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


(George Brooks) #873

Okay… I was wondering if I was going to need to invest more narrative on that point:

Looking at scenario (2) first, if a YEC wants to propose that Neanderthal (or other interbreeding) could change our analysis of possible bottlenecks, he would have to do two things at once:

a) that Neanderthals were an equally legitimate part of the human race per Genesis (I have very rarely found a YEC willing to do so); and

b) having done so, the YEC must somehow show that the Neanderthals introduced a completely different biology - - all the while being on par with the view that they are equivalent to Sapiens.

As for Option ©, it’s the same kind of issue… but instead of arguing for a different biology, the YEC has to simultaneously equate the contributors as “on par” with the rest of humanity … and yet also dramatically speed up mutation rates that the conventional analysis assumes for humanity.

Whenever we discuss how the scenarios could be changed, we really need to validate the proposed change with the likelihood that a Young Earth Creationist would tolerate the scenario change. Nothing important is accomplished to argue that there can be a single pair bottleneck one million years back in time when we can’t find any Creationist who accepts a million year time frame.

And if we find a creationist who says he endorses a million year time frame, the next logical question is how does he justify a million year time frame (and thus Rejecting the premise of 6 days of creation) while at the same time insisting on Special Creation a million years ago? This kind of creationist is neither Fish nor Fowl, and will be repulsed by Evolutionists (because of the feature of Special Creation) and by Creationists (because of the rejection of 6 days of creation).

Rather than making the BioLogos “spin” more palatable, it makes it likely that we will double our opposition, or at least double the apathy of a vast swath of our potential audience.


(Dennis Venema) #874

I don’t think we yet have a comprehensive picture of extant human variation in sub-Saharan Africa. In fact, I’m certain that we don’t - the question is merely how much a comprehensive picture would shift the TMR4A, etc. There’s only one way it will shift, based on new variants being discovered - it will shift to larger values, not smaller ones.

Another potential finding is new hominin remains we can get DNA out of. That could show us introgression events into Homo sapiens that could also push the date back.

Let me also push just a bit on that evidence for ancient DNA in Denisovans, and you can tell me what you think. Even if that ancient variation is not in present-day humans (and it is, as far as I know, in Oceanic peoples at least - why wouldn’t it be?) - but even if we assume it is not, if Denisovans are “in” then this is evidence that they interbred with another hominin. If that other hominin is also “in”, then the time for a last sole genetic couple gets pushed back. If that hominin is “not in”, then there is a introgression problem (interbreeding between humans and non-humans). I don’t see another option. Thoughts?


(Dennis Venema) #875

Of course, it could be selected against. Neanderthal variation was selected against…

Don’t forget the Denisovan DNA we have is fairly recent (last 100,000 years or less).

I’m going to go read that paper again…


#876

There were two implied conditions that often don’t get mentioned. First, there was the implied assumption that we were talking about the last 10,000 years or at most the last 200,000 years which corresponds to anatomically modern humans. The second, and related, assumption was that we were talking about the time period covered by the statistical confidence in the measurements and models themselves. If the 2 person bottleneck crowd has to retreat to time periods where population models are necessarily ambiguous then we go back to the burden of proof problem inherent in that bottleneck hypothesis. In order to work past the null hypothesis you have to have models that will detect a bottleneck if there was one. If the models and data do not allow you to reject the null hypothesis, then you stay with the null hypothesis.

My favorite way of tackling these issues is to just treat it as an interesting scientific question separate from any cultural or religious implications. Such research is probably not appropriate for scientists spending their official time on if they are being funded by other sources (e.g. NIH), but I think people can still approach this from an agnostic position and see where it leads.


(Peaceful Science) #877

Except that is precisely the assumption i’m challenging as absurd and unwarranted. It such a departure from our current understanding it cannot be justified and should certainly not be implicit.

That also is an unwarranted assumption. It is a scientific error to just assume this to be true of measurements.

This is in error. The choice of null hypothesis is subjective and is being used here to shift burden of proof. The right answer is that we do not know from the evidence. Any one who makes confident claims one way or another adopts the burden of proof, but the no bottleneck position is not epistemologically privileged.

That is a good approach. Most opposition to this inquiry has come from those theologically motivated agains Adam theology.


#878

But those assumptions were implicit in many of the debates prior to this one. That’s the point. It isn’t fair to suddenly change the parameters of the debate and expect older arguments to hold up. Remember, we are talking about a debate that is heavily influenced by young Earth creationism.

It isn’t subjective at all. The hypothesis is that there was a bottleneck down to two people in the direct human lineage somewhere in the past. If your models and measurements are incapable of differentiating between a 2 person bottleneck and a continuous large population then you can’t differentiate between the hypothesis and null hypothesis. This is straightforward statistics and hypothesis testing. You could say that the choice of alpha (i.e. p values) is subjective, but even then it is splitting hairs.


(Peaceful Science) #879

It is certainly fair to point out when conclusions depend on unwarranted and hidden assumptions. No one forced people to make those errors or to claim the evidence was on their side, when it was not.

That is not correct.

There are two hypothesis:

  1. No bottleneck in our lineage, ever.
  2. At least one bottleneck in our lineage.

We do not have the data, yet, it seems to distinguish these two hypothesis. The right answer is “we do not know” not “heliocentric certainty for H1”.


(Peaceful Science) #880

Please do. Let’s get the evidence straight.

As far as i know, we cannot find the entire Neandertal genome in human variation, just a small portion of it. Neither can we find the entire Denisovan genome in human variation either, just a tiny fraction of it. That means we do not expect any specific portion of the Denisovan genome, e.g. that tiny portion which was inherited possibly from an ancient hominin, to be in human variation. As far as I can tell, that portion of the genome is not found in extant humans.

Moreover, it only seems that a portion of the Homo sapien genome (i.e. loci) shows signs of interbreeding. Is that not correct?

If I misunderstand that status of the evidence. If I do, by all means please correct me. It is important to get this straight.

I do not know if the sole-genetic progenitor model specifies what happens to “humans” that do not ultimately contribute to extant humans. There are several shades of gray…

  1. Are genealogical ancestors that are not genetic ancestors allowed to descend from other lines?
  2. Are descendents of Adam and Eve that do not become ancestors of extant humans allowed to interbreed? (e.g. as put forth in all AIG models because of Nephilim)
  3. And as we have already covered, is interbreeding that contributes to extant humans allowed? (e.g. genealogical Adams)

Unless we can show that the variation from a 1 mya hominin appears in extant humans, and this is not incomplete sorting, then #2 and #1 are live possibilities. It would mean that there could be a bottleneck of a single couple in our lineage. Keep in mind also that we have no idea if that specific Denisovan was in our lineage or not. All we know is that there some fragments of human variation that seems to match that knuckle. As far as I can tell, there are severals ways this could have happened, not all of which would rule out sole-genetic progentiorship within the last 700 kya.

Of course, please do correct me if I am wrong or missed something important here.

True, and that is why I’ve pointed out 700 kya as a date that might stand the test of time, and also 2 mya. Conversely, 500 kya might ultimately be too early, even if we cannot definitively rule it out at this point.

As for what ultimately happened, and what the evidence will ultimately show, we can make guesses and take bets, but we should start by explaining honestly what the data shows us right now.
Of course it is also possible I misunderstood something in the introgression data (see above). Please do correct me if that is the case.


(Dennis Venema) #881

@Swamidass

I thought we had already covered this pretty thoroughly. I did not claim “heliocentric certainty for H1" in Adam and the Genome. Perhaps this is not what you are referring to, and I’ve missed a part of the conversation.


(Peaceful Science) #882

True. But you did claim very high certainty. You also retracted that claim. So I am not holding your feet to the fire on that one. Certainly there are other people making that claim, even now.

This graph from the paper seems to support my understanding. Looks like there is only weak evidence of less than 1%-3% of the genome showing interbreeding (contrast that with the higher certainty for Neandertal)…

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031459/

But there is a critical failure point in this analysis too. A large proportion of the data is in HLA and other immunity related genes. It is possible this might be convergent evolution too. I’m not entirely sure how important this wrinkle is, and it will take some effort to process. However, if convergent evolution was not tested for, and we do not see introgression evidence more widespread, that does weaken the claim.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031459/

That being said, I do think Neanderthals and Denisovans (and other hominins) interbred with Homo sapiens. Though, I’d resist using introgression claims two or three steps removed as evidence against a bottleneck.


(Dennis Venema) #883

These are the correct questions to ask, and I guess it would fall to those investigating a sole genetic progenitor model (@RichardBuggs @agauger , others?) to say what their preference is. My understanding of the motivations (which might be incorrect) is that the idea of getting back to a sole pair is so that you can have unique genealogical and genetic descent from that point on. If so, then introgression into the Denisovans becomes relevant. But I’ll wait to hear what @RichardBuggs and @agauger might have to say about these issues.


(Dennis Venema) #884

Ah - but as you phrased it in that quote, it’s at any point in our lineage. Well, our lineage is 3.5 billion years old, plus or minus, just like every other living thing on the planet. That’s a long time, and I certainly don’t claim certainty that there has never been a bottleneck to 2 in that entire time.


(Dennis Venema) #885

Yes, this is correct. But, we have found human remains that have a lot more Neandertal DNA in them than present humans do. At the point of hybridization, the first generation would have had the entire Neandertal set as one of their haploid sets. The same would apply to first generation hybrids of Homo sapiens and Denisovans. So, at some point in our prehistory, we had individuals that (most likely) did have that ancient Densiovan DNA in their genomes, even if it was later lost. Are those individuals “in” or “out”? That’s the question.


(Peaceful Science) #886

Yes yes, that’s right.

I think in the past (and you do not say this now), you have said going back 13 mya, or at least before we diverge from chimps. In the past too, I’ve agreed with that conclusion, but always had less certainty. A lot of people have made that mistake.

And you have retracted that any ways. So I was not calling you out. I was more pointing out it is totally fair to make that correction in the first place.

Sort of. That hybrid was more neanderthal than human (25/75), but point taken. Regarding the Denisovan, you missed my point. It is possible that the Denisovans that interbred with Homo sapiens did not have DNA or ancestry with that ancient hominin. In that case, our lineage would never have to account for them.

Keep in mind, however, that that ancient intebreeding even it is highly speculative. The authors write:

The evidence suggestive of gene flow into Denisovans from an unknown hominin is interesting. The estimated age of 0.9 to 4 million years for the population split of this unknown hominin from the modern human lineage is compatible with that it contributed its mtDNA to Denisovans since the Denisovan mtDNA diverged from the mtDNA of the other hominins about 0.7–1.3 million years ago41. The estimated population split time is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo erectus. This group started to spread out of Africa around 1.8 million years ago42, but Asian and African H. erectus populations may have become finally separated only about one million years ago43. However, further work is necessary to establish if and how this gene flow event occurred.


(Dennis Venema) #887

I also agree that the HLA data is very interesting. I think that introgression and selection makes a lot more sense than convergent evolution in this case, for the following reasons:

  • we know that Neandertals and Denisovans had certain HLA alleles, which are generally under strong selection, and it makes sense that they would have had time for their alleles to come under selection in their local environments outside of Africa since they were there longer than humans have been.

  • we know introgression took place, from the DNA evidence. As such, it is likely that those alleles entered Homo sapiens from these events

  • since there is good reason to suspect that those same alleles would be adaptive for Homo sapiens in those same environments, it’s not surprising that they were retained.

  • the alternative hypothesis, of convergent evolution, is possible, but it would take longer to act. I would also expect more molecular differences if ti was convergence, but I haven’t looked at it too closely.


(Peaceful Science) #888

And I do believe it is a tooth, not a knuckle. Is that right?


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306417/


(Peaceful Science) #889

That is possible but needs to be quantitatively tested. The qualitative arguments do not work here. Notice also how the divergence is extremely high? That appears to be because of very high rates of sequencing errors and DNA degradation. Inferences from sequences with this much error need to be made very carefully.

If convergent evolution has not been tested in the literature, we cannot rule it out unless we are willing to do the test ourselves. Given the extremely high rate of convergent evolution in HLA, I’m not convinced this is going to bear out.

The evidence for Neanderthals, however, is stronger, because it seems to be lower error data, from more individuals, and also include a greater portion of the genome. We also have direct evidence in the form of that 25/75 individual. The evidence for Denisovan interbreeding is just much weaker on several fronts.


(George Brooks) #890

@Swamidass

Do you write these things… just so you can get my reaction?

You have left out one last hypothesis, and it is the most crucial:

There are Three [two] hypothesis:

1] No bottleneck in our lineage, ever.
2] At least one bottleneck in our lineage, at any time. Or, most importantly,
3] At least one bottleneck in our lineage within the last 10,000 years.

The third one is the only one that matters… and I concur that we know that the
hypothesis has been disproven to the same level of certainty I have for a heliocentric solar system.


(Dennis Venema) #891

Hmm - the hybrid I was thinking of was more human than Neanderthal - let me see if I can dig up the paper.

Yes, the evidence for introgression into the Denisovans is tentative. I’m just pointing out the evidence is there, and that folks who are happy to camp out at 700KYA might keep it in mind. I’ll go out on a limb here and say that in the next decade, we will find more evidence for introgression events between different hominin species, and that it will further cloud the conversation about sole genetic progenitorship. The other thing to keep in mind is that I see the data progressively pushing us further back in time, not pulling us forward in time.

There is also some good evidence that there were introgression events into sub-Saharan Africans. If we ever find hominin remains with matching DNA that could shake things up as well. Too bad SSA is such a lousy location for obtaining preserved hominin DNA.


(Peaceful Science) #892

Um…the data just pulled us forward in time. =)

That is possible. We will see. At the moment, we need to give an accurate acount of what we know now.

Please do.