Jeanson is now finding a reason to ignore neanderthal DNA

[dsterncardinale]

@thoughtful

You are accurate but not as much as you think.

I would love to hear specifically what I am missing.

[misterme987 (Andrew P.)]

@thoughtful

I didn’t agree with Jeanson’s ideas about the recent history of R1b in Europe. Instead, I think it is French (who immigrated from Central Asia much earlier)… Over almost few centuries, but especially in the 1600s they fled to Basque country, northern Italy, the Netherlands, England, Ireland, the Americas, Australia, South Africa, etc… The R1b split seems to be somewhere in the line of Henry IV (because of a few papers confirming that).

I’m curious, how do you square this hypothesis with the fact that an individual with the R1b haplogroup has been found from late Neolithic Italy (Fu et al. 2016)? On the Masoretic-YEC timeline, that should be approximately 2100 BC at the latest, which is far earlier than Henry IV.

[Herman_Mays]

If you construct a gene tree from genes sampled from a stable population you still get a branching tree. That’s the most basic and frankly hilarious misunderstanding on Jeanson’s part. Given that fact you can not make the assumptions about growth from just counting branches on any single gene tree. You can’t do that therefore lining up the accumulation of gene tree branches against a population size curve is completely meaningless.

That’s it. That’s absolutely everything you need to know to debunk absolutely everything he’s trying to do here. The only reason anyone would jump through hoops to salvage what Jeanson is doing is because they desperately want him to be right because what he is saying affirms their religious beliefs

[thoughtful (Valerie (non-scientist))]

I can’t read the paper. You missed previous conversations - my hypothesis for the more ancient individuals is that it’s practically impossible to place them on a phylogeny. Too many of the same mutations with a fast mutation rate, and probably 1/3 to 1/4 of mutations are back mutations. All of that plus extreme drift means that lineage was likely lost and shares mutations with R1b.

@dsterncardinale

I would love to hear specifically what I am missing.

I guess I’ll state what I stated before with more clarity. I think it is misleading and inaccurate to leave out the context of your rebuttals. As far as I’ve watched your shows, you have not cited a paper that connects the y-chromosomes of modern individuals to a historical migration data point, oral history or genealogy. But yet those that aren’t really informed on the subject would get the impression that you do because you bring up mtDNA info like the Canary Islands (as one example). But yet, Jeanson’s phylogeny and timeline has confirmed half a dozen or so oral histories - he recently brought up Incan oral history on a podcast IIRC.

I’m waiting for you to use Balanovsky. Unless you think something’s wrong with that paper…

[John_Harshman]

I notice you didn’t respond to this, so I’m trying it again.

@John_Harshman

Think about what you’re saying here. A 4500 year old human population puts the origin at 2500 BC. This is younger than many cities and civilizations, younger than the pyramids, much, much younger than human remains and sites all over the world, including the Americas. Jeanson ignores almost all the data because he doesn’t like it. You appear to be OK with that and are willing to do the same. Are you actually willing to go full YEC?

Surely you aren’t ignoring the data, are you?

[Tim]

@thoughtful

At least if a hypothesis I barely hinted at is correct… I hinted a little in my conversations with @Tim that after some research I didn’t agree with Jeanson’s ideas about the recent history of R1b in Europe. Instead, I think it is French (who immigrated from Central Asia much earlier.)

Emphatically no Valerie!

This is errant nonsense.

The “French” did not ‘immigrate’ from anywhere.

What we now (heavy emphasis on that word) know as the French, are the end result of a complex process of population admixture and assimulation:

Western Hunter-Gatherers (15 kya), Neolithic farmers (7 kya), and later Steppe Eneolithic Age populations [2, 3], Celtic expansion, integration in the Roman empire, Barbarian migrations [Franks, Visigoths, and Burgunds], whose demographical importance remains to be assessed. France’s position at the western part of Europe has made it not only the final goal of a large number of, potentially massive, migrations but also a place of transit either to the North (British Isles) or to the South of Europe (Iberian Peninsula) and North Africa, as well as an important crossroad for trade and exchanges [4].

https://www.nature.com/articles/s41431-020-0584-1

Not only are the French not of homogeneous genetic origins, they remain genetically heterogeneous, due to natural barriers to gene flow (see above article). The most significant of which is (same article):

An important division separates Northern from Southern France. It may coincide with the von Wartburg line, which divides France into “Langue d’Oïl” part (influenced by Germanic speaking) and “Langue d’Oc” part (closer to Roman speaking)—Fig S20. This border has changed through centuries and our north-south limit is close to the limit as it was estimated in the IXth century [47, 48]. This border also follows the Loire River, which has long been a political and cultural border between kingdoms/counties in the north and in the south (Fig. 1).

So Valerie, my question is specifically which of the myriad constituent populations, that make up what we now know as the French, are you claiming “immigrated from Central Asia much earlier”, and seeded all of Western Europe (in spite of barriers to gene flow) with the R1b gene?

@thoughtful

Mainstream science thinks the western European origin is Spain and radiates from Spain probably because it’s high in the Basque country.

Citation please!

This claim likewise seems nonsensical. I have nowhere seen an ‘out of Spain’ explanation for the R1b in the scientific literature, and it would seem to be in complete contradiction to known history – which does not have Spain as an origin point for any population migration of any significance.

@thoughtful

But I think it’s radiates from southern France because of French Huguenot persecution.

This is likewise nonsensical. The Huguenot exodus was too recent, too small (“around 200,000”) and too marginalised (due to being a small and generally impoverished minority in the lands they fled to), to be responsible for R1b’s prevalence in Western Europe.

I would also question your claim that they migrated into northern Italy, as I have seen no documentation of this, and it seems highly unlikely, given Italy at the time was staunchly Catholic.

Do you have any solid evidence to back up this confected fantasy?

@thoughtful

The R1b split seems to be somewhere in the line of Henry IV (because of a few papers confirming that).

Citations please.

@thoughtful

The idea seems plausible anyway.

Not even remotely plausible.

[Mercer (John Mercer)]

@thoughtful

My opinion is that he sees those curves working, and he likes them.

And the pseudoscientist stops there!

@thoughtful

But he doesn’t have enough evidence yet to show that’s the case. He either needs a simulation or much more evidence that fits predictions.

A simulation won’t cut it.

[Rumraket (Mikkel R.)]

@colewd

I got it but based on this I would suspect higher similarity to H.S. Y chromosome if they indeed share a common ancestor

Why? Explain why!

[dsterncardinale]

Level of divergence from H. Sapiens depends on TMRCA. The question isn’t if there’s a common ancestor. Everyone agrees there is. The question is when.

I’ve referenced a number of papers on this over the years, I’ll dig them up later. I’m writing this on my phone so I don’t have access at the moment.

[misterme987 (Andrew P.)]

@thoughtful

I can’t read the paper.

My apologies. Here is what it says:

We were surprised to find haplogroup R1b in the ~14,000-year-old Villabruna individual from Italy. While the predominance of R1b in western Europe today owes its origin to Bronze Age migrations from the eastern European steppe, its presence in Villabruna and in a ~7,000-year-old farmer from Iberia documents a deeper history of this haplotype in more western parts of Europe.

On the YEC timeline, ~14000 years old translates to ~2200 BC and ~7000 years old translates to ~2100 BC.

@thoughtful

You missed previous conversations - my hypothesis for the more ancient individuals is that it’s practically impossible to place them on a phylogeny. Too many of the same mutations with a fast mutation rate, and probably 1/3 to 1/4 of mutations are back mutations. All of that plus extreme drift means that lineage was likely lost and shares mutations with R1b.

Okay. I’m not sure that’s right, but you’ll have to take that up with the actual geneticists here, I’m not nearly as knowledgeable as them.

[dsterncardinale]

@colewd

I got it but based on this I would suspect higher similarity to H.S. Y chromosome if they indeed share a common ancestor. Can you point me in the direction of papers pointing to sequence similarity? Are they Y chromosome sequences?

Okay, as promised, here’s one I’ve referenced in my videos on this topic that includes mtDNA, Y-chromosomes, and autosomal nuclear DNA: https://scholarlypublications.universiteitleiden.nl/access/item%3A2953429/view

You note that the Neanderthal sequences exhibit 1) high divergence from H. sapiens, and 2) form a nice neat clade themselves.

[evograd (Blogging Graduate Student)]

@thoughtful

I’m curious if @evograd has any relevant data from the programming he was doing for exponential growth scenarios. I was looking forward to that. If you have the time to indulge us (I mean, me) haha.

Unfortunately not. I got lost in grinding towards a way to draw phylogenetic trees according to different simulated parameters from scratch. It ended up taking too much of my time so I gave up on it and haven’t looked at any of the code for weeks now.

[Rumraket (Mikkel R.)]

@thoughtful

Too many of the same mutations with a fast mutation rate, and probably 1/3 to 1/4 of mutations are back mutations.

Wait, what? I’m going to need elaboration on this. Are you saying there are different individuals that have some extreme degree of homoplasy, and between a 3rd and 4th of mutations that occur are reversals? Please explain.

[Rumraket (Mikkel R.)]

@Herman_Mays

The only reason anyone would jump through hoops to salvage what Jeanson is doing is because they desperately want him to be right because what he is saying affirms their religious beliefs

Or that they just don’t get it and need it spoon-fed to them in tiny bites one at a time, which I’m sad to say I think is a really big problem with a couple of the ID/creationists who post here.

[Herman_Mays]

@thoughtful

As far as I’ve watched your shows, you have not cited a paper that connects the y-chromosomes of modern individuals to a historical migration data point, oral history or genealogy. But yet those that aren’t really informed on the subject would get the impression that you do because you bring up mtDNA info like the Canary Islands (as one example). But yet, Jeanson’s phylogeny and timeline has confirmed half a dozen or so oral histories - he recently brought up Incan oral history on a podcast IIRC.

There’s no supporting evidence for Jeanson’s conclusions. Period.

Read David Reich’s book on genetics and human population history. Reich was at Harvard when Jeanson was there yet I see no evidence at all that he has read his work or ever bothered to talk to him. If he were really interested in human population history he would have walked over to Reich’s lab while he was at Harvard and learned how to do all this. He didn’t because he’s not really interested in any of this as science. He’s only interested in rationalizing to others and himself of what he’s already decided he believes. That’s not science.

Read Jennifer Raff’s new book on the peopling of the Americas. Raff draws upon all sorts of data from archeology to linguistics to genetics. Jeanson ignores all that. Jeanson only cherry picks the stories and the data that serve his agenda.

Jeanson’s timeline says the entirety of humanity appeared out of nothing a mere few thousand years ago. That claim is contradicted by pretty much every line of evidence we have.

You Valerie are like any of Jeanson’s followers. You are primed to believe him because it’s something you want to hear. Jeanson himself is highly motivated, and contractually obligated, to tell a certain narrative and he’s simply not going to consider any evidence contrary to that narrative.

Wake up! You’re better than this. Jeanson is like all of these creationists peddling pseudoscience. I know it’s hard to do but stop falling for it.

[Herman_Mays]

@thoughtful

My opinion is that he sees those curves working, and he likes them.

Why does he like them?

[Mercer (John Mercer)]

@colewd

It’s false he ignores the data because he does not like it he is building his models independently.

We call that scientific misconduct in the biz.

[thoughtful (Valerie (non-scientist))]

@Tim

So Valerie, my question is specifically which of the myriad constituent populations, that make up what we now know as the French, are you claiming “immigrated from Central Asia much earlier”, and seeded all of Western Europe (in spite of barriers to gene flow) with the R1b gene?

Yikes. I meant R1b M-269. Sorry. I’ll find a paper for you on the distribution from Spain. Just wanted to reply quickly to clear that up.

@Tim

The Huguenot exodus was too recent, too small (“around 200,000”) and too marginalised (due to being a small and generally impoverished minority in the lands they fled to), to be responsible for R1b’s prevalence in Western Europe.

Read more of the history. That isn’t true. It was likely half a million just at the end of the migration. Editing Huguenots - Wikipedia

[Herman_Mays]

@Rumraket

Or that they just don’t get it and need it spoon-fed to them in tiny bites one at a time, which I’m sad to say I think is a really big problem with a couple of the ID/creationists who post here.

They don’t want to get it. It is extraordinarily difficult to teach someone something they don’t want to learn.

[Herman_Mays]

@thoughtful

I’m curious if @evograd has any relevant data from the programming he was doing for exponential growth scenarios. I was looking forward to that. If you have the time to indulge us (I mean, me) h

This all has been done. Consult virtually any textbook on coalescent methods and you’ll see all kinds of citations to simulations of gene coalescence under various population scenarios (growth, stability, bottlenecks). Programs like simcoal and fastsimcoal have been doing this for over a decade.