Immune cross on Science Origins blog; more at Evolution2009 at UNK

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Following up on the Science story on the origin of adaptive immunity and the role it played in the Kitzmiller case, the Science Origins blog has a short interview they did with me while writing the article. It didn’t make the final cut for the print version, but it is nifty for it to be online. I hope I sufficiently acknowledged my PT collaborators and all the other friends/enemies on the net that made that particular bit of the Behe cross-examination seem like a good idea.

Also, while I am on this topic, I should mention that I have been invited to speak about the role of evolutionary science in the Kitzmiller case, with special focus on the immune system science and how it was used in the Behe cross-examination. This will occur on September 3, 2009 at the University of Nebraska at Kearney. Here is the link for the meeting, September 2-4, 2009: http://www.evolution2009.org/. It looks like a fantastic lineup of speakers. The early (cheaper) registration deadline is July 31. And yes, I am mentioned in the same sentence as another speaker, Jack friggin’ Horner, which is just weird. (PS: Email me if you’ll be in the area and want to meet up!)

Here’s the flier the organizer, Brad Ericson, sent me, and asked to have put up: Evolution2009_poster_Univ_Nebraska_Kearney.pdf

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Evolution 2009, in Kearney, Nebraska from Millard Fillmore's Bathtub on May 29, 2009 3:42 PM

Evolution 2009 kicks off Wednesday, September 2, 2009 at the University of Nebraska atKearney. In honor of Darwin’s birth bicentennial and the sesquicentennial of his most famous work, the program is dedicated to evolution in different fields of ... Read More

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I might as well say it before someone else does: It takes a real geek to describe himself by analogy to a geek in a fictional movie who is a kid obsessed with another fictional (doubly fictional, this time) movie, which is based on a real-life fictional movie/TV series, which itself is adored by nerds. In a Science magazine blog.

Nick,

Not exactly on topic, but I was wondering if you had any thoughts on this paper, as it relates to your flagella evolution hypothesis:

“The Evolution of the Flagellar Assembly Pathway in Endosymbiotic Bacterial Genomes”

http://mbe.oxfordjournals.org/cgi/c[…]tract/msn153

Last year the creationists were crowing about it as a death blow to your argument:

http://www.uncommondescent.com/inte[…]ive-refuted/

Nick Matzke’s problematic evolutionary narrative of the Type Three Secretory System (TTSS) into the bacterial flagellum quickly made it into a peer reviewed journal while the response from the ID camp took two years longer. Our position, which I mentioned several times in the past, was that the flagellum preceded the TTSS in nature and thus the TTSS represents a devolution from flagella rather than flagella being evolved from a TTSS. Nick had it ass-backward. No surprise there. Devolution is much easier than evolution, Nick. Always look for devolutionary explanations first. I’d like to say that devolution being far easier than evolution is something that ID predicts but alas, it’s predicted by nothing more than common sense. Of course ID is predicated by common sense too so there is that kinship to consider.

and

Bacteria existed for over a billion and a half years before insects came along. IOW, the bacteria needed the flagella; then insects came along and, with the endosymbiotic relationship established, the flagella no longer needed those genes, and so, out of economy, eliminated them (this is one explanation for the putative “elimination”). Thus, the need to export proteins via the TTSS arises after the flagella have formed, not on the way to the formation of the flagella. This severely weakens Matzke’s argument.

If you’ve already addressed this elsewhere, could you provide a link.

Thanks.

Also, additionally, browsing the comments to that thread takes you to the following:

http://www.uncommondescent.com/inte[…]cy-or-other/

In which, in the comments beneath, a couple of the IDers try and do some probability calculations for the evolution of the flagella. Although found in the comments, this is apparently one of the main Uncommon Descent attacks on your hypothesis, so I was interested to see if you had any thoughts.

There are some obvious flaws, particularly in their treatment of beneficial intermediaries (as pointed out to them by Bob O’H), but I’d be interested if you had any thoughts. Here, for example, is one of the main points:

At this point, probably not knowing what else to say, you go back to the concept of gradual fixation. But what are you speaking of? Please explain how you pass from a function (T3SS) to another one (the flagellum) through 490 or so single aminoacid mutations, each one fixed in name of I don’t know what function increase. Are you thinking of, say, 245 gradual mutations improving at single steps the function of the T3SS, and then 245 more single mutations, building gradually the function of the flagellum? What a pity that, of those 490 or so internediaries, there is not a trace, either in existing bacteria, or in fossils, or in general models of protein functions

Or, if we want to exercise our fantasy (why not? in time I could become a good darwinist) we could split the cake in three: 150 mutations improving T3SS, 150 more to build some new, and then lost, intermediary function (double cooption!), and then 190 to build up the flagellum.

Obviously, all that would happen in hundreds of special “niches”, each of it with a special fitness landscape, so that we can explain the total diappearance of all those intermediary “functions” form the surface of our planet!

Is the number of mutations required in your pathway accurate? 490 seems rather high. Plus are any of the intermediaries still around? The reasoning behind 490 mutaions is, BTW:

However, let’s assume derivation as hypothesis. I think F2XL has reasoned very simply: we have 35 proteins which have changed. If there were no change, bacteria with T3SS would have the flagellum, but that’s not the case. How big is the change? Here F2XL has given an approximate reasoning, very generous indeed towards the other side, assuming high homology between the 35 protein pairs, calculating the number of different aminoacids between them according to that approximation, and then assuming that only a part of the aminoacid changes (10%, if I rememebr well) is really functionally necessary for the change from T3SS to flagellum. That’s how that number of 490 specifically necessary mutations comes out. OK, it’s an approximation, but do you really think it’s wrong? I think, instead, that F2XL has been far too accomodating in his calculations. The real functional difference is probably much higher. We are speaking of 35 proteins which have to change in a coordinated way to realize a new function. That’s the concept of cooption. I have always found that concept absolutely stupid, but that’s what we are discussing here.

Some of the main creationist posts:

http://www.uncommondescent.com/inte[…]mment-290187

http://www.uncommondescent.com/inte[…]mment-289966

Again, any thoughts much appreciated. The discussion strictly starts at post 90, with the following:

Moving on, what we will basically be doing is testing the claims of Nick J. Matzke.

The immune system and its evolution is a fascinating topic and a prime example of creationist head-in-sand-ness (and not the only one that came up in the Kitzmiller trial). Online efforts have illustrated this for years. Matt Inlay’s 2002 article Evolving Immunity brought together a large body of research that Behe was ignoring, and should have been “a word to the wise” to him on the subject.

Nick Matzke said: Also, while I am on this topic, I should mention that I have been invited to speak about the role of evolutionary science in the Kitzmiller case, with special focus on the immune system science and how it was used in the Behe cross-examination.

Has Behe been invited to speak? It would be a real hoot to invite him and then start your presentation by reading his invitation and then (1) read his weaseling-out reply or (2) look out into the audience and say “Behe? Behe?” Or if he accepted, it could get really interesting.

Paul,

I don’t think having Behe appear at this forthcoming Darwin celebration would be appropriate:

Has Behe been invited to speak? It would be a real hoot to invite him and then start your presentation by reading his invitation and then (1) read his weaseling-out reply or (2) look out into the audience and say “Behe? Behe?” Or if he accepted, it could get really interesting.

Anyway he’s still afflicted with a strong case of denial, as evidenced by his book, “The Edge of Evolution”. For example, he told me a few years ago that the audience at the AMNH ID debate (which was held in the Spring of 2002) wasn’t laughing at him and Bill Dembski (who were arguing the PRO; the CON was by Robert Pennock and Ken Miller, with Genie Scott moderating). I saw Ken last night and he remembers that the audience was laughing at Behe and Dembski.

Regards,

John

P. S. @ Nick, just for the record, weren’t you the one who found cdesign proponentist? I heard a slightly different version from Ken last night.

What a good idea! Invite Behe. I’ll put up the honorarium if necessary. We want entertainment!

Uncommonly Dense said: Thus, the need to export proteins via the TTSS arises after the flagella have formed,

So in order to obfuscate an evolutionary scenario they’re postulating a different evolutionary scenario but calling it “devolution” in order to deny that they’re suggesting evolution through natural selection. So somehow their adaptation of existing coding sequences is different than that postulated by real scientists?

You should consider contacting Nick’s co-author, British bacteriologist Mark Pallen:

mammuthus said:

Nick,

Not exactly on topic, but I was wondering if you had any thoughts on this paper, as it relates to your flagella evolution hypothesis:

“The Evolution of the Flagellar Assembly Pathway in Endosymbiotic Bacterial Genomes”

http://mbe.oxfordjournals.org/cgi/c[…]tract/msn153

Last year the creationists were crowing about it as a death blow to your argument:

http://www.uncommondescent.com/inte[…]ive-refuted/

Nick Matzke’s problematic evolutionary narrative of the Type Three Secretory System (TTSS) into the bacterial flagellum quickly made it into a peer reviewed journal while the response from the ID camp took two years longer. Our position, which I mentioned several times in the past, was that the flagellum preceded the TTSS in nature and thus the TTSS represents a devolution from flagella rather than flagella being evolved from a TTSS. Nick had it ass-backward. No surprise there. Devolution is much easier than evolution, Nick. Always look for devolutionary explanations first. I’d like to say that devolution being far easier than evolution is something that ID predicts but alas, it’s predicted by nothing more than common sense. Of course ID is predicated by common sense too so there is that kinship to consider.

and

Bacteria existed for over a billion and a half years before insects came along. IOW, the bacteria needed the flagella; then insects came along and, with the endosymbiotic relationship established, the flagella no longer needed those genes, and so, out of economy, eliminated them (this is one explanation for the putative “elimination”). Thus, the need to export proteins via the TTSS arises after the flagella have formed, not on the way to the formation of the flagella. This severely weakens Matzke’s argument.

If you’ve already addressed this elsewhere, could you provide a link.

Thanks.

A number of people have strongly criticized Behe’s absurd interpretation of the “irreducibly complex” flagellular motor, including Australian molecular biologist Ian Musgrave (who is a frequent PT poster), Brandeis professor emeritus David DeRosier (whose work Behe has incorrectly cited as proof of the flagellum’s “irreducible complexity”), and of course, Ken Miller (who of course mentioned this and, in particular, DeRosier’s discovery of the TTSS, in his talk last night here in New York City to the Brown University Club in New York). So of course the delusional IDiots at Uncommon Dissent have no rational ground to stand on, metaphorically speaking, in attacking Nick and Mark Pallen’s elegant refutation.

I’d rather see him invited to a “Star Trek” convention, so he can explain why he hasn’t followed up on Ken Miller’s excellent advice to write the definitive textbook on Klingon Biochemistry or mine to write - along with Bill Dembski - the definitive textbook on Klingon Cosmology:

Joe Springer said:

What a good idea! Invite Behe. I’ll put up the honorarium if necessary. We want entertainment!

I hope you will have time to cite, or even read from the Jones decision. Particularly;

Immune system page 77-78 of PDF “KITZMILLER, et al. v Dover, MEMORANDUM OPINION,” Judge Jones.

“The immune system is the third system to which Professor Behe has applied the definition of irreducible complexity. Although in Darwin’s Black Box, Professor Behe wrote that not only were there no natural explanations for the immune system at the time, but that natural explanations were impossible regarding its origin. (P-647 at 139; 2:26-27 (Miller)). However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system. (2:31 (Miller)). In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” (23:19 (Behe)).

We find that such evidence demonstrates that the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution.”

AND, Human Artifacts:

“ With ID, proponents assert that they refuse to propose hypotheses on the designer’s identity, do not propose a mechanism, and the designer, he/she/it/they, has never been seen. In that vein, defense expert Professor Minnich agreed that in the case of human artifacts and objects, we know the identity and capacities of the human designer, but we do not know any of those attributes for the designer of biological life. (38:44-47 (Minnich)). In addition, Professor Behe agreed that for the design of human artifacts, we know the designer and its attributes and we have a baseline for human design that does not exist for design of biological systems. (23:61-73 (Behe)). Professor Behe’s only response to these seemingly insurmountable points of disanalogy was that the inference still works in science fiction movies. (23:73 (Behe)). (pg 81)

The reason for the later is that neither the Science magazine material nor the Nebraska meeting acknowledge that there was any contributions made by anthropologists to the case, and leave the impression that the social sciences are merely represented by the likes of Steve Fuller.

P. S. @ Nick, just for the record, weren’t you the one who found cdesign proponentist? I heard a slightly different version from Ken last night.

I discovered the existence of (one) unpublished draft of Pandas. The lawyers then issued a subpoena and got 6 drafts. As we were going through them, it was Barbara Forrest that found the actual “cdesign proponentsists” term. I blogged it just after the trial in November 2005, acknowledging her. Cheers!

Nick

The IDist flagellum stuff quoted in this thread is so far off it’s not even funny. I.e. the “secretion systems” in insect endosymbionts are indeed reduced flagella, and phylogenetically nested within flagellar sequences, originating only a few hundred million years ago, but those systems are not the same thing as the classic nonflagellar T3SS, which at the very least are probably as old as eukaryotes.

In fact, IF classic nonflagellar T3SS *were* derived from flagella, we might well expect to see the same tell-tale “vestigial” traits that we see in the endosymbiont reduced flagella, e.g. P-ring, L-ring, and hook proteins. But we don’t see any of that in standard nonflagellar T3SS. This isn’t a knock down argument by itself but it is suggestive.

The bit about 35 proteins is just silly, they haven’t read the 2006 Pallen & Matzke analysis of how many proteins are actually universally required, how may are homologous, etc., or any of the updates since then.

John Kwok said: A number of people have strongly criticized Behe’s absurd interpretation of the “irreducibly complex” flagellular motor, including Australian molecular biologist Ian Musgrave (who is a frequent PT poster), Brandeis professor emeritus David DeRosier (whose work Behe has incorrectly cited as proof of the flagellum’s “irreducible complexity”), and of course, Ken Miller (who of course mentioned this and, in particular, DeRosier’s discovery of the TTSS, in his talk last night here in New York City to the Brown University Club in New York). So of course the delusional IDiots at Uncommon Dissent have no rational ground to stand on, metaphorically speaking, in attacking Nick and Mark Pallen’s elegant refutation.

Yes, I’ve read much of this and to me Nick’s model seems plausible. I was just wodnering if there was much to these particular criticisms (not being a biologist). One issue that springs to mind is that the UD people at no point seem to recognise is that the homologs are strong evidence for the model itself. They use them to try and provide a guestimate of the difficulty involved, but don’t recognise that, irrepsective of how it happened, the homologs are evidence that it did happen. At least that’s how I understand it. Nonetheless, I’d be interested in Nicks’ thoughts (but perhaps this is an inappropriate post in which to ask).

mammuthus said: Yes, I’ve read much of this and to me Nick’s model seems plausible. I was just wodnering if there was much to these particular criticisms (not being a biologist).

Mammuthus, I don’t know whether they are specifically making this error in the text you cite, but one probabilistic error creationists make all the time is to do a simple multiplication of individual event probabilities. This means that what they are actually calculating is saltation - i.e. the chance of every mutation happening in a single shot - rather than evolution.

My guess is, if you’re seeing them quote extroadinary odds of some event happening, this is what they are doing.

Well said, eric. BTW, your observation is the very one that Behe was rightly criticized for in his book, “The Edge of Evolution”, which, independently, Mark Chu-Carroll, Richard Dawkins and Ken Miller all pointed out in their respective reviews of that pathetic example of mendacious intellectual pornography:

eric said:

mammuthus said: Yes, I’ve read much of this and to me Nick’s model seems plausible. I was just wodnering if there was much to these particular criticisms (not being a biologist).

Mammuthus, I don’t know whether they are specifically making this error in the text you cite, but one probabilistic error creationists make all the time is to do a simple multiplication of individual event probabilities. This means that what they are actually calculating is saltation - i.e. the chance of every mutation happening in a single shot - rather than evolution.

My guess is, if you’re seeing them quote extroadinary odds of some event happening, this is what they are doing.

If you’re a subscriber to NCSE Reports, you may find especially fascinating, Johns Hopkins biochemist David Levin’s review of Behe’s “The Edge of Evolution”. He has an especially elegant example pertaining to “anti-freeze” in Antarctic fish in that review, as an important example refuting Behe’s inane claims for irreducible complexity from a molecular biological perspective.

Nick wrote:

“The IDist flagellum stuff quoted in this thread is so far off it’s not even funny. I.e. the “secretion systems” in insect endosymbionts are indeed reduced flagella, and phylogenetically nested within flagellar sequences, originating only a few hundred million years ago, but those systems are not the same thing as the classic nonflagellar T3SS, which at the very least are probably as old as eukaryotes.”

So in order to defend irreducible complexity they have come up with yet another system that appears to be irreducibly complex but which actually isn’t. Great. Once you get these guys arguing real science they always forget the point they were originally trying to make and shoot themselves in the foot.

Seriously, faced with the evidence that evolution is indeed capable of such things, you would think they would get the idea and shurt up already before they make themselves look even more ridiculous. Oh well, perhaps some of them are now willing to concede that someone actually does know something about the evolution of the immune system at least.

David Levin’s review of Behe’s The Edge of Evolution is also available on NCSE’s website.

Thanks for the plug, Glenn:

Glenn Branch said:

David Levin’s review of Behe’s The Edge of Evolution is also available on NCSE’s website.

IMHO, David’s is one of the very best reviews I’ve read. It ranks right up alongside Ken’s, and Jerry Coyne’s and, of course, Nick Matzke’s.

Yay, more festivities in waiting! Try to push Steve Steve into participation for his knowledgeable commentary, and have a beer from selected yeast for old Charlie.

5. ID guy: It’s not detailed enough, I need to see every single mutation and selection event detailed or I will still say that ID was responsible, not evolution.

As with the attempt of redefining evolution as “devolution”, I find this neglect of actual relevant, testable and tested, biological hypotheses (for example the phylogenetic nesting Matzke mentioned) irritating. I know that creationists like Behe is in denial, or otherwise are trying their best to pervert facts, but missing the blindingly obvious just seems so … perverse.

Ah, well, at least it is easy to recognize as blather for many or most casual observers.

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This page contains a single entry by Nick Matzke published on May 19, 2009 9:10 PM.

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