Article from Biologos on the recent mt-DNA barcode paper
Covered this already: Did All Species Arise about 200,000 Years Ago?.
The author at BioLogos @Joel_Duff was part of that discussion too. Too bad he didn’t link to us.
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@Joel_Duff I was curious about this statement:
What Stoeckle and Thaler have potentially discovered, by examining the variation of a single gene in the mtDNA, is that most species experienced a mitochondrial genetic “bottleneck” between 100 and 200 thousand years ago.
How do you derive this from the study? That seems to be an error in its analysis, even though the authors suggest it.
@wallischris10 welcome to the forum. I saw your comment on: Did All Species Arise about 200,000 Years Ago?. We can pick up the question here. You found Jeanson’s article on this paper.
I’d be curious to hear @Joel_Duff’s thoughts, but it appears there is an error in all this. Mitochondrial coalescence does not imply a bottleneck. Why would we grant that?
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Thanks for the welcome, this forum is great. Ive found that new articles, papers and books coming from YECs and ID proponents are generally ignored by relevant mainstream scientists, especially since the Pandas thumb is basically dead. Im glad you guys are writing about them.
I’ve found most of the criticism of the paper to reflect my own thoughts, however Jeanson’s response is very confusing to me. I hope Joel and others find time to dissect it.
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The article is “target rich.” It might help if you can put the excerpts you have questions about here.
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Ok, I will put in a few, but i find the entire thing confusing.
He seems to propose that population bottlenecks and species specific adaptions cannot explain the low mtDNA variation, but a recent creation (6k yrs) can. He defends this;
“We now have two decades’ worth of direct measurements of the rate at which human mtDNA mutates, and it matches exactly the 6,000-year timescale and rejects the evolutionary timescale (see “Genetics Confirms the Recent, Supernatural Creation of Adam and Eve” and references therein). Thus, taking Stoeckle and Thaler’s results to their logical conclusion, we can revise their statement to “Modern human [mitochondrial DNA] originated from conditions that imposed a single sequence on these genetic elements”14 about 6,000 years ago”
Im really not sure how you can jump from 100-200 thousand yrs to 6 thousand, and surely that includes not just a linear accumulation of mutations but also many “inter-kind” speciation events which alone must take ages. Later he even appears to acknowledge this:
“I’ve also documented that the process of speciation involves several steps—at a minimum, (1) the formation of one or more distinct individuals, (2) the multiplication of these distinct individuals into a population, and (3) the isolation of this distinct population from the parent species.”
There is much more i find confusing, but maybe I’ll leave it there for now.
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That is the keystone error. Take this out and whole deck of cards falls apart. Because of heteroplasmy, we do not actually have direct measurement of the rate and which human mtDNA mutates. Jeanson’s calculation of the rate is based on misreading sequencing errors as mutation rate in one study. From the statistics of his table themselves, it is easy to show that it is an error with a simple statistical test.
What we do have with increasing accuracy is direct measurement of mutations rates in the genome, which is much more data than mtDNA. Because we do not have the challenge of heteroplasmy, we can actually measure this directly. And, surprise, it does not match the YEC time line, not even close. I’m pretty sure (though I’ll have to check) that Jeanson notices this and reports it as an anomaly that he cannot explain. If he does, that is honest and I respect it. If not, he should be upfront about it.
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This article might be good to step through sometime. When another scientist (@Joel_Duff?) wants to do this with me, and there are enough requests, we might schedule an Office Hours for this.
A response is needed to clear up this mess.
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I’m thinking about it…time is crunched…
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Thanks @swamidass I have read plenty of evolutionary genetics papers, coalescence papers that strongly suggest the YEC timeline is WAY off, so I was really baffled how Jeanson could state the opposite with a straight face.
I did click the link to his Supernatural Creation of Adam and Eve (paper?) but its soo long and so full of errors, one would need something non-PhD students call “free time” to work thorough the entire thing. I would love to see you guys who have chops in this area take it apart, and he would probably enjoy responding.
In particular, his whole thing about dismissing hierarchies because designed automobiles can be arranged in to hierarchies drives me nuts. ANYTHING can be subjectively arranged in that pattern but only if you arbitrarily favor one character over another, any number of these trees could be drawn and all would be equally invalid. Decent with modification objectively finds trees because of the state of the ancestor is weighted.
Keep up the good work!
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The core problem is how he computes the mutation rate. This blog seems to hit most the main points:
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How have I never heard of that blog!?
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I’m probably not the right person to get into the weeds with on this article. I’ll just point out that among so many problems one that always hits me as I have read multiple YEC articles on this topic is that when I see the discussion of mtDNA variation in humans followed by the attempt to explain that variation within a 4300 year time frame, they leave out their analysis the Denisovan, Sima de los Huesos, and Neanderthal mtDNA sequences. I note that this time they throw in the caveat about Neanderthals to address this issue by stating:
" Without going into great technical detail, the short answer to the question of what Neanderthal DNA implies regarding the origins issue is that Neanderthal and ancient DNA samples appear to be too degraded and often untrustworthy for use in rigorous genetic analyses. In addition, analyses are perpetually plagued with DNA contamination from microorganisms and modern human DNA from lab workers.46 Finally, no one knows the rate at which Neanderthal DNA changes from generation to generation — and it might change at a rate much faster than that reported for modern human individuals.47"
The references to are previous YEC articles which reference yet older articles. The fact is that if the neanderthal mtDNA sequences are accurate then they are different enough that it significantly impacts their calculations and doesn’t fit the model they are trying to support. There are now sufficient mtDNA sequences of archaic humans and neanderthals that contamination and degradation effects can be accounted for and so those sequences need to be accommodated for in their model.
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I’m on vacation and have limited access and inclination to use it:-) But I should say a few things about this. The BioLogos article dropped the morning I left on vacation and I had little opportunity to see the responses and provide feedback.
I’ll say that the bottleneck argument was the simplest way to demonstrate how some YECs have sensationalized that Stoeckle and Thaler paper. I am in total agreement that mitochondrial coalescence does not imply or necessitate a bottleneck. I wanted to list multiple reasons why the pattern Stoeckle and Thaler observed–assuming that pattern is valid–but there was a severe space limitation. I had a much wider-ranging discussion on this point but agreed to the editing it down to one example. I’ve struggled to ever explain coalescence in less than 1000 words and several figures and so I knew I wasn’t going to go down that path but I should have mentioned it in the article and provided a reference. I have very much regretted leaving the impression after the Cheetah example that the same things could be responsible for the observed mtDNA patterns of most species. In writing these responses I struggle with the need to keep it simple for those that don’t know anything about population genetics and responding to the complexity of the article and issues with it with something that the lay reader will probably not grasp. In this case, the article was oversimplified giving too much fodder for the opponents of evolution.
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Thanks, looks like a good blog, I have never heard of this one. I notice that Jeanson has a lengthy response to the blog and it looks as though the author hasnt replied. One thing that stood out was that Jeanson claims circularity in phylogenetic measurments of the mtDNA mutation rate because they assume a priori that evolution is true. I dont think this works because the rate of evolution isnt assumed it is measured so im not sure what he is getting at.
“For example, Soares et al first assume an ancient timescale (the very fact that my research contradicts), and then fit DNA differences to this timescale. Not only is this circular reasoning (i.e., assuming evolution to prove evolution), it’s also indirect science. It’s analogous to trying to measure the rate of erosion in the Grand Canyon…by measuring the depth of the Canyon, assigning millions-of-years dates to each layer, and then calculating the rate of erosion…rather than actually physically measuring it. So the main claim of the blog you cited is not a logically sound or scientifically compelling argument against my published work.”
Looks like a great site with great articles. Thanks, I will add it to my bookmarks for viewing.
Why? It not like their wasting paper over there. Biologos needs to get with it. Give you all the space you need to explain in detail. oy vey Please, if you have more to explain, explain it here. We all have much longer attention spans than Brad Kramer. 
(See I got in a dig at Brad without being a mean and nasty militant atheist)
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Hi Guys, great discussion, do any of you, maybe @Joel_Duff, have any opinions on Nathaniel Jeansons recent post at AIG about the paper and the BioLogos blog? He makes a number of claims about how the work is consistent with a 6000yr origin of species, the unreliability of the fossil record for documenting speciation etc.
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