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

Faith & Science Conversation
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Hi Richard,

Yes, life gets busy. Ditto here.

I’ll be honest that I see this discussion as providing ever-diminishing returns. If you want to see your ideas get traction, it’s time for you to do some modelling. You also need to deal with the strongest evidence available, not simply pick at what you see as lesser evidence. For example, there are regions of the human genome that do have haplotypes that could fit into two people. Those are not the areas you need to deal with (!). The most variable ones are the issue.

For that reason it’s unclear to me why you want to continue picking at Zhao when there is stronger evidence to deal with, such as the other papers I’ve pointed you to. For example, the Alu paper, that paper with the haplotype blocks on chromosome 21, and so on. Even if you could shoehorn the data into 4 blocks for Zhao - and even that is not reasonable, as I will discuss briefly below - you just can’t shoehorn the variation on chromosome 21 into four blocks.

If you were my colleague approaching me with this as a hypothesis to be tested, I would immediately point you to the challenges - i.e. the haplotype diversity we see across the genome - and tell you that unless you have a reasonable explanation / mechanism for producing that diversity in the timeframe you propose that this is a waste of time. So would any other geneticist.

I’ll include a brief discussion of the issues here for the benefit of others, since this sort of thing also applies to any other part of the genome, including those haplotype blocks on chromosome 21.

For Zhao, you have in your second haplotype grouping more variation than reasonably can be attributed to one starting haplotype. For example, three individuals (3, 4 and 5) that share an “A” at the position in column six, and a “C” at the position in column nineteen. That looks like another haplotype to me. At position 15, you have about half in group 2 with either allele (A orT). Again, it would be more reasonable to have these as separate types. Ditto for that same column in your group 3. These are all types that have several people in the data set - these are common types.

If you try to start with four ancestral types and then produce the variant types within each of your groupings, you’ll see that you need to invoke too many rare events. For example, in order to produce individuals 3, 4, and 5 in group 2 from one of the other types, here’s what would have to happen:

We would need a mutation to an A at position six, followed by drift to make this variant more frequent. Then, one of the variants later would have to mutate to a C at position nineteen, and once again drift would have to occur to make the new variant more common. These two events could be reversed, of course - mutation to C19, drift, and then mutation to 6A, and drift. Once we establish the 6A / C19 variant, we need either (a) a third mutation at 15 to give 15T for some of the 6A / C19 descendants, or (b) a double crossover event in this region to pick up 15T from another type. This would be needed to explain the fifth individual in your group 2. Then, after these events, you would again have to have drift occur to make these new combinations reasonably frequent such that they would be picked up in Zhao’s sample size. That’s a large number of very rare events, and at least three instances where drift has time to work to take new variants to a reasonable frequency.

You don’t have enough time in your model to make this work. Rare events take a long time to appear, and then drift has to act between each rare event, and that takes a long time too. Multiple rare events interspersed with long times for drift = too much time.

It’s this sort of thing that would be even more of a problem for the chromosome 21 paper, to say nothing of looking at the scope of haplotype blocks across the entire genome as catalogued by the 1000 genomes database.

It’s just not going to squeeze into 4 (or two, which is what it should really be, if Eve was a clone of Adam). If you disagree, feel free to model it and present it for peer review - even the informal peer review that would result from discussing your model here.

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176

I do apologise to anyone who felt hurt by the brevity of my previous post. I had meant to spend longer on it but was interrupted by a PhD student with an urgent request. Once I had spoken to him I had to rush off to lead a class, and decided to sent the post in the minute of my lunch time that I had remaining. Perhaps it was a mistake to send it in such a brief form, but I did want to keep the conversation going. I will respond at greater length to Dennis and Steve soon. It is 9pm my time now, and I have to read three papers for a class tomorrow morning. Apologies.

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No worries - I for one did not take it negatively.

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This may have been raised before, but I’d like to mention the issue of Noah’s family, which is another putative bottleneck (down to eight people). I think any case for an Adam and Eve bottleneck of two people should also address whether or not a bottleneck of eight people occurred not too long after.

I thought it was perfectly reasonable, not a problem at all.

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Well, since someone already did the whole “Since Eve was pulled from Adam’s rib, isn’t it a bottleneck of ONE?” argument, I’ll have fun picking at your “bottleneck of 8”… Wouldn’t it be rather a bottleneck of five genetically speaking? It’s Noah & his wife’s genes that were merely recombined in Shem, Ham & Japheth (assuming Noah was monogamous, and the text gives no evidence otherwise), plus three daughters-in-law.

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FIrst, I want to emphasize the critical importance of taking the questions of the Church seriously. Few have done so, and so that is why there is high value in this conversation.

Though not relevant to this conversation, which is merely about bottlenecks, and not special creation.

Keep in mind that some creationists have proposed that Adam and Eve were genetic mosaics, with different genomes in each of their sperm/eggs. If this is the case, there certainly could have been a bottleneck of two. From a 100% genetic point of view (ignoring archeology), it could have even been a recent bottleneck.

That does not solve the problem of the subsequent 5 genome bottleneck of Noah. And it would also give Adam and Eve a very different sort of biology than us. It would also leave us with an “Appearance of Evolution” problem, because God did not make it clear we did not descend from Apes. It also raises theological problems in inferring incest in the first family. However, it would fit the evidence.

To be clear, however, @RichardBuggs been very clear about several things. Also, it appears @agauger has taken a similar view.

  1. He is not making the case for special creation. So the mosaic solution is off the table, but so is the restriction to one genome by jumping to Eve being a clone of Adam.
  2. He is not insisting on a recent bottleneck, and has even been happy to accept a provisional conclusion that "a bottleneck must have been before 500,000 years ago if it happened.”
  3. He has granted up front that a single couple bottleneck might not be most likely given the data, but he just wants to know of it is possible; e.g. has it been ruled out, even in the distant past?

This is not to defend his skepticism, but to make sure he is correctly represented. @RichardBuggs, as I read him, is asking a reasonable scientific question. I would instead point out that we are actually starting to engage the limits of science. Some of the discussion here seems to circle around trying to prove “what happened without a shadow of doubt.” This is not a reasonable hurdle for human inquiry. Moreover, there are some very subtle and interesting questions about the statistics involved here about rare outliers. However, these details cannot usually be resolved in public debate.

Instead, I emphasizes what @RichardBuggs appears to have already conceded, and what seems to be our common ground. Regardless of what happened, it really appears as if our ancestors never dip down to a single couple. Whether or not it is ultimately true, the evidence very strongly seems to show that, at least within the last 500,000 years, that our ancestors never dipped down to two.

While some have taken exception to their skepticism and questions, I must disagree. It is the essence of science to ask questions, even of settled answers. @RichardBuggs also is not a polemicist, but a practicing scientist who has earned the right to ask probing questions, even if he is ultimately wrong. I am not skeptical as is he, as I agree with that…

This is the type of inquiry where verbal exchanges have do begin to have limited value. Population genetics in particular is notoriously non-intuitive. Rigorous modeling of the data is the only way forward. Which brings me to what I think is another point of common ground.

While @RichardBuggs has an interesting hypothesis, that is not enough.

  1. At the moment, the only mathematical models that fit the full range of data we currently know about are those that show we arise in a population, that never dips down to 2.

  2. The only way to change that is to present a new model, that shows otherwise.

  3. Even if a model can be presented that fits the data, it may remain most likely that we arise in a population, not a couple. Consistency with the data is not the same as most likely.

As has been known for a long time, I am a frequent critique of ID. In this case, however, I think @agauger and others are taking the right path forward. They are not presuming divine action (directly or indirectly) and they proposing models of their own. They are doing the hard work of building them and plan to test them on data. That is a new and promising development in ID, even though this has nothing to do with recognizing design in nature.

Of course some of us have different beliefs about what the simulations will show. It is my hypothesis that they will end up confirming the consensus. If they do confirm the BioLogos position, and are honest about it, that will do great good for the Church, bringing them into an honest confession of the evidence. If they end up showing a new way forward, that has value on a purely scientific level. I commend them for it. I think the first option (confirming the BioLogos position) is much more likely. They might disagree.

Who cares. Let’s see what the data shows. Give them time.

Though I agree, in the meantime…

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C was actually my first programming language, so I would be happy to see the code whenever you have the time to post it.

Blessings,
Chris

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@Swamidass

I’m a little uneasy with how you expressing the target conclusion: “… it really appears as if our ancestors never dip down to a single couple.”

Now that you have inserted the “sperm and eggs as a mosaic”, we probably should add an additional clause, because all the results discussed so far has actually been more than limited to “a couple, yes or no”.

The conclusion that @RichardBuggs should agree on is not just regarding two (2):

“it appears as if our ancestors never dip down to either a single couple, or even fewer than 1000.”

And, further, the good doctor would immediately win support and credibility if he started telling the YEC audience that they have to drop the 6000 year time frame, because none of the evidence supports it.

I’m still waiting for someone in the I.D. crowd to step up and start pointing that out… while being a promoter of I.D.

For a while, I thought Dr. Gauger was going to be that person – and what does she do? She writes multiple chapters where she couldn’t bring herself to say anything like that… and instead buried her reputation even deeper into the YEC camp.

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As you note, making such a statement would alienate YEC supporters, and there seems to be an unspoken rule that you’re not allowed to say anything which might do that.

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@Swamidass

They are? Where can I get a summary of their model or models?

What I see is a continued (and baseless) attack on Evolutionary models, with not a wit of or trace of any replacement models.

If you have influence on them in respect to this particular issue, please continue to press them for replacement scenarios… so we can all join in the fun of figuring out what is workable and what is not workable.

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Ann has mentioned here and in the “Everything Wrong With TE” book that work on a model is underway and the results will be available RSN.

From Chapter 16 annotation:

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Not unspoken. They come right out and say it.

There is nothing like ignoring the elephant in the room.

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Looks like they actually shot the elephant in the room, then dragged it out of the room, and buried it in the yard behind the house.

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@Bill_II

Well, they certainly do “argue that”. And the last sentence says they Propose An Alternative Simulation. Yep, I agree. They are proposing it.

This should be amazing if one is ever produced… even a bad one would be amazing at this point !

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I don’t see the ‘mosaic’ proposal as viable for recent bottlenecks, without also introducing effectively miraculous genetic recombination and segregation events in subsequent generations across various populations. Perhaps if Adam and Eve were hugely polyploid and ‘mosaic’? I also believe that Buggs suggested a mosaic model when he referenced data and suggested that many alleles in one region of the genome could be traced back to four original regions.

In practice, I think that “two human bottleneck” models generally imply a mosaic starting point in which additional variation is added via later mutations. What the current models suggest is that it requires hundreds of thousands of years to reach a point where statistical uncertainty / noise finally overwhelms the ability to distinguish between 2- vs. multi-thousand population bottlenecks.

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That is not what mosaic is. It does not require high recombination or mutation rates or an increased genome size. It just means that Adam and Eve had different genomes in each of their gamete progenitors. This cannot arise in normal development, but perhaps God created them this way, with a different biology than the rest of us.

Lest there be any doubt, this is not my view. I am just explain an proposal put forward by others. Explication is not endorsement.

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@Swamidass

They might as well propose that God miraculously intervened into the population genome, to make people think there was no bottleneck!

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I thought the mosaic reference was as you referenced in Wikipedia. Thanks to recombination, I think almost every gamete carries a somewhat different ‘genome’ from the fertilized egg that started the parent.

Thanks for the clarification about “Adamic mosaicism” as gamete ‘frontloading’ with individual, unique and extremely diverse genetics . I understand you don’t endorse it. It’s not clear that Adam and Eve had thousands of children (some accounts suggest roughly 50) or that the current diversity reflected in modern day populations are compatible with the notion. I still don’t see how the Adamic mosaic model is a genetically ‘compatible’ view without additional miracles piled on to get around the issue of bottleneck size in a few thousand years.

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Well Eve, I suppose, would have to be a baby making machine. Let’s say she lives 900 years (like Adam) and is having a kid every 2 years; perhaps she has 400 kids, each of whom have two distinct genomes. So that would be 800 genomes. We could also wonder if they were in the Garden longer, and perhaps add to their numbers that way.

Fantastical. Yes. That seems implausible to me, stretching into comical. Poor Eve, consigned to be pregnant and nursing her entire life.

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Right? Yet strangely, there are a least a couple major religious organizations that support the notion of frequent childbearing as the desired state. It’s one of the reasons why I’m probably related to about half of the people in southern New Jersey.