Flagellum evolution paper exhibits canine qualities

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Today the prestigious journal Proceedings of the National Academy of Sciences (PNAS) put out an Advanced Online Publication paper on flagellum evolution entitled, “Stepwise formation of the bacterial flagellar system.” The paper is freely available via Open Access. I was initially excited that PNAS had published a paper on this topic, and furthermore that it cited the Pallen/Matzke essay on flagellum evolution, and Ian Musgrave’s excellent book chapter in Why Intelligent Design Fails.

Unfortunately, as I read the paper, my delight turned to concern, and then dismay. The paper makes some potentially useful points and explores new territory in a few areas. But much of it ranges from dubious to just irremediably wrong.

I am not talking about minor issues, like the fact that the authors endorse the “flagellum first, type 3 secretion derived” position, which is currently debated by the experts. I am talking about things like the conclusion of the paper, which is that

“we have shown the bacterial flagellum too originated from ‘so simple a beginning,’ in this case, a single gene that underwent successive duplications and subsequent diversification during the evolution of Bacteria.”

The authors argue, as have I and others, that the flagellar axial proteins, about 10 of them, evolved by duplication and diversification from a common ancestor. But this is miles away from demonstrating that all flagellar proteins come from one gene, and in fact the extra-flagellar homologies show positively that this cannot be true, as anyone who has read the literature on this topic should know (the authors exhibit some awareness of these homologies, but they don’t seem to see the implications). Frankly it is a flabbergasting thing to say, and I can’t understand how it got published.

There are numerous other detailed problems, especially involving the statistics of homology searches, and the authors’ truly weird interpretation of their phylogeny of the axial proteins (the phylogenies are in the Supplementary Figures). They all seem to point to unfamiliarity with the basic issues involved in these areas – and if I can perceive this as an amateur, you know something is wrong. To give this paper a pass as it is, the peer-reviewers must have been some combination of not in the right fields, too busy to do a serious review, etc.

Normally I would just ignore this sort of paper. Weird stuff gets published in obscure journals and ignored all the time. But it is published in PNAS, and PNAS has put it up free on the web, and a few pro-evolution blogs have already linked to it (1, 2 – sorry guys), and sooner or later the creationists will realize that the people who know something about flagellum evolution have major problems with the paper and start to make hay of it. And if we don’t stomp on this paper, more people who don’t know their flagella from their cilia will cite the PNAS piece as a competent rebuttal to Behe and co. So as painful as it is, and as much as I hate sticking my neck out against established scientists of good reputation, people who clearly could have produced a good paper with some more rigorous reviewing and background research, there is nothing for it but to suck it up and declare this paper a dog. In science, if the choice is between propagating error and being remorselessly negative, you’ve got to go with remorselessness. It sucks, and it’s nothing personal – everyone makes mistakes sometimes – but that’s science (unlike creationism/ID).

Am I being too harsh? It’s always possible that my inexpert self has missed something key that the experts are aware of. Read the paper, read the other flagellum evolution posts and papers (and more papers), and give your opinion. It’s even possible that we are accidentally seeing a rough draft or something.

PS: It would take all night to write a completely coherent analysis, but I should provide some details on just what the problems are that have me annoyed. Here is some initial analysis I made on email, after someone emailed me for comment (edited to remove specific people etc.):

[Note on terminology: the “axial proteins” make up the rod, hook, and filament of the flagellum. Together they form one long tube that constitutes most of what you see when you look at a flagellum. However a dozen other non-axial proteins secrete the axial proteins, provide the motor power, etc.]

[I was asked for reaction, and I replied as follows]

Positive points in the paper:

* (FliC + FlgL) are homologous to the (rod-hook proteins) on their analysis. I and I suspect everyone who thought about it always thought this was extremely likely, but AFAIK it had not been explicitly claimed in peer-reviewed publications, and it wasn’t claimed in the Pallen-Matzke paper, where we just traced the axial proteins back to 2 ancestral proteins. Whether or not the evidence is good enough to be considered demonstrated in a peer-reviewed journal is the real question.

* Identification of 24 ancestral core proteins, which we did not quite make explicit (but then I am dubious about a few of their decisions, see below)

* The comparison of flagellar systems to bacterial phylogeny is also worthwhile although their basic conclusion (mostly linear inheritance of systems, but with some lateral transfer) has been published before.

* Suggestion of homology of (unnamed???) flagellar proteins to Type V secretion, the P pilus, and prophage tail proteins. These would all be interesting if true. However, if it just the ATPase protein (which has endless homologs), or the muramidase domain of FlgJ, or other known bits and pieces, it is not new.

On the other hand, it is easy to get false positives in these searches for weak similarities, especially with certain domains that are widespread. These domains might share common ancestry or they might conceivably converge; and even if they do indicate common ancestry it might be from the evolution of the protein repetoire during the origin of prokaryotes, rather than any events occurring specifically with the origin of the flagellum.

Things I am dubious about:

* I have not delved into their methods in detail, but it looks like this was basically another exercise in BLASTing. They seem to be proposing a bunch of new homologies (see Figure 3, grey lines) based on extremely thin evidence. The homologies proposed between the various membrane proteins would be very important if true, but membrane proteins exhibit certain sequence patterns just because they are membrane proteins.

I tend to think some flagellum membrane proteins are homologous to some F1Fo-ATPase membrane proteins, but thinking it is different than proving it.

* They assert their preference for the flagellum-ancestral-to-NF-T3SS model, but don’t deal with the counterarguments or add any new data. To be fair, the sister-groups people need to produce better evidence on their side also.

* They don’t cite the Pallen et al. 2006 paper in Protein Science, documenting homology between FliH and ATPase components, even though it is extremely relevant to their topic and was cited by the structure people in recent papers.

* Asserting that the L- and P-ring proteins were not part of the common ancestor, based on the idea that gram-positive bacteria and spirochetes are phylogenetically basal, is fine, but it is no stronger than your confidence in the branching structure of the bacteria phyla, which for me is not very confident and plus depends upon the rooting of the bacterial tree.

* They claim their model is step-by-step, but it is less step-by-step than the Pallen-Matzke paper AFAICT.

* The paper could be repaired by removing the dubious points, but then there would not be much new about it, although the FliC-hook homology would be worth publishing by itself if they have a convincing case.

Overall (but very preliminary) conclusion:

* Confirms the basic results of previous studies, makes a few speculative suggestions and takes sides on a few issues of opinion, but mostly indicates that certain outstanding questions need to be worked on, e.g. the phylogenetic relationship of F-T3SS and NF-T3SS.

[after a more detailed read]

* The supplementary material has a useful attempt at a phylogeny of the axial proteins, and it is at least good to have someone making an explicit hypothesis – but the bootstrap values for the phylogeny are almost all 75% and below, i.e. not good. And the stuff about maybe all the membrane proteins also originating from duplication/divergence is not supported at all as far as I can tell.

* OK, I went and had a careful read-through. The paper is:

1. A perhaps-worthwhile comparison of flagella phylogenies to bacterial phylogenies

2. A perhaps-useful attempt to analyze the phylogeny of the axial proteins

3. But even if #1 and #2 are done right, this is hidden within lots of totally mystifying rhetoric stating that #2 explains the whole flagellum in step-by-step fashion, even though the axial proteins are really only about 1/2 of the “flagellar core”. And with many dubious interpretations on specific points.

The most mystifying sentence is this one. It is the last sentence of the conclusion:

As with the evolution of other complex structures and processes (29–32), we have shown the bacterial flagellum too originated from “so simple a beginning,” in this case, a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria.

There is just no way that the flagellum evolved by diversification of a single gene. If they meant that just the axial proteins (rod, hook, flagellin) originated from a common ancestor, that would be fine, but they seem to say the whole flagellum, based on a very muddled argument earlier that “we conclude that despite their antiquity, the similarities among core proteins to one another are more common and, on average, stronger than to nonflagellar proteins.” As if “on average” was relevant when it could be true (probably is) that half the flagellar proteins originated by internal duplications and the other half by cooption.

[…]

[talking about the interpretation of the axial protein phylogeny]

Yeah, I was going to mention the polarity problem also [with the interpretation of the phylogeny of the axial proteins]. Even if you assume the root is between (FliC+relatives) and (rod+hook) proteins, which IMHO is reasonable if not proven, and even if you accept the phylogeny despite the low confidence numbers (and it might be a reasonable phylogeny of the axial proteins), that *still* doesn’t tell you that FlgB/FlgC emerged first. What it would tell you is the first thing that happened is the divergence of the root into a proto-“flagellin” group and a proto-“rod/hook” group.

I think they get the bit about FlgB/FlgC coming first from the bottom of Supplementary Figure A, where that divergence is furthest to the left (by a tiny, tiny bit that is surely not statistically significant).

5 TrackBacks

There's a href=http://www.pandasthumb.org/archives/2007/04/flagellum_evolu_1.html a post at Panda's Thumb/a by Nick Matzke that illustrates why ID isn't science, and why science iis/i science. Matzke looks at a paper on flagellum evolution recently pub... Read More

Science at work from Uncommon Ground on April 17, 2007 12:51 PM

Renyi Liu and Howard Ochman describe in the Proceedings of the National Academy of Sciences a series of gene duplication and divergence events that could have been responsible for evolution of the core proteins in the bacterial flagellum (source). The... Read More

As the discussion over the Liu-Ochman flagellum evolution paper continues, it is clear that I need to do a little more arguing to defend my position. Although some were convinced that skepticism was justified based the previous PT posts... Read More

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

Yet more evidence of science (and scientists) at work. I've made two posts about the PNAS paper by Renyi Liu and Howard Ochman claiming that “core components of the bacterial flagellum originated through the successive duplication and modificatio... Read More

32 Comments

OK. Thanks for the write up here Nick. I’m one of the bloggers you mentioned that has already got a hold of this paper, and when I created a new thread at Infidels about it( http://www.iidb.org/vbb/showthread.php?t=203949 ), RBH expressed his concern and then linked to your post here.

Glad to see the quick turn around and the willingness to critique the paper.

The problem may be that PNAS does not necessarily use the Peer Review System. My understanding, based upon trying to get an article published in PNAS some time ago, is that if one of the authors is a member of the National Academy then the paper does not go out for peer review. This is why one should ALWAYS view PNAS articles with a grain of salt…

Nick Matzke Wrote:

Am I being too harsh?

No. You are just demonstrating why science is “no pain, no gain” and pseudoscience is addictive junk food. If ID were science Salvador Cordova (“YEC”) and Michael Behe (“frontloadingist”) would surely have heated debates about common descent.

What a fantastic demonstration that what scientists do is science and what creationists do isn’t.

About VAC’s comment on PNAS and peer review: Here’s their procedure. They do send the paper to referees.

Nick,

If this is a pre-publication maybe you can have some influence before it actually goes to press, or maybe it is too late already. I would recommend contacting the authors directly and letting them know of your concerns.

Assuming it is too late, I would recommend going to the editors and asking to be allowed to publish a rebuttal paper, or at least a letter to the editor. It might help if you could get some known people in the field to sign on as co-authors. This could have been avoided if you had been chosen as a reviewer.

I agree that the last thing we need is for the “other side” to see us arguing among ourselves. However, scientific integrity is a much more important issue. Thanks for standing up for the truth.

This paper was peer-reviewed as usual, the preferred method in PNAS these days, indicated by the “Edited by …” note under the title. Francisco Ayala was assigned as the editor, and he likely picked several reviewers to do the actual peer review. PNAS actually has three different methods for submitting and publishing papers (they used to be called Track I, II, and III; apparently that terminology has been dropped).

The first method is to get a NAS member that you know to “communicate” the paper to PNAS for you. This is sort of an inside track, as it gets the paper reviewed automatically, and papers submitted this way state “Communicated by [your NAS buddy]” below the title.

The second method is standard peer-review, where you submit the paper, no guarantees, and if the board thinks the paper is worthy they will assign an editor (Ayala in this case), who in turn assigns reviewers. The paper can be rejected at any stage.

The third method is for NAS members only – if you are an NAS member, you can get your paper published by getting a single friend of your choice to review it. These papers are indicated by “Contributed by [NAS member]” under the title. Carl Woese has used this method several times to publish his very speculative ideas on early evolution and the universal common ancestor.

Obviously, the first and especially last of the three methods are less rigorously reviewed. Most of us take anything “contributed” with a large grain of salt, as it really hasn’t been reviewed. However, the National Academy of Sciences is a very prestigious and elite organisation of scientists, scientists who have had to prove themselves scientifically to be elected for membership, and in this respect the track III contributions serve a worthwhile purpose for giving exposure to crazier ideas from good scientists.

One should always remember, in any case, that publishing a paper is really only the first stage in peer-review. The scientific community at large, over time, evaluates the worth of any work. Most papers are forgotten, others cited heavily.

Nick

I don’t think you have to worry about any ID/creationists actually reading a PNAS paper. They will just be content to let Behe tell them what it means. And there is sufficient information in there to damage his claims of IC that he probably won’t be too keen to call attention to it.

“I agree that the last thing we need is for the “other side” to see us arguing among ourselves. However, scientific integrity is a much more important issue. Thanks for standing up for the truth.”

I don’t agree with the first sentence above. Let the creationists and everyone else see how science works. Some things happen faster with the internet. Because some blogs had already mentioned the paper online, Nick’s strong reservations had to be published quickly. Otherwise perhaps the authors could have been contacted, and revisions suggested. Meanwhile back at PNAS they’re probably whapping themselves up side the head for not sending the paper to the right reviewers.

Way to go, Nick!

I think Dunkelberg’s right, there’s nothing that shows the worth and integrity of science so well as Nick’s quick and expert criticisms of an apparently second-rate paper.

However, it is decent of him to include all of his reservations as he does so.

Glen D http://tinyurl.com/35s39o

Pete and Glen:

You guys are definately right. That is why I originally said that the integrity of science was more important that the appearance of concensus. Let everybody see how science works compared to the ‘no criticism allowed’ approach of the ID camp. Maybe then people will see how the two approaches differ and why one produces results and the other one doesn’t.

I still think that it is important to present the concensus view of science in fields where concensus has been reached. Otherwise the other side is quick to play the ‘so you don’t know everything’ card. For example, when debating the age of the earth with YECs, it would not be productive to argue about whether it is 4.5 or 4.6 billion years old. The important thing is to emphasize billions rather than thousands. The topic would still be appropriate in certain journals, but not generally helpful in public debates. The more scientists are seen to agree, the more the public perception of integrity increases. After all, the reason we usually do end up agreeing is that our opinions are based on evidence, as compared to the ‘big tent’ approach.

However, this may not be one of the areas where there is yet a concensus. A good healthy scientific debate can only help to spur interest in research. Still, we should emphasize that ‘poof’ was not the hypothesis advanced in the paper, even if all the details were not concordant with other published work.

Very unfortunate. That journal better “unpublish” that article the same way the Stephen Meyer’s paper was dealt with or this is going to open up the whole bias thing again, and rightfully so.

I don’t know about you guys, but I have an issue with doing “peer-review by blogs”… Don’t call this peer-review. This is an opinion piece. If Nick thought he had any publishable material with this criticism, he’d submit it to a journal first, not to a blog. Criticizing science via this form of media smacks of the same tactics that IDers use all the time: i.e., utilizing popularist strategies to attack ideas, whatever their merit.

I don’t know about you guys, but I have an issue with doing “peer-review by blogs”… Don’t call this peer-review. This is an opinion piece. If Nick thought he had any publishable material with this criticism, he’d submit it to a journal first, not to a blog. Criticizing science via this form of media smacks of the same tactics that IDers use all the time: i.e., utilizing popularist strategies to attack ideas, whatever their merit.

If someone can up with some way this paper makes defensible the statement that all flagellar genes descend from one, I’m all ears and I will apologize. But the evidence for this idea is nonexistent and is contradicted by everything else we know.

New media and their effects take some getting used to. This Panda’s Thumb post is extraordinary, but the times they are a changing. PT is known for criticizing creationism, but we don’t want to support evolution other than correctly. Of course not every published paper is golden; but this one, on a favorite Disco topic, appears to be just too hasty and so PT, expected to know about these things, spoke up. This is certainly not a case of criticizing ideas regardless of merit.

This is not likely settled by this one post alone. Stay tuned. Let’s see how it plays out.

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Lurker wrote

I don’t know about you guys, but I have an issue with doing “peer-review by blogs”… Don’t call this peer-review. This is an opinion piece. If Nick thought he had any publishable material with this criticism, he’d submit it to a journal first, not to a blog. Criticizing science via this form of media smacks of the same tactics that IDers use all the time: i.e., utilizing popularist strategies to attack ideas, whatever their merit.

I see only three things wrong with Lurker’s remarks. First, once a paper is published, it’s fair game for commentary regardless of the venue of the commentary. “Peer review” is not merely what appears on dead trees in journals with a 12-month publication lag. It’s everything from the conversation around the departmental coffee pot to informal seminars to journal clubs to eviscerations in seminars and colloquia to published critiques. The Thumb is one such new-fangled venue.

Second, the difference between the ID “tactics” and this post is that the authors of the original paper are more than welcome to come here and defend their work. Try that on Unreliable Descent or the DI’s Media Complaints Division. We welcome it; they prohibit it.

Third, “whatever their merit” is a little off the wall, given that Nick gave reasons for the critique founded on some non-negligible expertise of his own together with some consultation with his peers. That crack is simply misplaced.

Lurker has clearly never stood up in front of a colloquium, presented, and then dodged slings and arrows for an hour of questioning. My most painful memory of an otherwise great sabbatical year at the U of Toronto was just such an experience. Thank the IPU for doctoral orals: they prep one for the real world of peer review.

RBH

Actually, Lurker has done all that, RBH. And it is manifestly different than having to do it in a forum where there is a bunch of unregulated, irresponsible commentary sometimes (if not often) from non-experts. That is what is different about blogs. It is mass-review. Peer-review is not merely any commentary on science. If that were the case, the notion of a ‘peer’ is rendered moot. So, Nick thinks he is a ‘peer’ merely because he got his name tacked onto some review article and because he spent years on a forum obsessing over this flagellum problem. Guess what: IDers think they’re ‘peers’ too. Most of them think they deserve to be acknowledged for doing all their reviewing and publishing. We don’t give them that kinda pass, do we? Finally, we may ‘welcome’ debate just like IDers welcome debate. Scientists aren’t coming to these forums, however. Why would they?

Look, I may be a bit harsh on Nick et al., but let’s be consistent. And show display a little humility about it too.

Lurker,

Normally I would agree with you. But whaddya do if you are pretty sure the irresponsible commentary is in the peer-reviewed journal?

I make no claims on this topic on any personal authority as a official peer, which I know I am not. But if I see problems or errors I’ve got to point them out. If people can find holes in what I am saying I would be happy to be proven wrong.

PS: Rather than the scattershot from-the-hip stuff in this post I am working on something more organized, probably for tomorrow.

Nick

Nick, I am concerned about people calling science-blogging as ‘doing science’ or an exemplum of peer-review. Don’t get me wrong. You’re doing the world an invaluable service by voicing your opinions, which are as informed as any from the normally aloof scientific body. But let’s not fall into the same hole that IDers are in by thinking this criticism is science.

What do you do if a peer-reviewed article is wrong and irresponsible? You do more science: correct it by offering a well-evidenced rebuttal. They we can all post about it and call _that_ peer-review and science at work.

Many people, when they can’t provide evidence for their theory, adopt the strategy of falsehood. Such is the case with many of those who have fallen victim to the propaganda of renowned evolutionists.

If evolutionists want to end the arguments all they have to do is, get their brilliant heads together and assemble a ‘simple’ living cell. This should be possible, since they certainly have a very great amount of knowledge about what is inside the ‘simple’ cell. After all, shouldn’t all the combined Intelligence of all the worlds scientist be able the do what chance encounters with random chemicals, without a set of instructions, accomplished about 4 billion years ago,according to the evolutionists, having no intelligence at all available to help them along in their quest to become a living entity. Surely then the evolutionists scientists today should be able to make us a ‘simple’ cell. If it weren’t so pitiful it would be humorous, that intelligent people have swallowed the evolution mythology. Beyond doubt, the main reason people believe in evolution is that sources they admire, say it is so. It would pay for these people to do a thorough examination of all the evidence CONTRARY to evolution that is readily available: Try answersingenesis.org. The evolutionists should honestly examine the SUPPOSED evidence ‘FOR’ evolution for THEMSELVES. Build us a cell, from scratch, with the required raw material, that is with NO cell material, just the ‘raw’ stuff, and the argument is over. But if the scientists are unsuccessful, perhaps they should try Mother Earth’s recipe, you know, the one they claim worked the first time about 4 billion years ago, so they say. All they need to do is to gather all the chemicals that we know are essential for life, pour them into a large clay pot and stir vigorously for a few billion years, and Walla, LIFE! Oh, you don’t believe the ‘original’ Mother Earth recipe will work? You are NOT alone, Neither do I, and MILLIONS of others!

Lurker, I have to disagree.

Science is the rational debate among those informed about scientific topics towards finding out how the world works, with the scientific method (making hypotheses and testing them against data) as a primary tool.

Scientific journals, full time scientists and references/peer reviewed articles are just a few of a variety of tools we can use for that. They are well established tools with a number of good sides - and still they aren’t everything. A lot of science has gone on in the form of informal discussions among the well-informed - think of discussions between Roger Penrose, Steven Hawking and Kip S. Thorne, or Oppenheimer, Dirac and Feynman - and the published material is in my opinion only a sort of skeleton. We need the rigidity of the published material to keep us honest - yet I think we also need the fluidity of the quick thought and comment to bring us forward at a reasonable pace.

I call Poe’s Law on the James Collins comment.

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James Collins:

A quick Google on your post came up with 39 hits. Have you learned nothing from all the previous times you have posted the exact same thing? For example, you say ‘It would pay for these people to do a thorough examination of all the evidence CONTRARY to evolution that is readily available: Try answersingenesis.org’. I certainly can’t find any evidence against evolution at that site - all I saw were assertions. In fact, there is no evidence contrary to evolution. If there were, biologists would be extremely excited and investigate it thoroughly.

Hi James Collins, you wrote “Build us a cell, from scratch, with the required raw material, that is with NO cell material, just the ‘raw’ stuff, and the argument is over.” When you use the word “us”, do you mean the same people that complain the Miller-Urey experiment is irrelevant? Or those that talk about how playing an 18-hole golf course doesn’t prove a golf ball can randomly do the same thing?

I very much doubt the argument will ever be over until a big booming voice declares the end-of-days for all of us (if that ever happens).

While I think Mark is correct in declaring “Poe’s law” I will take this opportunity to voice an opinion on mine. When I look at things like Maxwell’s equation and the existence of light, I tend to believe that if it can happen, it does. At least in this universe.

Having just read through the paper, I will disagree with Nick on the quality. There is a difference between papers whose results are questionable because the methods were questionable, and papers whose results are questionable because the relevant data are sparse or difficult to gather. In my opinion, the PNAS paper falls more on the side of the latter.

Homology assessments are difficult, especially with ancient divergences, and it isn’t clear to me that the authors could have done much better without spending decades working out the biochemistry of poorly-studied proteins. This is certainly NOT a “second-rate paper”. Rather it is a paper that, like most papers, contains results with varying degrees of support and varying degrees of speculation. It also contains about the same amount of arm-waiving I’ve come to expect of papers in top-tier journals, so it isn’t at all unusual in that regard.

Hi Alex,

There will be more on this later. Suffice it to say that the problems with the paper are even bigger than they seemed to me on Monday.

In the meantime, we have exactly what I feared, which is uncritical secondary reporting from Science and crowing from Behe.

Actually, Lurker has done all that, RBH. And it is manifestly different than having to do it in a forum where there is a bunch of unregulated, irresponsible commentary sometimes (if not often) from non-experts. That is what is different about blogs. It is mass-review. Peer-review is not merely any commentary on science. If that were the case, the notion of a ‘peer’ is rendered moot. So, Nick thinks he is a ‘peer’ merely because he got his name tacked onto some review article and because he spent years on a forum obsessing over this flagellum problem. Guess what: IDers think they’re ‘peers’ too. Most of them think they deserve to be acknowledged for doing all their reviewing and publishing. We don’t give them that kinda pass, do we? Finally, we may ‘welcome’ debate just like IDers welcome debate. Scientists aren’t coming to these forums, however. Why would they?

As a scientist, I’d certainly accept somebody who published a peer reviewed paper on a topic as potentially qualified to be a peer reviewer. However, peer review is pre-publication. Once something is published, it is open to criticism by everybody. Graduate students who don’t even have their PhDs yet routinely critique published papers in regular journal clubs. The quality of the critiques in a forum such as this is obviously going to be variable–but then, I’ve gotten some pretty off-the-wall comments from real peer reviewers as well. Ultimately, a criticism stands or falls on its merits, just like a scientific publication.

I’ve gotten some pretty off-the-wall comments from real peer reviewers as well.

you can say that again! I spent almost two yers bickering with various reviewers over a particular statistical method used in one of my papers, before finally managing to get them to all agree with my original usage.

some of the statistical models suggested by the reviewers were nothing short of whacky.

what will really clarify the situation in this particular case is finding out exactly why the authors chose the single gene model.

once that is clearer, the rest of the paper might be more favorably interpreted.

About this Entry

This page contains a single entry by Nick Matzke published on April 16, 2007 10:49 PM.

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