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


(Peaceful Science) #852

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.

Yes, that claim still stands.


(George Brooks) #853

@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 …

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) #854

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.


(Jon) #855

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) #856

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.


(Jay Johnson) #857

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?


(Jon) #858

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.

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

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) #859

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.


(Richard Buggs) #861

Hi Joshua,

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

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?


(Dennis Venema) #862

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?


(Dennis Venema) #863

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).


(Dennis Venema) #864

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

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) #865

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?


(George Brooks) #866

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 :

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).


(Richard Buggs) #867

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


(Jon) #868

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

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.


(Peaceful Science) #869

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.

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

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

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:

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.

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

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.

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).


(Peaceful Science) #870

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 =).


(Peaceful Science) #871

Help me understand that?


(Peaceful Science) #872

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.