Guest Contributor posted Entry 3270 on August 2, 2007 05:36 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3257

by Abbie Smith

Editor’s Note: This is a guest post by Abbie Smith, the blogger behind the Endogenous Retrovirus (ERV) blog (original post), who we marked early as having a special talent for this creationism-rebutting stuff. Abbie works in an HIV lab and has a few things to say about Behe’s argument in The Edge of Evolution that evolution hasn’t/can’t produced any novel adaptations, genes, or protein-protein binding sites during the evolution of HIV, the virus that causes AIDS, unless you are one of the several Discovery Institute fellows who denies this along with denying evolution.

Oh, and speaking of the Discovery Institute and Behe, Behe is apparently going to be on the Colbert Report tonight. Colbert has been setting an excellent example by making a point of it to bring scientists on his show – Kenneth Miller, Neil DeGrasse Tyson, Shubin I think. Hopefully Colbert knows that Behe isn’t quite like these other guys. I recall that Dembski claimed he was sick after he appeared on The Daily Show next to some weird new-ager in 2005.

Anyway, if Colbert doesn’t hit the appropriate snark mark tonight, you’ll get it from Abbie for sure. I thought I got Behe pretty good in Of Cilia and Silliness, but this really takes the cake.

—Nick Matzke


Michael Behe, please allow me to introduce myself…

I’m ERV. This is my dog, Arnold Schwarzenegger. And this is my friend, Vpu. I presume you and Vpu haven’t met, as you recently repeated in an interview with World magazine the same sentiment you gurgled ad nauseam in ‘Edge of Evolution’:

“Like malaria, HIV is a microbe that occurs in astronomical numbers. What’s more, its mutation rate is 10,000 times greater than that of most other organisms. So in just the past few decades HIV has actually undergone more of certain kinds of mutations than all cells have endured since the beginning of the world. Yet all those mutations, while medically important, have changed the functioning virus very little. It still has the same number of genes that work in the same way. There is no new molecular machinery. If we see that Darwin’s mechanism can only do so little even when given its best opportunities, we can decisively conclude that random mutation did not build the machinery of life.”

I find it rather difficult to believe that you two haven’t crossed paths, as Vpu turns up in a simple Google search. And as a matter of fact, Vpu is sitting right there in the totally unnecessary and worthless diagram in ‘Edge of Evolution’. See? Right there:

If you had taken the time to label this pointless diagram, you might have noticed your error, and we wouldn’t need to have this conversation. Alas, Vpu is a tiny molecule, and he’s easy to overlook if you don’t want to see him.

Vpu is, in fact, a new gene.1 Of the five major phylogenetic groups of SIV, Vpu is only found in one group– Chimpanzee SIV (SIVcpz) and its descendants – including HIV-1. It is absent in all of the other major lineages (Sooty Mangabey, African Green Monkey, Sykes Monkey, and L’Hoest Monkey). This means that Vpu is in HIV-1 but not HIV-2.2

Ah, Michael Behe, you might try to talk your way around Vpu now (though you were evidently unaware of its existence moments ago) by insisting that it is not *new* new. “Sure it’s new in chimpanzees, but its not *new* in HIV-1!” Sorry, you’ll find no escape with that limp-wristed, ad hoc parry. SIVcpz Vpu and HIV-1 Vpu act in different ways, biochemically, which is predictable enough when you do something as simple as comparing amino acid sequences. For instance, if you compare a laboratory strain gag to SIVcpz gag, you get a similarity of ~75%.3 Not too shabby. On the other hand, if you compare the subunit portion of env (the gene I use to create phylogenetic trees because it’s the most variable between viruses) you get an AA similarity of only ~59.5%.

The amino acid similarity between HIV-1 Subtype B Vpu and SIVcpz Vpu is ~37%. Ah but that study was published in 1990. Perhaps things are different now? I found the AA sequence of NL4-3 (lab standard Subtype B) and several recently entered SIV cpz sequences at the Los Alamos National Laboratory HIV Sequence Database4 – I got the same numbers. Highest was ~39% AA sequence similarity.

Turns out a LOT of evolution has been going on in HIV-1 since it was transferred to humans 50-60 years ago. What are the biochemical implications of these differences?

In humans, there are two functions of Vpu5 – one is inducing the degradation of CD4 molecules. CD4 is the host cell receptor HIV needs for infection. Removing CD4 from the cell surface prevents superinfection (more than one virus infecting the same cell) and helps prevent newly released viruses from turning around and infecting the same cell (also prevented by an HIV maturation step involving protease). To put this the simplest way possible, Vpu involves the evolution of at least two protein-protein interaction sites – one to interact with CD4, one to interact with the pathway that degrades the CD4.

The second function is to act as an ion channel in the host cell plasma membrane.6 Five Vpu proteins come together to form a Na+K+ viroporin.7 This has been shown to assist in particle release, making the cell charge more conducive to the release of new particles. This involves the evolution of more protein-protein interactions – the individual Vpu proteins must interact to form the pentamer, plus an action site that can be used to block ion flow.8

Viroporin capabilities have not been found with SIVcpz Vpu. Knowing what we know about Vpu, this is not surprising. If you scramble the transmembrane region of HIV-1 Vpu (the portion responsible for the ion channel formation), viral release is crippled.9 And when you compare AA homology between SIVcpz and HIV-1 Vpu in the transmembrane region is unremarkable (roughly two) – that’s as good as a ‘scramble’. So theoretically, ion channel formation evolved in HIV-1 when it infected humans to overcome a species specific and cell specific host factor.10 Though the list of viroporins discovered is continually growing, the evolution of a viroporin de novo is not menial task.

This seems like a pretty significant biochemical change in HIV-1, to me.

But the ‘pathetic’ evolution doesn’t stop there. The feature both Vpus have in common, CD4 degradation, is carried out in completely different ways. HIV-1 Vpu requires two casein kinase II sites. You could almost call it irreducibly complex – if you dont have both CKII sites, CD4 isn’t degraded. Yet some SIVcpz Vpus have only one CKII site, and instead utilize a simple string of negatively charged amino acids in place of the second site.11 Different ways of performing similar tricks with totally different amino acids. I think that’s biochemically significant as well.

Ah, Michael Behe, you might try to talk your way around Vpu NOW by saying, “Vpu might be *new* new in HIV-1, but its not *NEW* *new* new. It hasnt changed in HIV-1 since humans acquired it!”

Alas, ‘same number of genes that work in the same way’ goes beyond the differences between HIV-1 Vpu and SIVcpz Vpu. HIV-1 is divided into three groups, M, N, O. Group M is the one making a mess of the world right now, and is further divided into Subtype A, B, C, etc, and circulating recombinant forms of the subtypes (Subtype AG, for instance). Two relatively well characterized subtypes are Subtype B and C. Subtype C HIV can be defined by its Vpu, as it is so different from the other subtypes.12

For instance, Subtype C Vpus are characteristically longer than the others, have key phosphorylation sites shifted, have an extra CKII site, and its tertiary structure is totally different (Subtype B Vpus have an Mr of 43,000 in an SDS-PAGE gel, while Subtype C is 34,000). But what does this mean, biochemically?

It turns out that one of the biochemical differences is that Subtype B Vps have a Golgi retention signal in the second alpha-helix of the cytoplasmic domain.13 This means that Subtypes B Vpu prefers (if you will excuse me personifying a virus) to be in the Golgi, helping degrade CD4, while Subtype C Vpu prefers to be in the plasma membrane, assisting with the release of new viruses. Michael Behe, if you don’t understand the epidemiological and clinical significance of this ‘pathetic’ evolution, well, that might explain why you aren’t doing HIV research.

So here’s a quick time-line for the evolution of impossible genes and impossible protein-protein interactions, courtesy of Ian Musgrave (one of those dreadful PhDs/Professors that has something to teach this pre-grad student):

Michael Behe, as a courtesy to you, this essay isn’t even going to touch Vpx, a gene specific to the HIV-2 and SIV sm lineage. Vpx is one of those pesky gene duplications you say don’t exist in HIV (Vpr x2). I also won’t point out how silly it is of you to claim HIV has not evolved biochemically, when the HIV research community has barely scratched the surface of HIV’s biochemical evolution (for the love of Pete, we don’t even know what HIV-1 Subtype Cs gp120-gp41 look like!).

Look, the fact of the matter is, all of this information on Vpu is publicly available. No one was hiding this information. This wasn’t a ‘trick.’ Vpu was not discovered yesterday – it was discovered in 1988. There is no excuse for you to write an entire book on the premise of HIV not being able to do something, when it is clear that these impossible feats did happen. This is just one of a billion plus examples of lazy Creationists taking advantage of the ignorance of their followers. I’m just a friggen pre-grad student who knew what the HIV-1 genome looked like and had a few minutes to do a PubMed search. I haven’t even taken a course in biochemistry.

*sigh* So let’s hear it, Behe, what’s your excuse for missing this? Go ahead – run off to PubMed and find a paper to pubjack. I’m not going anywhere.

References:

1. A novel gene of HIV-1, vpu, and its 16-kilodalton product
2. Diversity and Evolution of Primate Lentiviruses
3. Genetic organization of a chimpanzee lentivirus related to HIV-1
4. LANL HIV Sequence Database
5. The HIV-1 Vpu protein: a multifunctional enhancer of viral particle release
6. The human immunodeficiency virus type 1-specific protein vpu is required for efficient virus maturation and release
7. The Vpu protein of human immunodeficiency virus type 1 forms cation-selective ion channels
8. Drug-protein interaction with Vpu from HIV-1: proposing binding sites for amiloride and one of its derivatives
9. Identification of an ion channel activity of the Vpu transmembrane domain and its involvement in the regulation of virus release from HIV-1-infected cells
10. HIV-1 Vpu Promotes Release and Prevents Endocytosis of Nascent Retrovirus Particles from the Plasma Membrane
11. Vpu-mediated CD4 down-regulation and degradation is conserved among highly divergent SIV(cpz) strains
12. Molecular characterization of the HIV type 1 subtype C accessory genes vif, vpr, and vpu
13. Identification of a region within the cytoplasmic domain of the subtype B Vpu protein of human immunodeficiency virus type 1 (HIV-1) that is responsible for retention in the golgi complex and its absence in the Vpu protein from a subtype C HIV-1

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Comment #191783

Posted by factician on August 2, 2007 6:45 PM (e)

Nice post, ERV.

Comment #191784

Posted by thalarctos on August 2, 2007 6:49 PM (e)

brava, Abbie!

nice and effective use of typeface styles, by the way.

Comment #191786

Posted by ERV on August 2, 2007 6:55 PM (e)

**Waynes-World-bow** I learned from the best!

I just dont know how Behe missed it.

*sigh*

Comment #191787

Posted by Jim on August 2, 2007 7:01 PM (e)

Is Behe even going to understand this? Real research and all …

Comment #191789

Posted by gwangung on August 2, 2007 7:07 PM (e)

I believe the term is “pwned.” In spades.

Comment #191792

Posted by Mike O'Risal on August 2, 2007 7:43 PM (e)

An IDspewer caught lying. What a surprise!

Comment #191795

Posted by Pete Dunkelberg on August 2, 2007 8:04 PM (e)

Behe invited:
People writing book reviews are limited in how detailed and technical the editor lets them be. But now there is an excellent opportunity for Dr. Behe to deal at a technical level with some questions about his book, and especially his statements on HIV:

ERV & HIV versus Behe. Behe loses.
http://www.pandasthumb.org/archives/2007/08/erv_…

Quite a few scientists read The Panda’s Thumb, so this is a chance for Dr. Behe to make an impression where it counts. The scientists who read and write PT would welcome Dr. Behe’s participation.

At his blog. It would be very helpful to hear his views on this interesting subject. I hope he will participate here, but you can also “talk” to him there.

Comment #191796

Posted by Ian Musgrave on August 2, 2007 8:05 PM (e)

Great work Abbie (and I say this not just because I drew a diagram for you).
(this is a copy of a comment left over at ERV’s blog)

This post is of great significance, because it not only shows that protein-protein interactions evolve when Behe claims they haven’t, but also hits at some other important claims by Behe.

Firstly, The formation of the Vpu ion channel and the Golgi targeting sequence results in a protein complex, the sort of thing that Behe say is vanishingly difficult for evolution. Secondly, this happened in historic times, not back in the Dreamtime, when the Rainbow Serpent^W^W designer could have popped some gene sequences into HIV without us noticing.

Thirdly, Behe claims zero new protein-protein binding sites in a population of 1020 viruses over 60 years (EoE figure 7.4 page 144 and page 143). In fact, in less than 10 years, HIV evolved two protein-protein binding sites that lead to the formation of a functional protein-complex in a virus population of much less than 1020, as this happened in the early stages of the disease, when the viral population was somewhere near 1012 to 1014, this strikes against Behe’s population size requirements (the effective population size was probably even smaller).

So Behe is defeated by his own example.

Comment #191799

Posted by Ian Musgrave on August 2, 2007 8:12 PM (e)

Pete Dunkleberg wrote:

[you can talk to Behe]At his blog. It would be very helpful to hear his views on this interesting subject. I hope he will participate here, but you can also “talk” to him there.

No you can’t, unless you have bought something from Amazon Books, even then, I have copies of “How to Build Dinosaurs from Chicken Bones” and “Vital Spark” on my book shelves, both purchased from Amazon, but Amazon says I haven’t bought anything from them and won’t let me comment!

Comment #191801

Posted by Pete Dunkelberg on August 2, 2007 8:19 PM (e)

Ian Musgrave wrote “Pete Dunkleberg wrote:”….

whozat? someone with a similar name to mine, but speled funi.
And my name is ez to spel, unlike Mierz.

Comment #191803

Posted by Torbjörn Larsson, OM on August 2, 2007 8:25 PM (e)

It is obvious Behe has caught some severe virus problems. Kudos, ERV!

Sigh. One would hope Behe would stop monkeying around, and start working on biochemistry. One would hope…

Comment #191813

Posted by deadman_932 on August 2, 2007 9:11 PM (e)

I hear the faint sweet sounds of wailing and gnashing of teeth.

Again, congrats, Abbie. Oh, and nice diagram, Ian. Cheers!

Time to assert that the lack of biochem evolution in HIV is just as valid science as is…well, astrology.., Mr. Behe. *snort*

Comment #191814

Posted by Jack Krebs on August 2, 2007 9:11 PM (e)

Great work - I especially like the personal challenge to Behe to respond. Time and time again these guys claim that things can’t happen when they do indeed happen, and we know it. How much will it take for someone like Behe to act like a real scientist and admit that the evidence falsifies his hypothesis rather than acting like a creationist apologists and constantly moving the goalposts.

Comment #191815

Posted by Jeffrey K McKee on August 2, 2007 9:11 PM (e)

ERV … you are letting science get in the way of presuppositions, posturing, and puerile propaganda.

(Sorry … Jon Stewart recently started me on an alliterative phase.)

Comment #191816

Posted by raven on August 2, 2007 9:14 PM (e)

This dissection of Behe needs to go into the list of claims at talkorigin. Given how desperate the creos are, I’m sure Behe’s quotes and examples will circulate for decades as an example of a real live scientist who has disproved evolution.

The fact that he is completely wrong and has no idea what he is talking about will, as usual, not be mentioned.

Comment #191817

Posted by 386sx on August 2, 2007 10:43 PM (e)

Great work - I especially like the personal challenge to Behe to respond. Time and time again these guys claim that things can’t happen when they do indeed happen, and we know it.

There you go. You know it, they know it, and everybody knows they read the same blogs too.

Nice job from Guest Contributor too. Take down yeah!

Comment #191820

Posted by Chris Harrison on August 2, 2007 11:02 PM (e)

Holy crap Behe looked bad on the Colbert Report. I’m not entirely sure, but I think he admitted that God was fighting back against science.

Oh yeah, great post Abbie! I knew something good was brewing coz you hadn’t blogged lately.

Comment #191826

Posted by The Primate Diaries on August 3, 2007 12:45 AM (e)

I saw the show tonight and it was excellent. Colbert stumped him on several points. He even got Behe to admit that his “Intelligent Designer” is God. I wrote up a review at my blog site The Primate Diaries.

Comment #191834

Posted by sparc on August 3, 2007 2:47 AM (e)

Behe loses

As if he ever had a chance

Comment #191835

Posted by Nigel D on August 3, 2007 2:51 AM (e)

Thanks for a very nice essay, Abbie.

Even though my knowledge of virology is, at best, a bit shaky, I found your essay clear, concise and compelling. Let’s hope it provides some enlightenment to the IDists, too.

Comment #191836

Posted by Cubist on August 3, 2007 3:49 AM (e)

ERV wrote:

I just dont know how Behe missed it.

Any time the stupid gets piled up as deep and wide as Behe piled it here, it would be imprudent to dismiss the possibility that the stupid-piler did not, in fact, “miss” anything, but, instead, is actively lying about the topic of the stupid.
Equally, it would be imprudent to dismiss the possibility that the stupid-piler is sufficiently deluded that they’ve managed to double-think themselves into sincerely believing that we have always been at war with Eastasia – sorry, I meant “that the evidence which blows their position out of the water doesn’t really conflict with their position at all”.
And, of course, there’s also simple incompetence.
Deceitful, Deluded, Doofus: The new trilemma?

Comment #191848

Posted by hoary puccoon on August 3, 2007 6:04 AM (e)

Cubist–
Deceitful, deluded and doofus have different probable outcomes.
If Behe is an incompetent doofus, he will acknowledge his mistake and print a retraction, now that he’s had the facts pointed out.
If Behe is sincerely deluded, he’ll come charging onto PT spouting incomprehensible but sincere “biobabble” (sort of like psychobabble, but without the incense.)
If Behe is deliberately lying, he’ll pretend he never saw ERV’s post, or it isn’t worth his while to interrupt his busy schedule, or… whatever. Anyway, he’ll cut and run.
Any bets which way he’ll go?

Comment #191855

Posted by Ian Musgrave on August 3, 2007 7:52 AM (e)

Erv wrote:

It’s amazing. I dont know how he missed this.

My hypothesis is that he can’t use PubMed boolean searches. Even a simple search such as
HIV AND “protein-protein interaction” AND evolution turns up this paper on evolution of CXCR4 binding sites during the duration of an infection.

Comment #191857

Posted by SteveF on August 3, 2007 8:23 AM (e)

Your first reference has only been cited 246 times, so it would have been pretty easy for Behe to miss in his extensive search of the literature.

Comment #191858

Posted by JimV on August 3, 2007 8:28 AM (e)

Sweet! But there is still this paradox which you haven’t explained: how can random chance have produced the outcome that you know at least three times as much as Behe about evolution, in about 1/3 the time? (And at least ten times as much as I do.)

Comment #191862

Posted by Flint on August 3, 2007 8:47 AM (e)

Any bets which way he’ll go?

I’d say there’s a 50% chance Behe will ignore this completely, and a 50% chance Behe will produce a denial of a total misrepresentation of this refutation, in such a way that the ID folks can say that Abbie was “definitively answered and shown to be wrong.”

If it’s the latter, I’ll bet the ID crowd will carefully never notice any of the many corrections to Behe’s misrepresentation.

Comment #191882

Posted by Blader on August 3, 2007 10:16 AM (e)

I’m sorry, what did you say, Abbie? I lost my train of thought because I was laughing so hard at the “hundred billion billion” remark, at Michael Behe, the self-styled Carl Sagan of intuitive biology.

Comment #191883

Posted by Austin D. Powers on August 3, 2007 10:22 AM (e)

Ouch, baby, very ouch!

Comment #191888

Posted by Warren on August 3, 2007 10:35 AM (e)

Colbert will nail him to the wall. He absolutely destroyed Dinesh D’souza a while back. I did something I hardly ever do while watching TV: I cheered aloud.

Comment #191889

Posted by Pastor Bentonit, FCD on August 3, 2007 10:37 AM (e)

Always with the crappy mousetrap argument, Dr. Behe…

Comment #191892

Posted by CJ22 on August 3, 2007 10:44 AM (e)

pwnage abounds. Good job.

I have no idea whether you’re right or not, but I’ll take it as a reasonable assertion. Unless of course MB can refute it?

Comment #191898

Posted by Frank J on August 3, 2007 11:39 AM (e)

The Primate Diaries wrote:

He even got Behe to admit that his “Intelligent Designer” is God.

Ah, but did he also mention Behe’s Dover testimony, in which he admitted that the designer possibly no longer exists? If so, did he ask Behe to reconcile the two statements? I’m sure that the fundamentalist YECs and OECs in the audience would be very interested in that answer, even if most of them close their ears whenever Behe admits common descent. Speaking of which, was it made clear that the most up-to-the-minute challenge to “Darwinism” completely concedes CD and a ~4-billion year history of life?

Comment #191919

Posted by zilch on August 3, 2007 2:04 PM (e)

Behe might still be right. Vpu might not be the result of a mutation, but rather of the Designer lending a Helping Hand to a virus in need.

Comment #191924

Posted by Brendan S on August 3, 2007 2:19 PM (e)

Here’s my prediction of the Creationist Response.

*ahem*

Everyone go and laugh at the pre-graduate student, who admits to NO BIOCHEMICAL TRAINING refuting a PhD! I mean, Dr. Behe is a respected PhD researcher, and ERD is just some kid with a search engine. Behe doesn’t even need to stoop to the level of these laughable and obviously false points.

*NOTE: Not what *I* believe, merely predicting the future…*

Comment #191926

Posted by Frank J on August 3, 2007 2:29 PM (e)

Zilch wrote:

Behe might still be right. Vpu might not be the result of a mutation, but rather of the Designer lending a Helping Hand to a virus in need.

I guess you meant that to be funny, and it would be if most people (especially the ID targets) took the time to unpack the statement. First, how could anyone show that some unknown designer didn’t create Vpu? Second, whether or not a designer was ultimately responsible for Vpu, what would its origin be if not by mutation? Behe has never claimed matter was created anew, and pretty much made it clear that the necessary changes occurred in vivo. So technically it would be mutation(s), however big, small or many. Which leaves the biggest question: “why on earth is Behe not testing what the designer did, when, and how, for those events that he claims are imppossible to occur by ‘evolution’?”

The answer is simple. He knows that he has no alternative theory, only a desire to fool (& possibly save) “the masses.”

Comment #191931

Posted by ERV on August 3, 2007 2:40 PM (e)

zilch–Vpu might not be the result of a mutation, but rather of the Designer lending a Helping Hand to a virus in need.

He cant go there. He would have had to make that his initial position. Instead he chose to make “Vpu does not exist” his position. “Vpu doesnt exist… oh wait. Gawd did it.” wouldnt convince a 3 year old.

:) Glad you all like it :)

Comment #191932

Posted by David Stanton on August 3, 2007 2:42 PM (e)

Frank J,

You are absolutely right. Even if the designer did this, it would still be, by definition, mutation. It just wouldn’t be “random” mutation and so would not violate the (imaginary) law of conservation of information or genetic entropy or something.

The point is that it would be impossible to disinguish between the results of random mutation followed by selection and “poof”. The only way to test the hypothesis would be to catch the designer in the act, something that he/she/it apparently doesn’t want to happen for some reason.

But of course the Behe claim was not that the designer could not do this, it was that it had not happened, period. So even that wacky designer cannot save him this time. Unless of course he now claims that the designer, since he/she/it not longer exists could not have done this. Then I guess he will have to admit that it evolved. Either way, he should really learn to do literature searches before publishing book on areas outside his expertise. Good thing his books undergo “peer-review” that is much more rigorous than for normal publications, or this kind of thing could happen all the time.

Comment #191933

Posted by _Arthur on August 3, 2007 2:46 PM (e)

Maybe that VPU-thingie was frontloaded in the HIV virus DNA/RNA/XNA since Day 4 of Creation ?

Comment #191936

Posted by Coin on August 3, 2007 2:56 PM (e)

I’d say there’s a 50% chance Behe will ignore this completely, and a 50% chance Behe will produce a denial of a total misrepresentation of this refutation, in such a way that the ID folks can say that Abbie was “definitively answered and shown to be wrong.”

I know that at one time it was pretty obvious Dembski read this blog. Are there signs that this is still the case?

Comment #191949

Posted by ben on August 3, 2007 4:05 PM (e)

Why would Dembski read this shit?

To read your insightful comments.

Comment #191951

Posted by raven on August 3, 2007 4:27 PM (e)

Moe, Larry and Curly

Why would Dembski read this shit?

Old European saying, “If you speak of the devil, he will come.”

Which one are you, Demski or Behe?

Comment #191952

Posted by Inoculated Mind on August 3, 2007 4:31 PM (e)

I saw the Behe-Colbert interview, and wrote a few comments about it. Apparently, Behe makes immodest claims, but tries to pass himself off as modest.

http://www.inoculatedmind.com/?p=207

Comment #191961

Posted by ERV on August 3, 2007 5:09 PM (e)

coin–I know that at one time it was pretty obvious Dembski read this blog. Are there signs that this is still the case?

He also reads IIDB, and I put a post on this there, too.
But, while I know we’re all chomping at the bit to see their ‘responses’ (assuming they dont ignore this completely), it took them well over a year to attack Chris Mooney for ‘Republican War Against Science’. And they didnt even remember Richard Sternberg ‘published’ a paper until six years after it was printed.

We’ll probably get a response around the time Im finishing my PhD.

Comment #191969

Posted by Jeffrey K McKee on August 3, 2007 5:32 PM (e)

Golly, gee whiz. The DI did not put up comment about their star, Father of ID, on the Colbert Report.

Maybe he needs to invent a new mouse trap.

Sheeesh!
Jeff

Comment #191980

Posted by Frank J on August 3, 2007 6:36 PM (e)

David Stanton wrote:

The point is that it would be impossible to distinguish between the results of random mutation followed by selection and “poof”. The only way to test the hypothesis would be to catch the designer in the act, something that he/she/it apparently doesn’t want to happen for some reason.

One of many ironies about the ID scam is that there are so many things that occur within development or in “microevolutionary time” that IDers could easily apply their spin to make it seem like “evidence of design.” The only thing that prevents them from doing that, and instead explicitly or implicitly placing design evens safely in the remote past, is because they need rank & file classic creationists for political support.

David Stanton wrote:

Either way, he should really learn to do literature searches before publishing book on areas outside his expertise.

Unlike most of his critics, I’m sure that he does do the literature searches. If he comes across something inconvenient to his argument, he’ll chuckle and say, “Hah! Those ‘Darwinists’ will rip me to shreds, of course, but my target audience will either not understand those high-tech arguments, or they’ll invoke Morton’s Demon. Meanwhile I’ll have even more juicy facts and quotes to take out of context.”

Comment #191986

Posted by fnxtr on August 3, 2007 7:09 PM (e)

Behe’s response to Colbert’s tease that the Bible says Earth is 6,000 years old went by fast, but he said “No, that’s physics”. Huh?

Comment #191993

Posted by Gary Bohn on August 3, 2007 8:13 PM (e)

[CrIDer mode]

But the HIV has not turned into a cat or a bird or something even after all the opportunity for it to do so.

[/CrIDer mode]

Comment #192004

Posted by Wesley R. Elsberry on August 3, 2007 8:52 PM (e)

Behe’s response to Colbert’s tease that the Bible says Earth is 6,000 years old went by fast, but he said “No, that’s physics”. Huh?

IIRC, Colbert had said he wanted Behe to slam the Darwinists over the issue of the age of the earth. Behe’s “No, that’s physics” actually sounded to me like he was saying that Darwinism was not the thing that needed critique on that particular issue. Which is nice that Behe recognizes that.

Comment #192019

Posted by 386sx on August 3, 2007 10:50 PM (e)

Behe said that both physics and Darwin’s theory say that the Earth is more than six thousand years old, but it’s more the physics than Darwin’s theory that says that.

At the risk of people having fainting spells and the onset of the Apocalypse and whatnot, I thought Behe did pretty well except for the parts where he completely ignores that he’s been debunked several times over and over and over and over on a daily basis for the past ten years or so. But hey, he knows who his public is.

Comment #192021

Posted by stevaroni on August 3, 2007 10:58 PM (e)

Holy crap Behe looked bad on the Colbert Report.

And once again, like every time an ID theorist speaks, he didn’t actually say anything.

Yes, I realize it’s a fast paced format and he only had seven minutes, but still, it was the same old pablum “We’ve learned a lot since Darwin’s time”, “Evolution is a theory in trouble”, and “The cell is full of complex machines and intricate computer codes”, with absolutely no real information.

Once again, he never actually said something solid like “and we know this because….” or - be still my heart - “and we have this new evidence to prove it…”

Classic Behe. All sizzle, no steak.

More is the pity that so many attention spans are just long enough to be caught with the sound of sizzling.

Comment #192051

Posted by dhogaza on August 4, 2007 1:11 AM (e)

Cobert was excellent when Behe raised the mousetrap argument. “when you take a piece away, you no longer have a mousetrap”. Cobert responded something like (liberal paraphrase), “and, yes, of course a piece of wood, and metal bits, can’t be used for anything else…”

I think Cobert understands a thing or two …

Comment #192061

Posted by raven on August 4, 2007 1:51 AM (e)

Behe lying on TV:

“Evolution is a theory in trouble”,

That is a false statement, a lie.

Evolution is a theory that a few people mostly from xian cults in the south central USA would like to be in trouble because it contradicts their mythology based on something near stone age sheep herders wrote 4,000 years ago.

Repeating a lie over and over doesn’t make it true.

This guy has the nerve to call himself a scientist while pushing grade Z and demonstrably wrong pseudoscience? I bet Lehigh U. is happy with this nonsense.

Comment #192062

Posted by Aagcobb on August 4, 2007 2:03 AM (e)

You poor saps. This doesn’t prove anything. Behe has already PROVEN that a gene like the Vpu couldn’t have evolved naturally. Thus, we can only conclude that the CIA really did invent the various HIV viruses as a biological warfare agent after all! Looks like Behe has rehabilitated the image of the KGB .

Comment #192096

Posted by Nigel D on August 4, 2007 4:42 AM (e)

Clarissa wrote:

Tough shit.

Clarissa, it’s not exactly clear to what you refer in Raven’s post. Is it the fact that Behe is lying; is it the fact that this particular lie has been repeated time and time again; or is it the comment about how Lehigh University must feel about Behe’s “science” standards??

Whichever, I’m not sure what point you are trying to get across. Should we not expect Behe to be honest? Should we have to tolerate his lying (and, come to think of it, that of most of the rest of the ID movement too)? What if someone started lying about your livelihood and field of expertise (assuming you have one)? How would you feel about that? Would you just shrug it off and say “that’s life,” or would you attempt to assert the truth? How about the potential livelihoods of your children (assuming that you have or will have them)? What then? Is that “tough shit” too? How about if someone tells a lie (repeatedly) that has the potential to affect the competence of every child in the nation? Should that be tolerated?

Meanwhile, addressing Raven’s comments in post 192061…

I don’t know about the terms of Behe’s employment, but if I lied in an official capacity (i.e. using my position of employment to impart authority to my statement or claim), I could be sacked. Whether Behe intends it or not, all of the other DI fellows seem to claim that Behe’s tenure at Lehigh gives his work some level of authority in the debate. So, I wonder if Lehigh could dismiss him from the faculty?

Comment #192112

Posted by hoary puccoon on August 4, 2007 5:40 AM (e)

Well, there you have it. On the side of accepted evolutionary theory, a tightly-reasoned, factual description of evolution in one, particular gene of HIV. And the ID rebuttal, in its entirety- “tough shit.”
May we quote you, Clarissa, in future scientific papers?
On second thought, never mind.

Comment #192124

Posted by Aagcobb on August 4, 2007 6:35 AM (e)

Raven:

I bet Lehigh U. is happy with this nonsense.

You can just feel Lehigh’s pride in their resident IDist oozing out of their disclaimer!

Comment #192153

Posted by Raging Bee on August 4, 2007 9:12 AM (e)

Whichever, I’m not sure what point you are trying to get across.

Neither is she. Tough shit.

Comment #192188

Posted by fnxtr on August 4, 2007 12:16 PM (e)

(shrug) Okay.

Comment #192256

Posted by Gary Hurd on August 4, 2007 4:28 PM (e)

Right on!

A wonderful spanking of a foolish man.

My thanks and congratulations.

Gary

Comment #192290

Posted by Henry J on August 4, 2007 6:58 PM (e)

Maybe some fiber might help?

Comment #192457

Posted by MartinM on August 5, 2007 9:17 AM (e)

“Vpu doesnt exist… oh wait. Gawd did it.” wouldnt convince a 3 year old.

Ah, but a 3 year old has no particular desire to be convinced.

Comment #192459

Posted by raven on August 5, 2007 9:30 AM (e)

Behe:
Yet all those mutations, while medically important, have changed the functioning virus very little. It still has the same number of genes that work in the same way. There is no new molecular machinery.

Behe is clearly wrong about where the edge of evolution is. Malaria can evolve double mutant resistance to chloroquine or quintuple resistance to another combo drug without even breathing hard.

abstract on pyrimethamine-sulfadoxine resistance: This ‘quintuple mutant’ is considered as a molecular marker for clinical failure of SP treatment of P. falciparum malaria.

There is also no problem with organisms evolving new “molecular machinery” as needed. Examples include the t cytoplasmic character in corn or the changes in HIV vpu.

I’ve argued elsewhere that he is on the wrong track to start with. There is a lot of evidence that what is rate limiting in phenotypic evolution is not mutation rates but natural selection pressures.

1. Look at the mammalian lineage. While the dinosaurs were around, mammals were small, inconspicuous, and many may have been nocturnal. One asteroid later, there was a lot of vacant ecospace and the furry guys grabbed it. It didn’t take long for a complete new megafauna to show up and small insectivores to give rise to complicated flyers known as bats.

2. Whenever environmental niches become available, the first organisms to show up seem to undergo rapid adaptive radiations. Galapagos finches, Hawaiian Drosophilia, African cichlid fish in lake Malawi and so on.

Evolution pushes organisms to local optimums in static environments. Once there, they tend to stay there until the environment changes. In the case of HIV, it is a demonstrably successful pathogen. Incremental improvements might occur it adapts further to its new host and it can and does evolve resistance to whatever new drugs are developed to treat it. But if it is near a local optimum, why should it look much different from generation to generation?

Comment #192636

Posted by John on August 5, 2007 7:42 PM (e)

Let’s challenge Behe and all the IDers on the nature and intelligence of the designer.

If the “designer” did design/redesign chimpanzee HIV to infect humans, then the “designer” (God) is a vicious and sadistic killer. A compassionate and loving God surely would not cause or even permit to happen the death and suffering of millions of people.

Let’s have an explanation from the IDers about why the “designer” redesigned HIV to kill humans.

Comment #192705

Posted by Rocky143 on August 6, 2007 12:43 AM (e)

Excellent! You cut out Behe’s gizzard and fried it!

Comment #192709

Posted by hoary puccoon on August 6, 2007 12:54 AM (e)

John–
I wonder, myself, why there isn’t more discussion of the moral implications of Behe’s argument. The Designer, according to Behe, is spending most of his time lately figuring out newer and more diabolical ways to kill people, with special attention to black Africans and gays. And is that giving everyone a warm, fuzzy feeling as they pray to Him in church?

Comment #192710

Posted by hoary puccoon on August 6, 2007 12:56 AM (e)

Oops. I thought that was going on another thread.

Comment #192839

Posted by Mark Studdock on August 6, 2007 9:51 AM (e)

For philosophy student trolls like myself….

Could you state for me (and others I imagine) where and how the above research, particularly the development of Vpu, crosses the line from HIV or SIV over Behe’s “Edge” of evolution.

Very impressive post.

MS

Comment #193157

Posted by ERV on August 6, 2007 11:07 PM (e)

Mark! I put up a ‘Translation for Laymen’ :) I really did try hard to keep this post from being too awful with the jargon, but I wanted to cut off any and all escape routes…

:)

Comment #193160

Posted by ERV on August 6, 2007 11:09 PM (e)

Ugh sorry. Right link.

Comment #193498

Posted by waldteufel on August 7, 2007 3:43 PM (e)

I see that our pal Casey Luskin has put up a post at the DI telling us that Ms. Smith has in no way refuted Behe.

Once again, Casey shows us his ignorance in the face of real science. Pathetic performance on his part, as usual. But, Casey’s real audiences are the ignorant and credulous denizens of the big round churches along the freeway …. .

Comment #193592

Posted by ERV on August 7, 2007 8:59 PM (e)

waldteufel– Once again, Casey shows us his ignorance in the face of real science. Pathetic performance on his part, as usual. But, Casey’s real audiences are the ignorant and credulous denizens of the big round churches along the freeway

Bingo!

Evidence #982369823653827659 that ID is PR, not science.

If it were science, Behe would have responded, and we could have had a fun conversation.

But its PR, so little Casey can write a note that says “Dont be scared, folks! False alarm! Move along move along!” to placate Average Joe Creationists who were thinking “Crap. Looks like Behe screwed up. What if hes wrong about…” Nevermind Casey doesnt appear to know the difference between biochemistry and genetics…

Meh.

Comment #194218

Posted by jmlawson on August 9, 2007 9:28 AM (e)

Abbie:

Excellently put. I’m a former lentiviral researcher myself, looking at phylogenetic trees of the non-primate lentivirus families. The data clearly shows a consistent, predictable level of mutation and adaptation that match the known mutation rates.

I worked with EIAV, the lentivirus of horses, which differs from SIV and HIV in encoding it’s own dUTPase, which is an adaptation to infecting macrophage, a terminally differentiated immune cell. SIV and HIV do not encode this gene, but instead have imperfectly adapted to “borrowing” the host cell’s Uracil DNA Glycosylase with vpr/vpx.

It’s a perfect “Panda’s thumb” for virus function. It doesn’t work as well as an attenuating adaptation to the host, hence the immunocompromise, because HIV shows such a preference for the actively dividing T4, which are so critical to immune response. If HIV/SIV had retained a dUTPase, it may have also retained the preference for macrophages over T cells. I should point out the EIAV does not cause profound immunodeficiency, just occasional episodes of fever and thrombocytopenia. Layman’s translation: Sick, but able to recover.

Another “Panda’s thumb” is the human resistance to HIV infection. It now appears that the delta 32 CCR5 mutation that causes HIV resistance in 1% of the population of European descent was the result of the plagues (Black Death) of the Middle Ages. Selection pressure produced survivor populations of the plague with this increased (but still very rare) phenotype. Darwin’s shield! For those of you unfamiliar with delta 32 CCR5, it’s a mutation of one of the possible receptors on the immune cell surface that facilitates viral entry. Inactivating it reduces the chance of initial infection, but once infected, has no impact on survivability. There are presently four commercial drug trials for agents that block CCR5-viral interaction.

Again, excellent article.

JML

Comment #194267

Posted by Mike on August 9, 2007 12:48 PM (e)

No, no, no, no, no. You guys just don’t get it. It’s STILL HIV! By now with all those ‘random’ mutations, if evolution was true, HIV should have evolved into something else, like fish or people! Until HIV involves into people who can wear suits and object to who other people love, your precious evolution stands refuted by the Einstein of Biology!

[Note: [Fx: spoken very rapidly] That was intended as parody, but, well, a minute of googling probably will reveal something even more daft said by an actual ID-creationist, so this disclaimer is, sadly, necessary to avoid needless heat. Void where prohibited.]

If there were some way to determine its outcome, I’d bet there are creationism consumers (i.e. the marks) out there who read Behe as suggesting just that: that with all those mutations, HIV should have eyes or fins or talk or something by now and until it does, well, they’re just not going to believe the evilutionists.

Comment #194279

Posted by Mike on August 9, 2007 2:04 PM (e)

No, no, no, no, no. You guys just don’t get it. It’s STILL HIV! By now with all those ‘random’ mutations, if evolution was true, HIV should have evolved into something else, like fish or people! Until HIV involves into people who can wear suits and object to who other people love, your precious evolution stands refuted by the Einstein of Biology!

[Note: [Fx: spoken very rapidly] That was intended as parody, but, well, a minute of googling probably will reveal something even more daft said by an actual ID-creationist, so this disclaimer is, sadly, necessary to avoid needless heat. Void where prohibited.]

If there were some way to determine its outcome, I’d bet there are creationism consumers (i.e. the marks) out there who read Behe as suggesting just that: that with all those mutations, HIV should have eyes or fins or talk or something by now and until it does, well, they’re just not going to believe the evilutionists.

Comment #194381

Posted by Collin on August 10, 2007 2:34 AM (e)

Not to burst your bubble guys but it seems that new research indicates VPU doesn’t produce a viroporin but triggers apoptosis in the cell (the cell self destructs in response to the inhibition of anti-apotosis factors in the cell… caused by VPU).

http://www.jem.org/cgi/content/full/194/9/1299

“ Both Vpr- and Vpu-induced apoptosis involve the activation of the caspase pathway (references 48 and 49, and this study). Although the precise mechanism for Vpr-induced apoptosis is still unclear, recent observations suggest that it might be caused by a Vpr-induced permeabilization of mitochondrial membranes resulting in the release of apoptogenic proteins such as cytochrome c or apoptosis inducing factor and the subsequent activation of caspase (50). While it was suggested that Vpu itself might have poreforming properties (51, 52) making a mechanism for induction of apoptosis similar to that of Vpr conceivable, our data suggest that Vpu instead functions by inhibiting the NF-{kappa}B—dependent expression of antiapoptotic genes.

Anyways the original post (while seeming incorrect on vpu proteins creating viroporins) does at least focus on the right stuff in trying to refute Behe. The same needs to be done in regards to the E Coli, Malaria, and Fruit Fly studies he mentioned. If it can’t be proven that evolution of biomechanical systems involving integrated complexity actually occurs when given very large generation times and population sizes… Well let’s just say the Dawkins meme might be headed for extinction.

Comment #194470

Posted by ERV on August 10, 2007 9:05 AM (e)

jmlawson– hehehe I think the Plague–>HIV thing is an old wives tale :) But CCR5-Delta32 is a very real and very rare mutation. It possible if HIV infection did a few million years ago what its doing today, we would probably all be CCR5-Delta32s… or dead…

Mike– Well thats the strawman behind all of this. What does Behe want HIV to do? Tap-dance? Its the old Creationist Claim “If evolution is true, how come humans dont have wings”.

Collin– What you have done, sir, is pubjack. Behe cant even defend himself with THAT, evidently. If youll take the time to search PubMed, youll notice that Dr. Strebel is the proponent of ‘Vpu does not form viroporins’. He might very well have a case. He might have just found ANOTHER way Vpu has evolved, biochemically. He might be totally wrong. The current consensus is that Vpu does form ion channels. Current paper:

Towards a mechanism of function of the viral ion channel Vpu from HIV-1.

Comment #194655

Posted by Nigel D on August 10, 2007 4:53 PM (e)

jmlawson -

Slightly OT, but…

I think for some viruses with small genomes that the loss of dUTPase may be an advantage, as it would increase mutation rate and lead to more rapid evolution. For larger viral genomes, some means of avoiding misincorporation of uracil into new DNA is an advantage. As you point out, some viruses encode their own dUTPase. To me, this is a sign of the importance of dUTPase in accurate DNA replication, and another strand of evidence supporting modern evolutionary theory (because AFAICT, all organisms that make DNA have a dUTPase).

I seem to recall attending a symposium (maybe in 2000?) that examined viral evolution rates in the context of a new type of antiviral agent. The idea was that some viruses mutate so rapidly that they are at the edge of evolution - i.e. their mutation rate is so high as to cause raid evolution, but just low enough so as not to compromise viral viability. The new approach was to apply mutagenic chemotherapy to push the viral replication over the edge into non-viability, hence allowing the host’s immune system to clear the infection.

Comment #194662

Posted by Henry J on August 10, 2007 5:12 PM (e)

Re “Its the old Creationist Claim “If evolution is true, how come humans dont have wings”.”

Lack of intermediate forms that would be viable? Then again, wings on something the size and approximate shape of a human wouldn’t be overly useful anyway, even if we had them. (Or is that being picky?)

Henry

Comment #194904

Posted by hoary puccoon on August 11, 2007 8:02 AM (e)

Henry,
Lack of viable intermediate forms is exactly the same argument that Sal Cordova gives for why birds couldn’t have evolved! In fact, some of our distant cousins, the lemurians, have developed skin folds for gliding, much like ‘flying’ squirrels. So intermediates are probably possible in primates. It just happens that our immediate ancestors were apparently moving away from a tree-centered existence, where flying might have been useful, to living more on the ground, where bipedalism came in handy. And what plausible ecological niche could one construct for an intermediate form that developed wings and bipedalism at the same time?

Comment #195517

Posted by ERV on August 12, 2007 2:27 PM (e)

I addressed Collins comment in a post here:

http://endogenousretrovirus.blogspot.com/2007/08…

Comment #195612

Posted by ERV on August 12, 2007 8:14 PM (e)

For Casey Luskin, ‘An Illustrated Guide to Vpu’.

YAY! Thank you Ian!

Comment #195808

Posted by RayGun on August 13, 2007 10:09 AM (e)

Although totally improbable, I would ratter believe that humans are the experiment of some Alien Race.
I like ERV’s view, and interesting info about the HIV mutation.
Now, how about a cure for HIV and Herpes-Virus (if pharmaceuticals would allow them)?

Comment #195851

Posted by Torbjörn Larsson, OM on August 13, 2007 12:40 PM (e)

Collin:

Collin wrote:

If it can’t be proven that evolution of biomechanical systems involving integrated complexity actually occurs

Not so. Lack of any set of observations wouldn’t be conclusive, since there are many more independent observations that already support the theory.

But as it happens evolution is observed in all these systems and more. That isn’t confined to biomechanical systems, but on the full range of observed phenotypes. Nor is “integrated complexity” necessary and in fact no one knows what observation you refer to there.

But FWIW there is an old evolutionary prediction roughly 80 years ago by Muller of interlocking complexity expected from phenotype change, if that is what you mean.

One such example would be the viroporin described in the post, confirming that old prediction for the umpteenth time.

Comment #196008

Posted by Shepherd Moon on August 14, 2007 12:33 AM (e)

Excellent smackdown, very methodical. The occasional sarcasm in the article is not to my taste, but I can’t say Behe didn’t ask for it. This should definitely be posted at the TalkOrigins web site.

Abbie Smith needs to write up a comprehensive article rebutting AIDS deniers, if she hasn’t done so already. As troubling as it is to know that IDers want to make inroads in school curriculums is the thought that there are also people who want to teach that AIDS doesn’t exist or is some kind of “behavioral disease” caused by sinful lifestyles.

Comment #196013

Posted by Eric Finn on August 14, 2007 1:16 AM (e)

Shepherd Moon wrote:

Excellent smackdown, very methodical. The occasional sarcasm in the article is not to my taste, but I can’t say Behe didn’t ask for it. This should definitely be posted at the TalkOrigins web site.

There is a short article at the TO site (see “What’s New” or talkorigins.org/faqs/comdesc/ICsilly.html)

Regards
Eric

Comment #196307

Posted by Richard Boyne on August 14, 2007 10:01 PM (e)

“It just happens that our immediate ancestors were apparently moving away from a tree-centered existence, where flying might have been useful, to living more on the ground, where bipedalism came in handy. And what plausible ecological niche could one construct for an intermediate form that developed wings and bipedalism at the same time?”

That sounds like the ‘ground up’ hypothesis for bird evolution. Though I guess they did evolve bipedalism long before they devloped flight.