Lents and Hunt: Behe And The Polar Bear's Fat

Science

(S. Joshua Swamidass) #1

Great article by @art and @NLENTS

Behe writes:

But what precisely did the changes in polar bear APOB do to it compared to that of other mammals? When the same gene is mutated in humans and mice, studies show it frequently leads to high levels of cholesterol and heart disease. The scientists who studied the polar bear’s genome detected multiple mutations in APOB. Since few experiments can be done with grumpy polar bears, they analyzed the changes by computer. They determined that the mutations were very likely to be damaging -that is, likely to degrade or destroy the function of the protein the gene codes for.

And there’s more. If we come back to APOB, the polar bear gene that Behe spends the most time discussing, we find that the authors of the study have a very different interpretation of the data than Behe does. Quoting the paper again [emphasis added]:

Substantial work has been done on the functional significance of APOB mutations in other mammals. In humans and mice, genetic APOB variants associated with increased levels of apoB are also associated with unusually high plasma concentrations of cholesterol and LDL, which in turn contribute to hypercholesterolemia and heart disease in humans (Benn, 2009; Hegele, 2009). In contrast with brown bear, which has no fixed APOB mutations compared to the giant panda genome, we find nine fixed missense mutations in the polar bear (Figure 5A). Five of the nine cluster within the N-terminal ba1 domain of the APOB gene, although the region comprises only 22% of the protein (binomial test p value = 0.029). This domain encodes the surface region and contains the majority of functional domains for lipid transport . We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood .

Clearly, the authors do not expect the polar bear APOB to be “broken.” Rather, a bare majority of the amino acid changes are in the most important region for the clearing of cholesterol from the blood. In other words, these mutations likely enhance the function of apoB, at least when it comes to surviving on a diet high in saturated fats.

To recap: 1.) There is no evidence for Behe’s claim that APOB is degraded or diminished in polar bears and everything we know about the protein from other mammals suggests the opposite. And 2.) Behe’s claim that the most common adaptive changes in polar bears are those that degrade or destroy proteins is not supported, and the evidence suggests otherwise. Those are just the errors that we found in his first example.

And yet Behe makes this bold claim:

It seems, then, that the magnificent Ursus maritimus has adjusted to its harsh environment mainly by degrading genes its ancestors already possessed. Despite its impressive abilities, rather than evolving, it has adapted predominantly by devolving. What that portends for our conception of evolution is the principal topic of this book.

Behe’s Response

Behe responds here: Behe: Responding to the Polar Bear's Fat. Unfortunately, he doubles down on his mistake.

That is on top of making a very misleading edit in his response:

This was just an unnecessary multiplication of existing error. What is in this table is beside the point.

Very unfortunate.


Darwin Devolves: The End of Evolution?
Behe on Lessons From the Polar Bear Studies
Behe on Lessons From the Polar Bear Studies
Detwiler: Questions Behe, Polyphen, and Ratchets
Did Behe mess up the science of "devolution" in polar bears?
Three Misrepresentations on Darwin Devolves' Back Cover
I Agree With Behe
(Nathan H. Lents) #3

Special thanks to @Art for catching this. I have to confess that I simply took Behe at his word regarding the evolution of polar bears involving mostly protein-damaging mutations. It’s his opening example. It’s the way that he chooses to introduce us to his concept of “devolution.” This example would have to be air-tight, right? I stayed up until 230a last night reading the Cell paper very carefully because I just couldn’t believe that Behe would be this careless. I’m almost HOPING Art and I wrong here because it can’t be this bad, can it?


(S. Joshua Swamidass) #4

Of note, @Joel_Duff has written much about Polar Bears too! The Polar Bear Diagnostic For Origins Views.


(S. Joshua Swamidass) split this topic #5

8 posts were split to a new topic: Lents Unmentioned


(S. Joshua Swamidass) #13

In the Science review, @NLENTS, we were necessarily focused on the larger arguments. There were beautiful gems through out the book, that would have been rabbit trails for the main review.

That’s great. Though, let me suggest we make it more about about how cool biology is than just litigating minor points. He has some good points too.

I thought the reference that explored why it is good to have a “backwards” retina was quite good. It is an example of how bad design argument are vulnerable, and reveals something really cool about how we see the world. And yes, there were gems that were mistakes too.

Maybe. We can dream, can’t we?

By the way, your T-urf13 article is in Zenodo, ready to reference.


(Nathan H. Lents) #14

Silent no more. Behe on Darwin Dissent List: “Overselling Darwinism Means Downplaying Its Difficulties” | Evolution News

No mention of the polar bears. They must be preparing a special hit piece for @Art and me, because this one really lays into you, Josh.

Btw, how’s it going with the piece on T-urf13? I mention that in my skeptic essay, so if you do something more recent then the piece at Panda’s Thumb, I can link to it on the e-version of the article.


(S. Joshua Swamidass) #15

@nlents and @art what do you make of it? They seem surprised I said something (many things) kind about Behe. I meant it too. I suppose it doesn’t fit their narrative. Cognitive dissonance?


(Nathan H. Lents) #16

I just finished reading your post. Of course it will confuse them. It also kind of confuses me. The tone is strikingly different than our review in Science. I can see how you are threading the needle, but I have to squint very hard. Oh well. I hope you’re not expecting a positive response. Olive branches don’t seem to be the specialty of the DI (with a couple exceptions). I’m not saying that Behe is mean or conflict-seeking, but he seems kind of shy and unwilling to engage much. Just my impression.


(S. Joshua Swamidass) #17

Hehe I can see what you mean. I figured I try and offer them an olive branch. I expected they would not know what to do with it. Oh well, maybe next time.

The thing is this isn’t a hit peice. We actually agree with him on a lot. The fairly remarkable thing is that he affirms common descent. More than once I’ve had people argue this isn’t true. I think pulling the quotes from the book where he affirms common descent would be educational.


(T J Runyon) #18

They are becoming really fond of the terms “hit piece” and “firing squad”. Also my favorite thing about ENV is when they link to another piece. More often than not it’s another ENV post… “As others have observed.” Yes, others that are in your tiny bubble. If Klinghoffer wasn’t there I probably wouldn’t mind the DI so much.


(T J Runyon) #19

I would like the reviewers opinion on this. So @swamidass and @NLENTS. And maybe even @Art and @John_Harshman.

Do you guys not think Behe’s latest argument is in tension with decades of ID/Creationist arguments (I’m not conflating the two Kinghoffer)? You always hear evolutionary processes can only cause a loss of genetic information or at most rearrange it. And you need an increase in information to have significant change. But then I think of this paper and others like it that show loss of function mutations can cause significant change. Like loss of limbs:

So I’m failing to see how most changes being “a loss of function change” is a problem. To me it seems like evolutionary processes don’t need lots of new info for macroevolutionary change.


(S. Joshua Swamidass) #20

@art’s T-urf13 paper is here:


(John Harshman) #21

It would be a problem because most changes that get selected are not loss of function changes, and there are plenty of gain of function changes. Of course it’s not a problem because those changes do happen.


(S. Joshua Swamidass) #22

However, the loose way Behe defines loss of function mutations means he might even call a gain of function mutation a loss of function.

A classic example is that of the polar bears. As they evolve white coats, he calls it a loss of function. As they gain more effective APOE, he calls it loss of function. In both these cases, they are better understood as gain of one function and loss of another.


(Arthur Hunt) #23

The DI mantra goes something like this:

Evolution can break proteins, which allows for small changes (like the color of polar bear fur). Evolution cannot create new functions, which would be needed for things like new body plans (Cambrian Explosion etc…). Since Behe has proven that evolution can only break proteins, then evolution can’t explain the Cambrian Explosion etc…

I know, I know, so many incorrect claims. That’s the point of the responses.


#24

Pace Lee Spetner a couple decades ago. How shocking that Dr. Behe should adopt Spetnerian metrics…


(Neil Rickert) #25

So we lost our fin function (from earlier fishes). That’s why we have to get by with walking. And we lost our gill function, so we have to get by with breathing. It’s front loading all the way. That’s possibly how Behe is thinking about it.


(Nathan H. Lents) #26

Still no response from EN or Behe about the polar bears (but they do have another article about us today, nothing new in it). Jerry Coyne did just blog about our post, though.


(Nathan H. Lents) #27

Maybe others answered this already, hard to keep up, but I think what they would say is that there are two kinds of adaptive evolutionary change. One is driven by mutation and generally involves loss/damage of something at the molecular level but bringing positive changes nonetheless (like polar bears losing pigment or wales losing forelimbs). This would lead to a gradual steady “loss of genetic information” (their words). So the other mechanism, and this is where the real innovation comes in, is the influx of new genetic information from the designer. They don’t say too much about that (wonder why) but when pressed, some say that “ongoing creation” is possible (or ongoing miracles, as it’s sometimes called), and others prefer the “perfect pool shot” that all the information is there in the genomes from the beginning of time, waiting to unfold at the right time. You will note the utter lack of evidence for either possibility. However, I don’t see a contradiction with Behe’s latest book. He threads the needle very carefully in that regard. That’s my $0.02


(S. Joshua Swamidass) #28

@Nlents and @Art repost on Panda’s Thumb.

https://pandasthumb.org/archives/2019/02/celebrating-darwin-day.html