Venema: The Argument of Allelic Multiplicity

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Science
Adam

(Matthew Pevarnik) #1

I am not really sure how to look at this paper, but it was brought up to me and it seems to have enough figures and lines that give the impression that this YEC duo completely have outdone the field of modern population geneticists:
The genetic effects of the population bottleneck associated with the Genesis Flood from the Journal of Creation

What are some helpful suggestions for someone who holds that this model is an adequate scientific explanation of the diversity among humans today?


(S. Joshua Swamidass) #2

This article engages the “Allelic Multiplicity” argument.

I note that the TMR4A evidence is unaddressed by this paper (TMR4A didn’t exist in 2016), but this paper does demonstrate that Venema’s argument against a bottleneck is false. We already know this though, but Venema has refused to retract this argument.

The fact that this article is even possible is a case study of the harm done by fallacious arguments against YEC, such as those offered by Dennis Venema. We should support YEC papers, such as this, that correct dispatch bad arguments against their position, so we have credibility to point to evidence that YECs have ignored, such as TMR4A. Let YECs win where they are right, and encourage them to engage the actual evidence instead of fallacious arguments.

Of course, many of the conclusion of the paper are incorrect (the evidence does not suggest a bottleneck). However their response to Venema’s argument is in fact correct. They also have not engaged the strong evidence against their position (such as radiodating and TMR4A).

Venema’s Fallacious Argument

The article quotes Venema:

This actually answers a challenge issued by several critics, specifically Francis Collins, who said:

“There is no way you can develop this level of variation between us from one or two ancestors,”

and his Biologos fellow, Dennis Venema, who said:

“You would have to postulate that there’s been this absolutely astronomical mutation rate that has produced all these new variants in an incredibly short period of time. Those types of mutation rates are just not possible. It would mutate us out of existence.”

This is an example of the fallacious “argument of allelic multiplicity” or “allelic numerosity.” It is invalid, depending on an incorrect claim about population genetics. I have explained Venema’s error at the ASA:

The argument from “Allelic Multiplicity.” This was published several times since 2010, online and in print, but never peer-reviewed. “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.” This is a fallacious argument that does not appear in the scientific literature.
http://peacefulscience.org/three-stories-on-adam/

By presenting this as a valid argument, claiming citations that do not exist, and refusing it to retract it, Venema is making an obviously false statement to those of us that know population genetics, that is trivially easy to falsify. William Lane Craig has written specifically in reference to Venema’s fallacious argument,

In fact, it is a good test of population genetics knowledge to parse out why this is a fallacious argument. This is not subjective or ambiguous. Once you see it, you will have learned something important about the non-intuitive realities of how DNA evolves.

Still No Retraction

It is disappointing that in his recent podcast appearance, Denis Venema did not retract this claim and, instead, reasserted it. He did this after being asked specifically about this claim, as it referenced the WLC quote above. It is disappointing that BioLogos yet to retract this invalid argument from its website, which is demonstrably false with precisely zero references in the literature:

Does Genetics Point to a Single Primal Couple?

First we ask how many different alleles there are for a number of genes within the current population. Correcting for the rate at which we know new forms of genes appear (mutation), we can calculate the minimum number of people needed to generate the current amount of diversity. Numerous studies analyzing many different genes all point to a bottleneck. However, these studies are all clear: during the bottleneck, there were several thousand individuals, not two.

It is all the more egregious in his recent comments that he makes no mention of valid genetic evidence that do actually does challenge the YEC position. For this reason, YEC will have no reason to address TMR4A. He is, after all, the leading BioLogos scientist on these matters. This is why Venema’s omissions here are so consequential.

With all this in mind, the YEC article is correct in pointing out Venema’s argument is false. It is a false argument, and that is why it should be retracted and abandoned. It does not appear in the peer-reviewed literature and demonstrates and teaches incorrect information about population genetics.

We should expect many more like it until BioLogos and Venema remove this invented argument from the public discourse by prominently retracting it.

Honesty, Trust, and TMR4A

I’m reminded that honesty is fundamentally important. False arguments are not excusable if they are advanced for the “right” conclusion. They are still false arguments. False arguments in service of correct conclusions do great harm to public understanding. It is important, for this reason, that YECS, ID (@Agauger/@Pnelson) and OECs (@AJRoberts) know that we will never advance a false argument against their position. I would advise them to point to this post every time Venema’s argument is raised against them. We will make more resources to make this clear if needed.

@pevaquark asks an important question:

I would do two things:

  1. Agree that Venema’s argument was fallacious and call on him to retract it. This will appropriately build trust, and indicate integrity and honesty in presenting science.

  2. Point people to TMR4A, which is very strong evidence against a bottleneck of two before 500 kya. Heliocentric Certainty Against a Bottleneck of Two? @pevaquark, would you like to write a blog post for us summarizing this for a broader audience? You are very well suited to do this, and it would serve many people outside your camp.

Honesty means opposing bad arguments everywhere. Remember, it not enough to be right. You also have to be trusted. Do not expect to be trusted if you are not trustworthy.


Side Comments on Allelic Multiplicity Argument
Side Comments on Allelic Multiplicity Argument
(S. Joshua Swamidass) #3

@pevaquark, I know you are not population geneticist, but you are a scientist with a leadership role at BioLogos as a moderator. Look at this scientific claim from the BioLogos blog:

Does Genetics Point to a Single Primal Couple?

First we ask how many different alleles there are for a number of genes within the current population. Correcting for the rate at which we know new forms of genes appear (mutation), we can calculate the minimum number of people needed to generate the current amount of diversity. Numerous studies analyzing many different genes all point to a bottleneck. However, these studies are all clear: during the bottleneck, there were several thousand individuals, not two.

If these claims were false (and they are), what do you think BioLogos should do in response? If you were the author of that statement, and came to understand it was false, what would you do in response?


(T J Runyon) #4

His argument seems successful against YEC timelines correct? Bottleneck would have to be 500,000kya maybe 700,000kya with introgression.


(S. Joshua Swamidass) split this topic #5

A post was split to a new topic: Side Comments on Allelic Multiplicity Argument


(S. Joshua Swamidass) #6

Good question. The answer is “no.”

First, the allelic multiplicity argument does not concern introgression. Even if the introgression argument worked against YEC, it would not some how redeem the allelic multiplicity argument.

Second, the introgression argument only works if (1) radiodating is valid and (2) Neanderthals and Denisovans are “non-human.” Reasons to Believe (e.g. @AJRoberts) take views like this, so it is a challenge to their model. YECs however reject both these claims. YECs do not affirm the accuracy of radiodating (disagreeing with mainstream science) but are entirely consistent with mainstream in arguing that Neanderthals and Denisovans were just other “human” species or sub-species that interbred with Sapiens.

In this single regard, YECs are more aligned with the consensus than Venema. Not accepting the premise of the introgression argument, it reduces down merely to another radio-dating argument without further work that Venema has not done.

So no, on both accounts. These are not effective or valid population genetics arguments against YEC, at least not as brought forward by Venema. As I understand it, he knows this too, but does not want to retract. I’ve invited him to comment here. Perhaps you can too @T.j_Runyon. I would welcome any clarifications he has to offer. Perhaps he does, in fact, plan to correct the record. If so, we should gladly welcome it. If not, I would like to see his response to the article in the OP.


(Matthew Pevarnik) #7

Do you naturally just turn everything into some kind of vendetta against Venema? You already changed the title of the thread and made it all about him. Since I kind of made the thread to discuss the actual YEC paper, I find your change of focus rather irritating.

Okay so your conclusion is that the YEC paper is correct then from what we knew in 2016. But with the advent of you calculating TMR4A which is quite similar to the TMRCA which they already don’t seem to care about then the whole paper is now wrong.

Could you unpack that for me now? Do you simply add the qualifier that the allelic diversity of the present human population could not have arisen from an isolated primordial pair with maximum created diversity and on average constant mutation rates within the past 500 kya? But you would say that it could have arisen from a primordial human pair before 500 kya? Or something other than this?

What are the TMR4A references in the literature that include the phrase ‘strong evidence against a bottleneck of two humans within the past 500 kya?’

I’m glad that you liked that part but apologize for getting you all riled up spending at least a good hour on this.

I still need to understand more what is fundamentally wrong or how allelic multiplicity + mutation rate is different from the TMR4A argument other than TMR4A is specifically asking when specifically 4 alleles were present on average in a population (which technically could be occurring in a bottleneck of two)?

Yeah I know, unless you’re Paul writing in Philippians 1:15-18.

I appreciate that and think your thread is very helpful, but at the same time - I still don’t get the problem with allelic multiplicity.

“Leadership” should be in quotes.

If I came to understand that and why something I said was false, I would correct my incorrect claims. I do it all of the time. It’s always challenging in today’s day and age though as kind of by default in an argument if one person admits something incorrect, typically the assumption is the other person is therefore correct. It’s kind of like someone writing a YEC and OEC article critiquing evolution. And then imagining that the theory of evolution utterly fails somehow, both of the articles independently will claim this as evidence that their position is therefore correct despite being in contradiction with one another.


(S. Joshua Swamidass) #8

No vendetta at all. Just hoping for clarity.

You have a good point though. Before I answer further, would you like me to split this thread for you, so you can be kept separate from this direction? I can do that, or I can leave it as is.

You have nothing to apologize for, as this was an excellent find. Glad you brought it to us.


(John Mercer) #9

I’m really disturbed by your persistent framing of issues as rhetorical (“arguments”) instead of focusing on the evidence. It cedes way too much ground to those who produce no evidence and do nothing but argue. It allows them to more easily deceive the public about the fundamental nature of science, in which we are required to be our own critics and attempt to falsify our own hypotheses.


(S. Joshua Swamidass) #10

Sure. I’m happy to change to discus evidence. The evidence of allelic multiplicity is not evidence against a bottleneck. It is the evidence of allelic divergence that must be grappled with, and seems to rule out a bottleneck.

Is that the shift you are asking for @mercer? If so, just explain a bit more why you prefer that framing. Maybe I will switch to it. From my point of view, I am currently ambivalent about the distinction, but it seems I am missing something you are seeing.


(John Mercer) #11

That’s 100x better!

As I said, it is the framing used by those who wish to hide the fact that they are not (or are no longer) actual scientists who strive to test hypotheses. I can easily teach third-graders the concept of hypothesis testing, but it’s all but impossible for adults to unlearn the false portrayal of science as debate.

Does that explain it more fully?


(S. Joshua Swamidass) #12

Please explain more. Perhaps you just want to rhetorically emphasize that we are talking about different dimensions of the evidence, rather than merely word pushing of arguments? Of course, that is what I mean, but you are just emphasizing that there is a rhetorical benefit to saying it the way I rephrased it?


(John Mercer) #13

Of course, I am not disputing what you mean.

I think that there is a huge benefit to framing issues as hypotheses and tests thereof, because laypeople don’t really see that aspect of science. They don’t get the idea that we’re supposed to use hypotheses to make predictions and test them. This is especially common for older laypeople, who were taught that science is just a bunch of facts, not something dynamic in which every conclusion is held tentatively.


(John Mercer) #14

Here’s an example:
Q. And you also propose tests such as the one we saw in “Reply to My Critics” about how those Darwinians can test your proposition?

A. Yes.

Q. But you don’t do those tests?

A. Well, I think someone who thought an idea was incorrect such as intelligent design would be motivated to try to falsify that, and certainly there have been several people who have tried to do exactly that, and I myself would prefer to spend time in what I would consider to be more fruitful endeavors.

Q. Professor Behe, isn’t it the case that scientists often propose hypotheses, and then set out to test them themselves rather than trusting the people who don’t agree with their hypothesis?

A. That’s true, but hypothesis of design is tested in a way that is different from a Darwinian hypotheses. The test has to be specific to the hypothesis itself, and as I have argued, an inductive hypothesis is argued or is supported by induction, by example after example of things we see that fit this induction.

Any working scientist that reads that immediately sees that Behe has abandoned the fundamental basis of science, but most laypeople won’t see it that way.

Thankfully, Judge Jones saw it in the way that we do.


(S. Joshua Swamidass) #15

Okay, you are convincing me. This is a very important point. Science doesn’t exactly producing a bunch of facts, nor is it a static unquestionable almanac. It isn’t merely argumentation either. It is, at least in part, a systematic process of proposing and testing hypothesis to judge evidential claims about hypotheses.


(John Mercer) #16

And it’s your duty to try and demolish your favorite hypothesis.

In the argumentative presentation of this, it’s not, “I’m right and this is the evidence that supports me,” but rather, “This hypothesis is consistent with the evidence, because if it wasn’t, we’d observe x, y, and z, and we don’t.”


(S. Joshua Swamidass) #17

Absolutely. It is also your duty to demonstrates where the evidence works just as well under a disfavored hypothesis. We are supposed to be our own adversaries to the extant that we can possibly do so.

Yes. Once again, this is why it is so critical to recognize when we are putting forward bad arguments. It is not merely about having the right conclusions or hypothesis in hand. It is about correctly working out our evidential case, and “showing our work.”


(George) #18

@swamidass,

I’m still plowing through the new postings here.

As you can see here, in this post, @pevaquark has the same befuddlement as I did! I assume you will be explaining (at some point, down below) that what is wrong is that Venema wrote:

“number of alleles” instead of writings “degree of divergence into multiple traits”, since counting merely the number of alleles is not a good methodology.


(John Mercer) #19

It’s also important to avoid personalizing our hypotheses, but instead seeing them as tools that work even when they are disproven. Personalizing makes that much harder to do.


#20

OK, let me see if I get.

Hypothesis: a possible explanation but not enough evidence to conclude.

Theory: a current best explanation for something with evidence we have.

Did I get this right?