I tried to cover a lot of ground in my April 16, 2022 review of Traced: Human DNA’s Big Surprise by Answers in Genesis representative Nathaniel Jeanson. But, like peeling away the layers of an onion, there’s more to discover and like a peeled onion reading Traced and its evangelism thinly masquerading as science is enough to make the reader cry.
Jeanson claims that his reexamination of sequence data from extant human Y-chromosomes has led to a stunning revolution in the science of human history. A finding that happens to also conveniently align not only with the religious beliefs he has harbored his entire life but also with the literalist Biblical interpretation he is contractually obligated to promote as an employee at Answers in Genesis. Jeanson’s revolutionary claim is that the entirety of the human population comes from the three sons of Noah and their wives a mere 4,500 years ago or so following their disembarkment from the Biblical ark.
This is an old claim. It was used by European colonialists to place indigenous peoples and their history within a Christian theology because without an accepted framework that viewed native peoples as descendants of Adam they could not be considered human. Arguably considered the father of modern young-earth creationism, Henry Morris, a fundamentalist Christian writer, engineer, and founder of the Creationist Research Society, is a role model for contemporary creationists like Jeanson. Morris promoted this same narrative regarding the three sons of Noah, and their wives, as the sole post-flood ancestors to all modern people and categorized modern ethnic and racial groups as being descendants of one or the other of Noah’s sons - Shem, Japheth, or Ham. Whatsmore Morris believed that each of these three lineages of human beings were imbued with inherent qualities relating to intelligence, creativity, and work ethic and those qualities coincided with traditional white, racist stereotypes.
Jeanson believes Y-chromosome sequences alone are sufficient to prove this very traditional fundamentalist Christian claim that all human beings are the descendants of the three sons of Noah.
How does Jeanson justify this conclusion?
The basis for Jeanson’s putative scientific conclusion rests on two things and two things alone.
A genetic tree based on the Y-chromosome sequences.
A measure of Y-chromosome mutation rates.
Demonstrating that Jeanson doesn’t know what he is doing on either of these metrics is enough to call everything he claims on the topic of genetic diversity and human history into question.
Trees
In my last post, I explained how a genetic tree is a diagram displaying information about genetic diversity among a sample of sequences. The same sorts of trees however can be constructed from measures of any sort of diversity, including morphology. However, in order for these trees to convey information about history, which is the sort of information Jeanson is after, they must be rooted. There are very well-established methods for rooting a tree but they typically involve comparing the sequences you are interested in with a sequence derived from an organism related to but outside the group of interest - an outgroup. Jeanson is ideologically opposed to this method no matter how scientifically warranted. So what does he do? He roots his trees in ways that affirm the groups he wants to see - groups he believes he can associate with the three sons of Noah. He then attempts to rationalize those arrangements of the branches of his genetic trees after the fact using justifications that are simply baseless. I went over this in some detail in my last post.
Mutation rates
Now, what about the other arm of this argument - mutation rates. Much has been said about Jeanson’s either reluctance or inability to distinguish between a de novo mutation rate (spontaneous changes in the bases of a DNA strand from one generation to the next) and a neutral substitution rate (the accumulation of changes that have little or no impact on the organism over long periods of time that become more or less prevalent due to the random action of genetic drift). The latter is relevant to the molecular clock approaches Jeanson claims to rely on and the former is not. But, let’s put that aside for a moment and look at exactly how Jeanson derived his Y-chromosome mutation rates that he claims are de novo.
The mutation rates Jeanson uses to draw his conclusions in Traced come from one of the many articles published in the Answers in Genesis in-house journal - which I will remind the reader is not a scientific journal in any meaningful sense as it operates under no legitimate peer-review process. That article is Jeanson 2019 Evidence for a Human Y Chromosome Molecular Clock: Pedigree Based Mutation Rates Suggest a 4,500-year History for Human Paternal Inheritance.
Jeanson focuses on one article in particular to, in his words, define the “upper mutation rate value for our calculations”, or put another way, the fastest mutation rate for his model. That paper is Maretty et al. 2017 Sequencing and De Novo Assembly of 150 Genomes from Denmark as a Population Reference.” Nature 548: 87–91. Jeanson correctly notes that this paper reports the frequency of structural mutations, deletions, insertions, rearrangements, but “did not explicitly report a per-generation Y chromosome single nucleotide mutation rate”. So, and this is typical of what Jeanson often does, he thought he could dig around the paper to derive what he needed. So, how did he do this?
Jeanson derived his Y-chromosome mutation rates from a figure in Marretty et al 2017 as follows.
“We extracted the father-son SNV differences from the Figure 4c Y chromosome tree of Maretty et al. (2017) as follows: First, a screenshot was taken from the published pdf containing Figure 4c, and the screenshot included the associated scale bar of “50 mutations” (see Supplemental fig. 1). (The raw sequence data for the Y chromosomes is restricted access.) After electronically expanding the screenshot to a large size (while keeping the proportions constant), we located the 17 pairs with the shortest distances between them, to identify the 17 father-son pairs. Then we used the scale bar to visually and electronically estimate the nucleotide differences between each father-son pair (see Supplemental fig. 1 and Supplemental table 1).” - Jeanson 2019
Remember Jeanson is only ever interested in the de novo mutation rate - the rate of spontaneous single base changes from one generation to the next, in this case, mutations occurring in a father that are passed to a son. But, Jeanson’s problem was that data was not reported in Marretty et al. 2017 so this was his creative approach to deriving those data. He literally made a screenshot of the figure from the paper - a distance-based tree from Y-chromosome sequences using the same method Jeanson uses (neighbor-joining, I included my own screenshot of the same figure below). The branch lengths on the tree represent the number of base changes along that particular branch. Jeanson zoomed in on the tips of the tree focusing on the 17 pairs of the shortest branches representing what he assumed were Y-chromosome sequences from fathers and sons. Then he used the 50 mutation length scale bar, essentially took a ruler to the screen, and measured the branch length for these 17 pairs of sequences at the very tips of the tree, and that is how he calculated his upper limit for the Y-chromosome mutation rate. That measure, along with the way he roots his genetic trees, lies at the crux of everything he is claiming in Traced - and neither is credible.
Figure 4c from Maretty et al 2017 Nature 548: 87-91.
It is very difficult for me to overstate this. Jeanson’s method for deriving a mutation rate by zooming in on a screenshot of a distance-based genetic tree and measuring branches with a ruler is probably the most amateurish thing I have ever seen from someone presenting themselves as a professional scientist.
So I wondered if these 17 bifurcations at the tips of this tree in Maretty et al. 2017 were actually father-son pairs or not, or was the tree just constructed from the paternal sequences. So I contacted some of the authors.
Turns out Jeanson’s assumption was correct. The tree does contain sequences from father and son Y-chromosomes and those father-son pairs are indeed these very short bifurcations on the tips of the tree. However, this is where everything goes completely off the rails.
As Jeanson noted, the goal of the Maretty et al. 2017 study was to look at structural variants and not the sort of single nucleotide differences between parent and offspring Jeanson was interested in, and yet even while making that observation he proceeds to ignore it and treats the data as if reliable single nucleotide variation (SNV) spanning a single generation is there to be tallied.
This is what one of the authors, Laurits Skov, conveyed to me in our personal communication (shared with the author’s permission) regarding Jeanson’s use of their article.
“One thing to note is that we mainly focused on structural variants in this paper (Maretty et al. 2017 Nature 548: 87-91) so we were not very conservative with regards to filtering of SNPs. So thats why the Y chromosomes are not completely identical.” - Laurits Skov, personal communication, April 19, 2022
That’s why the chromosomes are not completely identical. Not because of mutations, which is what Jeanson thinks he is measuring, but rather because of error. Jeanson is measuring very slight differences between sequences using a very crude method (i.e. zooming in on a screenshot of a figure) and treating those differences as if they are mutations and most differences very likely are not.
This is more from my correspondence with Laurits Skov, again, one of the authors of the paper Jeanson is misappropriating.
“No I think most of the differences between father-son pairs in this study are errors. I was looking through the supplement of my Y chromosome paper to find some numbers. So the phylogenetic tree is made using around 3000 SNPs and the error rate is around 1/1000. So while you can certainly use this data to construct a phylogenetic tree I would not use it for inferring mutation rates.” - Laurits Skov, personal communication, April 20, 2022.
“I would not use it for inferring mutation rates”, and yet that is precisely what Jeanson is doing and he is basing his entire argument on these contrived numbers. Making a distance-based tree from these data is not a problem because the deeper branches in the tree will certainly have many more differences than could possibly be explained by sequencing or alignment errors. But, you can not reliably distinguish the differences between father and son Y-chromosome sequences as being significantly different from zero because any small differences you measure are likely attributed to errors.
So, in short, not only is Jeanson relying on arbitrary approaches to rooting his trees - approaches with no legitimate rationale for rooting the tree one way versus the millions of other ways it may be rooted (see my prior post on this topic from April 16, 2022) - but also his mutation rate is relying on measures of diversity that not only are crudely derived but that may not be attributed to mutation at all. This is precisely what happens when someone dives into a field of study with strong confirmation bias, virtually no idea what they are doing, and working in a silo where no one will offer any critique of what they are doing so long as it conforms to Answers in Genesis orthodoxy.