Flagellum evo – further discussion

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For you flagellum wonks in the audience, an interesting and fairly detailed discussion of some of the science issues and, for lack of a better word, etiquette issues, took place over here at T. Taxus in “JCVI Evolutionary Genomics Journal Club on Liu-Ochman.”

(The discussion is also good for Esperanto wonks.)

P.S. added in edit:

FWIW (for what it’s worth), here is my list of online mentions/discussions of the L&O Flagellum Paper Controversy. (Rough draft and there may be some errors or misinterpretations. You have been warned.) It’s a pretty mixed bag for sure – some fairly creduluous citation of L&O which bugs me, some criticism of the PT blog criticisms, some ID piggybacking although most of them don’t even really get what the issues are (Dembski only caught on after I started noting that other IDists weren’t on the right track), etc. And in the grand scheme of things, this is not a huge amount of material – 45 items (if it was much bigger I wouldn’t attempt a listing anyway). We don’t have a “what if the PT blog criticism had been different” control group so any analysis will be dubious, but my suspicion is that whatever its flaws the PT criticism got a lot of people to look at the paper more carefully and may have stopped a lot of foot-shooting.

#DateTitleblogQuote or description of opinion statedUpdate
12007/04/16 0:00Stepwise formation of the bacterial flagellar system (online)PNAS online before printPaper online
22007/04/16 18:43Irreducible Complexity, IndeedJohn Dennehy, Evilutionary BiologistL&O disprove ID flagellum argument!
32007/04/16 19:11Stepwise formation of the bacterial flagellar systeminterrogatingnatureL&O disprove ID flagellum argument!updated with link to PT
42007/04/16 19:49Genome sequences reduce the complexity of bacterial flagella.Ryan Gregory, GenomicronSome enthusiasm for both of L&O & P&M)link to PT critique
52007/04/16 19:58Stepwise formation of the bacterial flagellar system [merged]IIDB Evo forumInitial enthusiasm (several different threads), later criticism
62007/04/16 22:49Flagellum evolution paper exhibits canine qualitiesNick Matzke, PTNick critique #1
72007/04/17 0:00The primary difference between science and IDClever Beyond MeasureCriticism of L&O praised
82007/04/17 0:00A Complex Tail, Simply ToldScienceNOWL&O disprove ID flagellum argument! Letter submitted to Science
92007/04/17 12:04When Scientists Go All BloggyCarl ZimmerCommenting on the controversy
102007/04/17 13:28Science at workUncommon GroundPraise L&O, note criticism
112007/04/18 0:00Skepticast #91Skepticast (podcast)Mention of ScienceNOW piece
122007/04/18 5:46In the News: A Complex Tail, Simply ToldTalk.Originslink, praise, links to critiques
132007/04/18 12:09You asked for simplicity and here you goKrish On PoliticsL&O disprove ID flagellum argument!link to PT in comments
142007/04/18 14:27ForumScandahoovian discussion board
152007/04/19 0:00Irreducible complexity - Eat your heart out!No More WallsL&O disprove ID flagellum argument!link to PT in comments
162007/04/19 8:37Sequence similarities in the bacterial flagellum: what do they mean?ARN blogMore IDists complaining about the very concept of sequence homology
172007/04/19 13:38DARWINISM GONE WILD: Neither sequence similarity nor common descent address a claim of Intelligent DesignMichael Behe/DIIDist doesn't get it: Even if there are sequence similarities it doesn't matter (i.e., Behe doesn't get the problems)
182007/04/19 13:49Inferring phylogenies + duplication and divergencesci.bio.evolutionDiscussion of further possible science
192007/04/19 15:53Behe's Black BoxEvil Under the Sun"Mit anderen Worten [in other words]: neeh neneneh neh."updated with link to PT
202007/04/19 22:58Uh-oh...poor science alert!PharyngulaProblems with L&O
212007/04/20 0:00Wie war das mit Leichtgläubigkeit ... ?German creationistsApparently chuckling over L&O
222007/04/20 0:00If Parody becomes the reality...German creationistsApparently chuckling over L&O
232007/04/20 2:28Update on PNAS flagellum paperNick Matzke, PTNick critique #2
242007/04/20 8:57All flagellar genes derive from a single gene"How could people publish such a ridiculous result, and in PNAS of all places?" [Dembski doesn't actually know enough to distinguish ridiculous from non-ridiculous -- Behe couldn't -- but he picked up on my statement.]
252007/04/20 10:00Scientific Controversiesevolgen, RPMProblems with L&O
262007/04/20 17:27Biologia Evolutiva O flagelo do "desenho inteligente"Citation of ScienceNOW piece
272007/04/21 10:49BOMBA! BOMBA! Falsificaram a complexidade irredutível do flagelo bacteriano!!!Nomenklatura CientificaMore IDists complaining about the very concept of sequence homology
282007/04/22 17:48ForumSkepChick.com forumAnti-ID citation, notes problems
292007/04/24 0:00Stepwise formation of the bacterial flagellar system (print)PNAS 104(17)Paper printed
302007/04/24 0:12Flagellum evolution kerfluffle continuedNick Matzke, PTNick critique #3
312007/04/24 10:22ForumVeganRepresentVegan weirdness
322007/04/25 13:20The great flagellum debateNsaundersDebate it but be professional
332007/04/25 15:31Stepwise flagella formation¡Viva La Evolución!L&O disprove ID flagellum argument! "NO fairies or little elves involved (in case you like it fantastic)"link to PT in comments
342007/04/26 5:38ForumEvolutionFairyTale.com"Behe's famous flagellum has been dissected aat the molecular level and an evolutionary pathway been built up showing the ancestory, see this link."
352007/04/26 13:07Peer review.Ryan Gregory, GenomicronAnnoyance at flagellum "spectacle "
362007/04/28 21:00Dishonest MoronsOJB42's BlogL&O disprove ID flagellum argument! "Just to completely destroy ID arguments, it has recently been found that 24 of the genes in the bacterial flagellum came from one gene,...Yes, that's right, the structure the ID supporters love to quote as their icon of ID, has become an example of evolution at work. OK ID, its time to give up. You can all go home now and stop deluding yourselves - evolution is a fact."link to PT in comments
372007/05/02 0:00Ayala (2007) Darwin's Gift: To Science and ReligionPrinted bookpp. 212-213, endnote 19 of chapter 8: Recounts L&O paper (in press at time of print, then...) "...The sequence similarity among all the flagellar genes in the 41 bacterial species has allowed Liu and Ochman to reconstruct the successive steps of addition and modification by which modern bacterial flagella have arisen." However the L&O paper is not cited in the main text.
382007/05/02 0:00Die Flagellumgeschichte geht noch etwas weiter.*Evil Under the Sun*Noting further debate over L&O
392007/05/04 21:50ForumOutdoorsBest forumuncritical citation
402007/05/09 17:00ForumRichardDawkins.net forumAnti-ID citation, notes problems
412007/05/10 2:56Re: Intelligent Design is NOT Science??? Apologetic.com forumAnti-ID citation, notes problems
422007/05/12 4:31JCVI Evolutionary Genomics Journal Club on Liu-OchmanT. taxusDiscussion of the discussionExtensive debate in comments
432007/05/14 0:00Microbiology: Building from the Inside OutRichardDawkins.net (not Dawkins himself)L&O disprove ID flagellum argument! link to PT in comments
442007/05/18 3:32Flagellum evo --- further discussionNick Matzke, PTlink to commentary
452007/05/18 8:20Peer review or peanut gallery?Ryan Gregory, GenomicronAnnoyance at blog critiicisms of L&O

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A correction to the paper by Liu & Ochman, “Stepwise formation of the bacterial flagellar system,” was just published in PNAS. PT readers will recall that I and others had many problems with the methods and conclusions of this... Read More

49 Comments

gee… TR Gregory is a douche.

I like the comments over at the linked blog, which seem to follow a completely different tone than they often do here. Even when people disagreed it still stayed pretty civil which is good. I know there are some rebuttals to the paper currently submitted in various forms and I’m looking forward to reading them. I didn’t agree with the conclusions of the paper, and the actual arguments put forth against it were very good. I only disagreed with the rhetoric and polemics being used in many of those posts. I recognize that the blogosphere is a very different beast than academia, much quicker and less formal. Still… to each their own I guess.

I have to defend Ryan Gregory, he is an extremely serious and knowledgable scientist, and conscientious about important issues like public understanding of science. He runs an very excellent blog, Genomicron, on noncoding DNA and related issues (where he is dissing me right now, but if I dish it out I have to take it also). We just have a disagreement over the did-Matzke-handle-the-L&O-situation-right issue – and there is some room for disagreement there, I probably could have done the initial posts in a better way.

There are Esperanto wonks?

and there is some room for disagreement there, I probably could have done the initial posts in a better way.

perhaps, but exploring the edges ended up provoking some interesting discussion, too.

I’m sure that wasn’t all a waste.

Gregory may or may not be a good scientist, but he behaves like a jerk.

First, this pathetic argument to authority:

http://genomicron.blogspot.com/2007[…]xity-of.html

“Moreover, the paper was edited by none other than Francisco Ayala, which are some rather large toes to be stomping on.”

Um, hello? How scientific is that?

Now in that last posting

http://genomicron.blogspot.com/2007[…]gallery.html

he loses all vestiges of logic:

“Reality check. I saw a grand total of three blog posts about the paper from pro-evolutionists.

[…]

I therefore reject the rationale of needing to protect evolutionists from shooting themselves in the foot.”

Um. Just because it didn’t become a PR catastrophe (probably in part (laaaarge part!) because of Nick’s whistleblowing) does NOT mean that Nick’s assumptions/worries were incorrect/implausible at the time when he was writing his initial posting. One just can’t dismiss it post factum, as Gregory does, just because “nothing happened”.

So it seems Gregory is just a stubborn person who will defend his current position no matter what.

http://genomicron.blogspot.com/2007[…]xity-of.html

“Moreover, the paper was edited by none other than Francisco Ayala, which are some rather large toes to be stomping on.”

http://genomicron.blogspot.com/2007[…]entific.html

“4) Eschew arguments from authority.

Arguments from authority are not acceptable in science. If you reject them when anti-evolutionists use them, avoid them in your own posts.”

And a hypocrite to boot.

Yeah, there are some issues with Ryan Gregory’s arguments, but then from his perspective I probably looked like just some twerpy blogger way out of my league (still possible!), and I am beginning to see that if you aren’t already a flagellum wonk with a lot of the background context, then many of my arguments were not self-evidently true, at which point it comes down to relative authority and I don’t have much. Also, Howard Ochman is a well-respected established figure in ev. bio. and rightly so. So you can see how twerpy blogger vs. PNAS + Ayala + Ochman can raise some skepticism.

I launched my little campaign after seeing only 2 random blogs praising the Liu-Ochman paper. But intuition said it would spread further than that, and this was proved somewhat right despite my efforts. I’ve accumulated a bit of a list, I might post it if I can get it together.

At first, when I was contemplating launching a scientific blog, I expected that I would probably come to face personal attacks and quote mining, since these are trademark behaviors of anti-evolutionary commenters. But I will admit that it is something of a blow to see this happening on Panda’s Thumb, which I normally think is a useful forum. I am disheartened to see the name calling, although I appreciate Nick’s comments. Nick, surely you know that nothing I wrote reflects criticism of you personally, only that the way that it was handled should be improved upon for the future.

For clarity, let me provide full quotes of what I said in the instances cited.

Careful criticism is, of course, how science proceeds, so I am glad that Nick has posted his thoughts on the paper. He has certainly done lots of reading and thinking about flagella. I have let Howard know about Nick’s comments, and the paper is open access so anyone else can evaluate for themselves. I’m not an expert on bacterial flagella so my role in this case is strictly to report on an interesting use of genome sequencing data. On a side note, I think calling someone else’s paper “a dog” (pretty much in so many words) does little to help one’s credibility among scientists, useful though it may be as a flashy headline. Moreover, the paper was edited by none other than Francisco Ayala, which are some rather large toes to be stomping on.

I in no way suggested that the science of the paper should be accepted because Dr. Ayala was editor, only that he is someone who has earned a tremendous amount of respect and that any implication that he shirked his duty in letting the paper through is unwarranted.

Reality check. I saw a grand total of three blog posts about the paper from pro-evolutionists. Mine, which gave equal time to Nick’s model. Dennehy’s, which, like mine, was tentative in its acceptance of the paper, and Harrison’s, which also mentions Matzke’s model and mostly just summarizes the paper. The first two bloggers are professional scientists, the third is a freshman student. There was also a story in Science, which I agree was not particularly well done. Readers of this blog will be aware of my complaints about scientific reporting and the all too common trend toward sensationalism at the expense of accuracy. That’s about it. None of the blog posts claimed that this study refuted ID (whatever it means to refute an untestable idea), they merely described it as further evidence that an evolutionary approach is applicable to the question of flagellar origins, and that genome data will prove useful in this endeavor.

On the anti-evolution side, I saw a similar number of posts. These said little about the science (no surprise), and focused mainly on Matzke’s rhetoric. I see nothing to be embarrassed about in the three evolutionists’ blog posts above, and lots to be concerned about in terms of arming the anti-evolutionists with sound bites that excuse them from even having to read the paper under discussion. I therefore reject the rationale of needing to protect evolutionists from shooting themselves in the foot.

The point I was making is not that no one would have commented with undue enthusiasm on the article (Science did, as I noted), but that the bloggers who did describe the paper did not misuse it in that way. I don’t doubt that the quick post by Nick had some positive effect, but it also had an adverse influence by giving sound bites to antievolutionists. The sentence that begins “Therefore, I reject the rationale…” is not even from the same paragraph as the first line cited.

I certainly agree with CJO’s note that this has led to some interesting discussions. I also think, on the whole, that Nick is right to have commented on the paper and in providing arguments rebutting its claims on scientific grounds. I only wish he had led with post #3 and skipped the rhetoric from post #1. And, despite this unpleasantness, I maintain hope that we can elevate the discourse on blogs so that scientists will feel enthused about contributing.

Yeah, there are some issues with Ryan Gregory’s arguments, but then from his perspective I probably looked like just some twerpy blogger way out of my league (still possible!), and I am beginning to see that if you aren’t already a flagellum wonk with a lot of the background context, then many of my arguments were not self-evidently true, at which point it comes down to relative authority and I don’t have much. Also, Howard Ochman is a well-respected established figure in ev. bio. and rightly so. So you can see how twerpy blogger vs. PNAS + Ayala + Ochman can raise some skepticism.

I really hope you don’t think that’s what I was saying here. I think you are more than qualified in this field. Indeed, I spent as much time on your model in the post about Liu and Ochman as I did on theirs (Science, by comparison, did not mention it). I also discuss your model with my students and direct them to the articles you wrote describing it.

The problem is that no arguments in science should be taken as self-evidently true. I said at the very beginning that I look forward to reading your formal rebuttal in published format. It is only the rhetoric, which I think was not necessary to accomplish your objective, that I questioned.

Thanks Ryan for your comments, which are fair enough. I officially rescind the suggestion that you think I am a mere twerpy blogger (although you might want to think twice about that!). I was hypothesizing one way someone coming to the PT posts out of the blue might view it. I will continue to ponder your criticisms also and may comment further on the meta-issue of the way the blog criticism was done once I get a little more perspective and see how the letter to Science plays out, etc.

There are Esperanto wonks?

Apparently Mark Pallen met his wife at an Esperanto conference in China. As Dave Barry would say, I Am Not Making This Up.

flagellum wonk

Is this the first time in history that this phrase has ever been used?

It’d make a good band name, I think.

IDiotoj kredas:

¡La tero planas, junas, kaj ne movas!

Mi Esperante skribas esperante ke oni povu kompreni min.

Horribly mis-formatted comment, I’ll try it elsewhere

Is this the first time in history that this phrase has ever been used?

It’d make a good band name, I think.

Possibly the only phrase rarer than “esperanto wonk”.

As of today both phrases still get zero hits on google. I guess we can watch the Google Fight progress.

Is this the first time in history that this phrase has ever been used?

It’d make a good band name, I think.

Possibly the only phrase rarer than “esperanto wonk”.

As of today both phrases still get zero hits on google. I guess we can watch the Google Fight progress.

from the list…

Vegan weirdness

how on earth did that happen?

I recall about six years ago that Nick was starting a very serious study of the bacterial falgellum. This was undertaken as a critique of the creationist work of Jon Wells. But, his ability and effort went far beyond this.

Ryan Gregory has offered nothing of substance. He asserts an elitist argument of certification (and then denies it), he argues for the sanctity of privlideged publications as opposed to profane blogs (in his blog). Thus, Gregory is a hypocrite.

Nick has far more years of work on this particular topic than Gregory, and I have seen over the last 6 years that Nick is a careful and thoughtful person. Gregory claims a personal relationship with Ochman. I assume he thinks that Ochman is a thoughtful person. Of course, Ochman is on the same faculty as Gregory, and will have some impact on Gregory’s future course assignments, committee assignments and even tenure. I consequently discard Gregory’s assement of Ochman as it is self serving. Nick and I have never even met face to face.

The Liu-Ochman paper was apparently a failure. If anything, this is a good example of a failure of peer review. If Nick had been a reviewer, Liu-Ochman and PNAS would have avoided a public embarrassment,

As I said on another blog, I seen several ironic arguments from authority over L&O versus Nick.

The irony is that L&O cite Nick as an authority on flagellar evolution. Citation number 13 in L&O is Nick’s Nature review paper of flagellar evolution with Pallen. Anybody who read the paper should have picked up on this. But I suspect that preconceived notions may have prevented some people from thinking that Nick might have a background in the topic.

The bacterial flagellum has received attention as an exemplum of biological complexity; however, how this complexity and diversification have been achieved remains rather poorly understood. Although several scenarios have been posited to explain how this organelle might have been originated (13), the actual series of evolutionary events that have given rise to the flagellum, as might be inferred from the relationships of all genes that contribute to the formation and expression of this organelle across taxa, has never been accomplished.

Insights into the evolution of the bacterial flagellum have been gained from the homologies between flagellar proteins and those functioning in other systems (13). …

13 Pallen, MJ & Matzke, NJ. (2006) Nat Rev Microbiol 4, 784—790.

I was in the same grad lab with Liu, interviewed for grad school with Ochman, and slept on Matzke’s floor. And from the very beginning I had no doubt that Nick knows what he is talking about when it comes to flagellar evolution.

I was in the same grad lab with Liu, interviewed for grad school with Ochman, and slept on Matzke’s floor. And from the very beginning I had no doubt that Nick knows what he is talking about when it comes to flagellar evolution.

This is a neat variation on the “small world” problem in social network studies.

TR Gregory seems unable to use a mirror. He threatens that Nick is facing retaliation from Francisco Ayala, but claims that he isn’t trying to intimidate.

Moreover, the paper was edited by none other than Francisco Ayala, which are some rather large toes to be stomping on.

I’ll be speaking with Ayala quite soon, and this assertion by Gregory that he (Ayala) has big feet and must defend L&O will certainly be worth mention. ;)

If Gregory had much experience as a reviewer or editor he would know better. I have noted that Greory’s CV included several book chapters he coauthored in a book he edited. That doesn’t count too much. The last journal article I “reviewed” was given to me by the editor with the request, “See what you can do to help this paper- it is going in the journal anyway.” From a 30 year perspective as a reviewer, this is not a rare instance.

My most recent rejected paper was trashed when I used a “global search and replace” for “Pb” instead of “Pd.” (The joy of dyslexia). You can imagine the hostile comments! Unfortunately, I went into hospital for a scheduled surgery counting on my coauthor to straighten out the mess I made. He went in for an emergency surgery the same week. The paper was never published.

Oh Well.

Syntax Error: mismatched tag at line 1, column 465, byte 465 at /usr/local/lib/perl5/site_perl/5.16/mach/XML/Parser.pm line 187.

Trying again…

Gary Hurd states… Ryan Gregory has offered nothing of substance. He asserts an elitist argument of certification (and then denies it), he argues for the sanctity of privlideged publications as opposed to profane blogs (in his blog). Thus, Gregory is a hypocrite.

I am not sure I follow what this is supposed to mean. I have been petitioning for a more respectful tone to discussions about science on blogs, and I have been doing it on a blog because I believe in the medium. That seems entirely appropriate to me. I think the fact that I am trying to make blogs accessible to more scientists and to have them take them seriously enough to participate such that the process is open proves that I am no elitist.

Gary Hurd states… Gregory claims a personal relationship with Ochman. I assume he thinks that Ochman is a thoughtful person. Of course, Ochman is on the same faculty as Gregory, and will have some impact on Gregory’s future course assignments, committee assignments and even tenure. I consequently discard Gregory’s assement of Ochman as it is self serving.

Howard Ochman is not in my department, nor even in the same country. I have not defended the science of Liu and Ochman even once. I have asked that scientists of their standing be treated with respect.

Gary Hurd states… TR Gregory seems unable to use a mirror. He threatens that Nick is facing retaliation from Francisco Ayala, but claims that he isn’t trying to intimidate… I’ll be speaking with Ayala quite soon, and this assertion by Gregory that he (Ayala) has big feet and must defend L&O will certainly be worth mention

I have never tried to intimidate anyone, and I made no threat to Nick. I made the comment in response to suggestions that 1) the paper should be “stomped on”, and 2) that it had somehow made it into print without being reviewed. Ayala does not have to defend the Liu and Ochman paper, but he deserves more respect than he received.

Gary Hurd states… If Gregory had much experience as a reviewer or editor he would know better. I have noted that Greory’s CV included several book chapters he coauthored in a book he edited. That doesn’t count too much.

To clarify, I have published > 30 peer-reviewed papers and have reviewed more than 80 manuscripts for journals including Science, Nature, Evolution, PLoS, Proceedings of the Royal Society, Molecular Biology and Evolution, and various others. This is all clear (I thought) from the CV you read.

Gary Hurd states… If Nick had been a reviewer, Liu-Ochman and PNAS would have avoided a public embarrassment

I agree, Nick would have made a good reviewer, and I look forward to reading his published, peer-reviewed rebuttal.

I must say that I am staggered that this is the reaction my comments have received from fellow science bloggers. I have simply expressed what I view as the need to treat these discussions more respectfully so that more scientists will be interested in participating. I have been reaching out to the blog community and trying in my own way to make it a medium for scientific discussion that would be worthy of being taken seriously by scientists. In response I have been misquoted, mischaracterized, misrepresented, and personally insulted. I have said a lot of positive things about Nick and his work, and my criticisms were about the process rather than the person – this has not been reciprocated here.

“In response I have been misquoted, mischaracterized, misrepresented, and personally insulted.”

Nobody likes whineys. Don’t be one.

Also, when you were criticizing Nick for his tone, you should have thought about your own tone. It’s not as if you were concerned about alienating someone.

I believe Gregory owes Nick Matzke a public apology.

Ack – guys, chill out, this is not some Matzke fan club. Like I tried to say before Ryan Gregory is a serious guy and I am taking him seriously.

If Nick has suffered personal offense even within an order of magnitude of what I have encountered on Panda’s Thumb, then I agree that he deserves an apology, and he shall receive it.

TR Gregory,

Thank you for coming to this blog to share your thoughts. I am sorry if some posters here have been less than polite. I for one need no further proof of your honest intentions than your willingness to respond in this forum. I hope you can understand that dealing with creationists can make one a little jaded after a time.

Now, about the paper. A wise man once said that extraordinary claims demand extraordinary proof. I believe that appplies in this case, considering that Nick published a reasonable scenario before you published something substantially different. If the paper is correct and all of these genes represent one gene family, descended from one anceatral gene, then is should be possible to perform a phylogenetic analysis in order to demonstrate how they are all related. The globin family story is a good example of this type of approach. Of course the situation here is a little more complex. However, if it is not possible to demonstrate the relationships between the different genes, that would not look good for your hypothesis. If you are unwilling to attempt the analysis, that would be even more telling.

In any event, I applaud your efforts to further the cause of science. Success in these efforts would mean that the God-of-the-gaps would get a little bit ssmaller and the empirical approach would once again be vindicated. I am certainly happy that you and Nick have such high opinions of each other. It would appear that both opinions are warrented.

David,

Thank you for your kind words, which have helped to restore my faith in this forum. Just to clarify, though, the Liu and Ochman model is not my work, and I am neutral with respect to whether it is refuted or not. I quite like Nick’s model, and as I said I use it in discussions with students and spoke favourably about it in my original post. I am glad that Nick posted his scientific comments. It is simply the tone and the blogosphere responses that caused me some frustration.

TR,

Sorry, my bad. I still think it’s not a bad idea though, for anyone interested.

Nick,

The table is a great summary. However, it is potentially confusing because it includes posts that are simply individual comments on discussion forums, were little more than footnotes or links to your posts, IDist posts, the paper itself (twice), your three posts, and discussions about the discussion. You probably stopped some foot-shooting – no one is claiming otherwise – but I think rhetorical ammo was also handed to the other side in potentially equal measure, and unnecessarily so. I think a more informative metric would be the number of pieces on scientific blogs or in print that uncritically accepted Liu and Ochman and used it as the and proclaimed that “L&O disprove ID flagellum argument!”. Mine, Dennehy’s, and Harrison’s don’t fall into that category, and they were posted before your critique arrived.

Dennehy: “The take-home message is that evolutionary theory [not this study in particular or its claims] is sufficient to explain even the origin of complex organs and organelles and we needn’t postulate intelligent designers.”

Mine: “This just goes to show the usefulness of genome data for addressing questions that, for the reason outlined by Darwin, seem unanswerable to some. It also opens the door to some exciting future work.” Equal time to your model, and mostly a summary of the paper, plus a comment from the author.

Harrison: “It looks like the coffin of one of ID’s major claims, that the bacterial flagella [sic] is a non-evolvable machine, just acquired another nail.” He then links to your model and just summarizes the paper. He also was the first to point out on other blogs that there was some controversy.

The Science story was a mess, I agree. So are many science reports, as I had noted on several posts. The difference, surprisingly, is that we only saw one of these (take credit if you like, but I doubt that’s why – reporters usually have access to papers long before they appear in press). By comparison, I saw multiple misleading stories in major publications (or their webpages) about recent articles on noncoding DNA (which is not irrelevant in the anti-evolutionism debate).

Finally, if I may state my position once more, I did not complain that the paper was critiqued via blogs, only about the tone of the discussion and the immediate acceptance of your claim by many others before you had even provided any backing evidence.

David,

Yes I think there are other interesting analyses one could do. And while the notion that all of the genes are descended from one ancestral sequence may be untenable, it would still be intriguing to consider the role of duplications in less restrictive capacities. I imagine that we will see a line of interesting papers coming from this topic.

Finally, if I may state my position once more, I did not complain that the paper was critiqued via blogs, only about the tone of the discussion and the immediate acceptance of your claim by many others before you had even provided any backing evidence.

I was willing to let you ramble onwards all the way until you said this.

In his very first substantive post on the subject, released the same day as his initial assessment, Nick did indeed provide supporting evidence for his claim that the authors were mistaken to use the single gene model.

so, I completely disagree that Nick did not provide any backing evidence before people started to run with it. At most, a warning was given at Pharyngula after Nick’s first post, to “stay tuned” for further details, which Nick did indeed rapidly provide.

again, you’re going overboard here and taking license with the leeway Nick has given you here to discuss the issue of the general issue of the appropriateness of discussing published papers via blogs.

This doesn’t give you the right to spin the history of the presentation into something it wasn’t.

Sir_Toejam

Fair enough. Let me amend the statement and note that the detailed arguments involving analyses of the data rather than general outlines of his disagreement with the article did not come until after some people had already called for the paper to be ignored or even retracted.

Fair enough. Let me amend the statement and note that the detailed arguments involving analyses of the data rather than general outlines of his disagreement with the article did not come until after some people had already called for the paper to be ignored or even retracted.

Hmm. I do recall exactly the unfolding of events surrounding Nick’s initial assesment, and the ONLY blog I saw with a response to his initial assesment was Pharyngula.

Please detail for me the blogs that “ran with this” before Nick released his first analysis of the data, a few hours after his initial post?

I think you might be confusing exactly who ran with what.

It’s quite possible many blogs ignored the details of Nick’s presentation, and simply ran with a byline, but that wasn’t Nick’s fault.

Is it even possible to really clear this up?

do you have dates and times as to when other blogs posted their own reactions?

let me add something to that:

There is a a legitimate discussion to be had about the very nature of commenting on research in public media. It certainly goes far beyond just the blogosphere, to all media in general.

surely you’ve noted the innumerable times mass media has fubared the reporting of an interesting or potentially controversial research paper, yes?

the bottom line is, the blogosphere is no better and no worse than typical mass media wrt to what can happen with the reporting of the results of scientific research.

It’s pointless to try to blame Nick for OTHERS deciding to run with the ‘story’ in their own fashion.

I was there, I saw the exact order and how careful Nick was not to make any foregone conclusions BEFORE he presented his second post on the issue, where he did present a detailed analysis of much of the data in the paper.

He was far MORE careful than most commenters have been in the past, that’s for sure.

That said, I really think there could be an interesting furtherance of the discussion of how reporting on research papers in the “blogmedia” could be done, but I really find very little to criticize Nick for in this matter.

Sir_Toejam

I don’t think we disagree for the most part. Science media can be quite problematic, as I have posted about several times previously. Just to be more explicit, I am not blaming Nick for the reactions of others. My comments were directed at both the original tone (only) and the reaction, which are separate issues. I didn’t use the term “ran with it”, so I’m not sure what you’re asking me to specify. The dates and subjects of the relevant posts are listed in Nick’s table above. Four days elapsed between his first post and his second. You’d also need to see the comments on various blogs where discussion occurred. Anyway, this wasn’t about science reporting, it was about scientific evaluation. I keep saying, I am glad Nick posted his critique, I want blogs to be a respectable format for this, I think he did prevent some inappropriate enthusiasm about the article, and that I consider him more than qualified to give an assessment of the topic. I am only saying that if you want scientists to participate, the discussion needs to be as scholarly as possible, with well-reasoned arguments backed up with data, and without people jumping on top of one another. It’s perfectly fine if that is not what this or any other blog’s aim is. Someone wondered why Liu and Ochman did not respond to Nick’s posts online. I think the comments in this discussion indicate the reason. That is what I am saying. Yes, there is a blog culture, and it is interesting and entertaining. But when you want it to be taken seriously as a medium for discussions on the merit of a scientific article, the tone has to be different. There is no personal criticism of Nick implied. He and I have spoken on email both before and after all of this about topics besides this one. I respect his work, I appreciate his contribution, and I am hopeful that he will be a prime example of bloggers as serious commenters. My worry is that most scientists are not going to take time to contribute to a blog if they can expect to be shouted down or insulted. Talking with scientists is not the same as arguing with creationists. Scientists will listen to reasonable arguments. They will admit errors. They will share data and discuss interpretation. But when the language is charged, they tend to pay less attention to the author. I am making my points because I want scientists to respect bloggers, but if it is not reciprocated this can’t occur.

As a meta-comment, my experience with using several fora similar to PT is that keyed-in words can easily be misunderstood and the misunderstandings can easily grow.

Personal conversations communicate much more efficiently and the emotive content is readily corrected.

It takes more effort to write in a way which accurately communicates. I commend the efforts of Matzke, Gregory and others to attempt to keep a civil tone…

“Why would anyone want to join a discussion with a bunch of partisans who are treating scientific arguments like a high school football rivalry?”

This is the question many people might ask when they see people rabidly come to Nick’s “defense”-

1) Nick doesn’t need to be defended.

2) Everybody is welcome to have an opinion, but as with many topics, many of us don’t know as much as we should or could. This is not an argument to STFU, this is an argument not to turn all PT discussions into the same poo-flinging that we normally enjoy when having arguments with people supporting absolutely illogical or crazy positions (anti-evolution, etc).

3) This is not a claim for blog commenting civility, although it would be nice.

4) TR Gregory is not a “douche”

5) If Nick were rebutting Ochman et al at a scientific conference with Ochman present, in a presentation and not on a blog, how would he go about it? Would he launch into his arguments as they unfolded here verbatim? No, most likely he would have contacted Ochman prior to conference, discussed his misgivings and stated his intention to discuss them in a public forum given the attention to the L/O paper. THIS IS NOT REQUIRED BEHAVIOR. It is merely polite and respectful. And in giving the presentation hypothetical Nick could have said “I have discussed this with Ochman and he a) respectfully disagrees b) will have a response shortly c) agrees with some criticism and will have a corrigendum/retraction shortly” and then WOULD PROCEED TO PRESENT HIS CRITICISM. Nick would not have to alter any substance just the way he communicated it. This is the difference between being outside of science and inside it as a colleague. As Nick is continuing his scientific career I think this is worthwhile advice. This is what many people were saying. This is not disrespectful to him, nor is it concern trolling nor is this an argument from authority, even though it is.

I think Pinko summarized the ideas well. I am not so much criticizing blogs as they are, but noting how they could be if people wish to have scientists participating. I may have mistaken Nick’s role here by considering him a colleague who had behaved with insufficient decorum rather than as a blogger who had exercised restraint. There are two cultures involved, and Nick straddles them as someone who works in PR and on blogs but who also has published in the peer-reviewed scientific literature. I was approaching him as the latter and reminding him that if you want to communicate with scientists and have them listen to your scholarly arguments, you need to leave the rhetoric out. If your audience is simply the blogosphere, and there is no intention of having Panda’s Thumb or any other blog be taken seriously by academics as a medium for scientific debate, then my comments are misplaced and I apologize. If anything, I hope the underlying assumption I made that Nick wants to be seen as a scholar first is received as a signal of respect. It is the difference between blogs as commentaries about science versus participants in science. I would like to see the process opened up such that a discussion on blogs is something to pay attention to as scientists, and so that non-scientists can see the arguments unfold as they actually do in science. Both scientists and blogs will have to adjust if there is to be more interaction – but if that is not something people want, then I admit that my arguments are misplaced.

I appreciate Ryan coming here and sticking with the discussion despite some unusually (or, well, perhaps usually, especially for Friday night) rude behavior from some commentators. Keep in mind that without a required login for commentators anyone can post under any pseudonym and we could always have a creationist or people with other issues coming in and posting to derail the discussion rather than perpetuate it. We can’t actively moderate the vast amount of PT commentating that goes on so generally only spammers, truly insane trolls, and flagrant obscenities reach the level where we get annoyed/disturbed enough to intervene (and typically summarily delete the post and ban the IP address), so rudeness and insults mostly have to be ignored or just pointed out (“That’s just pointless rudeness, not a serious response.” etc.)

Ryan – I agree with your points about the table, I will try to edit when I get a chance (it is all on a spreadsheet on a different computer at the moment).

Howard Ochman is not in my department, nor even in the same country.

My bad. I made an incorrect inference about your having frequent contact with Ochman. My apologies.

None the less, I see nothing that Nick needs to feel bad about, and the arrogance of your demand that he apologizes to Liu and Ochman is quite remarkable. Once a paper is public, the only possible response must also be public. Your insistence that you have been misunderstood does not suggest that you have given adequate thought to why so many people cannot understand your “true meaning.”

My only contacts with Nick have been related to the attacks brought by creationists against science generally and personally against those of us who are activists. Your (Gregory’s) experience is that of someone parachuting into a firefight; the view is lovely until the shooting starts.

Gary,

Your comments suggest your background is activism, partisan blog warfare and flame fests. Sadly, in the much more boring academic world, some people strive for more than that, even if they like to rip people new a-holes after hours at the bar. Nick doesn’t have to do anything he doesn’t want to, but imagine how much better a person he would look like if he said “Dear Howard, I’m sorry how this played out. I’d like to explain the initial frame of mind concerning my earlier rhetoric. In online discussion forums and in lawsuits concerning school curricula in many states, we are waging a battle for science vs. anti-science. One of the topics favored by the anti-science ID people is the origin of the flagellum, a complex molecular machine. Given that this area is a mine field of creationist disinformation I was extra-sensitive regarding the flaws I see in your work. Coupled with the non-critical media reaction to the work, I felt a strong response was in order. I apologize for etc. etc.” Nick would look like a true superstar without having to change any of the substance of anything he has done.

Frankly, I think the gnashing of teeth about the tone of scientific commentary in blogs is unwarranted. First of all, it goes without saying that blogs are not, and will never be, a substitute for peer-reviewed venues. This is not because peer-review weeds out all mistakes and nonsense (as this case shows), but because it provides a formal and permanent record of the progress of ideas, and indeed because it does make people adhere to certain standards, in format more than in tone, that have been developed to maximize the transmission of information between professional scientists while minimizing “noise”.

On the other hand, blogs are more like informal conversations among scientists - it is not just for cuteness’ sake that PT defines itself as the virtual pub of the University of Ediacara. Anyone who has even been at a scientific meeting knows that the way scientists talk about each other’s work over beers at the local bar late at night after a long day of talks is not the same as they would use in a Science commentary, or (in most, but not all cases!) even in the Q&A time after a talk. At the bar, some people may be pissed at the poor quality of someone else’s work, or at their unwarranted conclusions, and/or tipsy, and just let it rip. To me, that’s just dandy.

Clearly there is a space for both levels of discourse, and it sits with every blogger-scientist to gauge their tone to what goal they want to accomplish, or bar that (pardon the pun), to their mood/intoxication level. Perhaps Nick was a bit harsh in his first post, but I can tell you he was fuming. Indeed, to his great credit, if a similar paper had been published by a Creationist arguing for the other side, he would have been fuming just the same, and his criticisms would not have been different. (I am afraid, however, that there would have been fewer complaints about his tone.)

By all means, I agree people should strive to keep the level of their discourse up, because it allows communication channels to stay open and, frankly, you never know when you’ll be on the receiving end of harsh criticisms, so you may as well leave a good track record of expressing yours as civilly as you can. But “if you don’t have anything nice to say, don’t say anything” does not apply to science, even between scientists who otherwise agree on virtually everything else that matters. And most scientists have a thick enough skin to take it.

All of the above refers to actual substantial commentary. The peanut gallery is what it is (and sometimes it’s indeed too much), but that’s one of the things that make blogging entertaining, and you often do get insightful comments mixed in with the scatological material, so it’s definitely worth it to let everyone have their say.

I agree with Andrea, except that putting personal remarks in print in public is quite different from talking over beers at the local bar late at night. As a result, Ryan’s main point is reinforced: Personal remarks, not exclusively from the peanut gallery, both degrade the dialog we have and cause many scientists not to participate in the first place.

Perhaps just asserting that scientists are thick skinned is not enough. Could regular commenters here try to make the environment more attractive to more scientists?

I agree with Andrea for the most part as well. Blogs are not peer review (although some commenters seemed to be mistaking it as such in this case). I have tried to make that point, and I would never suggest that they could replace or even approach peer review. It doesn’t follow, though, that blogs have to be free for alls. They could be venues where scientists and non-scientists congregate to have rational, reasoned discussions about scientific publications. We did not get that in this case, and I think that’s a shame. That has been the basis of my comment more than anything.

Scientists do have thick skins. I have been involved in vigorous discussions in person and in print. That is not the point. The point is that scientists have a lot of things to deal with, and if we want them to be eager to participate in blog conversations, you can’t start it out with “oh, and you might be called names”. Very few would bother with that. As noted, disagreements in pubs are not public record, and debates in print are largely moderated by the combined influence of editors and academic decorum. That doesn’t mean that we haven’t all cursed at a lousy paper from time to time in our own offices.

My hope is that blogs can be more than a peanut gallery. If I didn’t care, I would not make any comments like those that I have, and I would simply retreat back into the ivory tower. I am trying to open the process up, but colleagues will not join me if I can’t convince them that it is worth taking bloggers seriously.

I would love to have seen an academic debate between Matzke and Ochman online. That would have shown many people what science is really like. However, I am relieved that Howard did not participate, given the way I was treated on this forum most recently.

if a similar paper had been published by a Creationist arguing for the other side, he would have been fuming just the same, and his criticisms would not have been different. (I am afraid, however, that there would have been fewer complaints about his tone.)

I do see a difference in expectation for tone when dealing with a creationist and with a respected scientist, in part because creationists do not do research, and thus don’t publish in prestigious journals, and are making their arguments on non-scientific bases.

Sorry I missed this the other day- I went fishing and I was in such a good mood.

PinkPunk, “Your comments suggest your background is activism, partisan blog warfare and flame fests. Sadly, in the much more boring academic world, some people strive for more than that, even if they like to rip people new a-holes after hours at the bar.”

I will wager the traditional bottle of single malt that I had a tenure offer before you were out of grad school. (My doctorate was awarded by the University of California in 1976 - I was 24 years old, (I’ll up-grade to a full liter if you can match that) I was offered tenure by the Medical College of Georgia in 1984 (or ‘83) - I realized I had to quit the same day)(Double or Nothin’ TR Gegory was not out of High School in 1976 (if not still in dippers). But, I also had early experience as an industry chemist which made me well aware of how easy it was to obtain a good income, pursue intellectually rewarding and interesting research outside of the “hallowed ivy covered halls.” Ivy is just a weed.

PinkPunk, “Nick doesn’t have to do anything he doesn’t want to, but imagine how much better a person he would look like if he said “Dear Howard, I’m sorry how this played out. I’d like to explain the initial frame of mind concerning my earlier rhetoric.

A “better person” to whom? Nick Mazke developed an impressive expertise on the biology and evolution of the baterial flagellum. His writing on this that I have read with interest dates back several years. He did this without a tax supported academic pillow. This has apparently been superior to so-called creationist experts such as Behe or Wells, who both have excellent academic credentials fully equal or superior to “dear Howard,” Ryan Gregory, or I’ll wager you, PinkPunk. And, when the final verdict is in on the L&O train wreck, I’ll bet that Matzke will be correct on the data, and their interpretation. Nasty way that data has of screwing pompous science academics who publish based on their positions and reputations rather than competence. If Nick sucks up to L&O, Gregory or PinkPunk, it is because he is young and was threatened politically by both the creationists and the so-called scientists named above.

Happily I have no need of the political, self-congratulary subculture of academic science. So I am even more ready to publically distain pompous assholes. If I were in Nick’s shoes maybe I would have caved in and waited a year or two for my work to be published.

I’ll make a counter offer- you apologise to me for you lame presumption regarding my academic experience, and you and Gregory appologise to Matzke for being pricks. Then you can skip the Scotch. Otherwise, my brand is The Macallan.

you guys act like little children

get a life

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This page contains a single entry by Nick Matzke published on May 18, 2007 3:32 AM.

Is Creationism Child’s Play? was the previous entry in this blog.

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