This is important because if we say, e.g., that Zhao 2000 is consistent with a MRCA 50kya, that does not contradict or overrule 10 other studies that say the MRCA was 500kya. Assuming such studies exist. In that case, we would have to (from the scientific perspective) say the MRCA was no fewer than 500kya, correct?

Thanks!


(Peaceful Science) #295

We are not going to get into a debate about what “human” should mean, but there is sufficient confusion in its use that it might be the entire reason for the disagreement. In @DennisVenema’s mind “human” = Homo sapien, but this not currently the dominant view in science. It appears @agauger thinks Homo genus = “human,” in agreement with the Museum of Natural History. Without having differences in these meanings clarified, I can see how confusion arose. In general, it is best to avoid the term “human” in making scientific claims for this reason.

It sounds like @RichardBuggs and @agauger would not have objected to a statement like this; and it also seems this is what @DennisVenema thinks:

Homo sapiens arise about 200 kya, and since that time we have very high confidence that our ancestors do not dip down to a single couple. In the deeper past, however, it is harder to know with such certainty, but one would have to accept a very ancient Adam who was not a Homo sapien.

And I agree, there is no positive evidence for a bottleneck of 2, but it just might be outside the genetic streetlight.

Correct. It just means we cannot tell for sure, and have no reason to think that it was a single couple. In fact, if the data is consistent with a single couple, it is probably also consistent with a group of 10.

Also, I’m not sure we concluded that Zhao 2000 is consistent with a MRCA of 50 kya, but that it might be consistent with a MR4A of about 250 kya. You are right too, that this does not contradict the studies that show 500 kya. The issue is that cherry picking locations is always going to be a problem. We have to look at the whole genome, as is done in some of the other papers. There is very high variance in MRCA time for genetics (but not for genealogy!), so we expect there to be different estimates. An average of across several portions of the genome would probably be best.

Also, it is important to keep separate the notion of an ancestor bottleneck and a single couple origin to “human.” Part of this gets to the fuzzy definition of species. From a taxonomic point of view, we have very sparse samples of a large population, and cannot really define with clarity any lines. In context of human origins, however, some people do think there was a “line” somehow. Perhaps there was, but we cannot discern it scientifically. There is an open question about what “human” is, but that is a conversation for another day.


(Dennis Venema) #296

Not quite. The (now infamous) quote says the following:

“As our methodology becomes more sophisticated and more data are examined, we will likely further refine our estimates in the future. That said, we can be confident that finding evidence that we were created independently of other animals or that we descend from only two people just isn’t going to happen. Some ideas in science are so well supported that it is highly unlikely new evidence will substantially modify them, and these are among them. The sun is at the center of our solar system, humans evolved, and we evolved as a population.”

I also say this in the very next paragraph:

“Put most simply, DNA evidence indicates that humans descend from a large population because we, as a species, are so genetically diverse in the present day that a large ancestral population is needed to transmit that diversity to us. To date, every genetic analysis estimating ancestral population sizes has agreed that we descend from a population of thousands, not a single ancestral couple. Even though many of these methods are independent of each other, all methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last three million years or more—long before our lineage was even remotely close to what we would call “human.” Thus the hypothesis that humans descend solely from one ancestral couple in has not yet found any experimental support,— and it is therefore not one that geneticists view as viable.”

So, I do discuss studies that go back past humans, and I show that there is not a case to be made from those studies that Adam and Eve are somehow not human and further back in time. The “heliocentrism quote” is more limited in its scope. It’s about humans.


(Mervin Bitikofer) #297

Had you (in true time-machine style) been able to look ahead to these threads and see all the kerfuffle raised by Dr. Buggs and others around the paragraph(s) above, would you have written anything differently? Is there a single change in any wording you would make were you penning those paragraphs now?

If this is a presumptuous question --feel free to disregard. Just my impertinent curiosity piping up here.


(Jon) #298

You’re missing the fact that Dr Buggs is doing a bait and switch.

But Dennis clarified that he was speaking of homo sapiens.

If you look at what they’ve posted, they haven’t been contesting the definition of “human”. Their concern has been placed elsewhere.


(George Brooks) #299

@Swamidass, what an odd question to ask.

When a scientist rules out a the possibility of something between 2 pm and 10 pm… would you ask him: “… are you suggesting that it could happen between 10 pm and midnight?”

If you got a major eye-roll, would you be surprised?

If the testing is designed to eliminate the possibility of something between 1 and 200,000 years ago … I think it would take a lot more testing to see what happens if you change the time frame beyond 200,000 years ago.

But you probably saw this quote from @DennisVenema by now, right?


(Richard Buggs) #300

Hi Joshua,
Very briefly as I have lots to do before the Christmas break.

I see a good mix of different races in all the major clusters of the network diagram. Indian/Hungarian/Franch/Papua New Guinean in one. Chinese, Kenyan, South African, Melanesian in another. Indian, Japanese, Mbuti pygmies in another. Nigerian, Chinese and French in another. This suggests to me that the clusters come from ancestral haplotypes. Even if they didn’t, one could explain it by population structure after a bottleneck with loss of haplotypes by drift in some areas.

I will respond at greater length as time is available.


#301

There is no confusion when a time frame is given. What they are saying is that the population leading to today’s human population did not dip to two people over the last 200,000 years. It doesn’t matter if you define those populations as human or bloppobops, all that matters is the time frame.


(George Brooks) #302

Yes, yes… @RichardBuggs… one could explain it … explain it away.

So when will you start lecturing @DennisVenema on the idea that no matter what his tests and experimental math shows, God could have just miraculously inserted maximum genetic diversity into the human race - - at any time after the Flood.

When it comes to cherry-picking special circumstances for how to get around the limits of scientific evidence, there’s really nothing like a few miracles of God… or a long series of miracles to create something that looks "just like evolution: … but really isn’t - - because God is quite the prankster (?!).


(George Brooks) #303

@T_aquaticus, perfect answer.

@Swamidass, it is clear that @DennisVenema has been avoiding the “bugaboo” of “Defining what is a Human” by simply ignoring the categories, and working with a single continuity of “common descent”.

While common descent is a maze of riddles if you are going from “older to newer” populations (because you never know when you are going to end up in a genetic cul de sac).

But if we are going backwards, from “newer to older”, there’s only path to follow, right?

Some might want to entertain the idea that one branch “cross-bred” with another branch… but is that in keeping with the Biblical model of human descent? Yes, there are the Nephilim … but is that how you and @RichardBuggs are going to solve the diversity problem?: “we get around the one mating pair bottleneck” by introducing a few hundred additonal breeding pair where one of the genetic contributors are Nephilim"

Even if we were to allow for that … it doesn’t look like you can get down to a single mating pair, or even a few hundred mating pair in just 6000 years.


(Dennis Venema) #304

Oh, I’m quite sure that bloppobops had a unique origin - right here! I guess if I’ve quoted your post that’s now N=2, and writing out the term once more bumps them to N=3. :slight_smile:

In all seriousness, I won’t be able to contribute much of anything to this thread for the foreseeable future. Merry Christmas, all.


(Richard Buggs) #305

Hi Dennis,

I would love to do this, but my offer of moving on was contingent on us agreeing that it does not provide a suitable citation to support your case in chapter 3 of Adam and the Genome.

Please let me just summarise why this paper does not support your case.

  1. The fact that the authors conclude from their data that there was not an out-of-Africa bottleneck is because they have data from both inside and outside Africa and they can compare the two sets of populations. It is the relative levels of diversity in the two populations that allow them to exclude an out-of-Africa bottleneck. They spell this out clearly even in the abstract (“The comparable p value in non-Africans to that in Africans indicates no severe bottleneck during the evolution of modern non-Africans”) They cannot exclude an earlier bottleneck using their data because they do not have genetic data for a population from which their African populations were derived. To do this they would, I guess, need to use ancient DNA from bones, and they were working before this was technically possible. Therefore you cannot claim that because they exclude an out-of-Africa bottleneck, they also exclude a bottleneck in the lineage leading to the African populations.

  2. The authors estimate a long-term human effective population size of between 8100 and 18800. These estimates are based on present day numbers of segregating sites in the sample sequences, and estimates of mutation rate. This method assumes a fairly constant population size over time. No historical reconstruction of effective population size at different time-points in history is given. Thus this does not exclude a bottleneck.

  3. The authors present a coalescent analysis for this region gave a mean estimate of time to the most recent common ancestor (MRCA) for this region of 1,356,000 years ago; and the 95% confidence interval was between 712,000 and 2,112,000 years ago. This is assuming a constant effective population size of 10,000. Using the approximation of @swamidass that the time to the coalescent of 4 alleles will be a quarter of this time, this means a bottleneck could have occurred between 178000 and 528000 years ago. And these figures do not include an adjustment in the light the point that I have made about rapid population growth after a bottleneck giving further reductions of these dates.

Therefore it seems to me very clear that this paper does not support your case.

I am puzzled as to why you are not willing to concede this rather minor point. After all, looking back over your previous posts in this discussion, your own understanding of the paper and its methods have clearly deepened during the course of our discussions, and your position has shifted somewhat.

You initially seemed to think that Zhao et al (2000) based their conclusions about effective population size on their coalescent analyses.[quote=“DennisVenema, post:87, topic:37039”]
Have a look at Table 5, which shows their data for the distribution of TMRCA values. This is the data and analysis they are basing their conclusions on. Bottlenecks increase the probability of coalescence (this is also how PSMC methods work). We see a distribution of TCMRA values for the alleles in the study. This is basically what a PSMC analysis does sequentially for an entire genome to get a much larger sample size.
[/quote]
I immediately showed that this was wrong, but you continued to believe this through-out most of our discussion until you finally re-read the paper.

You also thought that the method they used to calculate effective population size did not assume a fairly constant population size over time:

You were wrong on this point, so then you said:[quote=“DennisVenema, post:97, topic:37039”]
I guess I’m asking you to look at the TMRCA data there and think about your hypothesis (a bottleneck to two in the last few hundred thousand years).
[/quote]
You then appear to have made the mistake of thinking that a bottleneck could only have happened at the TMRCA. This is clear in the quote below, where you date any potential bottleneck at the TMRCA[quote=“DennisVenema, post:102, topic:37039”]
That study identified 75 variants in this region that have a minimum coalescence time of over 700,000 years. The mode is 1.2 million years, and 700,000 is the lower bound of the 95% confidence interval for the combined sample. So, how did all of that variation survive a bottleneck to two? It can’t. So, how did all of that variation arise after a proposed bottleneck to two? Through new mutations. How long would that take? Even with a steady-state population of around 10,000, about 1.2 million years.
[/quote]
You then made the mistake of suggesting recombination was unlikely to have occured much in a 10,000kb region[quote=“DennisVenema, post:109, topic:37039, full:true”]
Richard - are you aware how closely linked those variants are? They’re at most 10,000 bases apart. Are you seriously suggesting that they passed through a bottleneck en masse in two individuals and then recombined to the forms we see now?
[/quote]
I think that Joshua’s analysis has shown you to be wrong on this point.

You also suggested that the raw data presented by Zhao et al does not form clusters that could have been derived from four ancestral haplotypes:

By “eye-balling” in Excel and by drawing a haplotype network in Splitstree, I have shown this to be wrong.

You later expressed skepticism that three mutations could occur within a timeframe of a few hundred thousand years[quote=“DennisVenema, post:231, topic:37039”]
I’m still not seeing how you can fit everything you need into the timeframe you’ve allowed yourself. If there is a bottleneck to 2, every haplotype in the Zhao (2000) data set has to come from your four ancestral haplotypes. Why did you decide that three mutations was an acceptable deviation from those types? How do you have time for three mutations, each interspersed with drift?
[/quote]

However, the coalescent analysis of Zhao et al clearly shows that many cumulative mutations have occurred in this region in such a time-frame.

You also suggested that the low Ne after a bottleneck would reduce the numbers of mutations available[quote=“DennisVenema, post:231, topic:37039”]
Don’t forget that if you lower Ne to get a faster coalescence time, you also lower the number of forward mutation events that are plausible.
[/quote]
But I argued that if the population revered quickly, this effect would be small, and expansion to an Ne of over 10,000 would quickly allow far more mutations.

Thus, I am struggling to see how you can still think that this paper supports your case.

As we have been discussing the paper, you appear to have changed your position on when in history you believe a bottleneck has been shown to be almost certainly impossible. On page 55 of Adam and the Genome, you wrote:

"It seems our smallest effective population size over the last 18 million years was when we were already human, at around the time our ancestors left Africa…
All methods employed to date agree that the human lineage has not dipped below several thousand individuals for the last 3 million years or more – long before our lineage was even remotely called “human”.

You now seem to be saying in the current discussion that in fact you only think a bottleneck is excluded by the data in the last 200,000 years:[quote=“DennisVenema, post:247, topic:37039”]
A few questions for you - if we take as reasonable your suggestion that Zhao (2000)'s data coalesce to four haplotypes between 300,000 - 1,000,000 years ago, how does that help your case? In Adam and the Genome I consistently discuss humans as a species arising ~200,000 years ago. So, by your calculations, Zhao (2000) supports my case - human variation in this all region of the genome cannot be reasonably explained by a bottleneck to 2 individuals within human history, as I argue in AatG. Am I missing something here?
[/quote]
Yes, you do discuss humans as a species arising ~200,000 years ago, but you also say that “the human lineage has not dipped below several thousand individuals for the last 3 million years or more – long before our lineage was even remotely called “human””. Thus, it seems to me that a bottleneck between 300,000 and a million years ago would be a direct contradiction of the claim you make on page 55 of Adam and the Genome.

All in all, it seems to me that we have made considerable progress in our discussion of Zhao et al over the past weeks. It has helped us clear up several misunderstandings of the paper and of its methods. It has helped us all to think through how to think about a bottleneck in terms of a coalescent analysis. It also appears to have helped you to change your position expressed in Adam and the Genome – that a bottleneck could not have occurred in the last 18 or 3 million years – to a position that one could not have occurred in the last 200,000 years.

Given all this progress, it baffles me that you are not willing to now concede that Zhao et al does not support you case in Adam and the Genome, and is not therefore an appropriate citation. I honestly don’t think you have much to lose by making this admission. It is not as if you actually cited Zhao et al in your book. It is not mentioned there. Why not just admit that you were mistaken to cite it?

I also will struggle to contribute much to this discussion over the Christmas period. I will be reflecting on it though from time to time. I wish you and all other contributors and readers a very happy Christmas. Thanks for an interesting discussion so far, and helping me to try to answer my questions about bottlenecks.


(Tim) #306

Richard, while I think it’s very magnanimous of you to “offer” to review the stronger papers you demanded of Dennis 300 comments in on this thread, all for the meager price of his admitting something you’re demanding of him, I cannot help but notice you remain free of offering your own such admissions of whether the body of evidence compellingly attests to common descent, or if the body of evidence compellingly excludes a bottleneck of two in the human lineage within the past 10,000; 50,000; 100,000; 200,000; etc. years. Obviously basic questions of science highly relevant to this conversation.

I merely point this out as you’re drawing a link between what a scientist is willing to admit to what the evidence does or does not support, and ostensibly their credibility as well as how productive a conversation with them may or may not be. All the while you continue to refuse to admit to what the evidence does or does not support. On topics Dennis and others have repeatedly asked you to address.

I just thought I’d point this out. Since I believe in the golden rule. So please don’t do unto Dennis what you yourself are not prepared to have done to you. Or perhaps more aptly put:

Yet, as only a simple reader on this thread who only captures your interest whenever I elicit information from Dennis you find useful, I breathlessly await your ignoring what I’ve brought to your attention (or lack thereof) while you continue on your merry way of pushing the envelope on what double standards may achieve.