Side Comments on Allelic Multiplicity Argument

@swamidass,

This seems to be the heart of your objection to Venema’s position. But prior to the fairly complex discussion between Drs. @RichardBuggs and @DennisVenema on BioLogos (now a notorious discussion all around the English speaking world of Creationism), my understanding of the context would have been (and even now):

How to get from the diversity of a single mated pair to the Earth’s current state of human diversity in 6,000 years!

Prior to the rather fevered zeal of Dr. Buggs in that discussion, I had never encountered any Creationist who would have thought it important to show that a bottleneck occurring more than 500,000 years ago was at all relevant or useful to the YEC mission.

At the time of the thread (and I certainly made my complaints known on the thread), it seemed like a fishing expedition where Buggs was doing whatever he could to prove Venema was wrong “in some thing, in any thing!”.

And this feeling of mine is further confirmed by the complete lack of follow-through with the 500,000 year finding. It was an opportunistic discovery that there was any way to justify a bottleneck of one mated pair - - with virtually no relevance to the usual way these issues were discussed up to that point (namely, the usual YEC scenario of 6,000 years ago)!

So what exactly are you asking for in this retraction? Do you need Venema to publicly admit that it never crossed his (or anyone else’s mind) that a bottleneck was theoretically feasible if we extended the time frame back beyond, not just 6,000 years … back beyond the the rise of Homo sapiens sapiens… back all the way to before Creationists even believe “Humans” (as we understand them) existed?

I know you and Venema don’t exactly see eye-to-eye on such matters… but maybe Venema would be more forthcoming about the limits of his imagination if Dr. Buggs also confesses that he has no idea how a bottleneck more than 500,000 years ago would be helpful in a more “Biblically consistent” interpretation of the rise of humanity?

Maybe history (and lightning) can strike again in the same place - - if we arrange a “parlay”**[FN #1] between Venema and Buggs in their original canvas-floored arena at BioLogos.Org? (with over 1,050 individual postings!):

[FOOTNOTE #1: Parley … the term spelled as “parlay” on the Pirata Codex was known as a right in the Code of the Pirate Brethren, set down by Morgan and Bartholomew, that allowed any person to invoke temporary protection and brought before the captain to “negotiate” without being attacked until the parley is complete."]

“[PIRATE CODE] EXAMPLES: Nine complete or nearly complete sets of piratical articles have survived, chiefly from Charles Johnson’s “A General History of the Pyrates”, first published in 1724, and from records kept by Admiralty Court proceedings at the trials of pirates.”

“A partial code from Henry Morgan is preserved in Alexandre Exquemelin’s 1678 book “The Buccaneers of America.” Many other pirates are known to have had articles; the late-17th century “Articles of George Cusack and Nicholas Clough have survived intact.” [More ]…pirate articles [would] have survived [except] pirates on the verge of capture or surrender usually burned their articles or threw them overboard to prevent the papers being used against them at trial.”

You misunderstand @gbrooks9. Allelic multiplicity is not a valid argument against a bottleneck as recent as 6,000 years ago. It never was. It does not appear in the literature.

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Ok, I’ll bite. What exactly does appear in the literature? Who was the first (or last) Evolutionist to discuss the genetic diversity of the modern human population of billions of individuals?
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When I google your phrase “Allelic multiplicity”, I mostly get “hits” regarding “Mendelian disorders”:

“Allele multiplicity in simple Mendelian disorders. - NCBI - NIH”
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1685710/

We are not discussing all arguments. Why does it matter if there are other good arguments made? That is like arguing “Well, it is okay to argue 1+1=3, because in fact we know that 2+2=4”.

We are discussing a single specific argument. The topic of this thread is directed to a specific false argument offered by Venema “1+1=3”, and there is no relevance to the fact that we can demonstrate “2+2=4”. That is merely a change of topic.

I also add that several BioLogos scientists have agreed that Venema is in error. It is my understanding that he himself knows it is in error.

When I first read the criticisms regarding Venema’s “certainty” regarding the lack of bottleneck, my interpretation was very straightforward: Venema is absolutely certain that there was no bottleneck of one mated pair between 6,000 and 12,000 years ago. And this certainty seems to have been well justified.

I understand that the time frame was probably not explicitly stated, but that would not have been an mistaken assumption.

The fact that Buggs accidentally “struck oil” by demonstrating that there could have been one more than 500,000 years ago hardly seems to be something for which Venema has to confess anything.

I’m still waiting for my sudden realization of what Venema is refusing to “confess”?

This is not about the Buggs exchange @gbrooks9. This was a well known error before the Buggs exchange. Jeff Schloss confirms that it is an error. I apologized publicly for not making it clear that it was a fallacious argument sooner. Venema, it seems, knows that it is a fallacious argument but prefers not to retract it.

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@swamidass,

I was thus too easily persuaded? In fact, for 1 mated pair of humans to create a population of billions consistent with today’s diversity in the human population - - in less than 10,000 years - - would not require “…postulating mutation rates in excess of what we observe for any animal”?

This is the “benchmark” question, right? This is what is in error?

What would the more correct sentence have looked like?

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It is, as I quoted with reference several times:

“In fact, to generate the number of alleles we see in the present day from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal.”
http://peacefulscience.org/three-stories-on-adam/

The number of alleles is one measure of genetic diversity, but not the only one. There are zero papers that put forward “number of alleles” as a valid way of demonstrating no bottleneck, because it is in fact not a valid way. This is well known. It should be understood from entry level population genetics books.

The surrounding context of the quote does not improve things, but begins to rely on additional fallacious arguments.

Here is a revision that would work.

“In fact, the distance between alleles we see in the present day populations from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal.”

The important change is to reference the divergence or difference in alleles, not their numerosity or quantity. The surrounding context is problematic, because no papers have been published on this yet, except at Peaceful Science. So he is just incorrect.

@swamidass

Okay… so “number of alleles” is not valid. But I can only take this statement on faith. Because what I see you and others agree upon, is that 2 humans, regardless of how diverse their allele profile might be, cannot produce the current diversity in the human population within 500,000 years of the present day.

So - - what exactly is different from what we AGREE upon
(no 2 person bottleneck within 500,000 years)

VERSUS

what we DO NOT agree upon
(no 2 person bottleneck [unspoken time frame assumed to be less than 12,000 years ago])?

@swamidass

I don’t recall reading “divergence of alleles” instead of “number of alleles” in the “authorized” versions of the post-debate discussions. Isn’t there an “average divergence” within any collection of alleles?

ADDENDUM:
Are there known cases where multiple alleles are so similar to each other it is well known to be a terrible example of diversity?

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This is merely a high-level description of TMR4A. You have certainly heard of TMR4A a bazillion times. This is what WLC references too. He was immensely confused by Venema’s work until he read up on TMR4A. Then it made sense to him.

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That is my only scientific point here, my only point. Venema and I agree on the ultimate conclusion:

We may also agree that the argument is invalid (or not, let’s see what he says). We certainly disagree on the importance of retracting bad arguments. I think it does harm to understanding and trust to continue advancing false arguments. He appears to see no reason to retract them.

Do you now understand?

Yes. Every point mutation generates, a new allele that is very close to an existing allele. The number of these alleles is proportional to the population size now, not in the past.

@swamidass,

I really want to say I do understand. But I don’t see how we can cheer the 500,000 year conclusion, but using virtually the same vocabulary, condemn what appears to be also correct.

When I go back to your discussions with Venema in that thread, I found these three key postings (back in February of 2018 - - which is not that long ago !):

The first link is Chris Falter writing to you, @swamidass:

Then Venema writes these kind words (!) about you in response to Falter’s statement:

And then comes your lengthy reaction to Venema, where you invest considerable language to triangulate on his views. I note, with some disappointment (in connection to this sleuthing we are doing now) that I could not find any response from Venema. :frowning:

Maybe he wrote a response within a larger posting? I couldnt’ find it under the current time constraints.

Joshua, I have to wonder if we would still be having this dispute now if you had received some kind of an answer back then …

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My point exactly. Dennis goes into hiding on this one. This has happened several times. He does not want to clarify his error publicly. I understand. It is not a defensible error. It makes him look bad, as if he does not understand much population genetics. I would be concerned too. In the end, we all make mistakes that make us look bad. What matters is how we deal with it. Do we fix it when we say 1+1=3? Or do we ghost everyone?

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And yet the statement we all agree upon is that no 2 human sets of alleles could have produced the current human population within 500,000 years ago …

BUT… if someone says no 2 human sets of alleles could have produced the human population 12,000 years ago (implied time frame, not explicitly stated), he is wrong … unquestionably wrong.

This seems like an attempt to sqeeze Orang blood out of a Pongo specimen. It is not a useful application of your energy. You don’t appear to have a clean example of how his conclusion may have been right, but his terminology was wrong?

If you deserve justice from Venema, I would say the area you deserve justice about is more in: “Venema’s willing acknowledging the areas you were correct about” [aka: Genealogical Adam] - - rather than the areas "Venema may have been incorrect about."

Yes. It could, however, produce the same “number of alleles,” which is what the YEC paper is correctly arguing.

Do you meant to imply that Venema is incapable of honesty here? I hope that is not your claim. He is a good person doing the best he can. It is just hard to admit when we are wrong. I am sure he is capable of honesty.

I have been precisely claiming that he is incorrect. Is that what you think he is endorsing here?

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So… now we have the exact contrast!:
It is wrong to say:
“2 humans could not have produced the same number of alleles as today’s human population presents…”

But it is correct to say:
“2 humans could not have produced the differences seen in today’s human population”!

Wow… that’s a lot of heat for not much light! And I don’t think anyone even cares…

BUT. . .

I think the real problem was and still is that his book ERRONEOUSLY rejects the perfectly reasonable scenario of a Genealogical Adam - - where the genealogical aspects in question can and have been easily demonstrated by various computer simulations!

This is the “take away” that I think is fitting for your disappointment.

@swamidass,

I think the next time Venema is interviewed, he needs to come clean that the book was in error about its conclusion, and that he is now actually exploring the valid ramifications of your Genealogical Adam scenario!

Yes exactly.

That is not true. A lot of people care. There have been a disturbingly large amount of work responding to Venema’s claims, as if it was what population genetics teaches. That was a wild goose chase.

Why not during the podcast he recently gave? Nothing has changed over the last 8 months.

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