Critique of Behe and Snoke Available

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Michael Lynch’s critique of Behe and Snoke (2004) is now available as is a reaction by Behe and Snoke. Don’t forget to read the editor’s message about it as well.

We’re still discussing it, but here is Lynch’s abstract.

Lynch M (2005) Simple evolutionary pathways to complex proteins. Protein Science, 14:2217-2225.

Abstract: A recent paper in this journal has challenged the idea that complex adaptive features of proteins can be explained by known molecular, genetic, and evolutionary mechanisms. It is shown here that the conclusions of this prior work are an artifact of unwarranted biological assumptions, inappropriate mathematical modeling, and faulty logic. Numerous simple pathways exist by which adaptive multi-residue functions can evolve on time scales of a million years (or much less) in populations of only moderate size. Thus, the classical evolutionary trajectory of descent with modification is adequate to explain the diversification of protein functions.

Ricardo Azevedo has some view up on his blog: BS Model Gets Lynched.

28 Comments

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Hmmm. I may be the only one in the forum without a subscription to Protein Science, but the main link above requires you to be a subscriber to access. Anyone care to provide a synopsis?

My bad. Ricardo’s blog does provide some insight into Lynch’s critique and the BS response. Would be nice to see the original documents without violating copyright.

Behe and Snoke’s reply is a hoot.

1.) If Lynch assumed complete neutrality, then he’s making an unwarranted assumption. However, he went into extensive references, including those used by Behe and Snoke, to back up that part of the model. And there was a caveat which I didn’t catch–did anyone else catch it?

2.) Of course.

3.) Well, so Behe and Snoke are assuming that intermediate states always decrease function? That very well may be closer to the truth than Michael Lynch’s assumption, but they’re still assuming very broad things about the nature of mutation.

4.) But, if you first have to sacrifice function, then it’s a cost you pay up front. Or, as Bush would way, “I never said you had to give up your social security benefits, you simply forfeit them in order to possibly achieve more wealth under a privatized system.”

5.) Gee, gotta look these things up. The next part of Lynch’s sentence is “as the latter authors do not explicitly model the evolutionary process, whereas the stochastic computer simulations presented here precisely track the joint dynamics of allele frequencies.” It sounds pretty darned pendantic for Behe and Snoke to go telling Lynch about the fundamentally different models, which he stated very clearly himself. Lynch is saying that it’s hard to compare the models, because one is essentially invalid. But Behe and Snoke don’t let this opportunity to twist things slip by.

6.) Yes, IIRC Behe and Snoke used a general point mutation rate in their model and have no sleective effect operating on intermediates. This implies that the forward and reverse reaction rates are equal, which is what Lynch said. “But, officer, I didn’t speed through that school zone. I never accelerated past the 35-mph posted speed limit.”

7.) Perhaps Lynch is over-simplifying Behe and Snoke. But it depends on what they meant by “strongly selected against.”

8.) And that mutations are assumed to be deleterious is the fundamental reason that this is a non-Darwinian model, and an unrealistic one. This is the central point of Lynch’s critique, and one they seem to blithely ignore. “It’s because our model assumes this to be the case, of course. Oh, we didn’t realize he was criticizing the fundamentals of our model… well why didn’t he say so?”

9.) But it seems that it shoudl still hold for a model like theirs, even if mutations are always deleterious– 0 = 0.

10.) And they’re going for the gusto–no matter how bad their model is, they’re out to claim that Darwinian processes aren’t gonna cut it.

Behe and Snokes’s actual points (as opposed to Cerutti’s spin):

1. Experimental studies contradict Lynch’s assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function. 2. Lynch’s and our models are not mutually exclusive. Some evolutionary pathways might involve both deleterious and neutral mutations. 3. Lynch writes in the section “The Model” that we “imply that all amino acid changes lead to nonfunctionalization.” We imply no such thing. Although we assumed that intermediate mutations required for a new feature decreased function, we wrote, “it can be calculated that on average a given position will tolerate about six amino acid residues and still maintain function.” Our estimation of {rho} explicitly takes into account the tolerance of sites for substitution. 4. In “The Model,” Lynch writes, “As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein. …” We made no such assumption. In our model, the final mutation might restore and enhance the original function. 5. In the Discussion, Lynch writes, “It is difficult to pinpoint the source of the difference between the results of Behe and Snoke and those contained herein. …” The differences are largely due to opposing starting presumptions about whether mutations are deleterious. 6. In the Discussion, Lynch writes, “Behe and Snoke assume that the forward and backward point-mutation rates (per amino acid residue) are equal.” We do not. The mutation rate we use is the nucleotide point-mutation rate. 7. In the Discussion, Lynch writes that we assume mutations have “lethal pleiotropic effects.” We did not assume mutations to be either lethal or pleiotropic. We only assumed that they are “strongly selected against.” 8. In the Discussion, Lynch writes, “If the intermediate steps … are entirely neutral after gene duplication, as Behe and Snoke assume, then there is no compelling reason that ‘one-off’ (type-2) alleles should be absent from the population prior to duplication.” The reason for no “one-off” alleles before duplication in our model is that intermediate mutations are assumed to be deleterious in a singlecopy gene. 9. In the Discussion, Lynch writes, “Behe and Snoke failed to realize that a completely linked pair of duplicate genes has a mutational advantage equal to the mutation rate to null alleles. …” Such an effect does not hold for a model like ours in which intermediate mutations are postulated to be deleterious. 10. A recent report (Gao and Innan 2004) presents evidence that the gene duplication rate is lower by several orders of magnitude than that assumed both by Lynch and by us based on the work of Lynch and Conery (2000). If so, then both his and our calculations for the population sizes needed to fix a mutation in a duplicated gene are substantial underestimates.

Behe and Snoke’s actual points are available on the links provided at the top of the thread. I have responded as I see appropriate, but not being a geneticist I’m not authoritative. I was hoping that other PTers might be able to better inform me.

I love how this stuff works, though: presenting to an audience? Spin your case so as to appeal to the broadest number of people possible. Arguing with a scientist? Keep the burden of proof on him, and then (if he slips up or says something wrong) pound him for all you can, or (if he makes factual points that you can’t argue with) call it all a bunch of political spin and crown him with the encomium “oh, too good! You’re a better spinmeister than I, but someday you evolutionists won’t have all the money and choke-hold on what’s allowed to pass for truth!”

Behe and Snokes’s actual points (as opposed to Cerutti’s spin):

How come I, uh, don’t see any actual scientific theory of ID anywhere in Behe and Snoke’s, uh, actual points … ?

someday you evolutionists won’t have all the money and choke-hold on what’s allowed to pass for truth!”

Waterloo !!!! Waterloo !!!! Waterloo !!!!!!

I wonder why Behe and Snoke done have any, uh, actual scientific theory of ID anywhere in their, uh, actual points . …

When people read Behe and Snoke (2005) remember Behe’s statements at DDDV about his work:

So the point is that, whenever you have an apparatus that needs three or more proteins in order to work, that’s essentially beyond the capacity of random mutation and natural selection to produce. Even when you have something that only has two proteins stuck together, that’s a very very rare event in the history of life on earth. So the tentative conclusions from this–and there are a couple of caveats that I haven’t gone into but which I’d glad to talk about if you wanted to–two tentative conclusions: that is that the formation of new protein-protein interactions would be very rare in the history of life, and the formation of two such interactions in an irreducibly complex complex is practically impossible. So what I think is going to turn out to be the case–although we will be required to do it–is that design is going to be seen to extend very deeply into the cell and perhaps beyond that as well.

(Transcribed form an audio recording.)

Does Behe really not subscribe to triumphant views of his work?

Another variation on this theme can be found in an advance online publication in Nature Reviews Genetics: Missense meanderings in sequence space: a biophysical view of protein evolution. One of the authors is Daniel Hartl, author of a popular textbook on population genetics. (The link gets you to the abstract and a summary of the paper - you need a subscription to get the whole thing.)

These authors take a different view of point mutations from BS and Lynch - they claim that few missense mutations have an impact on a protein’s biochemical function; instead most mutations have an impact on a protein’s stability. This is a distinction not found in the Protein Science articles, as far as I can tell.

I think this paper is an even better answer to the BS one.

Taken as a whole, recent findings from biochemistry and evolutionary biology indicate that our understanding of protein evolution is incomplete, if not fundamentally flawed.

Michael, I seriously recommend you look over that article again. I’m no biochemicals expert, but that opening sentence really blows a hole in the propaganda this site seems bent on forcing into the minds of America’s shool kids.

When one of your own admits that evolution’s a bunch of hooey, the gig’s pretty much up, as they say…

When one of your own admits that evolution’s a bunch of hooey, the gig’s pretty much up, as they say…

Nice quote mining but you are ofcourse missing the point a bit. Of course even if our understanding is flawed, this does not mean that evolution did not happen nor that there is much support for the creationist ID viewpoint.

from the article Wrote:

# We propose a new model of protein evolution that is reminiscent of a constrained ‘random walk’ through fitness space, which is based on the fitness consequences and distribution of mutational effects on function, stability, aggregation and degradation. # This model can account for both the micro-evolutionary events that are studied by biochemists and the long-term patterns of protein evolution that are observed by evolutionary biologists

Now that is interesting…

typically confused creationist Wrote:

When one of your own admits that evolution’s a bunch of hooey, the gig’s pretty much up, as they say…

This is like saying that, if our understanding of star formation is incomplete, then stars don’t form.

Umm, you guys did realize from the name on my post that I was joking, right? Or shall I pull another admonitus and impersonate a creationist of some bizarre strain for many days before letting the cat out of the bag?

Umm, you guys did realize from the name on my post that I was joking, right?

Short of admitting it, parodies of creationist quote miners are not reliably distinguishable from the real thing, when we have folks like Sal Cordova referring to an “honest quote mine” maintained by IDists.

Oh, well, in that case I suppose it’s finally time to let the cat out of the bag.

I’m actually the one who posts as Sal Cordova.

The IP addresses show up differently because I only post as him when I’m in a certain building on campus, which I’m in frequently enough. He was a character I invented a long time ago, and trolling Dembski’s blog pretending to be a sycophant of that man has been more than hilarious, at least from my perspective. Of course I had to keep up the ruse, by insulting Sal now and then when I came to PT or Dembski’s blog as myself. But, it’s been fun. There may be periodic reappearances of Sal, but just know that he’s not in fact a real person.

I’m seeing it now … Dave Cerutti … D C … Designed Creationists … ah, my own Antony Flew moment.

When one of your own admits that evolution’s a bunch of hooey, the gig’s pretty much up, as they say…

“Intelligent design itself has no content”.

Is that a gig I see?

1. Experimental studies contradict Lynch’s assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function.

That assertion of decreasing function would be to ignore: that any optimisation has already taken place at all via evolution; that proteins can have more than one function which might be affected in different ways (eg acquiring a new useful one which offsets a slight reduction in effectiveness at an old one); that the environment can change to affect the relative fitness (eg some codings work better at higher temperature through being more stable against denaturing while others work more rapidly at a cooler temperature, or acid/alkali environment, or mineral-rich/poor environment etc).

In Comment #45964

Qualiatative Wrote:

1. Experimental studies contradict Lynch’s assumption of complete neutrality as a rule; the majority of amino acid substitutions decrease protein function.

This simply isn’t true. Lynch quotes several experimental studies (eg Guo et al. (2004)) that show that the majority (~70%) of substitutions are neutral, even the papers quoted by Behe & Snoke in their original paper show that the majority of substiutions are neutral (see Theory is as Theory does for a detailed discussion of this (you have to scroll down a bit)).

The rest of Behe & snokes points are like this one, either flat out wrong, or completely missing the point

Bottom line: Behe & Snoke are committed to their religious preconceptions, and are not going to ever concede anything. Do I “know” this, in the same way I know, say, vertebrates share a common ancestry? No. I “know” it in the same sense I know that Dubya will never concede that his Iraq adventure was miscalculated, and the same sense that I “knew” Clinton was lying about Monica.

Any of these pieces of “knowledge” I would be perfectly comfortable taking to the bank, but to try, through logical discourse, to get the principals to concede, would be tilting at windmills. All you can do is force them to retreat to ever more bizarre evasions. Sometimes that’s worth it; sometimes it’s not.

Comment #46003

Posted by Dave Cerutti on September 1, 2005 01:45 AM (e) (s)

Oh, well, in that case I suppose it’s finally time to let the cat out of the bag.

I’m actually the one who posts as Sal Cordova.

Yeah, right, and I’m Intelligent Design Theorist Timmy.

Ian Musgrave Wrote:

This simply isn’t true. Lynch quotes several experimental studies (eg Guo et al. (2004)) that show that the majority (~70%) of substitutions are neutral, even the papers quoted by Behe & Snoke in their original paper show that the majority of substiutions are neutral (see Theory is as Theory does for a detailed discussion of this (you have to scroll down a bit)).

Actually, the Guo paper (and others) show this proportion of substitutions maintain some function, not that they’re necessarily neutral. This is what B&S are dickering over. Lynch took pains to point out evidence showing that even substitutions that lower activity are tolerated and can be fixed. There is no reason to believe that just because an enzyme’s activity goes down by 20% that selection is going to weed it out. (For most enzymes, this would be selectively neutral, or nearly so.)

Yeah, right, and I’m Intelligent Design Theorist Timmy.

Intelligent Design Theorist Timmy, it’s time to really shake things up around the ID world.

For the time being, I have nothing to contribute. Michael Behe decisively refuted evolution. So did William Dembski. And David Heddle. And Charlie Wagner. And Ken Ham. And Kent Hovind. And myself. We have proven the same thing at least seven times conclusively. But there is a little delay in the recognition by the authorities-that-be. So now all there is to do is sit around and wait for the paradime change. Sometime soon it will happen. Beginning at Harvard and CalTech, and the other Ivies, and continuing through the lowly state colleges, and across the world, biology departments everywhere will cancel most of their erroneous research, empty their libraries of millions of disproven papers, and finally, replace most of their staff with experts in the new paradime. Freed from the clueless old evolution paradigm which has smothered biology for 140 years, biology will enjoy a huge rebirth, and finally be able to make some progress.

You accidentally spelled “paradigm” correctly in one place.

Henry

Can you evolutionists do anything other than Ab Homonym?

I have become bored of you people playing pretend creationists. Please cut it out for the rest of this thread.

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This page contains a single entry by Reed A. Cartwright published on August 31, 2005 3:27 PM.

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