Joel Duff: Animal Species Arising Same Time as Humans?

@wallischris10

Oh for goodness sake…

The study is being totally misinterpreted…

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I agree, but i was more interested in the group’s thoughts regarding his response to Joel’s BioLogos blog.

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No, I’m not YEC and do not think the paper argues for the creation of species 200kya. If anything, as a creationist, I’d say the paper argues for God’s continued Day 7 rest from creating abundantly since humans appeared, but that’s a topic for a different thread. Or, is it?

Admittedly Stoeckle & Thaler, 2018 is a horribly written paper. It’s as if they were in a rush to publish and avoided review. As a neutralist neophyte I’m hardly in a position to counter the criticisms, but are the authors as incompetent as portrayed in this thread? Fig 5 fascinates me. Why is synonymous APD within species so low across so many disparate species? Although the entire COI locus is under selection individual synonymous sites are neutral even in coding regions of the mitogenome per ref. [20] linked below. What’s your take on it? Coevolution with nuclear genome? Special environmental (read “just so”) circumstances? Because mitochondria are “honorary prokaryotes”? Accounted for in the theory of coalescence?

In Figure 7 they seem to expect that large census populations (under “naive neutral theory”) should have increasing variance with increasing population size presently, not historically. Their point seems to be that the measurements are not only similar across species, but significantly suppressed compared to Kimura’s prediction. Why? Of course birds may not have been the best choice, but they have the most reliable census data it seems. Ref [20], their previous paper in 2014, “DNA Barcoding Works in Practice but Not in (Neutral) Theory” gives their reasoning, but my new found neutralist glasses make me suspicious of the “just so” nature of it.

Relevant quotes from Stoeckle & Thaler, 2018 (bold added):

pp 21-22: “Purifying selection in linked genomes slows but does not stop the accumulation of neutral variation [139]. Drift and lineage sorting during population stasis or shrinkage decrease variation. The efficiency of decrease depends on the number of haplotypes in the population, as well as the numbers and distributions of female offspring among parents with different haplotypes [10]. A key prediction of naïve neutral theory that does not hold up against extensive barcode data from across the animal kingdom is that larger populations or older species should harbor more neutral variation [20, 140, 141]. The key incompatibility of naïve neutral theory with biological fact is that the theory considers populations at equilibrium in the sense that the population be at stable numbers for approximately as many generations as the mutation rate per generation. The evolution of modern humans offers a specific solution to the animal-kingdom-wide dilemma of missing neutral mutations.”

pp 22-23: “Modern humans are a low-average animal species in terms of the APD. The molecular clock as a heuristic marks 1% sequence divergence per million years which is consistent with evidence for a clonal stage of human mitochondria between 100,000- 200,000 years ago and the 0.1% APD found in the modern human population [34, 155, 156]. A conjunction of factors could bring about the same result. However, one should not as a first impulse seek a complex and multifaceted explanation for one of the clearest, most data rich and general facts in all of evolution. The simple hypothesis is that the same explanation offered for the sequence variation found among modern humans applies equally to the modern populations of essentially all other animal species. Namely that the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.”

Much thanks for any insight. I’m looking forward to sharing ideas and learning in this peaceful forum.

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Link to ref [20] did not come through. Here it is:
Stoeckle & Thaler, 2014
“DNA Barcoding Works in Practice but Not in (Neutral) Theory”

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Welcome to the conversation @EvolvableCreationist. Looking forward to learning more about you.

Fine for this thread, but there is a conflation between coalescence of mitochondria and speciation age. The two things are not coupled. So this does not argue for God’s continued Day 7 rest in any way.

It appears so.

Let’s define that number. For members of the same species. the synonymous APD is low, and this is true for many disparate species. This merely seems to indicate purifying selection. The argument that synonymous changes are unconstrained is not complete.

That would likely be since this DNA is not neutrally evolving, and should not their for be interpreted as they have interpreted it. This is not a failure of neutral theory, but a misapplication.

That is an erroneous interpretation. We do no believe that modern humans were mitochondrially uniform 200,000 years ago. The authors are revealing a basic error in their understanding of population genetics.

Incidentally, @Joel_Duff, Jeanson makes the same error.

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Glad to have you here.

You are not YEC. Does that mean you are OEC?

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That is unfortunate. @Joel_Duff, I hear Nathaniel Jeanson is chasing you down for comment. How about doing a dialogue with him here at Peaceful Science?

Incidentally, despite Duff’s large volume of anti-YEC blog posts on Naturalis Historia, Duff has not published a single critique of my book Replacing Darwin, and he has hardly attempted a robust rebuttal of any of my several technical research papers. Duff has publicly acknowledged my book; Duff has also publicly acknowledged my technical explanation for the origin of species. But Duff has not published a serious critique of it—despite Duff’s PhD training in biology. This silence is telling. Perhaps the “scientific facts from resources provided by a creationist organization” aren’t so erroneous after all.
A Response to “Talking Science as Christians” | Answers in Genesis

Though, I do understand if you’d rather not answer him.

@Joel_Duff don’t give Jeanson any oxygen. AIG like ENV needs oxygen generated by the controversy. Publish rebutal to editor of the journal paper appeared in.

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@Joel_Duff, Nathaniel Jeanson really wants a piece of you:

Dialogue is difficult with YECs (and AiGs specifically) about science because they are already “all in” for a literal, 144 hour creation period. I have heard Georgia Purdom admit that there is no amount of evidence that could ever change her mind. I don’t expect Jeanson to be any different.

I’m looking forward to talking with him. I hope he comes to Peaceful Science. We will treat him fairly.

Of course, I just don’t foresee benefit for Peaceful Science while an interaction could definitely be “kindling” for AiG’s fire.

If we treat him well when he comes, and carefully engage his work, it will be helpful for his base. They will understand that there are trustworthy Christians in science that want to engage his work. I’m curious to see how he answers for it.

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Yes, I’m OEC. It’s a long story, but my background is Geology and I now work as a home infusion nurse. I came to faith listening to Hugh Ross while in grad school at Caltech and pretty much hold to the RTB model. Only recently have I probed biological evolution. I consider myself an evolutionary Creationist in that I accept some mix of macroevolution and creation. I see OoL as super-, or hypernaturalistic. In general, I don’t hold to biological special creation ex nihilo because it’s nearly impossible to probe scientifically. If God did it that way so be it, but He gave me the mind of a scientist. I hold to what I can best describe as hypernaturalistic facilitated variation (after Kirschner & Gerhart). One topic I will pursue in a separate thread is the concept of evolvability and whether people reject it on scientific, or philosophical, grounds.

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When you say evolvability are you referring to the capacity or disposition of a population to evolve? @EvolvableCreationist

Yes, but more specifically a disposition for adaptive evolution.

Admirable work. You are helping people. I admire you for that and thank you for your efforts. How is new technology in this area improving how you can help people?

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Thank you. It’s a very difficult and at times uncomfortably emotional job. Basically, technologies that employ therapies increasingly as snipers vs. WMDs have a huge impact. An understanding of the mechanism of action, however, helps in mitigating side effects which in my analogy are basically collateral damage. Going into detail is too much for now, but if you’re not familiar with the MS drug Ocrevus it has a fascinating history from bench top to current use.

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Is your own work as an M.D, Ph.D, or both?

Agreed. If the low synonymous APD is due to purifying selection then the findings cannot be used to support God’s rest from creating, however I find the authors’ arguments for neutrality compelling. You seem to think the universally low APD is itself a clear indicator of purifying selection? I’ll have to read their arguments against this again. My apologies for harping on this paper which you consider junk. My take is the paper has a useful function! Familiar dichotomy.

Related questions (thinking “out loud”) that may help clear it up: Why doesn’t the mitogenome have junk DNA? Or, does it? Isn’t the argument for junk DNA in the nuclear genome neutrality? If the mitogenome does not even have a repair mechanism why hasn’t it accrued junk DNA? Why is it more susceptible to purifying selection than nuclear DNA? Aren’t they linked? How does population genetics of mitochondria a.k.a. “honorary prokaryotes” work compared to the natural selection dominated much larger populations of true prokaryotes?

Also, I obviously need to read a tutorial on how to reply in a more clear manner.

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