Dsterncardinale's Review of Traced by Dr. Nathaniel Jeanson

[Tim]

@thoughtful

AFAIK the choices are either you can believe that a Lenz/Lentz (a common surname) is the only descendent of certain Yamnaya to join a Family Tree DNA subclade project besides a few Turkic people and someone from Iraq (which seems very improbable after 5000 years because of the extreme drift of the y-chromosome)…

How extensive/pervasive is the coverage of this “Family Tree DNA subclade project”?

This would appear to be a classic Argument from Silence.

@thoughtful

…or mutations are common enough that they drift out of the population but occur again at the same position.

This appears to be a word salad. Please choose your words more carefully.

@thoughtful

I would hypothesize that it’s likeliest … that the Turks and the Europeans in the subclade project have a common ancestor sometime in the last two millennia and then accumulated some of the same mutations in their lineages at different times.

And Valerie, I would point out that given the massive amount of evidence (yes, we’re back to that word again) of R1b existing in Western Europe since the Stone Age (which, regardless of whether you take the consensus science date of that age, or the YEC date, was millennia before the Turkic peoples moved out of North East Asia around 1000 years ago), means that this ‘hypothesis’ is unlikely in the extreme.

I would also point out that slightly less than half Bashkir have R1b, meaning that, either way, about half of their Y-haplotype must have come from some other group(s).

Speaking for myself, “I would hypothesize that” Valerie will support ideas that are consistent with Jeanson’s claims in particular, and the YEC viewpoint in general, no matter how unlikely the evidence renders these ideas.

@thoughtful

… which seems very improbable after 5000 years because of the extreme drift of the y-chromosome …

Do you have any evidence of this “extreme drift of the y-chromosome” other than Jeanson’s amateurish, make-it-up-as-he-goes-along, thoroughly-debunked attempts at Population Genetics? This would seem to be nothing but ‘Begging the Question’ – assuming that Jeanson is right in order to ‘prove’ that he’s right.

@thoughtful

Hard to make an inference without the sample size to back it up. Get a huge sampling of Turkic people. I’d enjoy researching the history and figuring out that puzzle.

So how come Jeanson is willing to make such an inference with no data cited to back himself up – i.e. a sample size of exactly zero?

Also, this Wikipedia table shows that the Bashkir in fact may have the highest R1b of the Turkic peoples (the rest having 20% or less):

Y-DNA haplogroups in populations of Central and North Asia

This may be because the Bashkir, with their densest population in Bashkortostan, in the South West of the Ural Mountains, may well have been the Turkic people to have had the closest contact with the descendants of the Yamnaya.

@thoughtful

I never said it was predominate.

Please don’t quote me out of context Valerie. What I said was:

@Tim

Your quote from Cinnioğlu et al does not demonstrate that R1b is predominant in Turkey, let alone that it is the ancestral Turkic lineage. The fact that Turkey contains such a wide range of different haplotypes. that “[t]he major components”, “haplogroups E3b, G, J, I, L, N, K2, and R1” make up “94.1%” in fact indicates that Turkey is a ‘melting pot’ of many groups.

@thoughtful

I doubt there was any one ancestral Turkic lineage - just noticed that it’s curiously higher in Turkey than elsewhere in the region.

There are four problems with this claim:

1. Your Cinnioğlu quote demonstrates nothing of the sort.

2. This claim is false. As this map demonstrates that R1b is higher in neighbouring Armenia.

3. Even if your claim were true, the fact that the Turkish population is a melting-pot containing considerable non-Turkic elements (Greeks, other Balkan peoples, Armenians, other Caucasian peoples, Arabs, Kurds, etc) means that there is no way to attribute Turkey’s R1b to Turkic ancestry. In fact the fact that Greater Armenia once covered much of modern day Turkey, and that R1b is higher in Armenia than elsewhere in the region, may mean that Armenian inheritance is responsible.

4. If you’re not arguing for there being a singular “ancestral Turkic lineage” responsible for the R1b gene, it’s not at all clear what relevance Turkey’s genetic makeup has to your argument.

[Chris_Falter]

@thoughtful

this is the second thread of 3 I’ve been interacting with on this topic recently

In this thread, the fact that the genomes of Neanderthals and Denisovans strongly contradict Jeanson’s model was raised.

You have not addressed this strong contradiction in this thread.

I have not read the other threads. Did you address the contradiction in the other threads? If so, please share a link so I can peruse your contribution. If not, I invite you to respond in this thread.

Thanks.

[thoughtful (Valerie (non-scientist))]

@Michelle

From your last sentence here, @thoughtful, I’m wondering if you do not understand how @Chris_Falter and @dsterncardinale are using the scientific term “error”. Perhaps this point needs some more discussion for you to understand why Jeanson’s method is so flawed

Yes, I do understand, but I can see why you might think that. The scientists are saying the error rate is such per base pair (for whatever reason) that they think it created the appearance of the differences between the father and son pairs even though they didn’t actually have any.

Edit: All I meant by my earlier comment “they didn’t have any reason to think so” was that there wasn’t any evidence of double-checking or curiousity to make sure. I don’t know how the error rate is calculated or how it results or if there’s any way to check (although Jeanson claimed to). But when an odd result is fairly abundant, I’m a little surprised that they just said (paraphrasing) “I think it’s the error rate.”

@Tim

How extensive/pervasive is the coverage of this “Family Tree DNA subclade project”?

Good question. Whoever wants to join. I haven’t looked at how extensively they are used, but when I was researching ancestry a couple of weeks back it seems anyone who is interested in investigating ancestry at all is encouraging others doing the same to join them. With billions of people on the globe, as far as I can tell, they collect much, much more data than scientific papers, though it’s not as easy to place on the tree since they are just looking at markers AFAIK. It looked like I had to pay for a membership so I didnt get into them - I have only looked a little bit at what people have shared publicly.

@Tim

@thoughtful

…or mutations are common enough that they drift out of the population but occur again at the same position.

This appears to be a word salad. Please choose your words more carefully.

Basically what I’m saying is - consider a scenario where a male lineage has mutations at certain loci, but that male line ends. Ancient DNA is collected from the lineage that ended. Later another man (or someone from his male line) has a mutation at the same locus.

If mutations are understood to be uncommon, the conclusion would be that the man is directly descended through that male line, like the blog writer described. But if mutations are common, it’s a chance occurrence and they’re not male-line related at all.

@Tim

I would also point out that slightly less than half Bashkir have R1b, meaning that, either way, about half of their Y-haplotype must have come from some other group(s) .

Yes, but that doesn’t matter, because of drift. I’ve been trying to explain the ratios of haplotypes among groups doesn’t help to make historical inferences about the common ancestry of those groups. I haven’t done so very clearly, so that’s my bad.

@Tim

Do you have any evidence of this “extreme drift of the y-chromosome”

That’s just the science of it. You can find out faster through a web search or YouTube video than I can explain it to you.

[Mercer (John Mercer)]

@thoughtful

(which seems very improbable after 5000 years because of the extreme drift of the y-chromosome)…or mutations are common enough that they drift out of the population but occur again at the same position.

It appears that you are using the term “drift” in a very different way than it is used by geneticists.

[Chris_Falter]

@thoughtful

All I meant by my earlier comment “they didn’t have any reason to think so” was that there wasn’t any evidence of double-checking or curiousity to make sure.

As best I can tell, scientists typically make sure they understand the measurement errors in their methodology before they publish any conclusions. If they did not, their findings could be challenged on the basis of their not having taken measurement error into account.

Thus I do not attribute the conclusions of the researchers to lack of rigor or intellectual laziness, as you do.

I encourage you to reflect on this question: What kind of thought process impelled you to leap to the defense of Jeanson, who is untrained in the lab techniques used in the paper, rather than to trust the scientists who published the paper?

[Tim]

@thoughtful

That’s just the science of it.

I’m sorry Valerie. but given how much time the actual biologists on these threads spend telling you that you’re wrong (and you’re making errors that are even obvious to a layman like me) and trying, blatantly unsuccessfully, to educate you on the science involved, you are the last person whose word I’d be willing to take that “[t]hat’s just the science of it” (even if I were predisposed to accept such unsubstantiated claims, which I’m not).

@thoughtful

You can find out faster through a web search or YouTube video than I can explain it to you.

No Valerie. That is not how science works – the person making the claim is the person expected to have evidence to support it.

As it stands, your “extreme drift of the y-chromosome” appears to be entirely mythical, and your argument based upon it therefore collapses. That is just the logic of it.

@thoughtful

Yes, but that doesn’t matter, because of drift.

Balderdash Valerie.

As @Mercer suggests, you clearly don’t understand Genetic Drift.

This “matter[s]”, because while Genetic Drift makes some things possible, it does not however make them equally possible.

Even with Genetic Drift, it is far more likely for a large and distinct component of a population genetic makeup to be attributable to intermixing with a significant population, than for it to be attributable to intermixing with a smaller population, inflated by Drift.

This is especially true for (particularly tribal) human populations, where a small minority is likely to be at a competitive disadvantage, as it is likely to be treated as an out-group, having lower social status and lower access to resources and to potential mates.

@thoughtful

Basically what I’m saying is - consider a scenario where a male lineage has mutations at certain loci, but that male line ends. Ancient DNA is collected from the lineage that ended. Later another man (or someone from his male line) has a mutation at the same locus.

What is the probability of this? Without a probability calculation, this is simply more ‘My uncle is the Pope’ balderdash.

@thoughtful

Good question. Whoever wants to join. I haven’t looked at how extensively they are used, but when I was researching ancestry a couple of weeks back it seems anyone who is interested in investigating ancestry at all is encouraging others doing the same to join them. With billions of people on the globe, as far as I can tell, they collect much, much more data than scientific papers, though it’s not as easy to place on the tree since they are just looking at markers AFAIK. It looked like I had to pay for a membership so I didnt get into them - I have only looked a little bit at what people have shared publicly.

Shorter Valerie, ‘I have no idea how comprehensive this database is’. And therefore you have no idea whether the lack of further genetic ‘hits’ in it has any meaning whatsoever. Hence my earlier point that this is a fallacious Argument from Silence.

But even beyond that, it is entirely unclear that, even if this ‘silence’ were meaningful, that it supports your argument. Even if Lentz were a descendant of the Bashkir, you have presented no evidence that this is due to Jeanson’s three Turkic tribes (who vanished ignominiously several centuries before, and hundred of miles to the South East). It is perfectly possible that his mother simply had an affair with a Russian refugee who turned out to be of Bashkir extraction (or a hundred and one other explanations).

I am getting very very tired of all these almost-completely-undeveloped ideas Valerie, and of the sources, genetic mechanisms and effects, etc, that you have cited but which have completely failed to give any support whatsoever to your ideas. They have, to be bluntly honest, been a waste of my time and an insult to my intelligence.

This ‘throw everything at the wall and see if anything sticks’ strategy may be “imaginative”, but it falls woefully short of being “thoughtful”. It does not recommend you as somebody to have a serious conversation with.

We have ended up at where we started, with absolutely no evidence that any of Jeanson’s four tribes (three Turkic plus Magyar) are responsible for the presence of R1b in Western Europe. This dearth of evidence is matched by that for any of Jeanson’s other claims about the spread of Y-haplotypes. This in turn renders his entire book nothing but a fantasy novel.

[thoughtful (Valerie (non-scientist))]

@Mercer

It appears that you are using the term “drift” in a very different way than it is used by geneticists.

Ok, the use of the word “extreme” perhaps? There I meant its strong effect due to the y-chromosome’s small population size. It would be helpful if you pointed out exactly how I’m using “drift” differently.

Also to be clear, in case it was a poorly written sentence - I didn’t mean that mutations drift out of the population because they are common. I meant that if mutations are common enough, it’s reasonable to think that a few shared mutations don’t necessarily indicate a shared lineage.

[Herman_Mays]

@thoughtful

The scientists are saying the error rate is such per base pair (for whatever reason) that they think it created the appearance of the differences between the father and son pairs even though they didn’t actually have any.

Let’s stop and ask ourselves about this for a moment.

Stop on this point and think.

Think carefully…

WHO EXACTLY IS SAYING THIS?

WHAT SCIENTISTS ARE WE TALKING ABOUT?

THE AUTHORS OF THE PAPER JEANSON CITE FOR HIS MUTATION RATE ARE THE ONES SAYING THE MAJORITY OF THE FATHER SON SNV DIFFERENCES ARE DUE TO EITHER SOME SEQUENCING OR ALIGNMENT ERROR.

Are you saying that Nathaniel Jeanson knows the methodology of a study he never conducted BETTER than the actual scientists who actually did the work and published the paper? How exactly do you explain that? Doesn’t that give you at least some pause to think about what Jeanson is doing here? Jeanson never even conducted a similar genomic study of any kind! How could he know the methods better than the authors themselves to contradict them entirely on such a relatively simple matter?

Now how do I know the authors view these differences as errors? I EMAILED THEM AND ASKED AND THEY REPLIED AND TOLD ME AS SUCH!

[thoughtful (Valerie (non-scientist))]

@Herman_Mays

Are you saying that Nathaniel Jeanson knows the methodology of a study he never conducted BETTER than the actual scientists who actually did the work and published the paper?

Methodology no, of course not.

I don’t disagree with you on any of that. It’s just surprising to me that there are so few studies that publish a de novo mutation rate, and that there then isn’t more rigorous checking if some kind, especially if there is disagreement about the substitution rate, which there is, from what I’ve seen.

Two years ago, I was repeatedly saying for weeks on various threads that there were only 4 papers Jeanson could cite, and no one believed that. Perhaps no one realized Jeanson would specifically care about the de novo rate instead of the substitution rate, but still, I would be hard pressed to imagine those here weren’t surprised that more hasn’t been published. And no one else has come up with another paper with published father-son differences and shared it in this forum to contradict there are only these handful.

And I’m to blame for wondering about scientists’ curiousity? With my prior beliefs, it matters to me a little bit to see more certainty about their results…

@Tim

Even with Genetic Drift, it is far more likely for a large and distinct component of a population genetic makeup to be attributable to intermixing with a significant population, than for it to be attributable to intermixing with a smaller population, inflated by Drift.

This is especially true for (particularly tribal) human populations, where a small minority is likely to be at a competitive disadvantage, as it is likely to be treated as an out-group, having lower social status and lower access to resources and to potential mates.

From what I’ve seen of the radiation of R1b from western Europe (I’d need to gather more evidence), I would like to argue the exact opposite. My hypothesis is that if a new line is even slightly more fertile (possibly because of introducing new variety, or a specific y-chromosome affecting fertility), then it will quickly have the advantage in the larger population it’s introduced into via positive selection and drift. Also, opposites attract.

@Tim

But even beyond that, it is entirely unclear that, even if this ‘silence’ were meaningful, that it supports your argument. Even if Lentz were a descendant of the Bashkir, you have presented no evidence that this is due to Jeanson’s three Turkic tribes (who vanished ignominiously several centuries before, and hundred of miles to the South East). It is perfectly possible that his mother simply had an affair with a Russian refugee who turned out to be of Bashkir extraction (or a hundred and one other explanations).

No, I meant the Lentz and the Bashkirs both have an older Turkic origin. 1st millennium A.D. I wish written records from that time were better. I hope to research it more.

[Tim]

@thoughtful

From what I’ve seen of the radiation of R1b from western Europe (I’d need to gather more evidence), I would like to argue the exact opposite.

As far as I can ascertain, Valerie, you have “seen” no such radiation.

Jeanson simply assumes, without any evidence, that one of his four tribes carried R1b to the northwest shores of the Black Sea. He then assumes, without providing any details whatsoever, that it somehow spread thereafter to Western Europe and the British Isles.

But as he has not shown how this could have happened, you therefore can’t have “seen” it.

What we have in fact seen is a mountain of evidence that R1b has been in Europe since the Stone Age.

@thoughtful

My hypothesis is that if a new line is even slightly more fertile (possibly because of introducing new variety, or a specific y-chromosome affecting fertility), then it will quickly have the advantage in the larger population it’s introduced into via positive selection and drift.

My hypothesis is that the Moon is made of green cheese.

I have as much evidence for my hypothesis as you have for yours (none at all). This means that I’ve got as much chance of getting my hypothesis taken seriously as you do.

@thoughtful

No, I meant the Lentz and the Bashkirs both have an older Turkic origin.

Except that you have no evidence of this “older Turkic origin” of R1b, and in fact what evidence that we do have tends contradict this. The Bashkir, who straddle the border between Europe and Asia in the Urals have far higher R1b levels than the Turkic groups of Central and North Asia (to their east). That is strongly suggestive that the Bashkirs picked up this gene as they migrated westwards.

To quote Christopher Hitchens:

That which can be asserted without evidence, can be dismissed without evidence.

Lacking supporting evidence, I am perfectly justified in dismissing Jeanson’s book, your hypothesis, and any further unsubstantiated hypotheses you may confect,^[1] out of hand.

Jeanson’s book provides no more evidence for existence of his radiation of R1b into Western Europe, than The Lord of the Rings provides evidence for the existence of Dwarves, Elves and Hobbits.

Addendum:

We are left with two facts:

1. R1b existed in Western Europe in the Stone Age.

2. R1b exists in Western Europe today.

Yes, it is possible (but only the barest possibility) that (i) the Stone Age R1b population died out – but we have no evidence of this, and (ii) that some other groups migrated into Western Europe bringing R1b back with them – but again we have no evidence of this.

By Occam’s Razor, the simplest, and so best, explanation is that R1b simply continued to exist in Western Europe (being diluted in some areas by migrations of Carthaginians, Greeks, Germans, Norse, etc, etc) throughout history. This, I think, will remain the best explanation until some actual evidence can be found that casts doubt on it.

---

1. So please don’t bother sharing them unless you can cite relevant evidence to back them up. ↩︎

[CrisprCAS9]

@thoughtful

I would be hard pressed to imagine those here weren’t surprised that more hasn’t been published

If that’s what Jeanson cares about, then why isn’t he doing the actual research? Take some of the money his organization has and actually doing the sequencing? You know, like an actual scientist?

@thoughtful

And I’m to blame for wondering about scientists’ curiousity?

Why aren’t you wondering about Jeanson’s lack of curiosity?

[Mercer (John Mercer)]

@thoughtful

@Mercer

It appears that you are using the term “drift” in a very different way than it is used by geneticists.

Ok, the use of the word “extreme” perhaps?

No, I mean “drift.”

@thoughtful

It would be helpful if you pointed out exactly how I’m using “drift” differently.

It would be even more helpful if you demonstrated that you understand the fundamental concept of drift!

[Herman_Mays]

@thoughtful

Methodology no, of course not.

I don’t disagree with you on any of that. It’s just surprising to me that there are so few studies that publish a de novo mutation rate, and that there then isn’t more rigorous checking if some kind, especially if there is disagreement about the substitution rate, which there is, from what I’ve seen.

OK so if Jeanson knows less about the methodology than the authors shouldn’t you take what they have to say seriously and conclude that in fact Jeanson can NOT derive a mutation rate from their data?

I was sent no less than ten citations to Y mutation rates in humans by one of the authors of Maretty et al and the difference between de novo mutation rate and a neutral substitution rate IS EXPECTED. It’s not some discrepancy that needs resolving rather it’s what we would expect to see based on evolution and population genetics.

Jeanson does not know what he is doing Valerie. At all. And he shows no willingness or ability to get any of it right. I really don’t know how that’s not clear to you by now?

[Herman_Mays]

@thoughtful

And I’m to blame for wondering about scientists’ curiousity? With my prior beliefs, it matters to me a little bit to see more certainty about their results…

You are desperately probing around trying to find any way you can to salvage Jeanson’s conclusions for really no other reason than those conclusions agree with your prior beliefs.

Scientists in these fields are quite certain Jeanson is wrong. There aren’t lingering questions as to whether or not humanity is only a few thousand years old. There’s not disagreement in regard to how Jeanson reads a tree or interprets mutation rates. He’s wildly, demonstrably wrong about virtually all of it.

Your beliefs, or Jeanson’s beliefs, simply do not matter when it comes to the science.

[Herman_Mays]

@thoughtful

My hypothesis is that if a new line is even slightly more fertile (possibly because of introducing new variety, or a specific y-chromosome affecting fertility), then it will quickly have the advantage in the larger population it’s introduced into via positive selection and drift.

Positive selection and drift are two different things. Molecular clocks rely solely on NEUTRAL variation (variation without a selective advantage). If selection is going on that changes expectations pretty dramatically. So if we go by your hypothesis then we could not apply a molecular clock to these data.

[Mercer (John Mercer)]

@CrisprCAS9

@thoughtful

I would be hard pressed to imagine those here weren’t surprised that more hasn’t been published

If that’s what Jeanson cares about, then why isn’t he doing the actual research? Take some of the money his organization has and actually doing the sequencing? You know, like an actual scientist?

I would be interested in how you rationalize Jeanson’s inaction here, given its alleged importance to both of you, Valerie.

[swamidass (S. Joshua Swamidass)]

@Herman_Mays

I was sent no less than ten citations to Y mutation rates in humans by one of the authors of Maretty et al and the difference between de novo mutation rate and a neutral substitution rate IS EXPECTED.

Do you mind reproducing that list of references please?

[thoughtful (Valerie (non-scientist))]

@CrisprCAS9

Why aren’t you wondering about Jeanson’s lack of curiosity?

I have. I feel like I’ve said something like this more than once when replying to @mercer, but I could only find this instance quickly.

One of his audiences is mainstream biologists and he’s just needs more lab data to back him up; any argument about new theory just isn’t going to be accepted without it. Yes, it is frustrating that AIG doesn’t make lab work a priority.

Replacing Darwin Made Simple

Why not, other than the obvous tribal reasons? Well for one thing I don’t see the argument comparing the phenotypic development of a frog to the phenotypic diversity of cats as a bad argument. But it only makes sense from a creationist perspective. Because if the genome controls for phenotype then that means it can contain the diversity in both cases if it is originally created. I also think what he is trying to do to advance his ideas is very difficult, in terms of writing. As I see it, he has three audiences to appeal to with new ideas, well, now 4: One of his audiences is mainstream biologists and he’s just needs more lab data to back him up; any argument about new theory just isn’t going to be accepted without it. Yes, it is frustrating that AIG doesn’t make lab work a priority. Another audience is mostly lay creationists, the vast majority who have no idea what the state of mainstream science is and need complicated concepts explained in a digestible way- not easy. A third au…

@Herman_Mays

Positive selection and drift are two different things. Molecular clocks rely solely on NEUTRAL variation (variation without a selective advantage). If selection is going on that changes expectations pretty dramatically. So if we go by your hypothesis then we could not apply a molecular clock to these data.

Ok, good point.

@Herman_Mays

You are desperately probing around trying to find any way you can to salvage Jeanson’s conclusions for really no other reason than those conclusions agree with your prior beliefs.

Well, because of my prior beliefs I’m curious how well his conclusions hold up scientifically. And I keep pressing to see how much is due to bias or differing interpretations of the data. And asking questions and engaging in conversation has been worthwhile; it challenges me and then I learn something new.

[Herman_Mays]

An email to me from Laurits Skov regarding Jeanson’s misuse of the Maretty et al 2017 paper.

[Herman_Mays]

@thoughtful

Well, because of my prior beliefs I’m curious how well his conclusions hold up scientifically. And I keep pressing to see how much is due to bias or differing interpretations of the data. And asking questions and engaging in conversation has been worthwhile; it challenges me and then I learn something new.

Maybe you should forget about your prior beliefs for once, at least in this context as they really don’t matter.