Dr. Joshua Swamidass and TMR4A: Some Major Modeling Problems for Young Earth Creationism

Did all those papers which have been linked demonstrating Y-chromosome and mtDNA data in keeping with evolutionary timelines - just disappear? vamoosh? :hole: :open_mouth:

If the evidence does not support Carter, Jeanson, and Sanford’s conclusions, - and I think that in fact the evidence is solidly in favor of the mainstream - , then their conclusions cannot be used to buttress other inferences.

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It is tiresome to see you repeat this falsehood when it’s been explained to you multiple times how and why that statement is wrong. We recently had an extended exchange where I tried to get you to understand that there is and must be a time-dependent rate of mutation.
You mysteriously stopped responding in that thread (shouldn’t you be finishing Sanford’s book and then some other stuff before you argue about this?).

Now you’re suddenly back here arguing as if demonstrable history did not in fact occur. Of course, that seems to be the entire basis for your creationism in the first place.

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I guess so. Please show me where they have been linked.

I checked back when I came here and literally knew not a thing about genetics and asked about Jeanson’s y-chromosome work back in July.

Now I see @evograd gave me this mess with a rate that probably wasn’t pulled directly from a y-chromosome study. No one has shown me that there are more than 4 y-chromosome studies - maybe he can show me where the rate is in one of those studies.
Testing Jeanson's Model: Y Chromosome Mutation Rates - #32 by evograd

And then @swamidass basically rebuts him and says, we calculate the rate based on the evolutionary time scale

I finally realize that @swamidass is concentrating on the genome and ask him why. Testing Jeanson's Model: Y Chromosome Mutation Rates - #25 by thoughtful

I finally realize maybe no one here is getting why anyone would focus on the y-chromosome. Valerie: Questions about TMR4A - #39 by thoughtful

And then recently @Rumraket asked about this, and I said Jeanson tested both the evolutionary time scale and a creationist time scale. Valerie: Questions about TMR4A - #225 by thoughtful

And he never replied to rebut it.

So what am I left with? All I can tell is that @GutsickGibbon has given me the best argument so far on why Jeanson and Carter are wrong, and that it’s this:

See below. I did respond.

Why haven’t you, as someone who claims to be excited about uncovering evidence, found them?

But you didn’t look at the evidence. All hearsay.

So you’re not at all excited about uncovering new evidence and you’re not at all focused on the Y-chromosome. You claim that others are obligated to spoon-feed it to you, then you’ll ignore it anyway.

I believe that Jeanson tells you for two of them: Helgason et al. 2015 and Xue et al. 2009.

Here’s another one:

If one is truly excited about the evidence, there’s a lot to examine.

There’s no need to evaluate an argument. You should be evaluating the evidence that Jeanson presents in the context of all of the available evidence.

That’s what someone truly focusing on the Y and excited about evidence would do.

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I’m sorry you thought this comment of mine was a “mess”. What was unclear?

I explained that both pedigree and “evolutionary” studies of Y-chromosome mutation rates are consistent with long timescale and inconsistent with YECism. Those pedigree studies are among the ones Jeanson cites.

The issue is that Jeanson has decided, with no background in this field, that those pedigree studies missed a lot of mutations, and got data from two other studies in which he (not the authors) claims to have found those many extra mutations, using his own method of extracting mutations from the sequence data. That’s the suspect part.

The fact that he chose to publish these claim about radical new results in his employer’s vanity “journal” rather than a proper scientific journal is a red flag. If he’s correct and he’s managed to find the “true” mutation rate, then that would be certainly be a result of great interest to the broader scientific community, and I’m sure he’d be able to publish the results in a good scientific journal. That would certainly be worth more than publishing in AIG’s “journal” It would be a great coup for AIG, to have one of their scientists publish in a real scientific journal about some secular results that have implications for human origins.

Either he tried and didn’t pass peer-review, or he didn’t bother, likely because he has little confidence in his claims. I don’t see any other reason that he would not want to publish in a secular journal.

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No, you aren’t. You’re focusing only on what creationists say about them. You’re ignoring all of the evidence.

You don’t care about any evidence, you only care about hearsay. Yet you relentlessly pretend to be using evidence. Why?

If you are focusing, demanding that others show you is not reasonable.

That is literally false. Anyone with any curiosity about the evidence can falsify it in seconds.

That is consistent with your complete lack of interest in the evidence.

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If this thread is going to descend into Valerie bashing, I will close the comments. We can and should do better.

@thoughtful - I am acting to keep you from being ganged up on, but not all the criticisms have been unwarranted. Please be more … thoughtful … I know you can do it! :slight_smile:

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So he explains the method in the paper, and gives you examples of how you could criticize it. I guess we can have different views of what “suspect” means.

I’m sure he has so little confidence in his claims that he spent 25 hours explaining history to the general public that’s available on YouTube to watch, and then also wrote 2 more papers that followed that one.

Also Carter and Tompkins agree that the y-chromosome is young, so what do you think of that?

So then do you need to explain to @GutsickGibbon that Jeanson is wrong because his methods are suspect since he did not publish in a secular journal, and not that he has “bad sampling” and “incredible error bars”?

There were twelve links total in this post:

I have bookmarked over 20 Y chromosome papers, and I do not even have access to an academic account. When a paper comes up on NCBI website, it lists similar papers and citations, and if you follow these you will be up to dozens of Y chromosome studies minimum.

You seem to under an impression that Jeanson et al are blazing an investigative trail, the significance of which has been overlooked by mainstream science. This is not the case at all, Y chromosome and mtDNA has been studied by hundreds, probably thousands, of scientists.

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Yeah you responded by saying you don’t understand the subject and you’re “a baby scientist”, which you clearly don’t since you refer to the graphics in that crap AIG article and saying you’re “assuming are testing time-dependent rate”. But they are not anywhere. The subject of deleterious mutations being removed by natural selection, resulting in a lower long-term rate of mutation is not discussed at all in that AIG article. Nor is it included in any of the figures.

So your response doubly reveals you’re defending things you don’t understand. It’s ridiculous.

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Look at what you listed:

Xue is included. Karmin is included. Helgeson is included. Francalacci, Poznik, Mendez are referenced.

And he discusses those papers and their methods.

This was made even more clear in how Karmin et al. (2015) defined the accuracy of their filtering strategy: “The number of FS [i.e., Father-Son] differences was approximately 10-fold higher than the expected number of de novo mutations considering the range of published Chr Y mutation rates (Xue et al. 2009; Francalacci et al. 2013; Mendez et al. 2013; Poznik et al. 2013). This finding prompted us to explore additional filters” (page 4 of the Supplementary Information). Of the four studies they cited—Xue et al. 2009; Francalacci et al. 2013; Mendez et al. 2013; Poznik et al. 2013—only the Xue et al. study represented a pedigree-based Y chromosome mutation rate. The other three studies derived a mutation rate via the historically circular evolutionary geology-based molecular clock method—see Introduction—or by extrapolating the autosomal mutation rate onto the Y chromosome.

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There have been dozens of populations which have been studied by means of Y chromosome assays. One of particular interest is the Mongols.

The Genetic Legacy of the Mongols

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ∼8% of the men in this region carry it, and it thus makes up ∼0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia ∼1,000 years ago…
The Y chromosome of a single individual has spread rapidly and is now found in ∼8% of the males throughout a large part of Asia. Indeed, if our sample is representative, this chromosome will be present in about 16 million men, ∼0.5% of the world’s total. The available evidence suggests that it was carried by Genghis Khan. His Y chromosome would obviously have had ancestors, and our best estimate of the TMRCA of star-cluster chromosomes lies several generations before his birth. … The historically documented events accompanying the establishment of the Mongol empire would have contributed directly to the spread of this lineage by Genghis Khan and his relatives, but perhaps as important was the establishment of a long-lasting male dynasty.

Here is more:
The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan

Y-chromosomal analysis of clan structure of Kalmyks, the only European Mongol people, and their relationship to Oirat-Mongols of Inner Asia

The takeaway in regards to this conversation is that these studies are based on and incorporate the Y chromosome mutation rates as established in the mainstream literature, and they line up with a fascinating if terrible history of pillage, rape, subjugation, and ultimately assimilation. The latest victims of the Mongol hoards are Jeanson and Carter.

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Of course. I stated in my post that Jeanson referenced a number of these papers. That does not mean that he properly represented them or is correct in his interpretation of the data. He strongly disagrees with the authors he quotes, and the question is who is correct.

It would be so helpful if only there were a paper which verified such Y chromosome studies with actual descendants of a known individual of a millennium past. Ta Daaa!

Evaluating the Y chromosomal STR dating in deep-rooting pedigrees

Four sets of Y-STR mutation rates were applied in the estimations. These are a widely used evolutionary mutation rate, two observed genealogical mutation rates, and a genealogical mutation rate adjusted for population variation using logistic model. A generally accepted generation time of 25 years was used to produce a time estimate in years.

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I had a very long conversation with @CrisprCAS9 about why Jeanson’s mtdna work is so horrendous. I’ll link the video and timestamp below, for your convenience.

Timestamp: 1:06:00

The TLDW though is this: Jeanson uses Parsons et al. (a secular scientist) for his insane mutation rate. Parsons et al. is a bad paper, for one because it includeds samples from individuals with a high contamination risk (soldiers) and two because it’s error bars have the mtdna “eve” in a wild range that (guestimating as it’s been a few weeks) has the upper end at only a few hundred years ago, and the lower end at a few million. That is not good.

Jeanson additionally references NGS studies, but OMITS the difference between pedigree and phylogenetic mutation rates (See Santos 2008 for more).

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I’m pretty sure that he is paid to do that.

The measure of confidence in his claims would be talking AiG to fund an actual study, not a cherry-picked review, in which he produced new data by testing his hypothesis.

I see no such confidence.

I don’t think much of what they claim. I’m more interested in evidence.

All three are true.

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Fine. Just let creationists explain ALL of history and migration. Then maybe you will listen.

Yes, he has laid out his method. That’s great. I’m not currently able to evaluate how valid it is though, because like Jeanson, I’m have no background in this specific area, and I don’t have the time to dedicate to figuring it out. That’s why I said “suspect”, rather than “wrong” - I’m being honest and generous. As I said, I’m skeptical of his method being accurate given that Jeanson has no background in this field, and it contradicts previous research by scientists that do have expertise in the field. On the other hand, you seem to take Jeanson’s method and results as accurate purely on the basis that he uses big sciencey words and is a YEC just like you. We’re not on equal footing.

I’m sure he has so little confidence in his claims that he spent 25 hours explaining history to the general public that’s available on YouTube to watch, and then also wrote 2 more papers that followed that one.

It doesn’t take confidence in his claims to spend time pontificating about them to laymen if he’s not interested in being accurate. Writing “papers” in ARJ is no different. He’s done the same thing about other demonstrably ridiculous claims, why should this time be any different.

Wait, what? Two other Young-Earth Creationists also believe something is young!? Well that changes everything! /s
Tomkins is the only big YEC “scientist” I respect even less than Jeanson, given that he is even more brazenly wrong in his claims that Jeanson is. I don’t know as much about Carter’s work.

I don’t remember example what context the “bad sampling” claim is about, but I suspect the “incredible error bars” comment is in reference to his mtDNA work, not the Y Chromosome. There’s so many more problems with his work than just sampling and error bars though, as I think @GutsickGibbon realises.

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They have been scooped in that regard. Have you checked out the David Reich book I suggested earlier? Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It is very thorough, and discusses population movements out of Africa, Neanderthal, Denisovan, Eurasian and Oceana, and new world migrations.

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Yep, the Y chromosomal work is a completely different, albeit similarly flavored, can of worms.

So the bad sampling and error bars is in reference to the Parsons et al. study. Those problems are specific to that work. Jeanson uses that work in part to justify his mtdna mutation rate. So what I was pointing out is that Jeanson’s own sources are ALSO frequently problematic.

Not a great way to bolster his point.

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