Last weekend we went on a tour to Pres’quile Provincial Park here in Ontario to see the duck migration. The park is about half way between Toronto and Ottawa and our guide could easily tell which birders were from which city. The Ottawa contingent was flipping out over the hundreds of long-tailed ducks sitting on the water, whereas here in Toronto we can practically pet them at will, they are so common.
Anyway, my wife referred to them as “little sweeties” and our guide readily agreed with this appellation. Not sure whether “little sweetie” falls into the category of handsome or cute, or is a separate category onto itself.
Surveying various studies, I see Y chromosome SNP mutation rates given in the general range from about 0.5 to 1.0 x 10^-9 per bp per year, more frequently in a tighter range of 0.7 to 0.8 x 10^-9 per bp per year. Jeanson argues for higher, but looking at his molecular clock paper, I did not see an actual number. Does anyone have a reference for the plug and chug Jeanson rate?
I understand that mutations in extinct lineages will be lost. What I don’t understand is why the mutation rate wouldn’t be the substitution rate of there were actually an average of 3 mutations per generation. I’ve been pondering how it couldn’t be the same if the population has continued to grow. I’m coming up with a blank, and I really do want to know if I’m just missing it.
Oh it gets better. I’m sure you’ll find a lot to disagree with.
You’ll get to it later in the book several times, but so far no one responded to what I thought was the most important part of the book - what I quoted earlier from the book about the tree showing minimum population size. It was discussed in the forum before, but not understood. In an interview, Jeanson alluded to that idea, explaining that was what convinced him this was working.
Isn’t that a big problem for the book? He contradicts mainstream science while ignoring most of the contradictions. If I advance a theory that the moon is made of cheese, and I present as my evidence that it’s exactly the same color as Swiss cheese, and it has visible holes in it, am I free to ignore all the other data, for example the samples of moon rocks brought back by the Apollo missions? Jeanson is in exactly the same position except that he dresses up his cheese in more sciencey language, and you are predisposed to believe him.
I’m not explaining this again. You don’t want to get it and so aren’t going to get it.
The entire timeline he constructs is built on this mutation rate error. Everything about his findings flows from that, and it’s all wrong. The entire book is undercut, the entire thing, by the errors in about a three page span in chapter 6.
But @dsterncardinale is pointing out something that it seems clear that you don’t understand. That mutations in existing lineages will be lost. It’s basic population genetics.
Here’s my response: you haven’t pointed to a speck of evidence supporting Jeanson’s idea.
Why are you labeling what should be (scientifically) a hypothesis as a mere “idea”?
Sigh. Yes, I don’t get it. I’m not sure why @dsterncardinale thinks I don’t want to get it when I’m specifically asking. I understand there could be back mutations. I understand how alleles could be lost in autosomal DNA. I understand how mutations could be lost if there’s less than 1 mutation per generation in mtDNA or the y chromosome. I don’t understand how they can be lost if there’s multiple mutations per generation in uniparentally inherited DNA. If every male passes on 3 mutations approximately, someone is going to have a male child if the population is growing, so I don’t understand how the mutation rate and substitution rate would be different over time.
I DO want to understand it. I think population genetics is interesting but I know it’s not intuitive, so I do know the likeliest outcome is that I’m drawing a blank because I’m not understanding correctly and I would like to get it. Hopefully my explanation is helpful to see where my misunderstanding lies.
You’re right; I haven’t. I just was curious if anyone disagreed outright with the hypothesis on the face of it. But I couldn’t tell since no one responded.
Yes, it is a hypothesis. And I very much doubt the book would be written without it. The Y-chromosome mutation rate is important, but Jeanson puts forward evidence that that hypothesis about the tree and minimum population size is working in several places in the book.
There are lots of haplogroup that have their origin in Central Asia. And Jeanson has Turks as J2 and G, which you can see from your map. The general theme in the book seems to be that the highest haplogroup levels in any given area are the most recent migrants, and that some migrations generally happen as a slow outward spread, but otherwise there are specific historical events that move a group in or push it out. In the case of R1b into western Europe, obviously the suggestion is that it migrated quickly from eastern Europe and spread out quickly, based on the distribution of various recent subgroups of R1b.
Reset Y-chromosome chronology by dating nodes in y-chrom phylogeny based on incorrect rate.
Eyeball real-life historical events that could correlate with revised node dates and say “could be that <event> (e.g. mongol invasion of europe) is apparent in <node> (e.g. divergence of central asian haplotypes into european lineages)”.
Conflate phylogeny and genealogy in order to overlay revised, incorrectly-dated y-chromosome tree onto Genesis-derived pedigree starting with Noah.
Do (3) but for Genesis stories rather than historical events.
Claim you rewrote the history of humanity and confirmed Genesis.
When a male dies without having any male children, what happens to the 3 new mutations they experienced? What about any unique mutations from their father? Grandfather? Great-grandfather?
They’re gone. Their lineage could very well persist, if they have daughters, but the diversity unique to their Y-chromosomes will vanish. This is just something that happens by chance each generation - some fraction of the variations in the Y-chromosome are lost.
So you have opposing forces - mutations generating new variants, and drift (and selection) removing them. Over many generations, these opposing forces reach equilibrium. That is the long-term substitution rate, the rate at which new mutations accumulate in the Y-chromosome. It’s a slower rate than the one-generation mutation rate, because the mutation rate only considers one side of the equation - new mutations - but hasn’t yet been affected by the other - drift and selection.
Jeanson uses the one-generation rate and projects backwards, acting as though drift and selection never operate. He’s been doing it since at least 2015 with his mitochondrial DNA TMRCA calculations. And it invalidates basically all of his work.
There’s your problem. Not every male passes on his Y chromosome. That only happens if he has sons. All the mutations that happen in males who have no sons are lost. Further, given most reasonable assumptions, every strictly male lineage except one will eventually be eliminated because all it’s various branchings will end in daughters (or extinction, which is the same thing as far as Y chromosomes are concerned). This is true whether the population is expanding, contracting, or stable.
Then again, barring selection, that one remaining lineage will have experienced a number of substitutions per generation equal to the mutation rate per generation unless selection has been operating. And if there’s no selection, population size is irrelevant.
I will note that this is in response to a post I made 6 days ago. The conversation has moved along quite a bit since.
Yes, and there is evidence that R1b arrived in Europe during the stone age, long before Jeanson’s time-frame.
So if it wasn’t the Turks, was it the Huns or the Mongols, or some other lesser migration, and what is Jeanson’s evidence that they had R1b?
That is a ludicrously simplistic claim. It fails to account for the fact that (i) relative sizes of the migrant and pre-existing populations would affect the balance, and (ii) that if the migrants had gone through multiple migrations, they would likely already be a genetic mix.
It also does not account for the fact that R1b is highest in the areas of Western Europe that saw the least migrations during the last two millennia – Ireland (particularly the West-- the Vikings had a colony around Dublin in the East), Wales, the Scottish Highlands, the Basque country, Brittany, etc.
I.e. Jeanson’s “general theme” does not fit the evidence.
… where there is no evidence that it was predominant.
Where the evidence suggests it has existed since the Stone Age.
The more I learn of Jeanson’s claims the more the following analogy comes to mind. That of a demented amateur taxidermist, who is attempting to stretch a zebra’s hide over the skeleton of a rhino. It simply doesn’t fit!
I’ve been scratching around on the genetics of some pre-Roman Empire populations, and then looking for what Jeanson had to say about them. In doing so, I came across this little ‘gem’:
I would note that the Etruscans,[1] Celts[2] and Basques[3] are all pre-Roman Western European ethnic groups, known to have the R1b haplogroup.
Making claims about the migration of R1b to Western Europe without tracing these groups, is ludicrously blatant negligence. I must assume that Jeanson omitted them because he knew that their inclusion would blow his thesis out of the water.
I think this puts the last nail in the coffin of Jeanson’s “supposed” understanding of human genetic history, and his “supposed” claims to being a real scientist.
By contrast, the newly reported central Italian individuals from 800 to 1 BCE show ~75% frequency of the Y-chromosome haplogroup R1b, mostly represented by the R1b-P312 polymorphism and its derived R1b-L2, that diffused across Europe alongside steppe-related ancestry in association with the Bell Beaker complex (16). This suggests that this R1b Y-chromosome lineage spread into the Italian peninsula with steppe-related movements during the Bronze Age. In the first millennium CE, its frequency is reduced to ~40% with higher occurrence of Near Eastern–associated Y-chromosome lineages such as J (fig. S5B).
This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.
The majority (about 86%) of the Basque Y chromosomes belong to haplogroup R1*(xR1a,R1b3f)-M173, of which R1b3*-M269 accounts for 88% (Figure 1). As this haplogroup is also the most abundant type in all Western Europe16 it places the Basque Y chromosomes within the European landscape. The above data are reflected in the low diversity values for the Basque populations (Table 1). Within R1b3*-M269, Basques also show a reduced STR diversity (Table 1). Thus, compared for instance to the non-Basque Iberians, the average number of mutations in our sampled Basques is significantly lower (Mann–Whitney U-test, P=0.009).
Thanks for the explanation. I really do want to know. I got that part.
Yeah, I wasn’t sure about his specific mtDNA paper after watching your videos, but I didn’t think that was such a big deal for the hypothesis about mtDNA being young in general, since in your debate with SFT, he was mentioning that the mutation rate for the more sequenced part of mtDNA left time for drift. Hopefully I’m summarizing correctly.
Thank you. This is what makes discussing population genetics more fun. I got that mutations will be lost, but since the tree that we’re looking at is survivors, if there were multiple mutations per generation, why can’t we just count backwards, (barring possibly the tips of the branches maybe really skewing the average over time because of a lot of drift)? Meaning the ancient branches should show a stable mutation rate though…?
My question above is also related to this comment.
But I had read the section in Wikipedia and y chromosome again and it was explaining why selection probably doesn’t operate. But I don’t understand what you mean by “if there’s no selection, population size is irrelevant”?
Most basic result of neutral theory: the number of fixations in the population per unit time is equal to the number of mutations in the average individual per unit time. This is because Nµ mutations happen in the population each generation (or whatever period of time you’re measuring µ in), while the probability of fixation for each mutation is 1/N. (Here I’m talking about the Y chromosome, and N just means the number of males in the popuation). Since the number of fixations is Nµ * 1/N, the N cancels out. Population size doesn’t matter.
I talk about Traced for a good 30 minutes at the beginning of my recent episode of This Week in Creationism. I hadn’t intended to say so much at this time but couldn’t stop talking about it. With regards to the science, @dsterncardinale pretty much says all that needs to be said about the book. The book is disappointing to me personally in the sense that there is nothing new in it for those that have watched all of Jeansons videos and read his papers over the past 5 years. Also, the book doesn’t include enough science for any scientists to know what he has done because he is trying to write much more simply than he did in “Replacing Darwin.” In fact he doesn’t include many things I had thought he would try to provide (and very much needs to!) a fuller explanation for (e.g. Neanderthal and other members of the hominin “kind” are missing from the book and his radiometric dating chronology converter system he promoted in early videos is not there)
I can’t add much to what Dan has said because the underlying the basis of Jeanson’s ancestry analysis is already been laid bare well before this book came out and Jeanson does nothing to respond to those flaws but rather seems to just double down on them.
I am more interested in how the book will be marketed and how it will be used (or not used) and accepted by other creationists. As I say in the video, so far this is a stand-alone product of one person (though very much leans on the work of Robert Carter at CMI who receives for to little credit for his apparent influence, as I point out Carters paper in 2018 draws many of the same conclusions as Jeanson so the hyped novelty of Jeanson’s work does not ring true to me) and Ken Ham cannot expect this product which he has paid for to be taken seriously by other scholars until Ham can convince other YEC biologists outside of AiG to strongly endorse this analysis. The only reason I or others will critique this book at all is because so many lay-Christians will pick it up and think that it provides a trustworthy response to the conventional scientific consensus.
I will also say, I feel a bit bad for Jeanson, he has a real passion for this and has done a huge amount of work to write this book. But there is such a dearth of expertise in the multiple disciplines that he touches upon within the YEC community that he is drowning in a sea of information that I wouldn’t’ expect any one person to be able to become an expert on. He needed multiple co-authors which don’t exist and the insular nature of YEC ministries doesn’t provide a mechanism to enable. He is out there on his own. Yes, he had some reviewers but his entire thesis is built on populations genetics/phylogeny reconstruction/molecular evolution and for that he lacks internal checks and balances. He doesn’t want to take advice from non YECs but he doesn’t have any YECs that can really understand what he has done and give him any constructive advice except may be Robert Carter who seems to have helped him quite a bit but I’m not sure has the ability to do this sort of analysis himself.
It’s been pointed out before that Jeanson seems not to understand the simplest things about phylogenetics: how to read a tree, how to root a tree, whether there’s such a thing as a “main line”, and so on. And as far as I can see he’s never done any analyses on his own, just relying on trees published in the mainstream literature.
I’m sure you’ll find a lot to disagree with.
I got that mutations will be lost, but since the tree that we’re looking at is survivors, if there were multiple mutations per generation, why can’t we just count backwards, (barring possibly the tips of the branches maybe really skewing the average over time because of a lot of drift)? Meaning the ancient branches should show a stable mutation rate though…?