Ann Gauger's latest salvo against Dennis Venema's arguments against an original pair of human beings

Faith & Science Conversation
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Gotta stop using my phone to type these forum posts.

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I for one have grave doubts about my own historicity.

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I should clarify that I do not favor a recent date, not at all. All I said is that if it is true that there was a 2-individual bottleneck, it has no bearing on Biblical exegesis because the bottleneck would have been more than 105 kya, whereas Adam and Eve were (to the extent they could be regarded as historical) no more than 104 kya.

By all means, Dr Gauger, build your model and get it published in a well-regarded peer-reviewed journal. You seem to recognize that just criticizing someone else’s model is not enough; you have to present a better model in the right forum. You have indicated that you plan to do so, and I wish you success in the endeavor.

Grace and peace,
Chris Falter

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:slight_smile:

What I find interesting is that no one I know argues for the divine special creation of Melchizedek, even though the author of Hebrews explicitly states that he is without ancestors.

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As I have already pointed out, Buggs says that a first pair is possible under certain conditions. Those conditions include common descent, evolution, and a first pair being the descendants of a previous large population with a common ancestor with apes.

As I have already pointed out, when you truncate Bugg’s statement to simply “Does Science Rule Out a First Human Pair? Geneticist Richard Buggs Says No”, then you misrepresent what he said, by omission. Significant omission. What you should have said was “Buggs’ comments support the idea that Adam and Eve were not created by God but were in fact the descendants of pre-human ancestors”. Why did you not say that?

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That would be part of the problem. If you are going to claim that the evidence could be consistent with the population bottleneck of just 2 people then you need to mention a timeframe.

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This goes back to the thousands of HLA alleles I was talking about earlier. With just two people you would have heterozygosity for just 4 alleles at each locus. This is true for every gene locus and DNA that appears to be diverging through genetic drift (i.e. not under selection). If there was a population that preceded these 2 people that also had a large number of alleles for HLA genes then that would have been a massive reduction in genetic diversity, contrary to what Buggs is trying to claim.[quote=“agauger, post:59, topic:36790”]
By ‘first human pair’ I meant the first pair to be fully human, coming from a bottleneck of two, which is what Buggs said could not be ruled out. A bottleneck of two can happen at least three ways I can think of: by a sudden reduction in population size from a pre-existing population because of isolation or who knows how, by de novo creation, or by the sudden imparting of a different character to two individuals. Buggs suggests the first is a possibility. I did not contradict him or misrepresent him, despite what you may think. I think you have read into my words what was not there.
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What I find lacking is scientific support for the suggestion that a bottleneck down to two individuals is a possibility, or even how much of a possibility it is. Is it a 1 in a million possibility? 1 in 5?

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Perhaps you’re in a witness protection program.

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This argument has descended into the absurd. I would encourage everyone to take a big step back and deal with the problems in their own camp. Back of a clearly unwinnable argument. There is plenty of blame to go around.

Let us keep in mind that one cannot claim to have ruled something out if one has not considered it. Science does not in any way consider the miraculous creation of Adam and Eve, so it unequivocally has not ruled it out. We can legitimately say that the DNA evidence appears to indicate a large population that shares common ancestry with the great Apes. However, if we believe that God exists and can do miracles, we cannot totally foreclose the possibility more has happened.

To shut down the sincere beliefs of others with the “findings of modern science” as some have done here is to misrepresent the claims of modern science, which does not consider miracles like the special creation of Adam and Eve. That is a scientific error. So, if you care about science, back off the clearly incorrect claims.

First off all, I want to thank @agauger for participating here. Do not underestimate the difficulty of arguing with a large number of people who disagree with you. This takes great bravery.

Second, @T_aquaticus is correct about this…

None of the model I have seen produced by the ID camp have explained trans-specific variability, as Ayala and others have unequivocally demonstrated in the data. This is appears to be a very strong hard stop lower limit on the total population of our “ancestors” (whether they be “human” or not) as we go back in time.

There is one effective rejoinder to this, that fits the evidence, but raises other questions. It is possible that Adam and Eve have different genomes in each egg/sperm. This may possibely solve the problem if Adam and Eve are situated far enough back in time, and if they have a large enough number of children. Fantastical, yes. But technically possible if we allow for one grand starting point miracle. I do not think @agauger can declare success here yet. It is not appropriate to declare success without doing the mathematical modeling, which they have planned to do but have not yet done.

This solution, however, does raise an important theological claim. Why did God make us in a way that looks like we evolved if we did not? The best theological response to this comes from John Sanford. He argues that God intentionally designed ambiguity, for a purpose, into creation. Perhaps he is wrong, but this is the beginnings of a coherent case that needs to be dealt with on those terms. That is a philosophical and theological argument that deserves consideration. Claiming falsely, however, that science has ruled his position out is not legitimate.

We are now in the realm of science-engaged theology, not science. Science makes no pronouncements here.

I do understand that there are theological agendas at play here. Some are on an agenda to affirm a historical Adam and Eve. Some are on an agenda to deny a historical Adam. Do not claim the authority of science for your agenda. ́[content removed by moderator]

Finally, I do not think @agauger (and Richard Buggs) has fully made her scientific case. Demonstrating that @DennisVenema may have slight overstated a point here or there, or explaining part of the patterns we see in the data, is not the same thing as presenting a cohesive mathematical model for all the data we can currently explain in evolution. I encourage @agauger to try, and will gladly acknowledge when they are correct.

However, there is a better option. As I have explained, and is widely accepted among BioLogos biologists,

Therefore, entirely consistent with the genetic evidence (Figure 1), it is possible Adam was created out of dust, and Eve out of his rib, 10,000 years ago in a divinely created garden where God might dwell with them, the first beings capable of a relationship with Him. Perhaps their fall brought accountability for sin to all their descendants.17 Leaving the Garden, their offspring blended with their neighbors in the surrounding towns.18 In this way, they became genealogical ancestors of all those in recorded history.19 Adam and Eve, here, are the single-couple progenitors of all mankind.20 Even if this scenario is false or unnecessary, nothing in evolutionary science unsettles this story. So, evolution presses in a very limited way on our understanding of Adam and Eve, only suggesting (alongside Scripture) that their lineage was not pure. Any case claiming that evolution itself requires more dramatic rethinks of Adam is in scientific error.
http://henrycenter.tiu.edu/2017/06/a-genealogical-adam-and-eve-in-evolution/

This would make Adam and Eve the first “humans” as we understand the meaning of “human” today, though we can imagine other types of God-Imaged humans before them (following the exegesis of @JohnWalton. Remember, that “human” is an ambiguous term was we move into the distant past.

There is exactly zero scientific evidence against this view. And it demonstrates exactly @agauger’s point, that science has not ruled out a first couple.

To the regular commenters, why not give those with deeply held beliefs a way to affirm those beliefs in a manner consistent with our mainstream understanding of science? @agauger, also, I would love to hear what you do or do not find acceptable about this model. As I hear your position, I do not see a strong insistence against the notion that Adam’s offspring ended up mixing with other lines (Genesis 6:2). I know first hand that many in the ID camp are comfortable with this solution.

Now please, everyone, stop with the needless fight. Do your best to understand and be understood. This is not about winning. Honesty is more important.

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T_aquaticus:
I hope by now you have read my earlier answers and know that I do propose a time frame.

HLA is a special case, because of balancing selection for heterozygosity, elevated mutation rates, and gene conversion rates, (and recombination rate within alleles I think, I am not sure). I know that recombination is suppressed throughout the region). The fact that HLA-A has 4000 alleles does not surprise me. HLA-DRB1 probably has over a thousand by now as we detect rare alleles.

The HLA genes generate new alleles at an astonishing rate.One study among an isolated tribe in S America found that had generated new alleles in just 20 years, I think it was. An older 1980s paper found a mutation rate of on the order of 10^-4 in sperm. All of these citations are published in my book Science and Human Origins. This area of research is what led me to consider the possibility of a first human pair. Ayala claimed 32 alleles I think (memory being not what it was) as the number of alleles in the population we last shared with chimps some 6 million years ago, in order to account for all that diversity. Further work by Bergstrom et and von Salome proved him wrong, precisely because of the odd behavior of the HLA-DRB1 gene. At last count the estimate for the number of founding alleles is four or five. Full stop.

I would love to verify that this true for HLA-A etc. because I think there is something very special going on in the region, precisely to maintain a high level of diversity, for immunological and fertility reasons.

You heard it here first, folks. But most of this was published with Science and Human Origins. If you are an immunologist, just measure the father to son mutation rate using deep sequencing, and see if all the HLA genes show this trait. There you have it. A testable ID prediction. You could get a paper out of it, maybe multiple!

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I haven’t read very far into those papers, but I did find this tidbit:

An example of trans-species polymorphism is depicted in Figure 3. Here, two human alleles at the DRB1 locus (HLA DRB1 * 0302 and * 0701 ) differ in the exon encoding the PBR by 31 nucleotide substitutions, whereas one of them (HLA DRB1 * 0302) differs from the corresponding chimpanzee allele (Patr DRB1 * 0305) by 13 substitutions, and the other (HLA DRB1 * 0701) differs from the corresponding chimpanzee allele (Patr DRB1 * 0702) by 2 substitutions only. In terms of genetic distance (the number of nucleotide differences divided by the total number of sites compared), each of the two human alleles is more closely related to a chimpanzee allele than the two human alleles are to each other. This relationship is reflected in a family tree of the four alleles, which shows that the two human alleles diverged from a common ancestral gene before the ancestors of the human and chimpanzee species separated from each other around 6 Myr ago.
Reference

As Dr. Swamidass mentions, the trans-specific variation appears to be good evidence that there has been a substantial human population since divergence from chimps since a large proportion of trans-specific variation should be lost in a bottleneck, if my popgen knowledge is correct. The production of HLA variation after the bottleneck would not be able to recreate alleles that were lost as part of the bottleneck.

As far as the overall scientific approach is concerned, there appears to be a conclusion in search of evidence. Some people have started with the conclusion that there were two founding members of the human population when there is simply no evidence that would lead them to that conclusion, at least no evidence I have found. What we have instead is a lot of evidence for a substantial and continuous human population. No population model that I have seen is biased against the hypothesis of the Adam/Eve archetype bottleneck. In fact, scientists were even comfortable labeling the mitDNA and Y-chromosome MRCAs as Eve and Adam respectively, so it isn’t as if there is some aversion to the concept. If there really was a severe bottleneck then I see no reason why the standard models found in thousands of popgen papers would not point to that conclusion.

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Venema’s heliocentrism analogy might be useful here. Can science say that Geocentrism has been completely ruled out? No. Science is always tentative. While it may be a bit hyperbolic to claim that the certainty of past human population sizes is equivalent to the confidence we have in Heliocentrism, the comparison isn’t that far off.

Can science rule out the possibility that there is a super-intelligent alien species messing with human minds in a way that makes it appear as if Heliocentrism is true when it is really not, with the caveat that the aliens are able to mess with our minds in a way that is completely undetectable? No, science can’t rule that out. Is that a bad thing? Does that mean we should doubt Heliocentrism just because we can invent miraculous and undetectable scenarios that would falsify our theories? I don’t think so.

In my experience, science is more about ruling things IN than ruling things OUT. Instead of making claims about ruling OUT a 2 person human population bottleneck we should instead point out that there isn’t strong evidence ruling it IN, and that we have a lot of evidence that rules IN a substantial and continuous human population going back quite a ways.

If there is one thing we can all agree on is that we shouldn’t overstate our conclusions, and I think it is fair to point out that nothing in science is ever treated as an absolute. We would be better off describing the level of confidence that the evidence affords.

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You do me a disservice there. You know nothing about my thought processes. I went into this research open to any result, including the possibility that we shared common ancestry with chimps. I was on the EC side of the ID spectrum. I took Ayala’s work to be strong evidence that a single pair was not possible. But what I found in the literature was that he was wrong. I know, shocking isn’t it? Read Bergstrom et al and Von Salome et al.

It’s an open question as to what the cause of the “trans-species polymorphisms” are.

As Dr. Swamidass mentions, the trans-specific variation appears to be good evidence that there has been a substantial human population since divergence from chimps since a large proportion of trans-specific variation should be lost in a bottleneck, if my popgen knowledge is correct. The production of HLA variation after the bottleneck would not be able to recreate alleles that were lost as part of the bottleneck.

That depends on the rate of allele generation and the time involved. I saw what happened to Ayala’s numbers. They went from 32 to 4 or 5 at the time of our split from chimps. What would be the predicted number for HLA-A?

There are other suggestive bits in the literature–bottle-necked mouflon sheep that have higher than expected HLA diversity.

As far as the overall scientific approach is concerned, there appears to be a conclusion in search of evidence.

I repeat, it was the data that led me to consider the possibility of a first pair. Not as you suggest. I would like to ask everyone here to stop trying to read my mind or my motivations, based on what you think you know about ID or ID people. Ask me. I will tell you. Don’t assume.

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[content removed by moderator]

I did ask you. I asked you directly, very early on. Here’s the question again.

You didn’t answer.

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First off, I wanted to thank you for participating in this thread. My posts may come off as a bit gruff at times, but it is not meant in a mean or spiteful manner. Think of it more as the pseudo-combative nature of scientific conferences where ideas are hotly debated among peers who respect one another. Again, I really appreciate your time spent here and your willingness to discuss the subject in a somewhat hostile environment.

In reading Bergstrom et al. (1998) I have to wonder why you would look to this paper as supporting the type of bottleneck you are proposing. First, the 6 allelic lineages Bergstrom et al. talks about (which only covers a little over 90% of the alleles, not all of them) have coalescence times that range from 0.18 to 0.89 million years. I would expect those dates to be a lot closer if they came from a single bottleneck. Bergstrom also lists the effective population size as 10,000 over the last 1 million years, the time span during which these lineages were apparently founded.

It is also worth mentioning that there are 2,103 alleles listed in the HLA database compared to the 135 alleles compared in this paper. The authors are certainly not to blame since the paper is from 1998. However, I think we could both agree that a new analysis with a larger database would certainly be of interest.

I will also admit that popgen is a field that I am not as familiar with. If my understanding is correct, coalescence is not evidence of a bottleneck. For example, if you had a population of 100,000 people and that population was held steady for a million years you would have genes in the descendant populations that coalesce to different time periods in that million years. This is certainly true for MRCAs for mitDNA and the Y-chromosome. It is my understanding that alleles will naturally increase and decrease in number in any population. If this is true, then why would the coalescence of alleleic lineages point to a bottleneck if you don’t need a bottleneck to cause coalescence?

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I have read all the comments, and it appears possible that I am the only biologist here who has actually read the book “Adam and the Genome”. (Although others are familiar with Dennis’ arguments from other sources). The book is excellent, and makes the case for a large population size accurately and with scientific precision. And as Dennis has stated here, he uses allelic diversity, ILS and standard pop gen models, nicely explained for lay readers to make the case. I will not go further, since the author himself has said he will weigh in when he can.

There have been some suggestions made that if Adam and Eve were in fact miraculously created, then perhaps other miraculous events might also explain modern human genetic diversity (this is similar to the AiG idea that pre flood lifeforms were full of “genetic diversity” allowing for very rapid evolution to modern forms by loss of "genetic information), or that Adam and Eve didnt live 6000 ya, but were actually members of an earlier species in the human family line.

I truly do not understand these desperate appeals to magic to try to insist that Adam and Eve were the first and only (or only surviving) humans, when the Bible says nothing of the sort. The AiG interpretation of Genesis 1 and 2 and of Romans, is the problem here, not the science. The complex theology around Adam and Eve is beautifully addressed in the same book by Scot McKnight, and of course elsewhere by John Walton.

If we want to assume a historical Adam and Eve, with theological and biological connections to all of us, there is no reason to reject those parts of Genesis 1 and 2 that clearly indicate Adam was not the first or only man on Earth (in contrast to YEC’s very troubling interpretations). If Adam and Eve were truly alive at roughly the right time, we are all their descendants (@Swamidass)

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I of course have read the book =).

And I largely agree with Sy. It is worth asking exactly what we are arguing about here.

Exactly.

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Because it’s not true. Being the descendants of pre-human ancestors does not rule out God’s involvement. You are operating from a strictly materialist worldview, where evolution is sufficient explanation for everything, and evolution means a strictly material process. But the realm of possibilities is larger than that, and the kinds of transformations we are talking about may require more than that.

No more responses. I have answered your questions but you do not accept my answers, and keep harping on the same point.

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In defense of Jonathan, that’s not his worldview, nor does he believe any of that. You are inferring these things without warrant.

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I have to wonder why you would look to this paper as supporting the type of bottleneck you are proposing.

Good question. I don’t actually look to this paper concerning bottlenecks. The main things that caught my attention were:

  1. The decrease in number of founding alleles and 2. The ages of those founding alleles. Ayala had been trumpeted as disproving the possibility of a founding pair based on his count of alleles at our split from apes. Later data showed him to be wrong.

The time frame of 1 million years gives me no problem. I place the origin of humanity with the appearance of homo erectus.

However, I think we could both agree that a new analysis with a larger database would certainly be of interest.

Yes, more work would be good. von Salome does some of it.