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

Faith & Science Conversation
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But this is precisely the question that I am interested in, regardless of Dennis never meaning it. I want to know about our homo sapiens ancestors. Otherwise this has absolutely no relevance to the issue of Adam and Eve at all.

All I have seen from your own scientific bottleneck testing is that there’s no bottleneck going back even 500,000 years which could remotely be identified as evidence that either homo sapiens or our ancestors were bottlenecked down to a single pair.

I don’t see how this establishes your claim.

But it’s incredibly unlikely that it was only one person who started it; it was more likely to be a group of people. I just don’t find other scientists saying what you’re saying. I find them saying things like “There was no first human”. And they say things like this.

The first thing you see is obvious: our ancestors went through two different phases of population “bottlenecking” (constriction): one occurred about three million years ago, when a large population declined to around 10,000 individuals. The authors note that while this may reflect population size decline associated with the origin of hominins after our split with the lineage that produced modern chimps, they also say that this could be an artifact of ancient genetic polymorphisms maintained by natural selection.

The second bottleneck is the one of interest, for it’s the one associated with a reduced population size as humans left Africa. For the Chinese, Korean, and European genomes, effective population size fell from about 13,500 (at 150,000 years ago) to about 1200 between 20,000 and 40,000 years ago. Now this is the effective population size, almost certainly an underestimate of census size, but that only makes the problem worse: we never went through a bottleneck of anything near two individuals, as the Biblical Adam-and-Eve story suggests. This, of course, means that theologians have to scramble to save that story, turning it, as always, into a “metaphor”. (In science, a falsified hypothesis gets tossed on the scrap heap; in religion, a falsified hypothesis becomes a metaphor.) And it also suggests that Jesus died for that metaphor.

But enough of Biblical exegesis. While the bottleneck for non-European populations was probably associated with a group leaving Africa and subsequently colonizing the world, we also see a somewhat less severe bottleneck in the African samples: from about 16,100 people about 100,000-150,000 years ago to 5,700 about 50,000 years ago. It’s not clear why the populations in Africa bottlenecked as well.

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Sorry, but this makes no sense. Adam & the Genome was published in Jan. 2017. You first published something on “genealogical science” on your blog in April 2017. How, exactly, did you expect Dennis to take into account a “discovery” that was still four months away from being published? And to imply that it might have been a case of “intentionally misleading” people is just irresponsible, unless you think that somehow Dennis had advance knowledge of what you might publish about “genealogical science” back in 2016, but he intentionally choose to conceal his knowledge of the future from the rest of us.

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Thanks for asking to clarifying this point.

@DennisVenema did have advanced knowledge. He claims to have known about this for years (since graduate school), and the two of us had discussed this several times over 2016. In 2017, I was honestly surprised that he had not included in Adam and the Genome.

Regardless, let me be clear that I do NOT think he was being intentionally misleading. I think he did not understand that significance to the conversation. So it is better understood as an unintentional error to omit this. The error was in being imprecise in his language, and not realizing how some people would find this important. A lot of people made the same mistake. @DennisVenema is not unique here, and he certainly is not to blame any more than everyone else who did the same over the last couple decades.

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Yes, that is correct. Jerry Coyne makes illogical statements, and random youtubers misunderstand science. This is a widespread misunderstanding. Even many scientists are making these logical errors. No big surprise there.

That is the great thing about science though; its self correcting, and scientists themselves are not the ones having a problem with what I am saying. I’ve made the case, and its correct. In the end, appeals to what others are saying are an ineffective rebuttal when clear logical and scientific errors are identified.

Well it’s a good question. From a scientific point of view, we know that they go down to ZERO, so they certainly dip below 10,000. The exactly generation-by-generation counts at their origin are unknown, and likely unknowable, and likely dependent on the precise definition of Homo sapien we use.

Though, this may or may not have any relevance to Adam or Eve. There is no a priori reason to think Homo sapiens = the “adams” of Scripture.

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So you are saying that the “real science” is that humans originated from a single couple, not as a population? I would love to see all the other scientists saying this, but I haven’t found any yet.

This doesn’t seem like a sensible statement to me. It looks like an apologetic dodge.

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I cannot imagine this scenario. How is this possible? You are saying there were humans and then because of some event, were no longer any humans. But then humans reemerged at some point in time?

I don’t understand. The word “dip” implies a population that falls to a lower number, not a population that simply doesn’t exist yet. What kind of semantic game is this? I assume when anyone says that there are zero humans at 300 kya it is not because their population has “dipped” to zero, but because their population has not yet arisen. If the entire evolving population in which the boundaries between species are fluid and in which the designation “human” is philosophical, not genetic or biological, why does it matter exactly when a part of the population gets what label? If there was no two person bottleneck along the whole continuum, then there was no two person bottleneck.

I don’t understand this contradiction you are pointing out. The question was whether or not there was a two-individual (whether they are designated ancestor, homo sapien, or human to me is irrelevant) bottleneck in the last 300,000 years. The answer was no, right?

I disagree. French does not begin with a single couple. Any such designation would be totally arbitrary and not based on linguistic realities. It takes generations for given linguistic distinctives to solidify in a population. As transitions are happening speakers go back and forth. @AMWolfe 's "first people to say “oui” almost certainly also said “oïl” some or most of the time. Plus one linguistic distinction doesn’t make a new language out of two speakers. Those things are only useful in retrospect. No one in a given population would have recognized a single individual or pair of individuals in their population as speaking a different language. Similarly species don’t have solid boundaries. Anyone who labels a particular individual “the first homo sapien” is making an arbitrary choice that is not based in genetic or biological realities. “Human” is different because it is a different construct than “species” but if you want the first “humans” to not belong to a large population of other creatures who share their same biological species and live contemporaneously, we agree that did not happen within the last 300,000 years, correct? And pushing the designation of “human” back beyond 300,000 years ago to me sounds quite controversial and dubious.

“Human ancestors” has two meanings, depending whether you mean “ancestors of humans” or “ancestors who are human.” For the record, when I say “human ancestors” I mean “ancestors who are human” not “ancestors of humans.” Is it not true that our human ancestors (wherever in time you arbitrarily designate “human”) did not dip down to two?

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That is exactly how I have been reading this.

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You have to be much more precise in your language. That is not what I am saying.

The claim is not about the the origins of Homo sapiens, but whether they go below 10,000 in the last 300 kya. Everyone who thinks that Homo sapiens arise later than 300 kya will say that they dip below 10,000. That is just an obvious statement.

Whether they arise as a population or not depends on how we define them. Whether or not this has anything to do with Adam and Eve (which think not) depends on how we define the “adams” of scripture.

No. That is not it.

For example, Dennis has argued that “humans” = Homo sapiens, and they arise about 200 kya ago. That means they do not exist at 250 kya. That means their population count at 250 kya is ZERO, which is less than 10,000. So the population count of humans is then less than 10,000.

This is just one scenario where they dip down to zero as we look back in time.

Its about if we are using reverse or forward time. It’s common in population genetics to talk reverse time, which means we start in present with a high population and it “dips” as we go back in the past. Another direction insensitive way of making the same claim is that “humans never have less than 10,000 members”. That is just false.

It’s not a semantic game. It’s just taking a claim seriously and seeing if it is supported in the evidence or not. It’s worth asking, also, why @DennisVenema is no longer defending that claim. The reason, it seems, is that it is not defensible.

It matters if there is a sharp theological or cultural transition at some point. Remember we are talking about Adam and Eve too, so at the core the theological question is whether or not Adam and Eve existed and if their is a sharp theological transition that comes about because of them. Ultimately, we are going to be dependent on our understanding of Scripture and theology to definitively answer these questions. Science does rule out some possibilities (it seems) but it certainly does not answer them.

That is true! In context with Dennis, we clarified his meaning, but perhaps others take a different meaning.

Using your definition, we just do not know from science. The question is underspecified because there are so many ways to understand “human”, and we both agree that our ancestors include at some point ancestors that are not “human.” At any generation, or the first generation, was there just a single couple of “human”? There is no way to know from science. It is certainly not settled, as there is raging debates about what “human” is in anthropology, and they are not considering things like “The Image of God” and “souls” and a historical Adam etc. From a purely biological point of view we cannot answer the question. Neither can we come to consensus when taking theology into account.

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To “dip below 10,000” presumes a population of 10,000 exists, though right? At some arbitrary point in time a population that was once labeled, “pre-Homo Sapiens” gets labeled “Homo-sapiens.” The population is a continuum. Or do you conceptualize that individuals “emerge from their ancestor population” one at a time and form a new species population, so at some point in time there were fewer Homo sapiens than the total population of the species continuum?

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Can you answer this yes or no, if we are going with the anthropological definition of human, not a theological one: that is, anatomically and behaviorally human.

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(also @swamidass)

I don’t really have more time to clarify my thoughts too much today (big move coming up) but just to agree:

My comment about “first speakers of French” only makes sense (if at all) with an absurdly reductionist definition of “French,” and after the fact, almost as a useful fiction, one might say.

In the linguistics version of this sort of shift, at least, the change is gradual in several respects. (In fact, I don’t know to what extent the metaphor even holds at this level of detail!)

I mean, yes, as @Christy said, speakers have variation from one communicative setting to the next. But also, initially, probably all Franco-Occitan speakers said both hoc and hoc illud in different contexts, and one community gradually conventionalized things so that when someone asked a question, they would tend to use hoc illud more than hoc. (This is sort of like, if you imagine a hypothetical English-speaking community where people started using the word “exactly” to mean “yes.” They would say “exactly” in many other situations, and only over time would people realize that “exactly” had come to mean “yes.”)

Then you have the gradual loss of the medial consonant c until it was [h]o[c]il[lud], which probably happened over generations of reanalyzing, like when one of my kids started writing and wrote “gragon” for “dragon” because that initial “d” had come to sound like a “j” to her. This sort of reanalysis happens extremely gradually and probably went something like [k] > [g] > [ɣ] > ø over successive generations.

In genetics, I imagine there are similar complications when you try to isolate the particular innovative string of AGTC that you’re going to artificially designate to be The Thing That Makes Us Human. But I’m not a geneticist, so I’ll leave that question to others.

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If you didn’t explicitly connect your conversation about pedigree collapse to Adam and Eve, I do not see how you can fault Dennis for not making the connection himself. I could go back and look up a conversation about pedigree collapse right here on the forums that many of us participated in, and none of us made that connection at the time. I might as well ask why you didn’t publish in 2016, if you had that conversation way back then.

The fact that you would be surprised that a conversation you had in 2016 was not reflected in a book published in Jan. 2017 just reflects your own ignorance of the book publishing process. I would bet that final proofs were due to the printer at least 8 weeks before the book actually went on sale, and the author would have turned in his “final” draft months before that.

But, I should let Dennis speak for himself, if he cares to revisit the subject at all. Personally, I’m done with it.

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In reverse time, it is self evident that there is > 5 billion people alive now. So as we go back in time, we see the population “decrease” or “dip” over the last 10,000 years (its increasing in forward time). In that sense we will see a dip at origins. But we are also conflating our ancestral population with “human”.

What I would insist upon is that there is a distinction between taxonomic categories and theological categories. In science, we only deal with taxonomic categories that are themselves very poorly defined (e.g. Homo sapiens). However, in theological origins, we are talking about the origin of a particular theological category. It is the dangerous type of concordism to equate a taxonomic kind with the theological kind.

So the real question is how do the theological category of “adams” arise. That is the story told in Genesis, and it is concordism (i.e. eisogesis) read Homo sapiens into “adams.” To understand how this theological kind arises, we have to think about different models. In many models already proposed by others (e.g. Kinder and Walton), “adams” arise as a single couple, even though Homo sapiens may or may not arise as a couple.

So if they are anatomically and behaviorally human, we are talking behaviorally modern humans? The answer is that we do not know. We do not have the resolution down to a single generation to know if all these cultural innovations (or the critical ones) arise from a single couple or not. We just do not know.

Yes there are, but in a complex way. If we are going to identify Homo sapien by a genetic sequences (dubious) then it arises in a single person, but is not going to transmit to all his/her offspring reliably.

However, if we are going to identify “humans” behavior, that can reliably transmit.

Agree. Let him speak for himself, or let’s just let sleeping dogs lie. I’ve just said it was an unintentional error that a lot of others have made too. He should not be scapegoated over that. A lot of other people made the same mistake.

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Just an analogy. We should just let it be, as the analogy will eventually break down. Probably already has.

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Where did I equate taxonomic kind with theological kind? In the part you quoted I only talked about homo sapiens and the number of individuals in the population continuum. That is all I am concerned about at the moment. Where you assert “humanity” in that 300,000 years doesn’t affect the question did the population of organisms that eventually transitioned to Homo sapiens ever have a bottleneck of two. The answer is no, correct?

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The puzzle as I see it is to identify the start of the human race. From what I have read here, the modelling cannot identify a time when “any” number can be given to a start of humans, and try as I may, a time when the model states, “here we are modelling human beings of an x number”.

I am also puzzled by an absence of any evidence of events that are thought to eliminate populations of any number of pre-humans in the model.

These are important concerns to those such as myself, who are not overly concerned with modelling techniques, and more interested in a narrative derived from such work, that identifies a start, and subsequent development, of human beings and communities.

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Okay, that puzzle cannot be addressed by science.

But we can answer the question “In the population of organisms from which humans emerged at some point over the last 300,000 years, was there ever just a single pair?” The answer is no as I understand it. The fact that science can’t prove that there never was a possible two organism bottle-neck somewhere in some population of organisms that are a common ancestor with humans a million years ago is totally irrelevant to me personally.

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Hey @Christy with this…

I think I can see what you mean, and think you are correct. However, your phrasing is not precise enough to be clear. There are some conceptions of it that may be possible. I do not think that, however, is what you mean. So the answer is “no”, it does not appear so.

First, a more clear way to phrase this that is precise…

It seems that in the last 300 kya, our ancestors never had a generation with just a single couple.

Here ancestors would include all ancestors, without raising questions about who is human or not. We could also add…

There seems to be strong genetic evidence that in the lsat 300 kya, our ancestors never had a generation with just a single couple.

However, we should always be aware, that this is an assessment made while barring ongoing miracles. That is a standard caveat in scientific findings, but seems worth pointing out here. If we allow for God’s action, and for unusual biology in Adam and Eve (e.g. if they were mosaics) it might be possible that at our origin (with one big miracle) there is a single couple, less than 300 kya ago. Of course, this last possibility is not “what the data looks like” but it is technically possible.

I’m not just being difficult or playing with words. Precision in stating the claims of science is important. Its part of honesty here. The evidence shows us some things. I does not show us others.

Even if these options are personally not relevant to us, they may be relevant to others. And we have the responsibility to honestly explain what it does and does not say. I think this cuts both ways.

  1. I think @DennisVenema has the responsibility to acknowledge what the data does not say here. (as has been detailed in the last several posts).

  2. I think also (once he has settled this for himself) that @RichardBuggs has a responsibility to acknowledge what data does seem to say (i.e. that a single couple bottleneck before 300 kya seems ruled out).

Both types of public acknowledgement are important. I press for BOTH of them to be honest about what the data does and does not seem show. It cuts both ways. Part of our service as scientists in the Church is to be honest about these things, not selectively but in full. Honesty is just extremely important.

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That’s a helpful correction, especially with the caveat you give prior to that…

If it doesn’t work to say that Adam was the first “human” in terms of genetics or behavior, we can, of course, still say that God initiated a special kind of relationship with him as (or as being “in”) His “image,” and posit that this was passed down to others. That is, it could be a relational definition rather than genetic or behavioral. This is not something that science could ever really speak to, though, as it completely divorces the categories “Adamite” and “modern H. sapiens.” If I understand correctly, this is roughly what you’ve suggested elsewhere, or it’s compatible with it anyway.

I will add that the whole exploration of the linguistic metaphor above actually really helped me to get my mind around just how difficult it is to talk about some individual early human being singled out as “the first H. sapiens.” I started with the idea that surely there must have been some kind of first 100% H. sapiens (intuitively this has long been a hard notion for me to shake… there’s that intuition thing again), but it quickly became apparent how problematic that really is when you try to zoom in and look at the issue in high resolution, as it were. So I want to thank you and @Christy for helping me do that.

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You are starting to get it =).

The relational definition is exactly the one that @Jon_Garvey has been developing on his blog.

However, it actually could make sense to see Adam and Eve as the first with a certain behavior. That does make sense. Or at least it can make sense. Its not at all different than proposals by John Walton about original sin. Defining them genetically, however, is more difficult.

Regarding the Image of God, it all depends exactly what you mean. Though Scripture barely speaks about the Image of God, it’s a very loaded term. Some people have a difficult time with interbreeding between those with and without the “Image of God” because of a lot of meaning they import into the term. If we just mean “appointed to a role” (as many people believe), then this need not be a problem. If we mean “of different intrinsic capability” or “with a soul” then there might be some problems that arise.

I think it is clearer to explain that Adam and Eve (the first theological “humans”) are defined by a particular relational status with God, and they eventually (by one of several possible means) transmit this relational status to all of us. I would associate this relational status more with the Fall than with the Image of God, but that is just me. I think, for example, @Jon_Garvey understands God’s Image as “appointment to a purpose” so he is less concerned about saying that Adam’s descendents are the only ones with this Image.

Ultimately, all these options should be on the table, as long as we affirm the unity of all mankind in the present day. So both my inclination and @Jon_Garvey’s are both in the zone of safety. Of course, that status can transfer to all of us many ways, and different theological models can take different paths. Most importantly, whether or not its important, genealogical descent is available as one method of transmission if that is what is needed within theology.

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