"I'm treating the mutation rate as a substitution rate" - Dr. Nathaniel Jeanson

So I want to ask what is obvious to me, but no one is saying - how much can selection actually affect his work? How much different would/could the substitution rate be?

My question after reading Genetic Entropy probably a couple of years ago was - how could we lose that many men? The main point of GE wasn’t that mutations weren’t neutral; the point was that they don’t affect fitness to the degree that there will be purifying selection (as @Giltil said). I agreed with Sanford’s description of how natural selection works (it seems obvious - because the population sizes you’d otherwise need for purifying selection aren’t available), so I didn’t see how these mutations could be selected against.

So I quite well remember that selection was mentioned in Jeanson’s paper…and I just checked and he already answered you all fully on this point. Anticipated your move…

How might the evolutionary model adapt to these contrary data? With respect to pedigree-based analyses, evolutionists might invoke natural selection—a mechanism by which a high mutation rate could be converted to a lower substitution rate. Alternatively, evolutionists might hypothesize that the mutation rate has recently sped up—that it was much slower in times past. Either way, for these hypotheses to be scientific they must make testable predictions. For example, can any of these evolutionary hypotheses predict the pedigree-based mutation rate for A00 individuals? Or African individuals in general (since no African father-son pedigrees were part of the Karmin et al. 2015 and Maretty et al. 2017 studies)? Or Asian individuals, or Native American individuals (none of whom were part of these same father-son pedigree studies)? Unless the evolutionary hypotheses can meet this standard (i.e., the standard to which evolutionists have held creationists for many years; see Eldredge 1982 and Futuyma 2013), then these hypotheses cannot be considered scientific.

In contrast, our YEC-confirming results led to several testable predictions. These testable predictions add scientific weight to the YEC conclusions found in this paper.

Let’s remember something Valerie.

Jeanson on the one hand complains that evolutionists say that mutation rates may be different at different times and then he himself uses that very excuse for explaining why the branch on his Y-chromosome tree for Africans is longer than he expected instead of adopting the obvious explanation that those branches are longer because they are older and he’s rooted his tree inappropriately. If he really believed that the rates were different on different branches of the Y-chromosome tree he would use a relaxed clock model with his data. He didn’t do that because he doesn’t know what he’s doing and he’s fumbling around to get something that seems to support what he wants to believe.

Substitution rates don’t cause mutation rates. They are a consequence of selection acting on genetic diversity. So it’s kinda stupid to say that one should predict the other. We can measure selection in populations and know that many of these mutations have fitness effects.

I’m going to add a wild misunderstanding of correlation and causation to the long and growing list of scientific concepts Jeanson doesn’t understand.

You are desperately probing for some excuse that will make Jeanson right because you have an interest in him being right that has everything to do with your religious beliefs. You really need to consider that when evaluating people like Jeanson. Jeanson is completely ignoring the mountains of evidence outside of genetics that demonstrably shows that the earth and life is old, much older than a few thousand years. You can’t just focus on this one thing (genetics of one or two loci just in humans) and pretend the rest doesn’t exist. That is the smoke and mirrors that Jeanson is using and when his audience is motivated to believe his conclusion because they share his religion they will always desperately look for rationalizations to say he’s right. He’s not.

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This should help explain the discrepancy and yes it would be significant over long periods of time.

And here is a graph displaying long term substitution rates and showing the difference between those rates and per generation de novo mutation rates.

evograd has done an excellent job explaining this literally years ago as it relates to Jeanson’s first book, Replacing Darwin.

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We’ve made and tested predictions. I’ve done it directly myself - mainstream substitution rates against Jeanson’s strict molecular clock. The best case scenario was that Jeanson was off by a factor of 5x. At worst his model overestimates the rate by 120x.

His excuse was that well maybe we don’t have a sufficiently accurate history of the people from which we collected our samples. For to fly, we’d have to be wrong about basically everything over the last 2-3 thousand years.

Also, this work had already been done when he wrote that.

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Let me count the ways. Henry VIII went to extremes and beheaded wives and advisors, split from Rome, and went to war to pass on his Y chromosome mutations, all in vain. Czar Nicholas II took his dynastic duty seriously but to tragic end. Louis XVI’s Y chromosomes were lost when his young dauphin died in captivity. William Shakespeare’s son Hamnet died at eleven, so he lives on in his sonnets and not his mutations. One can be fit and successful, and still be favored with only daughters. Half of all men with a single child will not pass on Y chromosomes; likewise one quarter of all men with two children, an eighth of men with three, and so on. That is a huge carve out right there. Of course, not everyone’s sexual preferences is conducive to producing offspring. Then there is ever present war, pestilence, plague, and famine, which have reaped the common man by the untold millions century after century. It is a risky business, this being born.

The Bible recognizes the male line may come to a dead end. Genesis 34 tells of the killing of all the males of a small city in retribution for a rape, and the women taken as plunder. Genesis 38 recounts the strange story of Onan, who was supposed to provide for offspring in place of his deceased brother to the widow, but instead was derelict in his duties and practiced coitus interruptus. The apostle Paul advised that men would be better off celibate as himself.

That Y chromosome mutations often fail to substitute in the population I do not think can be in serious dispute.

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Jeanson’s “anticipated response” boils down to: “well sure you have an explanation, but if it doesn’t make the specific set of predictions that I claim it has to, it’s not scientific”.

He simply ignores the many actual fulfilled predictions made by the hypothesis of natural selection. For example, from one of my blog posts responding to “Replacing Darwin”:

Another prediction this hypothesis can make is that synonymous sites should display far less signature of time-dependence than non-synonymous sites, as mutations in these sites would be less likely to cause any fitness effect that could be acted upon by natural selection. For example, mutation rates estimated from 3rd codon positions should be fairly similar regardless of timescale, while the estimates from 1st and 2nd codon positions should differ, following the trend in Figure 5. This is a prediction that has been fulfilled (Endicott and Ho, 2008; Subramanian et al., 2009). Put more simply, deeper (older) branches in the phylogeny should display a lower ratio of non-synonymous to synonymous mutations than more recent branches, which is what we find (Kivisild et al. 2006).

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At 2h32m into the Traced video, Jeanson argues that his population growth curve provides an independent data set against which the reliability of ancient DNA can be experimentally tested. Under his methodology the inclusion of early specimens of haplogroups and Neanderthal DNA would violate the correlation with historic population, and on that basis he dismisses such specimens.

Jeanson discusses Neanderthal DNA at length in his Answers Research Journal paper Testing the Predictions of the Young-Earth Y Chromosome Molecular Clock

My results show that the hypothesis of reliable Neanderthal DNA sequences makes poor testable predictions. This is in contrast to those hypotheses that treat Neanderthal DNA as unreliable and modern DNA as reliable, which make successful population growth curve predictions.

Jeanson is being duplicitous here. He is attempting to steer the conversation so that a challenge of his work is somehow a challenge to the population growth curve. The general shape of population growth over historic times is not what is in dispute here. The record of population does not validate Jeanson’s methodology with respect to haplogroup accounting, nor does it confirm his model. The growth of the world’s population fits just fine with the conventional genetic narrative, so that hardly qualifies as a differentialing test.

His complaint with Neanderthal DNA is that it leads to a poor fit with the population growth curve given a 4500 year horizon. Dr. Jeanson, we have just the fix for that - a much longer extent of time.

Jeanson has it backwards, his work is a model, not an independent data set. Ancient DNA is data, not a hypothesis. Tests for the validity of ancient DNA extraction and sequencing are performed with such tests and best practices that are relevant to DNA, and population has sweet nothing to do with that.

That Jeanson sweeps aside Neanderthal DNA ( his paper completely ignores the Denisovans ) is instructive. If it were possible to accommodate the Neanderthals in his model, he would. Jeanson cannot make the catalog of human genetics work within a post flood framework. This is a tacit admission that ancient DNA, including the extensive record of European haplogroups, invalidates his model and realistically any model positing a 4500 year horizon leading back to one family.

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I think it’s very much worth it to go straight to the source of the original figure and see what the authors write about it:

Box 1

Mutation rates versus substitution rates

It is important to distinguish between the rate at which spontaneous mutations occur and the rate at which genetic changes accumulate in a surviving lineage. The MUTATION RATE reflects the probability of a change in genome sequence between a parent and its offspring. It is the compound result of unrepaired DNA damage, polymerase errors, intragenomic recombination events, movements of transposable elements, and other molecular processes that introduce errors during the transmission of genetic information. However, only those mutations in lineages that persist — typically in the face of selection — contribute to the SUBSTITUTION RATE measured by whole-genome sequencing. The failure to carefully distinguish between these two types of rates is a persistent cause of confusion and misconceptions about whether mutations are random. In the same vein, the frequency of a mutant allele in a population generally does not equal the rate at which the corresponding mutational event occurs.

Mutations can be broadly categorized as beneficial, neutral, deleterious, or lethal with respect to their effects on BIOLOGICAL FITNESS88. In a variety of organisms, many or most new mutations are thought to be neutral or nearly so, and deleterious mutations greatly outnumber beneficial mutations under most circumstances89. Some mutations may change the magnitude or even sign of the fitness effects of other mutations, a phenomenon known as epistasis90. Nevertheless, each new mutation in an evolving lineage can be classified into one of these categories depending on its fitness effect at the time and in the genetic context in which it appears. In this review, we discuss two kinds of evolution experiments where these different categories of mutations make very different contributions to the substitution rate.

In MUTATION ACCUMULATION (MA) experiments, populations are continually forced through a bottleneck of one or a few breeding individuals, so the probability that any given mutation survives is essentially random and independent of its fitness effect. Thus, all mutations – except lethal or extremely deleterious ones – accumulate at rates close to their underlying mutation rates (shown as dashed curve) in surviving lineages (see the figure, part b). The overall fraction of mutations in these highly unfavourable categories is usually thought to be small, and it is therefore common to equate substitution rates and mutation rates in MA experiments, although this will slightly underestimate the true mutation rate. The ultimate MA experiment is to sequence large numbers of parents and their offspring to avoid changes in environmental or genetic factors that might affect mutation rates during a longer experiment91.

In ADAPTIVE EVOLUTION (AE) experiments, by contrast, beneficial mutations typically drive the genetic dynamics. The substitution rate of beneficial mutations exceeds the actual mutation rate (shown as dashed curve) for this category because lineages with these rare mutations increase in frequency as they outcompete their ancestors and lineages with other mutations. Deleterious mutations, by contrast, are underrepresented in AE experiments because they are usually purged by selection, although slightly deleterious mutations can sometimes hitchhike with beneficial ones. The nature of competition between genetically diverged lineages will affect the extent of mutational diversity in a population, but the expected rate of accumulation of neutral mutations in any one surviving lineage will still equal the underlying mutation rate for this category.

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Well, buckle up folks. It’s a new day. :slightly_smiling_face: I will post about a new paper on that topic but it should be a new thread. I’ll respond to the other replies later when less busy with the kiddos

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I feel like I buckled up for nothing

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Some of us didn’t even bother. Listen to us next time. :wink:

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I don’t think he’s burying things (and I don’t think he’s arrogant). A good indicator is the following from him at the end of his book (From p. 221, reproduced here for those of you who did not fully read the book):

How can you not have a good deal of respect for those words? As a YEC myself, I’m completely fine with waiting it out, and seeing what future data reveals.

Dr. Mays, I’m actually rather curious: Why the ad hominem posts? Why not just wait it out, as he suggests?

The problem is that current data are sufficient to falsify his hypothesis, so his predictions are irrelevant. I predict that at some unspecified time in the future, it will be discovered that things sometimes fall up, thus proving that Newton’s theory of gravity is wrong. Are you willing to wait?

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“Wait it out?” I’m assuming you are serious?

The notion that the earth is young and life on it appeared suddenly in a bout of special creation hasn’t been in line with the available evidence for over 150 years. What exactly are we waiting for?

Jeanson doesn’t know what he’s talking about. That’s not an ad hominem but simply a fact. He doesn’t understand modern coalescent theory that is the basis for virtually everything we do in molecular systematics and population genetics, he fails to understand very basic concepts like how to read and interpret gene trees, he has shown he doesn’t know what effective population size is (in Traced he makes up his own definition saying it is something akin to net population growth, it’s not), he continuously confounds de novo per generation mutation rates with long term substitution rates, and he virtually ignores data from radiometric dating (except when it suits him), ancient DNA, biogeography, paleontology and paleoanthropology.

Jeanson wants to be taken seriously as a scientist. When I say he buries things I’m referring to him presenting his findings on religious ministry websites (AiG’s journal is not a peer reviewed scientific journal in any meaningful sense). If he wants his ideas to have scientific legitimacy he has to convince experts in these fields that his results are sound and that means submitting results to real scientific journals that working scientists in these fields actually read and have an impact on the field. That is what I mean by buried.

So why doesn’t he do that? He can’t. He can’t because his methods are so flawed, his findings so at odds with the available evidence, and his approach so divorced from how science is done that none of this would survive any meaningful peer review process. That’s not because he’s a Christian and scientists are biased against Christians. MANY Christians are working scientists. Many of those Christians are here in this group and they strongly reject Jeanson’s claims.

He is arrogant. He’s acting as if he has some monumental, unassailable findings and he is some lone misunderstood genius. None of those things are true. Jeanson by his own admission is looking at the data through “Biblical lenses” and bending the evidence to fit a religious ideology that he is contractually compelled to adhere to. None of this is mere ad hominem. It’s all simply true.

Someone from outside of science looking at Jeanson to determine if he is credible should consider all these things.

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Only in a sense which is predicated on the larger validation of scientific ideas. The goal of science is understanding the basic principles which govern nature; so the hallmark of scientific claims is validity as a generalization, the concept which applies across time, past, present, and future, and space. That is what YEC misses in terms of its distinction between observational science and historical science - all science generalizes from observational science. The boiling point of water may be an observation, but that is just a data point at a particular set of conditions. The generalization is statistical mechanics, and that can be applied to phenomena from boiling an egg to stellar equilibrium, in any place and at any time. The successful range of application is the validation of the principle. There is no requirement for patience in evaluating Jeanson’s claims, as his ideas concerning speciation and haplogroups are in conflict with solidly established data and principles as concerns both the past and the here and now.

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I think very often in this arena people are quick to cry “ad hominem” to shoo someone off who is telling them they don’t know what they are talking about.

If I was making up things as I went along about quantum mechanics (a field where I have zero expertise) and coming up with grandiose claims about the importance of my ideas, drawing conclusions at odds with decades of scientific consensus, and all the while demonstrating I’m incapable of grasping the most fundamental concepts in the discipline while expecting everyone to take me seriously I fully expect someone is going to tell me I don’t know what I’m talking about. I can’t expect just to cry “ad hominem” and have those criticisms disappear. Jeanson and his followers should know better than to expect that.

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We don’t need to wait for more data to be able to determine that Jeanson’s work isn’t valid; we can test his models against real-world data and see if they match. I’ve done it myself, and he’s WAY off, while those same directly observed data are in line with standard evolutionary theory.

His excuse is that we’re assuming we know things like the actual timeframe for the sequences we’re comparing, but you can’t use that excuse to invalidate literally dozens of datapoints without throwing out essentially all of recorded human history.

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True.

Personally I’ve had to get accustom to hearing the ad hominems. I usually just read past them. I’m generally not one to throw the “ad hominem” card of dismissal so quickly.

My question was actually a sincere one.

SUPER short background: After a year away from this site, I came back to hear critiques of TRACED (I always like to hear critiques & rebuttals of new material. I try very hard to avoid confirmation bias).

I started with your article here.
Although you did address technical issues, I was a bit surprised at the amount of discussion that was not technical, and more along the lines of ‘religious motivation’ and the like (about a third).

Understand, I don’t bring that up as a critique, but more of a curiosity.

My question is (and I don’t know how to word it better to make it sound more sincere): There is a whole world of people putting out “miss-information” (as we each perceive it). Why so much attention on this book? And on Jeanson? (And on AiG? And perhaps religion in general)?

Because so many of us here are biologists, and evolutionary biologists, and deal with molecular evolution. We thus tend to pay attention to claims about molecular evolution purporting to be scientific research. If there’s something you would prefer people here to be paying attention to, all you have to do is start a new thread.

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We always tend to treat creationists in general as good-faith actors in these discussions and in the spirit of that good faith stick to the science. The problem with that is that they seldom are good-faith actors. The attention is on religion because special creationism is all about religion. Period. You can’t just pretend that isn’t there. Jeanson himself says he is looking at data through “Biblical glasses”. Modern intelligent design began not with a scientist but with a lawyer who wanted to press the evolution issue to create a wedge into which he hoped to insert very parochial religious views to replace a secular society. Between all the exhibits about floods and kinds at Ken Ham’s creation museum are exhibits about the moral decay they believe is caused by evolution.

I have no problem with people’s religion so long as they aren’t harming themselves or others in the name of those beliefs, coercing others to share those beliefs, or presenting their beliefs as something they are not. Professional creationists like Jeanson operate under the auspices of conservative fundamentalist ministries who are out to do just that and the trick they play on everyone is getting them to just discuss mutation and gene trees and sedimentary geology while insisting they ignore everything else that motivates them. We make a mistake when playing that game.

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