Dsterncardinale's Review of Traced by Dr. Nathaniel Jeanson

Conversation
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Video review from 4/13/22:

Text version (not a transcript, not by a long shot):

“Traced: Human DNA’s Big Surprise” is the new book by Dr. Nathaniel Jeanson of Answers in Genesis. In Traced, Dr. Jeanson uses Y-chromosome haplotypes to argue that the Y chromosome supports a Young Earth history, specifically the AiG version.

His argument works like this:

  1. Establish a Y-chromosome mutation rate based pedigree studies to calculate a Y-chromosome time to most recent common ancestor (TMRCA) approximately 4500 years ago.

  2. Reinterpret the Y-chromosome phylogeny and chronology based on this earlier TMRCA.

  3. Correlate historical events, like migrations, to nodes in the Y-chromosome phylogeny.

  4. Overlay the Y-chromosome phylogeny onto the pedigree for Noah and his sons derived from Genesis.

  5. Do (3) for Biblical events (e.g. the Flood, Babel, etc.)

  6. Claim you rewrote the history of humanity and confirmed the AiG interpretation of Genesis.

There are, uh, significant problems with the case Jeanson makes.

The first, which underlies much of his analysis, is that he treats genealogy and phylogeny as interchangeable.

They are not interchangeable. Genealogy is the history of individuals and familial relationships. Phylogeny is the evolutionary history of groups: populations, species, etc. A phylogenetic tree may superficially look like a family tree, but all those lines and branch points represent populations, not individuals. This is an extremely basic error.

There are additional problems with each step of the case he makes.

In terms of calculating the Y-TMRCA, it’s nothing new: He uses single-generation pedigree-based mutation rates rather than long-term substitution rates. It’s the same error that invalidates his work calculating a 6000kya mitochondrial TMRCA. He even references a couple of studies that indicate the consensus date of 200-300kya for the Y-MRCA, but dismisses them as low-quality (he ignores that there are many, many more such studies).

He is constrained in an extremely narrow timespan for much of the Y-chromosome branching due to its occurrence after the flood (~4500 years ago) and running up against well-documented, recorded human history (he ignores that Egyptian history spans the Flood). So he has to squeeze a ton of human history into half a millennium, at most.

In correlating his revised node dates on the Y-chromosome phylogeny with historical events, he employs some really half-as…uh, amateurish “analysis”. Like, “the ancestral population for sister haplogroups existed along the line between the geographic homeland for the derived groups, and the descendants migrated in opposite directions” amateurish. I’m not exaggerating; this is how he explains how and where E1b1a and E1b1b descended from E1b1.

He also just ignore inconvenient data that refute his model. Just straight up. Thanks to the crew on the Peaceful Science forum, my favorite example of this is R1b in Europe, and specifically Italy. Jeanson claims haplotype R1b arrived in Europe between 700 and 1400 CE, and specifically in Italy in the 14- or 1500s. Exceeeeeeeept…we have DNA from a stone age burial in northern Italy dated to about 14,000 years ago, and that individual was, you guessed it, R1b.

Even if we take Jeanson’s YEC timeline at face value, a stone age specimen would be pretty close to the flood, about 4kya, which also directly invalidates his model.

Moving on, the next step in his argument is to overlay the Y-chromosome phylogeny (now with incorrect new dates incorrectly correlated to historical events) with the pedigree of Noah and his sons and their descendants derived from Genesis. To do this, Jeanson egregiously acts as though a phylogenetic tree and a pedigree are interchangeable, treating nodes on the phylogeny as specific individuals rather than populations.

And finally, he correlates the haplotypes on the phylogeny (now incorrectly overlayed with Noah’s family tree) with Biblical groups and events.

That’s how Jeanson rewrites the history of humanity. That’s it.

…

It’s actually worse than that. Because he ignores Neanderthals. Neanderthals interbred with Homo sapiens. Most YECs have Neanderthals (and Denisovans) as descendants of Adam and Eve, and living post-flood. This means that Noah is also their Y-MRCA. The problem is that we have Neanderthal genomes, and their Y chromosomes are highly divergent. This necessarily pushes the MRCA back far beyond the YEC timeline, even using Jeanson’s incorrect mutation rates.

How does Jeanson deal with this?

He completely ignores it.

Really. There are a grand total of three (3) mentions of Neanderthals in this book. At no point does Jeanson engage with the fact that Neanderthal genomics refutes the foundation of his argument – the recent Y-MRCA. So…that’s not great.

The last thing I want to mention is that, so far, no other YEC “scientists” have gotten on board with Traced. Not many people have commented on it, really. AiG is in full hype mode, but that’s about it. Dr. Rob Carter published a piece answering a question about a secular paper, and the degree to which his qualifications and critiques apply to Traced is…notable, I think.

So Traced doesn’t do what we’re told it does. It’s too full of basic errors and shoddy analysis.

It’s not designed to convince real biologists that AiG is actually right. And I don’t even think it’s designed to convince non-YECs, Christian or not, that YEC is right. I think this is designed to reassure people already on board with AiG’s version of Genesis that they have “science” to back up their beliefs. It’s to make a subset of YECs feel good, and not much more. There are too many errors, basic, obvious errors, for anything else.

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So from what I have gathered, Jeanson’s argument is his method of using the Y chromosome explains mutations as a series historical events. That you can watch human migration patterns and correlate it with mutations.

I am curious if you have noticed any migration patterns which are documented in historical records that do not line up with Jeansons prediction. Such as the Visigoths conquering Spain and leaving behind blonde hair blue eyed people, then the Moors conquer Spain and take the blonde hair blue eyed people back home to Northern Africa to interbreed with.

I am curious since what I have gathered as a ‘layman’… The foundation of his argument lies in it correlating with human migration patterns. And from reading your summary the only time you mention a mismatch is with R1b from a fossil that is 14,000 years old or the Egyptian record predates his assumptions. Which would not be considered proof by a YEC.
Do you have examples of a mismatch in migration that YEC’s would take as credible evidence due to it not predating the time of the flood?

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No, that you can PRETEND that there’s a correlation.

Pretty much all of them.

It doesn’t correlate.

YECs ignore any evidence that would falsify their assumptions. YEC leaders routinely misrepresent the evidence itself.

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It’s more that Jeanson is assuming that migrations carried genes into areas, where there’s no evidence from burials associated with those migrations that they carried these genes (e.g. R1b coming westwards from “far Eastern Europe or Central Asia” in the “the a.d. 700s to 1400s”). Even worse his model predicts major migrations where there were none, e.g. “into France and the Iberian Peninsula (S116), in Switzerland and Italy (U152), and in the British Isles and Ireland” “in the a.d. 1400s and 1500s”.

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I’ll reply over here about Jeanson since you made a thread for your review and my comments are in response to that.

The paper you cited mentions the strait HAS been a historical migratory route. The obvious implication from your words was that Jeanson thinking there was any migratory route across the Red Sea is ridiculous, when it is clearly not. I also mentioned you skipping the figure from the book, since you mentioned line-drawing as if there was no historical inference at all.

So…Dan’s mention of Jeanson’s conflation of phylogeny and Genesis 10 genealogy was one other place where I thought, if Dan had any creationists in his audience, he really lost them there. They’d be scratching their heads, what? Lol, how can he be criticizing that? :slightly_smiling_face:

And the only thing I can think of is that as undergrads,
biology students must get drilled into them that nodes on phylogenies are not individuals and are populations (because we are all used to family trees and want to think that way all). And of course this makes sense for phylogenies based on phenotype or autosomal DNA. But I see no validity in using this as criticism for phylogenies of uniparental DNA that have multiple mutations per generation where the substitution rate is going to be the same as the mutation rate in the ancient branches. The creationist with no science background is thinking to himself, “Dan, I really didn’t think that only those men were at the tower of Babel, I kinda figured there were populations with women and kids too.” :wink:

It’s getting late, so I gotta respond to more another day.

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Do you think the branches and nodes on a Y-chromosome phylogeny represent either a) individuals, or b) populations with zero polymorphisms? Those are the only two ways for this to work. And both are, to be blunt, laughable suggestions.

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Thank you, I have not read the book nor do I plan on buying it. I was curious as to defeating the arguments with it’s own claims (something I believe should be possible if an assumption is false).

By 700ad to 1400ad is this in reference to the Mongolian Conquest or the Muslim Conquest?
Mongolians being the tail end of this time period and the Muslims being the first 2/3rd’s. They are the only two major events that come into mind when thinking about Eastern Europe and Central Asia at this time period.

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Why couldn’t they represent individuals, in this case, if there are multiple mutations per generation? How wouldn’t they?

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Since you label yourself as imaginative, you might want to imagine the possibility that you have a profound misunderstanding of both how genetics is taught and how we learn it, as none of it is by rote–it comes from a mechanistic understanding of how meiosis works, something you appear to lack. Genetics tends to cause a lot of trouble for those who thrive on rote learning (premed stereotype) for that very reason!

You might want to consider the real reason–Jeanson is making a laughably basic mistake (if indeed it is a mistake and not an attempt to deceive people like you, of course). I didn’t merely learn genetics as an undergraduate, of course; I have done original work in genetics and taught it. Has Jeanson?

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Aside from Jeanson’s choose your own adventure methodology of migration studies, and assumption of a fixation rate that implies every male child in history has, without exception, in turn sired another male child, Dan’s review highlighted a show stopper. Where does Neanderthal fit in? We can add the Denisovans as well.

Answers in Genesis - Neanderthal People

Neanderthals were a group of humans, descended from Adam and Eve, who lived in the harsh post-Flood world. Archaeology confirms they made instruments, make-up, jewelry, weapons, and ritually buried their dead. Many humans today share DNA with Neanderthals. This fully human lineage died out sometime after the Flood.

Answers in Genesis - Humans Only 1.5% Different from Neanderthals and Denisovans?

These post-flood peoples are descendants of Adam and Eve (and of Noah and his family), made in God’s image, and therefore fully human.

By Y chromosome studies, both Neanderthals and Denisovans have divergence times far earlier than any haplogroups.

The evolutionary history of Neandertal and Denisovan Y chromosomes
The Divergence of Neandertal and Modern Human Y Chromosomes

It is not possible that Noah’s sibling children or more distant offspring include modern human, Neanderthal, and Denisovan Y chromosomes, but do let us try. Indulge the identification of haplogroup divergence with individuals. Imagine that Shem, Ham, and Japheth between them represent these three lineages, or in more mainstream terms - three human species. The immediate collapse of this idea lies in that the Bible itself already assigns nationalities to descendants of the three sons, and as Jeanson and numerous others have laid out, these correspond to populations with familiar haplogroups. There are no sons to spare. So it is not possible to get from Noah to Neanderthal and Denisovan Y chromosomes, and even if it were, it is not possible to reconcile the Biblical genealogies with their presence in post flood populations. In contrast, the genetic evidence all aligns comfortably with the evolutionary time scale and conventional description of human dispersal.

For the most part, AiG has in the past simply acknowledged Neanderthals and Denisovans as descended from Noah while avoiding any discussion of the genetic challenge posed. With the publication of Traced, we can now thank Jeanson for making this omission explicit and overt as the mammoth in the room. The post flood existence of the Neanderthals and Denisovans is incompatible not just with Jeanson’s exposition of genetic history, but any conceivable YEC harmonization which places a bottleneck at the three sons of one couple 4500 years ago. This is bound to be noticed, and it may be the unintended consequence that Jeanson has lobbed a grenade into his own enterprise.

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Well, how fortunate that @thoughtful is open enough to the evidence not to fall for the deception.

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If that were true, every modern individual would need to be classified into a separate genotype. Is this what happens?

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Actually, the paper merely mentions the strait as one expected (i.e. possible or potential, not necessarily actual) migration route, with a land route via the Sinai and the Mediterranean coast being the other, not as a “historical migratory route”.

Can you provide any evidence of a major migration of Eb1b-carrying people across the strait into southern Arabia, in Jeanson’s required time period (between the 400s BC and the 700s AD)? If not, then this is just another of Jeanson’s fairy stories – a fact-free fantasy to tell YECs to make them sleep peacefully at nights.

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An excellent question, and one that Jeanson unfortunately does not appear to be willing to offer a definitive answer.

After stating that:

Together, these data suggest a migration route (Color Plate 74):
  • In the a.d. 400s to 700s, the ancestral population of R1b men resided somewhere in far Eastern Europe or Central Asia.
  • Then, in the a.d. 700s to 1400s, a subgroup of these men started moving westward, leaving the M73 lineage behind.
  • Some of the migrating men settled down in places they crossed, like western Russia, the Caucasus, Turkey, the Balkans, and the former Eastern Bloc European countries. The ones who stayed in these places gave rise to the M269 and L23 lineages.

He then goes on to discuss a grab-bag of potential candidates: the Magyars, the Turkic “Pechenegs, Oghuz, and Kipchak” and the Mongols. These groups apparently fit the compressed timeframe of Jeanson’s Y-haploid mutation model, so he’s happy to suggest them as candidates, without bothering to check if there’s any evidence that any of them carried the R1b gene in any particular concentration.

Jeanson’s map (plate 74) suggests that the point of origin was at, or close to, the southern Ural Mountains, in what is now southern Russia (near Magnitogorsk, if I’m comparing his map to Google Maps correctly).

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What do you think when you look at this figure?

1-s2.0-S0092867421008394-figs2_lrg
1-s2.0-S0092867421008394-figs2_lrg1920×1854 444 KB

https://www.sciencedirect.com/science/article/pii/S0092867421008394?via%3Dihub

[quote=“John_Harshman, post:12, topic:14979”]

Yep. Not yet. They haven’t sequenced a full Y chromosome, well, as far as has been published. I’ve been reading the news from the T2T consortium but they haven’t released the y chromosome paper yet AFAIK. It will be a while until the science catches up to finding each unique genotype. But it’s not hard to find online in ancestry forums where people have found a fairly modern surname specific SNP already. At least I noticed one already while browsing just a little.

And also thank you for clueing me in that I’m not missing something and Dan is not granting Jeanson’s multiple mutations per generation when Dan criticizes overlaying phylogeny onto Genesis 10. I’m sure you can all imagine what impression I have now. Disappointed is one word.

I’ll have to come back to this later as I wanted to discuss ancient DNA, Joseph’s famine, Carter, a recent paper I read, and what this book shows. But I have to pull a bunch of thoughts together to link all those threads and need a chunk of time.

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Please don’t thank me for supporting your misunderstandings. It’s just rude. And it’s not true.

What do you think? It seems to have nothing at all to do with the matter you were asked to provide evidence for.

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At first glance, that it’s a massive dump of data, without anything to really contextualise it.

In the context of my question, that there doesn’t appear to be anything showing a “major migration of Eb1b-carrying people across the strait into southern Arabia” from East Africa (or anything about East Africa at all).

It therefore seems to be irrelevant data, rather than relevant evidence.

In fact, looking at the paper it’s from, it comes straight after a chart showing migration going the opposite way:

1-s2.0-S0092867421008394-gr2_lrg
1-s2.0-S0092867421008394-gr2_lrg1660×1571 250 KB

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Is @Herman_Mays here? Looks like he is! Awesome. He also reviewed the book, and then went further and dug into Jeanson’s methodology in way more detail than I did, and it’s so, so much worse than I thought. My mindset was “Jeanson’s mutation rate calculations are always iffy, but that’s not the biggest problem here”, but it turns out…that may actually be the biggest problem here. Because Jeanson’s techniques are bananas.

Via @Herman_Mays:

Remember Jeanson is only ever interested in the de novo mutation rate - the rate of spontaneous single base changes from one generation to the next, in this case, mutations occurring in a father that are passed to a son. But, Jeanson’s problem was that data was not reported in Marretty et al. 2017 so this was his creative approach to deriving those data. He literally made a screenshot of the figure from the paper - a distance-based tree from Y-chromosome sequences using the same method Jeanson uses (neighbor-joining, I included my own screenshot of the same figure below). The branches on the tree represent the number of base changes that have occurred in the past along that particular lineage. Jeanson zoomed in on the tips of the tree focusing on the 17 pairs of the shortest branches representing what he assumed were Y-chromosome sequences from fathers and sons. Then he used the 50 mutation length scale bar, essentially took a ruler to the screen, and measured the branch length for these 17 pairs of sequences at the very tips of the tree, and that is how he calculated his upper limit for the Y-chromosome mutation rate.

[…]

This is what one of the authors, Laurits Skov, conveyed to me in our personal communication (shared with the author’s permission) regarding Jeanson’s use of their article.

“One thing to note is that we mainly focused on structural variants in this paper (Maretty et al. 2017 Nature 548: 87-91) so we were not very conservative with regards to filtering of SNPs. So thats why the Y chromosomes are not completely identical.” - Laurits Skov, personal communication, April 19, 2022

That’s why the chromosomes are not completely identical. Not because of mutations, which is what Jeanson thinks he is measuring, but rather because of error. Jeanson is measuring very slight differences between sequences using a very crude method (i.e. zooming in on a screenshot of a figure) and treating those differences as if they are mutations and most differences very likely are not.

This is more from my correspondence with Laurits Skov, again, one of the authors of the paper Jeanson is misappropriating.

“No I think most of the differences between father-son pairs in this study are errors. I was looking through the supplement of my Y chromosome paper to find some numbers. So the phylogenetic tree is made using around 3000 SNPs and the error rate is around 1/1000. So while you can certainly use this data to construct a phylogenetic tree I would not use it for inferring mutation rates.” - Laurits Skov, personal communication, April 20, 2022.

“I would not use it for inferring mutation rates”, and yet that is precisely what Jeanson is doing and he is basing his entire argument on these contrived numbers.

It’s soooooooo bad, y’all. Worse than I realized. Nobody should take any of this seriously.

But that’s not really the point, right? If he wanted it taken seriously, this book wouldn’t exist.

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Here is the context in the paper for E1b1b which is what we you were discussing:

The haplogroup common in Natufians, E1b1b, is also frequent in our dataset, with most lineages coalescing ∼8.3 (7–9.7) kya, though we also found a rare deeply divergent Y chromosome, which coalesces 39 kya (Figure S2).

So they’re saying the rare divergent chromosome on the top right is 39 kya - that isn’t relevant to the map you shared from the paper which shows the spread of language and how many thousands of years ago that happened, and I don’t think they’re saying it’s relevant to haplogroup E either.

BUT it is relevant to Jeanson’s book because his hypothesis is that E started in Africa, E1b1b migrated to the South Arabian peninsula in the early A.D. era, and migrated back to Africa with Muslim conquest into Africa. On that figure, E1b1b2 on the top right is located in Yemen. The mainstream view is that E originated in Africa. And now somehow a lineage that broke off early is in the Arabian peninsula. That fits the book. I don’t think it matters whether there was a large migration or not - it could have been one person. It just matters that there was a reason for one person to migrate - trade opportunity is enough of a reason. AFAIK, chances are that it was a large migration of that lineage for it to still exist today, but it doesn’t have to be.

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The notion that anyone take Jeanson seriously is frankly absurd, and yet I myself fall for it every time and in the end regret it every time.

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