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


(Ann Gauger) #691

@Swamidass, Hi Josh.

I have a great deal of respect for Jon Garvey, and you, Josh, but I am going to disagree with his and your claim that “God wouldn’t have done it that way.”

Jon left off a critical part of the context of his verse: 2 Peter 3:8.

8 But do not let this one fact escape your notice, beloved, that with the Lord one day is as a thousand years, and a thousand years as one day. 9The Lord is not slow about His promise, as some count slowness, but is patient toward you, not wishing for any to perish but for all to come to repentance.

And Habukkuk 2:1-3

  1I will stand on my guard post 
        And station myself on the rampart; 
        And I will keep watch to see what He will speak to me, 
        And how I may reply when I am reproved.

 2Then the LORD answered me and said, 
        “Record the vision 
        And inscribe it on tablets, 
        That the one who reads it may run.

 3For the vision is yet for the appointed time; 
        It hastens toward the goal, and it will not fail. 
        Though it tarries, wait for it; 
        For it will certainly come, it will not delay.

6000 years is a long time to us in terms of our life spans, but only 300-400 generations. 60,000 years is 10 times and 600,000 years 100 times that-- 30,000-40,000 generations. I hold to an old age for the universe. If God can take 14 billion years to form the universe we see, including the 4 billion year old earth, and then took more than 3 billion years to create life as we see it now, it’s clear he’s not in a hurry.

As to the awfulness of leaving so many generations in sin, there is this: there are many icons that depict Christ descending to the dead to redeem Adam and Eve. It’s probably based on these verses: 1 Peter 3:19 and following.

19 After being made alive,[d] he went and made proclamation to the imprisoned spirits— 20 to those who were disobedient long ago when God waited patiently in the days of Noah while the ark was being built.

Maybe there was the offer of redemption for those who had no opportunity before Christ. (This verse is interpreted in various ways. I have given the Catholic version here.)

Let the buyer beware. I am not a theologian. I have no axe to grind about Genesis interpretation (YEC or OEC) except for the historicity of Adam and Eve. I agree with Josh that the Gospel is central. Others have made the arguments about whether Adam was figurative, representative or a single actual person. I came to the idea of an old Adam because of the science, because I couldn’t reconcile multiple hominins running around with only some bearing God’s image. H. erectus is so much more similar to us than chimpanzees ever were. The chief argument against a H erectus Adam for me is that technology did not advance much, at least as far as we can tell. But then at that distance in time, the only things to preserved will be the kinds of things we see.

I also agree that some are exhibiting prejudice against “brow ridges”, and a tendency to underestimate the abilities of H erectus or Neanderthals.

As for the apparent presence a neolithic culture at the time of early Genesis (though written language?), I attribute that to whoever recorded the stories remembered from long long ago. The essence of the family history was preserved, but because they had no detailed description of things, anachronistic details were added.

Now I could well be wrong. It wouldn’t be the first time. But you asked.


(Peaceful Science) #692

Thanks for the response.

For the record, I do not know how God did it. I’m just curious how you are thinking about these things. I think there will be interesting things in the conversation. The goal, to be clear, is not to convince you to change. Any of us could be wrong about these distant details of the past, and it would not make any difference in the end.

I think there are many that draw the line here too. Though I would say you also seem to think sole genetic progenitorship is important too. Why do you think genetic sole proprietorship is so important?

Someday we’ll have to talk about a recent genealogical Adam model that does not have that problem. In the Genesis narrative, Adam is tied to the Fall, not God’s Image. Perhaps all our ancestors equally bear God’s Image at any given point in time, but Adam is more important for the Fall.

I’ve heard this view before. It is very catholic. =).

Amen.


(Dennis Venema) #693

Thanks for your comments, Ann.

It’s a beautiful axe, to be sure. I too “see a mind there” - but I also see minds of varying degrees in nature. My dog has more going on than the zebrafish in my lab. Among fish, cichlids like angelfish seem to have more going on than the zebrafish. Bowerbirds make things we think of as aesthetic. So do octopuses. Crows plan ahead and make / use tools. So, I guess I’m more comfortable with seeing a gradient of “mind”.

I too agree that the gospel is central. I just don’t see a historical Adam as part of that. When Paul summarizes the gospel, he does not reference Adam (and of all the New Testament authors I would expect to use Adam as part of the gospel, Paul would be the one). For example, here’s 1 Cor 15 (the very chapter where Paul gets into Adam theology in the letter) in the NIV:

Similarly, in Romans 1 (also NIV):

I see Jesus’s lineage from David, his death, burial, resurrection, and exaltation as Lord as the key elements. I just don’t see Adam on the radar here.

Now, I too am not a theologian, so, as you aptly said, “buyer beware”. But I don’t think a historical Adam is part of the gospel according to Paul.


(Peaceful Science) #694

To be clear, neither @agauger or myself are saying Adam is part of the Gospel. Several times I have made this point, often in your defense. This is a conversation between those of us together in the Church, and this community is defined by Jesus, not Adam.

That is a valid interpretation too.

Right now, I think there is a lot up for grabs in our understanding of human origins. So much so that everything from @agauger position to yours is consistent with the evidence, at least somewhat represented within mainstream science.

Also, if the goal is merely to affirm a sole genetic progenitorship, we could possibly imagine that taking place about 700 kya with the common ancestors of Homo sapiens, Denisovans, and Neanderthals.


(Chris Falter) #695

Hi Joshua - I agree with you on the object of our confidence. However, I disagree with you that science rules out miracles. I would contend quite adamantly that a one-time miracle is not subject to scientific research, which requires repeatability.

Best,
Chris


(Peaceful Science) #696

One time events are the subject of scientific study. That is how we study the Big Bang.

I would agree however, that science has not precisely ruled out the Resurrection. It does not consider God’s action, so it is more accurately silent on the Resurrection. The claim is that God Himself rose Jesus from the dead, breaking the natural order of things. That is a hypothesis outside the realm of science.

The point, however, in context is that we believe things beyond science. The fact that science is silent does not mean nothing of interests exists in its blindness.


(Dennis Venema) #697

Exactly. Jesus is the gospel. There are some non-negotiables in the faith, and other matters which are open for discussion.

Thinking about fish, minds, and aesthetic artifacts reminded me of this video from the BBC on pufferfish. Imagine if we found a carving like this in the hominin record?


(Jon Garvey) #698

@Chris_Falter
Hi Chris

I would agree with you that science properly only “does” repeatability, except that it may document unique phenomena on the possibility of future repeatability of some kind. But the recording itself is really history rather than science.

But on “ruling out miracles”, a few years ago I set up (here) a scenario of an essentially miraculous overnight transformation in a lab petrie dish. Can’t remember the details, but it was designed to ask “How would scientists deal with an apparent miracle?”

Almost universally I got the reply that the true scientist would always be looking for the natural cause, and suspend judgement on a miracle, even if no plausible natural possibility existed. Strictly speaking this is not to exclude a miracle - but if ones agnosticism is so absolute and unconditional, then effectively miracle is excluded.

Th question is what one actually means by “science does not rule out miracles”. Since “science” always means “scientists,” wouldn’t it be true to say that a scientist practising methodological naturalism consistently cannot accept a miracle, including the resurrection? He/she either has to suspend the methodology in that case (in which case it becomes a methodology with ad hoc exceptions), or believe “as a human” whilst remaining agnostic “as a scientist”.

The trouble is that the resurrection is not simply a factual proposition to be accepted or not, but a demand for total commitment - in other words, the scientist part of one has no warrant to cut itself off from that commitment to the risen Christ.

So on what basis can methodological naturalism continue for the person who has suspended it in the case of the resurrection? Is there any longer any rational basis to use naturalism as a reason to doubt, at least, an historical Adam if the methodology is no longer used to doubt the resurrection of the second Adam?

My own solution: free science from the dead hand of “naturalism” altogether and deal only with your excellent concept of “repeatability,” which is entirely metaphysics-free. One can also allow the recording and investigation of isolated events, like the Big Bang (which can hardly be naturalistic as it preceded the laws of nature), and that also is metaphysics-neutral.

False metaphysics only gets a look in when (1) regularity is assumed to be an alternative to divine action, excluding the latter in favour of some demigod called “Nature” or (2) when metaphysically loaded (and spurious) concepts like “chance is a cause” are allowed in as explanations of non-regular phenomena.


(Jon Garvey) #699

@DennisVenema
The “Adam was a puffer fish” hypothesis?? Good for the theory of universal redemption, I guess. Especially if diatoms get in on the act:
diatom

More seriously (slightly), unless one found human eggs at the centre of the artifact, it would in the hominin lineage be evidence of culture and symbolic thought, because it would be in direct continuity with our use of symmetry, and not that of teleosts or diatoms.

But that is only a problem if one has already taken the common conceptual leap of equating the defining nature of Adam in Scripture - ie the first physical being to come into covenant relationship with Yahweh - with some measurable cultural attainment in a particular area like symbolic thought.

But why on earth should those two be any more equivalent than expecting born-again Christians to be measurably more culturally advanced than unbelievers?


(Steve Schaffner) #700

It could have been one location, it could have been a broad range, or it could have been patchwork evolution across multiple locations with limited gene flow between them. We have lots of evidence for multiple range expansions by hominins, but they really don’t provide evidence for rapid expansions from a small founding population. My impression is that such a rapid expansion is unlikely, given what we know about the reproductive capacity of hunter-gatherers.


(Jay Johnson) #701

By 1.8 million years ago, just 100,000 years after H. erectus appeared, three different species of hominin and A. sediba were co-existing in East Africa, as well as the smaller-bodied H. erectus in Dmanisi, Georgia. Considering the mosaic of features present at the time, anthropologist Susan Anton termed this early phase of our evolution “a period of morphological experimentation." In which species did the literal Adam appear?


(Richard Buggs) #702

Hi @Swamidass, thank you for such a quick response. It looks as if you had a busy Sunday!

I felt an obligation to give a response in that: (1) it is a loose thread that needs to be tied up, and (2) it is a public blog that mentions my name in the title and (3) because I said I would and (4) because it is interesting. I also feel obligated to continue to reply and deal with the four papers that @DennisVenema references in the blog, even though you have already dealt quite effectively in their conceptual content within this discussion forum. If Dennis were to formally retract the blog, I would not need to do this, but otherwise I need to do this for the sake of completeness.

I think that you and I are essentially in agreement, and where we appear to differ it is mainly because we have different interpretations of what @DennisVenema was saying in his blog, or you are making additional comments that complement mine, or you have misunderstood what I was seeking to say.

I think you are saying the same thing as I was my statement:
“The loss of alleles via the sampling effect of the bottleneck will not show up as coalescence events in a coalescence model. These are two separate effects of a bottleneck.”

When you say this, do you mean (1) any lineage, or do you mean (2) a lineage that has a mutation that makes it a different sequence (allele) to other lineages?

I agree, and I agree that my figure shows that. That was not unintentional! :slight_smile:

I am not sure what conditions you mean. Yes, I deliberately showed three lineages going through the bottleneck, two in a heterozygote and one in a homozygote. I tried to illustrate as many processes as I could in the figure.

I agree: three identical alleles in three different individuals coalesce into a single identical copy in a one parent.

I think we are misunderstanding one another here. There is no reduction in number of alleles from g1 to g0. There is a reduction in the number of copies of alleles (= a reduction in the number of lineages) but not a reduction in the number of alleles. By an allele here I mean a DNA sequence that is different in nucleotide sequence to the other alleles - as I explained in the text describing my figure, I show different alleles in different colours. There are three alleles in generation g1 (one red, one blue and one yellow, with copy number 1, 3 and 2 respectively) and three alleles in the g0 generation (one red, one blue and one yellow, with copy number 1, 1, and 2 respectively)

I agree. In the text that accompanied this second figure I wrote:
“How would coalescence to one lineage occur after a bottleneck? Figure 2 shows a scenario in the minimum possible number of generations.” The figure does not claim to show a single coalescence - it claims to show the most rapid possible coalescence back to a single lineage that passed through a bottleneck of two. (The significance of this is that it was the nearest thing I could think of that would to some extent correspond with what Dennis seemed to be writing about in his blog. A problem here is that Dennis’ blog was so off the mark that it is hard to reinterpret it in terms of actual coalescent scenarios.)

I think you are misunderstanding what I am seeking to do here.

I agree that this could be developed into that, but my aim here was simply to show how unlikely it is that three lineages would be lost after a bottleneck of two, leaving just one of the four allele copies that was present in the parental pair.

I agree that coalescence analysis is normally done with a sample, not the whole population. This is why I wrote: "Similarly, if we only sample a subset of the lineages, the probability of all of our sample coalescing at the bottleneck is slightly higher than the probability of all lineages coalescing, but again, this will not make a huge difference. For example, if we sampled four individuals in generation g2 the probability of all sampled lineages coalescing in the bottleneck would be 0.000977. "

I agree. Coalescence and fixation are completely different things.

That was not my case. There seems to have been a degree of misunderstanding in your reading of my blog.

I don’t dispute that, but the number of extant lineages in a coalescent analysis is simply our sample size. Every sample we take is a lineage. It doesn’t matter if they differ in their nucleotide sequence (i.e. are different alleles) or not.

I agree. This is a point I have been trying to make all along in this debate.

In summary, Joshua, I am glad we agree on the big picture, but I think you have misinterpreted some of what I was trying to say, especially (a) the distinction between lineages and alleles, and (b) what I was seeking to show in figure 2 and the calculations accompanying it.


(Peaceful Science) #703

Okay, I’ll mainly let @DennisVenema respond then.

I mean #1. In coalescence, we only care about direct descent of the samples. At particular times, we entirely expect different “lineages” to have exactly the same sequence, such as right after they split.

But that is all that matters. In coalescence based estimates of Ne, we are just estimating where in time these coalescents fall. They can all be identical sequence, but they are still different lineages.

I’ll let Dennis defend himself. As in understand it, has already retracted several things from that post here on this thread. I suppose it’s up to you how you would take it from here.

It seems now that @DennisVenema agrees now too. That it seems was the conceptual error that’s been fixed.

Okay, I’ll let you work it out with @DennisVenema then.


(Dennis Venema) #704

Yes, I agree with this. I pointed that out ^ up there ^ somewhere.


(Richard Buggs) #705

Hi Dennis,
That’s great. Would you also agree that the points made in the four papers you refer to in your “Part 2” blog have also been dealt with adequately on this thread, or would you like me to respond to them also?
best wishes
Richard


(Dennis Venema) #706

I think so - I haven’t read the entire thread, but I think we’ve covered what needs to be covered. Like I said to Josh before, I think that the ArgWeaver paper covers the same territory (and does it more thoroughly) than those papers. If we’re agreed that a single - couple bottleneck is not supported in the last 400+ KYA then I don’t really have a dog in the fight any longer, since that goes beyond even what the (now infamous) “heliocentric” statement in Adam and the Genome was defending. It simply becomes a question of “how far back can we exclude this?” now, which of course is very interesting in its own right.

I will be away for the next few days, but I’m hoping to get the PSMC modelling results from Charles Cole up on a private thread for you, myself and @Swamidass to look over later today (dv).

Hope you’re doing well. I’ll send a PM once the PSMC data is up.


(Richard Buggs) #707

Hi Dennis,

Thanks for your reply. I am glad to hear that you consider that the four papers you refer to in your “Part 2” blog have also been dealt with adequately on this thread. That potentially frees up a few of my evenings, for which I am very grateful!

Just to be clear, are you saying that you now no longer hold this view, described on page 55 of Adam and the Genome:

“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 one another, 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 close to what we would call “human.” Thus the hypothesis that humans descend solely from one ancestral couple has not yet found any experimental support, and it is therefore not one that geneticists view as viable.”

If that is no longer a “dog” you have in the “fight” then we have come to a good degree of agreement

I am really glad that Charles Cole has done some more work on this. I will look forward to hearing more.

best wishes
Richard


(Richard Buggs) #708

Thanks Joshua. It seems we are entirely in agreement. :slight_smile:


(Dennis Venema) #709

This remains accurate, even with our ongoing conversation. All methods employed thus far do indicate that we descend from thousands. What we’ve been discussing is whether or not these methods have the power to detect the sort of bottleneck that you are proposing. That idea - 10,000 down to 2 in a single generation, followed by exponential growth - was not on my radar at all when I wrote that. Nor had I seen anyone else suggest anything similar. If I were to write the book today, I would discuss this idea and talk about what we have learned together (especially the ArgWeaver data). But it wasn’t on my radar in 2016.

This also remains the case. At best, we can say that your specific idea cannot be conclusively ruled out further back than 400 KYA. We do not have any evidence that supports the hypothesis - we only have a limit to our current methodology that does not allow us to rule it out in the deep past.

I hope to have the Cole data ready for later today, but it might be tomorrow.


(T J Runyon) #710

Erectus did have some modern behavior. But also lacked some. What pretty much rules out an ancient Adam for me is its very unlikely Erectus could even speak. Like us at least. Definitely more complex than say chimps. But what we know about their anatomy I just don’t see much speaking ability.