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

[Swamidass (Peaceful Science)]

@gbrooks9

It was wrong? Aren’t you quibbling a bit here?

As far as I can tell, for “presenting evidence against a bottleneck ever in our lineage as a settled finding” to be wrong, somebody has to show that evidence that there is evidence for a single mating pair bottleneck.

Didn’t we only prove that there could be a bottle neck far enough back that it can’t be detected? And isn’t “far enough back” well beyond the 6000 year range?

So, I would think you should be more “wordy” about what we have proved or not proved. I think we have quite clearly showed that there cannot be a single pair bottleneck within a 10,000 year time frame - - don’t you agree?

The claim that was wrong was that there is solid evidence against a bottleneck of 2 in our lineage, including the time between now and when we diverge from chimps. Some have even argued the evidence goes back 13 million years. That claim about what the evidence showed us was false. It was overstated.

@gbrooks9

So, I would think you should be more “wordy” about what we have proved or not proved. I think we have quite clearly showed that there cannot be a single pair bottleneck within a 10,000 year time frame - - don’t you agree?

Yes, that claim still stands.

[gbrooks9 (George Brooks)]

@Swamidass

The claim that was wrong was that there is solid evidence against a bottleneck of 2 in our lineage, including the time between now and when we diverge from chimps. Some have even argued the evidence goes back 13 million years. That claim about what the evidence showed us was false. It was overstated.

gbrooks9 writes:
So, I would think you should be more “wordy” about what we have proved or not proved. I think we have quite clearly showed that there cannot be a single pair bottleneck within a 10,000 year time frame - - don’t you agree?

Yes, that claim still stands.

@Swamidass, I hope you can see how differently your discussion/conclusion sounds immediately above - - when compared to the much more severe statements you made in the post(s) prior …

@Swamidass

For a long time, people have presented evidence against a bottleneck ever in our lineage as a settled finding of population genetics. However, it is not a settled finding, as we have just unsettled it. However, for a long time, questions have been silenced because of the total certainty of that finding. Yet it was wrong. So how do we avoid that mistake again?

If someone were to read your quote from post 848, they would no doubt conclude something very different from your clarified comments found in this paragraph: “The claim that was wrong was that there is solid evidence against a bottleneck of 2 in our lineage, including the time between now and when we diverge from chimps. Some have even argued the evidence goes back 13 million years. That claim about what the evidence showed us was false. It was overstated.”

[Jon_Garvey]

https://en.wikipedia.org/wiki/Association_fallacy#Guilt_by_association_as_an_ad_hominem_fallacy

Not for the first time - no doubt not for the last.

[Jonathan_Burke (Jon)]

@Jon_Garvey

Not for the first time - no doubt not for the last.

This is the guilt by association argument.

Guilt by association as an ad hominem fallacy

Guilt by association can sometimes also be a type of ad hominem fallacy, if the argument attacks a person because of the similarity between the views of someone making an argument and other proponents of the argument.[1]

This form of the argument is as follows:

Source S makes claim C.
Group G, which is currently viewed negatively by the recipient, also makes claim C.
Therefore, source S is viewed by the recipient of the claim as associated to the group G and inherits how negatively viewed it is.
An example of this fallacy would be “My opponent for office just received an endorsement from the Puppy Haters Association. Is that the sort of person you would want to vote for?”

I did not make that argument. I didn’t say anything whatsoever about you as a person. I am talking about your argument, not you. How is your argument any different to the argument made by Ken Ham?

[Jon_Garvey]

That’s very simple.

Ham says the Holy Spirit was a witness to events (which is orthodox), and inspired history according to Ham’s understanding (which is interpretation), which is therefore a defeater for any other understanding, including evolutionary science (which is fallacy).

I say the Holy Spirit was a witness to events (which is orthodox), and inspired Scripture (which is orthodox), which is therefore authoritative data to bring to the table of understanding, as is evolutionary science.

Different presuppositions, different argument, different conclusion. But superficially similar enough for the careless thinker to confuse them.

[Jay313 (Jay Johnson)]

@Jon_Garvey

I say the Holy Spirit was a witness to events (which is orthodox), and inspired Scripture (which is orthodox), which is therefore authoritative data to bring to the table of understanding, as is evolutionary science.

To say that the Holy Spirit was a witness to the events of creation is an entirely non-controversial statement, and to say that the Scriptures are inspired and authoritative is equally non-controversial. As well, neither statement espouses or entails a literalist interpretation of Genesis. So, where exactly is the beef, @Jonathan_Burke? Must you argue with every statement that Jon Garvey makes?

[Jonathan_Burke (Jon)]

@Jon_Garvey

I say the Holy Spirit was a witness to events (which is orthodox), and inspired Scripture (which is orthodox), which is therefore authoritative data to bring to the table of understanding, as is evolutionary science.

You don’t just say “the Holy Spirit was a witness to events” and “inspired Scripture” (a phrasing designed to make your argument look at least slightly different to Ham’s). Like Ham, you say Genesis 1 is “an authoritative eye-witness account from the Holy Spirit” of creation. So you don’t just say the Holy Spirit “inspired Scripture”, like Ham you say the Holy Spirit inspired an authoritative eye-witness account of creation.

And you use that to challenge certain conclusions of evolutionary science, just as he does. So you use the same argument, in the same way.

@Jay313

To say that the Holy Spirit was a witness to the events of creation is an entirely non-controversial statement, and to say that the Scriptures are inspired and authoritative is equally non-controversial.

If that was all Jon had said, it would indeed have been non-controversial.

@Jay313

Must you argue with every statement that Jon Garvey makes?

I make about one comment on his posts every month. It’s not like I argue the toss with every statement he makes; most of what he posts, I don’t even read.

[Jon_Garvey]

Jon

I suggest you stop digging. It would be more plausible if your post had set out to refute Ham’s argument, or even mine. Instead, it was enough for you to link my name to his, knowing how much weight he carries with the EC community.

I’m out of here.

[RichardBuggs]

Hi Joshua,

Reworking the Science of Adam

Thank you very much for posting this summary; this is a helpful service to us all.

@Swamidass

However, I think I understand @Jon_Garvey’s motivation. We do not want to state these claims with too much certainty, as we have just seen a large shift in our understanding here. I’d point, again, to my invitational epistemology as a solution to this paradox. I’ve already pointed out three ways a more recent bottleneck might be possible:

Adam and Eve had totally different biology than us (e.g. genetic mosaics)
Ongoing miracles that diversify us more than is possible by natural processes alone.
Much higher mutation rates in the distant past than we can imagine or observe in humans (perhaps miraculously?)

I agree with you that @Jon_Garvey has made valid points, and I respect him for that. We would not want to fall into the trap of attaching too much certainty to any of our claims. This is a very complex field, where direct testing is difficult and sometimes impossible. I have made this point previously in this discussion with reference to the Lenski LTEE experiment.

To my mind, there are three lines of evidence before us now that a bottleneck could not have happened in the last 500,000 years. These are (1) @glipsnort’s allele frequency spectrum argument (2) your TMR4A calculations and (3) evidence for introgression from Neanderthals into European and Asian humans.

It is the third one that I think is the strongest argument, as it relies upon archaeological findings that can be dated, as well as sequence data.

However, if someone wanted a more recent Adam and Eve: they could claim (as I think have been claimed previously in this discussion) that Neanderthals were not fully human and not descended from Adam and Eve (perhaps invoking Genesis 6:2). Thus a bottleneck could have occurred in the human lineage even while Neanderthals were co-existing elsewhere. Thinking this through, it has just struck me that your TMR4A argument might also be vulnerable to this argument, if the loci with large TMR4A were also shown to be loci in which there is evidence for polymorphism due to Neanderthal introgression. Is this something that you have thought about?

[DennisVenema]

@RichardBuggs

evidence for introgression from Neanderthals into European and Asian humans.

I assume you mean Neanderthals and Denisovans, correct?

There is also that evidence that the Denisovans have an introgression event into their genome to keep in mind - something that would suggest that part of their genome is older than the last common ancestral population of Neanderthals and Denisovans.

One interesting finding from the recent Denisovan paper in Cell is that some human groups in the present day have a lot of Denisovan ancestry. I think this makes it problematic to try and excise this ancestry from the discussion. Thoughts?

[DennisVenema]

@RichardBuggs

Thinking this through, it has just struck me that your TMR4A argument might also be vulnerable to this argument, if the loci with large TMR4A were also shown to be loci in which there is evidence for polymorphism due to Neanderthal introgression. Is this something that you have thought about?

My feel for the data is that there is not a lot of Neanderthal DNA left in present-day humans, so it wouldn’t have a large effect. There are also really ancient TMRCA values in SS Africa (and thus not due to Neanderthal or Denisovan introgression). That said, in re-skimming the Argweaver paper, I don’t see where they tested SS African DNA apart from the entire set (which includes non SSA samples).

[DennisVenema]

In case anyone is interested in the data supporting introgression into Denisovans - it comes from this paper, and the relevant section is as follows:

We tested three non-mutually exclusive scenarios that could explain these observations. First, gene flow from the ancestor of Neandertals after the split from Denisovans into the ancestors of all present-day humans would result in more sharing of derived alleles between present-day Africans and Neandertals. However, because gene flow contributes alleles at low frequency the sharing of derived alleles with Neandertals would grow weaker with higher African derived allele frequency (SI 16a), whereas we observe the opposite (Fig. 7). Second, gene flow from the ancestors of present-day humans to Neandertals after their split from Denisovans would also result in more sharing of derived alleles. However, the amount of allele frequency change (genetic drift) that has occurred in present-day Africans since the split from Neandertals is too small to explain the extent of sharing of derived alleles fixed in Africans (SI 16a). Third, we considered a scenario where Denisovans received gene flow from a hominin whose ancestors diverged deeply from the lineage leading to Neandertals, Denisovans and present-day humans. We find that this scenario is consistent with the data, as also suggested by others29, and estimate that 2.7–5.8% (jackknife 95% confidence interval) of the Denisova genome comes from this putative archaic hominin which diverged from the other hominins 0.9–1.4 million years ago (SI 16a). An approximate Bayesian computation30 again supports the third scenario (SI 16b) and estimates that 0.5–8% of the Denisovan genome comes from an unknown hominin which split from other hominins 1.1 and 4 million years ago.

We caution that these analyses make several simplifying assumptions. Despite these limitations we show that the Denisova genome harbors a component that derives from a population that lived prior to the separation of Neandertals, Denisovans and modern humans. This component may be present due to gene flow, or to a more complex population history such as ancient population structure maintaining a larger proportion of ancestral alleles in the ancestors of Denisovans over hundreds of thousands of years.

So, if Denisovans are “in” as it were, then we need to account for the introgression (or ancient population structure) we see in their genomes. This would seem to push the magic date back past 700KYA towards something closer to 1MYA.

This also highlights the problem with deciding on a specific date. I can see new data pushing it further back, but I can’t as easily foresee a mechanism to pull it forward. I’ll welcome the thoughts of @RichardBuggs and @Swamidass.

[Chris_Falter]

@RichardBuggs

if someone wanted a more recent Adam and Eve: they could claim (as I think have been claimed previously in this discussion) that Neanderthals were not fully human and not descended from Adam and Eve (perhaps invoking Genesis 6:2). Thus a bottleneck could have occurred in the human lineage even while Neanderthals were co-existing elsewhere.

The claim under scrutiny is that a single couple were the sole genetic ancestors of all humanity. Or so I thought, until you suggested that the single couple was only the head of one of many genetic lineages for humanity. Is this really a hypothesis you wish to defend? If so, how would you reconcile the hypothesis with the traditional theological concerns of someone like @agauger?

[gbrooks9 (George Brooks)]

@RichardBuggs

To my mind, there are three lines of evidence before us now that a bottleneck could not have happened in the last 500,000 years. [ The 3rd reason is ] . . . evidence for introgression from Neanderthals into European and Asian humans.

How is evidence for introgression an indication of anything? One could assert that the introgression is by a hundreds of random contributions… or by a single mating pair.

The evidence against a bottleneck remains the same in:

(1) @glipsnort’s allele frequency spectrum argument; and
(2) @Swamidass’ TMR4A calculations .

And the only way to arrive at some other conclusion is still the three methods outlined by @Swamidass :

@swamidass

…there is not a single model proposed that can account for the data with a single couple origin less than 200 kya, without either

(1) inferring ongoing miracles,

(2) totally different biology for Adam and Eve (e.g. genetic mosaics), or

(3) mutation rates an order of magnitude (or more) higher than we have ever observed in humans.

No matter how many contributors there may have been to the human genome, the contributors have to participate in a favorably harmonious way with Option (2) or (3), or be completely by-passed by Option (1).

[RichardBuggs]

@Jon_Garvey

I’m out of here.

Dear moderators,

I would like to note that I think it is very regrettable that @Jon_Garvey has apparently been hounded out of this discussion by @Jonathan_Burke

@Jon_Garvey’s contributions to this discussion have been erudite, humorous and good natured, and clearly come from his experience of a long career as a physician. He has expressed views that are probably held by many other Christians, and he has defended them well and with good grace.

It appears that he has now left this discussion due to what he (in my view legitimately) feels is an ad hominem attack by @Jonathan_Burke.

My understanding of the role of this Biologos forum is to allow debate from people of all perspectives on science and faith. However, it does seem that someone like @Jon_Garvey who holds a perspective that perhaps differs from the majority of participants is being unfairly targeted by @Jonathan_Burke and this is undermining the purpose of this discussion forum.

best wishes
Richard

[Jonathan_Burke (Jon)]

@RichardBuggs

I would like to note that I think it is very regrettable that @Jon_Garvey has apparently been hounded out of this discussion by @Jonathan_Burke

He hasn’t. He just told me he wasn’t going to reply to me.

@RichardBuggs

However, it does seem that someone like @Jon_Garvey who holds a perspective that perhaps differs from the majority of participants is being unfairly targeted by @Jonathan_Burke and this is undermining the purpose of this discussion forum.

Nonsense. I made less than a dozen comments over six days, none of which constituted unfair targeting. I note you make absolutely no mention of how Chris Falter and George Brooks have been repeatedly challenging Jon Garvey’s perspective on this thread and others.

[Swamidass (Peaceful Science)]

@RichardBuggs

However, if someone wanted a more recent Adam and Eve: they could claim (as I think have been claimed previously in this discussion) that Neanderthals were not fully human and not descended from Adam and Eve (perhaps invoking Genesis 6:2). Thus a bottleneck could have occurred in the human lineage even while Neanderthals were co-existing elsewhere. Thinking this through, it has just struck me that your TMR4A argument might also be vulnerable to this argument, if the loci with large TMR4A were also shown to be loci in which there is evidence for polymorphism due to Neanderthal introgression. Is this something that you have thought about?

Yes, I have thought about that! =)

If you allow for interbreeding all bets are off. Adam and Eve could have been 10,000 years ago in the middle east, or 200 kya as the sole-couple progenitors of Homo sapiens, etc. None of the genetic work we have done here has any relevance to the question if interbreeding is allowed.

@RichardBuggs

To my mind, there are three lines of evidence before us now that a bottleneck could not have happened in the last 500,000 years. These are (1) @glipsnort’s allele frequency spectrum argument (2) your TMR4A calculations and (3) evidence for introgression from Neanderthals into European and Asian humans.

That’s about right, but do not forget Denisovans.

@RichardBuggs

It is the third one that I think is the strongest argument, as it relies upon archaeological findings that can be dated, as well as sequence data.

#2 is pretty strong too, as it is very easy to explain to non-experts, and is also very well supported in the data.

@DennisVenema

There is also that evidence that the Denisovans have an introgression event into their genome to keep in mind - something that would suggest that part of their genome is older than the last common ancestral population of Neanderthals and Denisovans.

@DennisVenema

So, if Denisovans are “in” as it were, then we need to account for the introgression (or ancient population structure) we see in their genomes. This would seem to push the magic date back past 700KYA towards something closer to 1MYA.

That is not really relevant to our question.

We have only 1 Denisovan genome (from a single knuckle, now destroyed), and do not know of we descend directly from this Denisovan. It is possible that Adam and Eve are our sole genetic progenitors, but some Denisovans interbred with another hominem, then subsequently died off without ever contributing to all of us. Unless we can show that those genes appear in humans too, and do not push the TMR4A back, then it does not give us a confident way to push back our date.

They also give an alternate hypothesis:

@DennisVenema

a more complex population history such as ancient population structure maintaining a larger proportion of ancestral alleles in the ancestors of Denisovans over hundreds of thousands of years.

The issue is that we cannot actually untangle this knot in most cases. In extant scenarios, migration can only measured by getting serial measurements over time and comparing them. Without serial measurements (multiple time points) its not possible to determine the direction of interbreeding events, or distinguish it from incomplete sorting. This, therefore, is just not strong evidence against a bottleneck at 500 kya - 700 kya.

@DennisVenema

My feel for the data is that there is not a lot of Neanderthal DNA left in present-day humans, so it wouldn’t have a large effect. There are also really ancient TMRCA values in SS Africa (and thus not due to Neanderthal or Denisovan introgression). That said, in re-skimming the Argweaver paper, I don’t see where they tested SS African DNA apart from the entire set (which includes non SSA samples).

That has never been done. But also we have no way of parsing out what is what that far back.

@DennisVenema

This also highlights the problem with deciding on a specific date. I can see new data pushing it further back, but I can’t as easily foresee a mechanism to pull it forward.

I agree that this will always be subject to revision. However, it is hard to imagine the evidence what would pull the date back earlier than 2 mya. The most likely thing, I would guess, would be trans species variation, having ruled out convergent evolution. To do that, we would need to get a much better census of great ape genetic variation, and do a very careful (and frankly difficult) analysis to make sense of that. Still, it is possible that at a future date a single couple of bottleneck would be ruled out.

Then, however, if we allow for interbreeding (whether it be sanctioned by God or not), all bets are off. We do not think a single-couple origin of our kind needs to correspond with a single couple bottleneck.

@Chris_Falter

if someone wanted a more recent Adam and Eve: they could claim (as I think have been claimed previously in this discussion) that Neanderthals were not fully human and not descended from Adam and Eve (perhaps invoking Genesis 6:2). Thus a bottleneck could have occurred in the human lineage even while Neanderthals were co-existing elsewhere.

The claim under scrutiny is that a single couple were the sole genetic ancestors of all humanity. Or so I thought, until you suggested that the single couple was only the head of one of many genetic lineages for humanity. Is this really a hypothesis you wish to defend? If so, how would you reconcile the hypothesis with the traditional theological concerns of someone like @agauger?

As we have shown, if we allow for interbreeding, all bets are off. Adam could be very recent, or at the origin of Homo sapiens, or really any where or time we like.

How would this reconcile with @agauger? Well, that requires theological reflection. If we’d like to change @agauger’s view of this, it would probably be best to engage catholic theologians and philosophers (e.g. @AntoineSuarez).

[Swamidass (Peaceful Science)]

@RichardBuggs

I would like to note that I think it is very regrettable that @Jon_Garvey has apparently been hounded out of this discussion by @Jonathan_Burke

@RichardBuggs

It appears that he has now left this discussion due to what he (in my view legitimately) feels is an ad hominem attack by @Jonathan_Burke.

I agree.

However, this is not the moderators fault. It is more regrettable that an apology from the responsible party is not not forthcoming. We should not interpret @moderators inaction as endorsing poor behavior. They may not have seen the exchange, or may be trying to resolve it privately. The best way to bring it to their attention is flagging posts as inappropriate.

Also, @Jon_Garvey will be back. He is not banished for good =).

[Swamidass (Peaceful Science)]

@gbrooks9

No matter how many contributors there may have been to the human genome, the contributors have to participate in a favorably harmonious way with Option (2) or (3), or be completely by-passed by Option (1).

Help me understand that?

[Swamidass (Peaceful Science)]

@RichardBuggs

To my mind, there are three lines of evidence before us now that a bottleneck could not have happened in the last 500,000 years. These are (1) @glipsnort’s allele frequency spectrum argument (2) your TMR4A calculations and (3) evidence for introgression from Neanderthals into European and Asian humans.

We should also remember that these lines are not yet evidence against it, but become so in the future:

1. Trans-species variation
2. HLA exon diversity
3. HLA intron diversity

Those, historically, have been the strongest arguments against a single couple bottleneck, even though we found them wanting. Science, however, progresses. This assessment could change in the future. To this we could also add TMR4A, which could move upwards if we include more extant (or ancient) samples and recompute it in the future.