Part 2 of Polar Bear Seminar

Polar bears don’t have lower plasma cholesterol levels compared to brown bears. There doesn’t appear to be any significant difference between plasma cholesterol levels for the two species, higher or lower. Therefore, there is no phenotype consistent with a damaged APOB protein.


I don’t care if DI responds. Who are they?

I care if Behe responds. Real scientists don’t point to anonymous posts from a non-scientific advocacy group to deal with critique. Behe knows this of course. As for me, I await his response. Of course, he likely has no response that he is willing to put his name on, so I’m happy to take it as a concession.


Behe responded personally to Lenski and indirectly to you and lents. You would consider a response only when your and Nathan Lents names will be mentioned with high prestige at the beginning of the post? like he did with Lenski,

Professor Lenski is perhaps the most qualified scientist in the world to analyze the arguments of the book. He is the Hannah Distinguished Professor of Microbial Ecology at Michigan State University, a MacArthur (“Genius Award”)

so, the whole issue is the term “some other guy’’

Actually, I am a computational biologist that has actually published on PolyPhen 2, more than once. I can tell you that Behe does not understand the output of that program and Lenksi, even though its outside his field, understood it precisely correctly. The right way to characterize Behe’s response is “non-responsive.” Do you know what that means?


You can blame about the methodology of the program with the author of the paper, Behe did not run program and wrote the paper and concluded damaged

This is falsehood. Total falsehood. Why continue to lie about it? The paper did NOT conclude damaging.

Please stop lying. I rarely say this, but this is one of those times it is necessary. Stop lying.


If he is going to make the output of the program the key example that demonstrates his thesis, then yes, he better be damn sure he understands the program and its limitations.


Actually, DI responded to this in the second Polar bear Seminar, i was not attentive

When Lents and Hunts claim that the mutations in APOB “likely enhance the function of apoB,” that is their own speculation. They focus on a statement in the paper that the adaptive changes in APOB “enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.” Perhaps that is true, but the paper presents no evidence that the removal of cholesterol was accomplished by constructive mutations. Indeed, as Behe [pointed out](Lessons from Polar Bear Studies | Evolution News), cholesterol may be removed by decreasing the activity of APOB .

This was answerend in the second Polar bear seminar, indeed they mentioned your name, and i have not heard your view, respons to this, aahh because it was not Behe personally

@davecarlson, what is fairly remarkable about this is that the best move for him to do would have been admitting error, and making his case with other data. That would have given his thesis a fighting chance. They have not done this, but doubled (trippled?) down. Now, the whole ship goes down on this misquote of a paper. Very bad move for them.

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The paper did not conclude “damaging,” but the opposite. Saying otherwise is not truthful. You can disagree with the authors, but you can’t claim they said something they clearly did not. Do not lie.

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Good luck with this guy, lol.

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Just noticed this update to the article:

Update: Joshua Swamidass now writes in response to this post “Are they just ignoring the fact that the authors concluded that the mutations were not damaging?” This is a false accusation because the authors of Liu et al. (2014) did not conclude that the mutations were not damaging. Rather, as we have repeatedly documented throughout this post, they concluded, “[W]e assessed the impact of polar bear — specific substitutions on human proteins for top-20 genes under positive selection by computational predictions: a large proportion (ca. 50%) of mutations were predicted to be functionally damaging .” (Emphasis added.) That was their conclusion. They concluded that the mutations were “predicted to be functionally damaging.” There is no language to the contrary in the paper, and the burden is upon critics of Behe to provide language which shows that the authors specifically argued that the mutations were not damaging.

I’m going to bed now, but I will pull the quotes tomorrow that show that the authors did not conclude they mutations were damaging. These quotes have already been shown to DI, and it is fairly remarkable they have, apparently, forgotten them.

Note, the text the quote by DI is not a conclusion but an observation.

The claim that the authors concluded they are damaging? That is total falsehood. They did iobserve the prediction of “damaging”, but went on to conclude that they were not likely damaging. Behe is free to disagree with the original authors but they absolutely did not conclude that the mutations are damaging.


This looks like a losing hand to me.

The point should be that Behe has a hypothesis and Behe should be testing it, but he’s not. This is what scientists do, and Behe isn’t doing it.


I am happy to explain how to test their hypothesis on polyphen too. The misquote is important at the same time.

Wow. They’re shameless.

Here is the whole part 4:


Behe et al. need to be reminded that a mutation predicted by PolyPhen2 to be benign is not necessarily a neutral mutation. Especially if it is positively selected. Part 4 provides more evidence that Behe does not understand the tool and its use.

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Wow. Throughout the article they continue to misunderstand PolyPhen with quotes like this:

Data only challenges Behe’s thesis when a mutation is shown to be constructive. In this regard, it’s crucial to point out that the mutations that Behe didn’t list from the chart that were not said to be damaging were also NOT said to be “constructive.” They were said to be “benign.” That’s a key point that completely undermines Lents’s charge that the data Behe doesn’t list is somehow “contrary” to his position.

This passage seems to assume that the 3 possible predictions PolyPhen can make are “damaging”, “benign”, and “constructive”, which as we’ve been over time and time again is NOT the case.