Mito and Y-MRCA Appears to Rule Out Recent Bottleneck


#1

Continuing the discussion from Heliocentric Certainty Against a Bottleneck of Two?:

I’ve been getting some questions on why I think a recent bottleneck (before 100 kya) is ruled out by the evidence. I noted several times in this series the reason why.

Mito- and Y-DNA

Let’s say (as most YECs do) that we rule out any scenarios that imagine Adam and Eve with very different biology than us (e.g. mosaics), or imagine God was constantly adding mutations to our genomes. A 50k bottleneck seems pretty well ruled out by the mitochondrial and Y-chromosomal data. Y- and mito- DNA has some very favorable properties in comparison to autosomal DNA for our purposes.

  1. There is no recombination, so these DNA stretches are much easier to analyze.
  2. Because of recombination, and perhaps by luck, neither of these are obviously contaminated by interbreeding.
  3. They are both are transmitted independently of one another.
  4. The mutation rates of both are well studied. They are directly measured in Y-Chromosome too, though this has not yet be done for Mitochondria (because it is really hard).
  5. One is transmitted exclusively by fathers, and the other exclusively by mothers, so they are independent of one another.
  6. Men/women have only one copy of y- and mito-genomes, so we do not need to worry about TMR4A vs TMRCA.
  7. We consistently get MRCA for y-chromosomal and mitochondrial genomes > 100 kya.
  8. Both YECs and others agree with each other on the source of variations in mitoDNA and yDNA (it is all mutations, and none of it is de novo created diversity).

So these are two essentially independent tests for a recent bottleneck. We also know many of the factors affecting increased mutation rates, and know they are not relevant on this timescale, and work differently for y and mito DNA. So this seems like a plausible bound. There will be debate on exactly where we drop down the line on what is ruled out by this evidence, but I do not think one can plausibly put a bottleneck at 50 kya. A very generous cut off seems to be 100 kya, though some will insist is must be 150 kya or even earlier.

For a 50 kya bottleneck (or a 6 kya bottleneck), there would have to be miracles and substantially different biology in Adam and Eve than we observe in humans today. One can believe that, but we would then be outside the realm of scientific inquiry.


#2

But Dr. Thomkins And Dr. Jeanson say…

I was contacted with some questions about this article by two AIG scientists: https://answersingenesis.org/human-evolution/origins/did-humanity-arise-from-large-population-or-pair-individuals/ This article claims that mitochondrial DNA disproves evolution. This is false, and I’ll explain why, but I want to point out what this so fundamentally correct about this article first.

Perhaps the authors most insightful comment is this.

Both sides may claim that the data fits their view, but claiming that the data support a view to the exclusion of the other is very challenging.

They are exactly correct. As we covered already (and Drs. T and J also explain), theistic evolutionists and evolutionary creationists have unfairly dismissed single couple bottlenecks at times by using a cartoon version of the theory: assuming Adam and Eve were homozygous clones. The fact that such a strawman theory is disproven does not reall tell us anything about the plausibility of the actual theories being put forward.

As is pathologically standard in the origins debate, almost everyone (there are exceptions) builds arguments by misrepresenting the otherside. TE / EC authors comically misrepresent YECS, but the same happens the other way too. The second half of this article claims to disprove evolution by comically misrepresenting the theory and the evidence too.

True to form, Drs. J and T go on to present evidence against evolution, making some gross errors as they do so. I’m including the figure below, but also linking here (http://www.phylotree.org/) to relevant data.


#3

Loyalty or Dishonesty?

The errors in that figure are obvious. I’m not going to explain them at first. They are just too obvious; and I wonder if giving it some time to percolate before answering might be more instructive. Dr. J, however, is a puzzle in this story. He is a Harvard trained biologist and surely understands the error in this argument and graph.

I’ve often been quick to call this dishonesty, but I wonder if instead it might be something else, a false sense of loyalty. As I’ve looked into this (as I’ve interacted with Thomkins’ work), I’ve been more sympathetic to scientists working with AIG. They have all signed a belief statement that requires them to misrepresent the evidence:

Scripture teaches a recent origin for man and the whole creation, spanning approximately 4,000 years from creation to Christ.

The days in Genesis do not correspond to geologic ages, but are six [6] consecutive twenty-four [24] hour days of creation.

By definition, no apparent, perceived or claimed evidence in any field, including history and chronology, can be valid if it contradicts the scriptural record.
https://answersingenesis.org/about/faith/

That means they have promised to ignore all data that demonstrates the earth is old. All such evidence, by definition is invalid. After making such a promise, one is obligated to misrepresent the data. After ruling out all evidence (by definition) that show a theory wrong, then the theory will look correct. No surprise there.

As scientists, this surely puts them in a conflicted place. They cannot make honest statements about the data, as does Todd Woods (a YEC too) when he writes:

There is evidence for evolution, and evolution is an extremely successful scientific theory. That doesn’t make it ultimately true, and it doesn’t mean that there could not possibly be viable alternatives.
toddcwood.blogspot.ca/2009/09/truth-about-evolution.html

As a confessing scientist, I have much more respect for Todd Wodd’s position. Honestly representing the evidence is an intrinsic good; I do not believe God needs misrepresentation.

I am also sympathetic to Dr. Tompkins And Dr. Jeanson. It is not their choice that AIG insists they misrepresent the data; and if one is a YEC scientist, AIG is the elephant in the room right now. If one wants a stable job as a YEC scientist, they may just have to accept AIG’s terms.

What About Scripture?

I also would clarify with high emphasis that I certainly affirm the inerrancy of Scripture too, but I also emphasize the fallibility of human interpretation of Scripture. We can be wrong in how we interpret Scripture, especially on non-essential details of our distant past.

I confess the evidence for evolution is strong. However, it is also possible that God still make things differently. That is a dignified position, but we have to ask and answer a theological question: why God would make a world that could so easily be mistaken for an old, evolved world?

There are some answers. Among my favorite:

And as I wrote recently:

With quantitative and mathematical detail, evolutionary theory explained the patterns of similarity and dissimilarity between the human and chimpanzee genomes. God could have falsified common ancestry in our genomes, for all the world to clearly see. He did not. Why not? At the very least, my Creator was much less intent on disproving evolution than I. Whether evolution is true or false, it certainly looks like our genomes descend from common ancestors with the great apes. Even if it is ultimately false, evolution is the plain reading of genomes.
http://henrycenter.tiu.edu/2017/06/a-genealogical-adam-and-eve-in-evolution/

I add these final thoughts to emphasize we are just discussing the plain reading of the evidence, not what actually happened. These two things are separate. Whatever really happened, it is an intrinsic good to be honest about that evidence, even if it is ultimately incorrect.


#4

I’m curious the thoughts of the YECs on this (@J.E.S). Would you prefer your scientists were honest with you about the evidence, even if it ended up challenging your view of origins?


#5

@swamidass

Before I answer your question, let’s talk about some specific cases of science being misrepresented…

Somewhat off-topic: a major disconnect I often see in the origins debate is evolutionists accepting whatever a scientist (nay, an evolutionist scientist) says as indisputable truth, and dismissing whatever YEC scientists say as “pseudoscience.” I ultimately came to the conclusion that evidence is interpreted through a dogmatic “worldview” and that evolutionist’s worldviews were different enough from my own as to create this disconnect. When it comes to the Creation/Evolution debate, the playing field is not at all level. That aside, I am ready to discuss specific events of YEC falsehood. :wink:


#6

I agree. That is not fair, and is especially problematic when YEC scientists have a point. I hope you’ve seen that has not been my pattern. It should be clear that I’ve been calling out evolutionary scientists on their mistakes too. Right?

I’m not intending to take you to task on that. It’s not your fault if another YEC is not honest. You do not have to answer for them. And many YECs are honest too (see Todd Woods). So I am not at all claiming that all YECs are dishonest. Even in the case under question, I do not know if I can call it dishonest. They are in a difficult position, because they work with an organization that requires them to leave out evidence.

Once again, you do not have to defend or answer for that. I have a different question.

It’s about what you prefer? Do you want to hear only version of the evidence that supports your view? Or would you rather that the evidence was completely explained to you?

Case in point is the argument against evolution being offered here. It’s representation of the evidence is just flat out wrong, but it supports your view. I’m not even showing you how its wrong. You can find out yourself by looking on the internet. How do you feel about that?


#7

I would say that your data would rule out certain OEC models as well. For example the idea that there was a flood which extincted all humans except for one Y-DNA chromosome within the last 50K years.

Fortunately the Christ-centered model of early Genesis does not require such a bottleneck. As Genesis ch. 11 makes clear, others besides the clan of Noah survived the flood.


#8

@swamidass
I have respect for you due to this fact.

The latter.

However, when it comes to researching alleged claims of YEC dishonesty, it can be quite frustrating because who do I believe? The original AIG etc. article, or the random person (scientist or not) on the internet that “disproves” it with:

  • Seemingly Sound, But Occasionally Convoluted, Scientific Information That Does Not Necessarily Seem To Explicitly Contradict The YEC paradigm

  • Repetition Of The Premise Refuted By The AIG Article As A Dogmatic Fact (This Irks Me To No End :wink: )

  • Or The Arrogantly Condescending Railing Against YEC’s (and sometimes christians and/or theists) in general.

I almost always run into one of these three when I seek to find evidence against a YEC claim. This makes things very difficult, because 1 automatically becomes 2 if it does not specifically address the YEC argument, and 2 often becomes 3 when it is addressing the YEC argument…I hope this little insight proves enlightening for you all…:wink:


#9

Playing devil’s advocate for a bit, is it really a cartoon version? What is present in a literal interpretation of Genesis that indicates that Adam and Eve were not homozygous clones?


#10

@cwhenderson
Nice to see you here!


#11

Thanks @J.E.S , working back into re-engaging my brain before the Spring semester begins!


#12

Where does Genesis tell us Adam was homozygous? Where does it tell us that Eve was his genetic clone? Where does Genesis talk about DNA?


#13

Maybe not homozygous, but if Eve was taken from the literal rib, wouldn’t she be a clone?


#14

Why would we assume that when AIG itself does not take this position? Where does the passage say that God did not give her a new genome?


#15

Hi everyone,

I think we need to distinguish between what Genesis explicitly teaches and what the default assumption would be from a plain reading of Genesis. Nowhere does Genesis teach anything about Adam’s DNA. But if the first man were created from the dust of the ground and the first woman were made from his side, then the default assumption would be that since he had no parents, the first man would be homozygous, and the first woman would share his DNA (or more precisely, the only differences one would expect to observe would be those required to make her into a woman). Thus when I read discussions about TMR4A, for instance, my reaction is that this proposal really only makes sense in an evolutionary context. I’m not saying it’s impossible if you’re a creationist, but I do think it would be unexpected. My two cents.


#16

I completely agree, Vincent. Homozygosity might be debatable, but any explanation involving something other than a cloned genome of Eve requires adding to the Genesis account. Isn’t that contrary to the AiG approach to Genesis?


#17

AIG and other creationists and have been complaining loudly for years that they are being misrepresented. Most, pretty much has been ignoring them. What we should have been doing is trying our best to make the model work with the data, with a real sympathetic reading. That way we’d not be relying on a strawman when we claim to demonstrate their position wrong.

From the article, they make this clear. By the way, I’ve heard this repeated over and over. There is nothing new here. It’s our fault for not taking it seriously:

If we assume, for sake of argument, that mankind did indeed arise from two supernaturally created people (regardless of how long ago it was), and if we further stipulate that genetic differences can arise only via mutations, then we would be forced to conclude that Adam and Eve did not have any genetic differences between them (aside from the X and Y chromosomes, since these are involved in specifying gender).
https://answersingenesis.org/human-evolution/origins/did-humanity-arise-from-large-population-or-pair-individuals/

This, by the way, is Dennis’ model of the YEC position. https://discourse.biologos.org/t/adam-eve-and-population-genetics-a-reply-to-dr-richard-buggs-part-1/37039/133?u=swamidass Which is why, his argument ended up being so fragile (e.g. TM4A). I understand that shift was surprising to some (@vjtorley and @cwhenderson), but it is just taking what they are saying seriously, without inputting absurdity where it does not lie.

Any ways, Drs. T and J concede that this model is totally inconsistent with the data. They are pointing out its a strawman. In my view, they should be justifiably angry about it. And the fact their model was not engaged is just going to provoke a great deal of distrust of those who imputed absurdity onto them.

Why They Reject Homozygous Clones (and just Clones)

They even go to some of the philosophical and theological reasons (non evidential) that they reject this model.

But this hypothetical scenario leads to some bizarre conclusions. If Adam and Eve decided to fulfill God’s command to be fruitful and multiply, they would have passed on two identical DNA sequences to their offspring. Aside from the few mutations that may have arisen (representing 0.00000001% of the billions of DNA3 letters in our cells — a negligible fraction), Adam and Eve would have basically produced copies of themselves — not slightly modified versions of themselves as we are used to observing in our own children, but identical copies of themselves. Offspring that are completely identical to parents receive a particular label in genetics: clones. Cloning as a means to fulfill the dominion mandate is a strange position to maintain. With all the debate that currently exists over the ethics of human cloning, it is somewhat disturbing to think that God instructed the first man and woman to fill the earth by this process.

I’d say that is a plausible reason to reject the homozygous clone model on theological grounds.

A very simple alternative hypothesis resolves the conundrum and also makes straightforward scientific sense: God could have created Adam and Eve with genetic differences from the start (Figure 1). In fact, all of us possess not just 3 billion letters of DNA in our cells. With few exceptions such as red blood cells, the cells of our body possess two versions of our 3 billion letters, which means that each of our cells has 6 billion letters. Each parent passes on only 3 billion in sperm or egg, keeping the total of 6 billion letters constant across generations. Going back in time, Adam would likely have had the same cellular arrangement — two versions of his 3 billion letters — and the same would have been true of Eve.

And that is exactly the hypothesis that YECs and OECs have been working with over the last decade. Anyone who does know this has just not been listening.

What if Their Scenario Could Work?

Wouldn’t that be great? Would it not be really exciting to demonstrate such an non-intuitive finding? I certainly think that would be newsworthy.

Honestly, I think it would be really great if we could find a way for YEC time scale to work with the evidence without abusing. I’m rooting for them. In some ways, that is exactly what the genealogical Adam is doing; given them a way to hold a 6,000 ya timeline for Adam if that’s what they think is important.

Instead, when we ignore their own models, and declare victory by deposing a strawman, it leaves us very overconfident. Maybe even heliocentric confident ( :slight_smile: ). More importantly, it leaves us untrusted. If we cannot sympathetically and accurately represent YEC positions, and we cannot acknowledge when they have a point, why should they trust us? If we are not rooting for their success, why should the trust us?


#18

I think a better approach is to ask the question. Are there any good theological reasons offered for why God might make Eve from Adam’s rib, but not as his clone? It turns out that this question has already been floating around for long enough, that they have actually offered plausible answers.


#19

I suppose that is one reason why I respect you.

I’m not asking you to assess their honesty. I’m not even sure if this dishonesty. I do know, however, that they excluded data that demonstrated they are wrong. Moreover, they are obligated to exclude evidence like this by their employer.

Just giving you a chance to look at it.


For everyone, let me know when you want the next hint.


#20

If this site is now going to be an apologetic project for YEC, then I’m not interested. I see no value in torturing the scientific data until it can be presented in some way that it supports a position which we know from many other lines of evidence, to be non-factual.

I do not believe it is our responsibility to do their work for them, especially where that work consists of attempting to give people reasons for believing a falsehood. More importantly, you completely omit the fact that the YECs have given us absolutely no reason to trust them, or accurately represent our positions.

I am not rooting for their success, for the same reason that I am not rooting for the success of Flat Earthers or white nationalists. They teach dangerous falsehoods. I have seen too many people lost to atheism as a result of YEC, to want them to succeed. I have seen too many people turned away from Christianity by YEC, to want them to suceed.

In most nations, YECs are a tiny minority. In Australia only 9% of the population rejects evolution, and that includes non-Christians. The fact that the numbers are significantly higher in the US, is the kind of problem which Christians in the US need to solve.