Testing Jeanson's Model: Y Chromosome Mutation Rates

So, he is lying when he says there are only two studies?

“To date, two published studies explicitly attempt to obtain the pedigree-based per-generation mutation rate for the Y chromosome (Helgason et al. 2015; Xue et al. 2009). Both studies have reported results to be consistent with the evolutionary timescale.”

I would not call this lying. He is writing about a topic way outside his expertise and may not realize how wrong he is. I would say that this is a totally false claim, whether Nathaniel realizes it or not.

As it is, you can see for yourself though, he does not meantion this study (and many others like it):

I do think it is interesting that he acknowledges that “Both studies have reported results to be consistent with the evolutionary timescale.” However, as I already explained, the way he computes the mutation rates is not valid.

Is this lying? Is it incompetence? Is it loyalty to the AIG belief statement? Something else or some mix of all these? No one can know for sure but Nathaniel. So I don’t want to call it lying.

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Lol, I’m laughing because what he’s saying is pretty bold. I’f I’m understanding right, he’s saying that there’s only two studies determining pedigree rates, and he came up with a third one based on screenshots of some raw data from a few others that didn’t explicitly try to do so. haha. That would take a lot of hubris if he was wrong and be embarrassing science.

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@thoughtful that’s exactly right. It is incredible hubris.

Keep in mind his whole argument relies on evidence that scientists are eager to collect. We are measuring and refining our observations of human mutation rate now quite often, not because we are trying to prove evolution true, but because it is immensely important in understanding human disease.

There is a gigantic incentive for scientists across the globe to show that everyone else got it wrong and the mutation rates are in fact 50x faster than we expected. That would be big news. It would be in the leading journals and likely even in the news. There is no conspiracy of evolutionary scientists that could possibly prevent this, because the people who measure these rates are not even evolutionary scientists!

Yet we don’t see Nathaniel’s prediction confirmed in the literature. That doesn’t make any sense if he is right. That alone should be enough to see the problem with his argument. Just sit back and watch over the next decade. If you ever see a secular scientists in a leading journal claim that mutation rates are 50x more than we had thought for decades, and other scientists agree, then Nathaniel is vindicated. Until then, the evidence is just solidly against him, so solidly you don’t have to be an expert to see it clearly.

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Maybe it’s worth asking him why he doesn’t mention that study. It’s worth the professional courtesy.

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Nathaniel has never answered a single of my emails or messages on FB. He has obviously read my comments on how he misrepresented me (Would Jeanson Please Correct A Clear Misrepresentation?), but hasn’t fixed the misrepresentation. So I’m not sure how to ask him other than to write it on this forum.

Do you think that is trustworthy? Do you trust the science of someone who acts this way?

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Incentive yes. Incredibly challenging, yes. That’s why tenure was created. But in an academic setting you’ve got to test and retest and get your ducks in a row even with tenure, I bet? You can’t just go out and be Galileo with no repercussions. It’s easier to say you did it wrong and filter the data to match, IMO.

That is a misconception. In this specific case, it would be very very easy. In fact, it would be so easy, that with new technology yet to be invented I wouldn’t be surprised if in 20 years high school students are measuring mutation rates as a take home lab for biology class. Every year it gets easier to do.

As for push back? If you had the data, and it really showed this, it would be research misconduct to manipulate the data to show something else. @glipsnort and @sfmatheson can give their comments, but I’m pretty sure the result would be quadruple checked (which is a good thing) but no one would stand in the way of its publication. It would likely be a Science or Nature paper. It would be a career maker if that result were true.

Well yes, you do have to make sure you aren’t putting out bad science, but that is always the case.

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To echo what @swamidass said, it is really just a question of willpower and money. The cost of sequencing a human genome is less than a $1000 dollars. There is bioinformatics software available that anyone can purchase, and anyone can assemble the reads and compare the different genomes themselves. For that matter, scientists download their sequencing data onto public databases as part of the peer review and publishing process, so anyone can analyze it for themselves.

I would strongly suspect that Answers in Genesis pulls in more than enough money to pay for some next-gen sequencing runs. Why don’t they do it?

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To be clear, it costs more usually (at least at this time) to get high coverage sequencing done. Without high coverage sequencing, errors dominate the calculation because mutations are so rare.

The software, by the way, is free.

So actual costs would likely be more. Still one could do a study for just a few hundred thousand dollars, use data collected by others, or just trust the competition between scientists trying to one up each other in the literature.

In the future though, it might be possible for far far less money.

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That’s true.

Going by the most recent quote I have, 10x coverage (60 Gb of data, 150 bp reads) would cost just under $2,000. 20x would be twice that. This is assuming 150 bp reads would be sufficient for this purpose.

True. The free stuff tends to be less user friendly, so newbs like me prefer the paid software. We have to put up with the computer nerds looking down on us for our lack of Linux skills. :wink:

Indeed. The ingenuity among biotech companies continues to amaze me, with nanopore sequencing being one of the more recent advances.

You usually need paired ends, longer reads (to disambiguate CNVs), and more than 100x coverage to get error rates low enough. It isn’t trivial, except that it’s done all the time.

20x coverage is not sufficient for this analysis.

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Thanks for the info (and @swamidass)!

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What if his prediction had somehow been confirmed? Would that support YEC? Clearly not, as a 6000-year-old universe, or earth, or life, or even Homo sapiens, is contradicted by much more than human genetic diversity. What we would have had would be a strange mystery, but YEC would not be a possible solution to that mystery. You can’t just ignore the evidence against your hypothesis, even if it comes from a different field from the one you happen to be looking at right now.

It would be epic, New-York-Times-front-page-level misconduct.

Lesser misconduct, more relevant in this discussion perhaps, is selective citation (aka cherry picking). I say “lesser” because some kinds of selective citation are mostly obnoxious (citing friends, failing to cite competitors) while not usually rising to the level of “misconduct.” At our journal and our sister journals, we very rarely (as a matter of policy) require correction when the authors should have cited particular papers but didn’t. More serious misconduct would be selective citation that amounts to misrepresentation of the literature. For example, an author who cited only a single paper in 2004, since shown to be incorrect about X, in support of a claim of X, is not merely omitting citations–they are misrepresenting the literature. Such things are rare at our journal and very few can make it through peer review uncorrected, but that is actual misconduct IMO, subject to correction or retraction.

So, if this author has misrepresented the literature, making it appear to support a claim that is known to be false, they are obligated to correct the error once it has been pointed out. I am not taking a position on whether this has happened.

What is much more of a concern to me is that the author has engaged in public accusation while not engaging in professional correspondence about the science. If that is the case, then the author has, IMO, left scientific discourse and should not be given a prominent platform among scientists. This can of course be fixed, by engaging in professional correspondence, correcting errors, and seeking the company of more-qualified colleagues.

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OK - I’m a little slow to understanding what you meant and what he’s referring to. He is referring to just the Y-chromosome mutations and you say he’s ignoring the whole genome, which fits with what you said. The links you provide are sequencing the entire genome.

However, for what he’s saying, do we need the entire genome? Why run into all these complicated mathematical problems when we know Y chromosome is inherited from a father who passes it down to his son and so on? Wouldn’t that yield a more accurate pedigree rate for each generation of males rather than sequencing the entire genome?

The entire genome includes the Y chromosome. The authors would be trumpeting it from the rooftops if they found that the Y mutation rate was 50x higher than the rest of the genome. That is not what they found.

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Why would it be expected to be the same? I don’t see a reason that it has to be…

And maybe as creationist we would expect that they should be different. We could share similar genetic makeup as animals but X, Y chromosomes would be different.

AND…in the middle of typing I decided to do a quick Google search. First hit :wink: do chimpanzees have y chromosomes - Google Search

I have to read the paper through later.

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Great questions!

Turns out that evolutionary science predicts that X and Y have different rates than the rest of the genome. We expect Y chromosome to have a bit higher mutation rate (not 50x higher, but maybe 1.5x) and X chromosome to have a bit lower mutation rate.

So here is the thing, by measuring the mutation rate across the whole genome, they also measured the rate of mutation in the X and Y chromosome. They include a table of data in (if I remember correctly) 10,000 bp blocks showing the mutation rate for each block across the genome. So we can directly look at the Y Chromosome mutation rate specifically, what Nathaniel needs to test his hypothesis, and it is exactly what evolutionary science predicts. It does not confirm the YEC hypothesis he puts forward.

This, also, is why the paper is a higher quality than those he cites. The best technology works in such a way that it makes little sense to measure Y-chromosome mutation rates in isolation. I just makes most sense to measure the mutation rate across the whole genome (including Y Chromosome), but in a way that we can measure it specifically in Y Chromosome if we want to. That’s what they did here.

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