The controversy expands

I'm getting increasingly uncomfortable with this situation. We just know that "it's not our policy to promote creationism" is going to be spun and used as evidence by the persecution-complex creationists.

We need to hear from the reviewer and figure out just what went wrong before papers start getting pulled and the liars start screaming censorship.

Or maybe, as some have speculated, something got inserted after the review.

It should be easy enough for them to check versions for that, surely. Nothing like the amount of work Barbara Forrest undertook to eventually uncover the cdesign proponentsists evidence.

Oh, and the link doesn't work for non-UMM students or faculty.

Might retract it? It hasn't gone to press yet (it was an ePub ahead of print) and it is plagiarized, not to mention the other issues. What's to decide?

I would think the plagiarism issue would lead to an automatic retraction, whether the paper is creationist crap or not.

and it is plagiarized

I was baffled by this until I rechecked the first thread on this paper and saw the comparison by John H. McDonald--way to go Pharygulites!

This kind of stuff just shows how little respect creationists have for the scientific process. PZ's comparison to D- students in another thread seems more apt every day.

I guess if you're a traditionalist decrying anything modern (like uppity broads getting jobs and all) you see no reason to synthesise anything new. I mean, if it was correct in a previous paper written by somebody else, why bother retyping it?

And in a way, the rampant plagiarism makes the 'controversy' sort of moot. The authors and whoever their ID puppetmasters are can piss and moan about censorship and 'academic freedom' with all their might, but at the end of the day it's just like the Gonzalez tenure thing--shoddy science, and purveyors of same, are the losers.

O Lordy! I just today heard what became of one of my old ferry-mates, one of those guys who thinks (and whose "education" tells him) the Bible is the font of all knowledge.
He's head of the Sociology Department atr Nazarene Bible College! Biblical Sociology! I wonder what that is like?

Oh yeah, he's an ID guy. And his big moral crusade? "Bring back shame"!! Oh yeah, he's department head material. And Good Lord, he has two young daughters. Thank God, they'll never lack for shame.

As my wife said, laughing so hard she almost choked: "Shame! Come back, Shame!"

She added: "He's not educated, he's indoctrinated!"

See, but he's read the Bible, so he know's everything. Everything that matters, anyway.

Sorry, that was way OT. But you have got to see these guys in their natural habitat, in all their uninhibited glory! It's an amazing show!

Biblical Sociology! It is to laugh. Or cry.

Um, the link to the Chronicle points to a UMN subscription page (the article itself is behind a paywall, those bastards).

Ok, mistakes happen. This was a rather infortunate one, but still. But why in the world is the article still available? The people at Proteomics seriously need to get remove their thumbs from their a** and start pressing the "retract" button.

As my wife said, laughing so hard she almost choked: "Shame! Come back, Shame!"

Now that is comedy gold.

It looks to me as though without the blogosphere screaming about it, there'd be next to no chance that Proteomics would even consider getting an anal phalanxectomy.

I've screwed up a lot in my life, and as far as I can tell, I've never had a bad outcome when I've admitted it when I discovered it and worked to make things right. But I've had endless trouble when I've hemmed and hawed and tried to be all political about it. Makes me concerned that the journal thinks it has so much at stake here that it has to act like members of congress when it gets caught with its pants down.

Now that is comedy gold.

Posted by: Tulse

She is, in fact, really funny. When she gets going she keeps me in stitches. She also is great at "gross outs". (Can't really explain that, but you know what I mean) I'm very lucky, cause laughter is good medicine.
And then I think about her first husband ( she shot him, as I may have mentioned) and I laugh even harder. Sometimes hilarity is preventitive, if you get my meaning.

He's head of the Sociology Department atr Nazarene Bible College! Biblical Sociology! I wonder what that is like?

About as informative as Biblical Biology. Then again, anyone with a CV or resume that lists Nazarene anything goes in the circular filing cabinet.

Surely, PZ has earned his place in Himinbjorg in the service of the Watchman of the Gods.

I strongly believe that the journal had better come completely clean in public about the review process for this paper, including providing the version of the paper that went to the referees and was recommended for acceptance by them. Dunn -- the editor -- has made one unfortunate remark so far, the "promote creationism" comment. Someone who knows him should clue him in that that's not the issue.

The three issues are (1) a comparison of the version that was published online with the version that was sent to referees; (2) was the reviewing competent, in the sense that the reviewers actually attended to (and perhaps commented on) the relationship between the research reviewed and the 'soul' conclusions reached; and (3) the plagiarism.

It would be too easy for Dunn to pull the paper just on account of the plagiarism and not address the other two issues, but they are also critical here. Someone who knows him might do some coaching.

#1: that's exactly the first thing I thought. I cringed when I saw the wording they used. That's just such easy fuel for the idiot's fire.

Surely, PZ has earned his place in Himinbjorg in the service of the Watchman of the Gods.

I know I've spent too much time studying the sexual politics of the theocrats because I firt saw this as a form of "hymenborg."

Biblical Sociology! I wonder what that is like?

Blank tablet instead of blank slate?

Michael J. Dunn, the editor of Proteomics and a professor at University College Dublin's Conway Institute of Biomolecular and Biomedical Research, told The Chronicle that "it's not our policy to promote creationism" and added that the journal might retract the article.

Michael J. Dunn should consider what happened to Nixon when he stonewalled and Bill Clinton when he lied about his plump girlfriend.

After the bacon is in the fire, stonewalling becomes counterproductive. It isn't the crime that nails these guys, it is the coverup.

As a responsible party, at this point he needs to exert some leadership and lay it all out in public.

We need to know where the system at Proteomics broke down, who was responsible, and what will be done. At this point, thinking about a retraction isn't an option. He has to investigate, make a determination, and if it is warranted (obviously it is), don't stall, beat around the bush. Retract that paper.

I hope his comment that the, "journal might retract the article" is just British understatement. Even though he is in Ireland. Understatement tends to go over the heads of Americans.

That journal must have a pretty generous policy when it comes to changes to the manuscript after acceptance if people think that is what happened. Maybe its just because I'm a n00b, but I didn't dare make very many changes to accepted MSs with Elvesier. I don't know what Wiley's policies are though.

Doh! Elsevier, that is.

That journal must have a pretty generous policy when it comes to changes to the manuscript after acceptance if people think that is what happened.

What if someone added the crazy stuff to the version sent to the proofreaders, after the paper was already accepted and the revision done? Do editors regularly check the papers after proofreading?

(The problem with these "switch" scenarios is that this paper does not look like it was very good to begin with, though)

But why in the world is the article still available?

I think it perfectly reasonable to leave it for the present.
a) It's got a lot of attention at the moment, and it's possible that interesting new information about it may yet arise.
b) The authors whose work was plagiarised should have the chance do their own checks, should they wish.
c) It's reasonable that the editors want to examine the situation closely and understand what happened before pulling the paper and providing a statement to replace it. And editors tend to be busy people.

But if there isn't at least some sort of warning notice about disputed content by the end of today then I'd join you in complaining about the lack of action.

I find it hard to believe that the title of the paper, let alone an entire paragraph like,

Alternatively, instead of sinking in a swamp of endless
debates about the evolution of mitochondria, it is better to
come up with a unified assumption that all living cells
undergo a certain degree of convergence or divergence to or
from each other to meet their survival in specific habitats.
Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.

...would get by the reviewers and editors of a reputable journal. Has anyone considered the possibility that a copy editor inserted the offending passages into the manuscript at the very last minute, just before it was published online as a PDF? It could've been a joke on their part, or perhaps an earnest attempt at ID arguments.

That doesn't explain the gross plagiarism, though.

Re #26, if you're going to speculate about the offending passages being inserted by an insider at the journal/publisher, then you could just as well postulate that the whole article was replaced, which would explain the plagiarism as well. As a hypothesis, it has in its favour the need for but a single point of failure.

But it doesn't explain the title. However if you bend over backwards to be charitable the title could be taken as an attempt at metaphor - a riff on the stock phrase "keeping body and soul together".

I think we're going to have to wait for the journal to explain what when wrong - there's more than one possible explanation, and I don't want to rush to judgement.

Jeff @15,

anyone with a CV or resume that lists Nazarene anything goes in the circular filing cabinet

A trifle hasty, surely? People might have gone to a church-run school because their parents made them do so. They might have gone because, at that time, they still bought the package, but later got better.

I mean, PZ has had a guest poster here who went to Pensacola Snake-Handling Academy, or whatever it's called. (You'll be glad to learn that he has since recovered.) If he wanted to take one of your courses or whatever, would you keep him out on the basis of a line in his CV?

After the bacon is in the fire, stonewalling becomes counterproductive. It isn't the crime that nails these guys, it is the coverup.

There's procedures to follow when an article is disputed, and one of the first is to allow comment from the authors. If Proteomics retracted the paper without opportunity for comment from the authors, then they really would have a valid grievance. While Proteomics is not a prestigious journal, it is respected and I imagine it wishes to remain that way. So I have every confidence that Prof. Dunn will handle this thoroughly (if a bit methodically). I am very interested in finding out where the errors occurred in the reviewing process.

I mean, PZ has had a guest poster here who went to Pensacola Snake-Handling Academy, or whatever it's called. (You'll be glad to learn that he has since recovered.) If he wanted to take one of your courses or whatever, would you keep him out on the basis of a line in his CV?

Teachers (perhaps mercifully) don't see students' CVs; when you see a CV, it's a hiring situation. In the academy, that's a huge commitment you're considering making, because you don't just dump someone immediately when they don't work out. With a bazillion well-qualified candidates for every academic position out there, going to such a third-rate school, and then hoping to regain lost ground afterwards is to hobble yourself in an already extremely-competitive race against many candidates who don't have that handicap.

As you said, some people can't help it, and some people do actually wise up afterwards, but it's still an anticompetitive path to take in a job hunt that's extremely competitive.

I know I've spent too much time studying the sexual politics of the theocrats because I firt saw this as a form of "hymenborg."

Hmm. I wonder if Borg nanites would interpret the tearing of the hymen as physical damage severe enough to repair it, thus making the term technical virgin a double entendre in Borg culture.

I just downloaded the paper. Freaky stuff. To me, the strange comments read more like New Age woo than Islamo-Judeo-Christian creationism. On the non sequitur front, it reminds me of the college friend who suspected that his English prof wasn't actually reading student assignments. So, in the middle of his term paper on English-language African poetry, this guy inserted the line "I like pizza." And, a few pages later: "With pepperoni." Prof. Oblivious never noticed.

I went to the journal's homepage to see if the editors had made any comment. Nothing there yet, but will keep checking.

thalarctos @30,

fair enough. I'm not in academia, but now you mention it, I can see that CV = hiring situation more than anything else.

Even so, I'd be surprised if church-affiliated schools (on the whole) didn't turn out a fair few decent scientists. Binning a candidate because s/he was previously connected with a religiously-affiliated school seems a bit harsh, is all. (Or are the Nazarenes such a bizarre cult that having a degree from a school affiliated with them is per se conclusive evidence of whackjobbery? I know noting about them.)

And conversely, I'd note that Kurt Wise has a perfectly respectable Harvard Ph.D.

You're right, Mrs. Tilton, that any heuristic is going to yield some degree of false positives and false negatives. And I had a pleasant surprise, once, when looking into an option a student wanted for grad school, and that I was concerned about, that the sciences program were not fifth-rate, as I had feared. The school still wasn't competitive with a state university, but it wasn't just "Godidit. Test on Thursday." as I had incorrectly expected. They actually did make an effort to try to teach real science. Given the challenges of building a career in the sciences, though, I still advised him to go to a state school instead, in order to increase his competitiveness in the job market. In other words, I thought he should go to the most reputable school he could get into. He took my advice, and is succeeding in a way that he should be very proud of.

I agree, heuristics like the one above can yield false positive and false negatives (as my investigation of *mumble* findamentalist-denomination *mumble* College turned up), but at the same time, places like Liberty University taint the whole concept--it's an understandable impression. So it's still a competitive disadvantage for the student in sciences, even if some schools are more and some are less doctrinaire. That's why some of the previously more religious schools have taken historical overt religious references out of their names--they want to communicate that they take education seriously, wherever that mission leads.

Here is a direct link to the article: http://chronicle.com/daily/2008/02/1552n.htm

It is simply inconceivable that the journal Proteomics would not make a swift respone. The editor's (Michael Dunn) comment to the Chronicle doesn't go nearly far enough.

Also, there have been many comments regarding the author's poor command of English (as a partial explanation/excuse). Although it pales in comparison to creationism and plagiarism, there is another point to be made about poorly (in this case very poorly indeed) written reviews. I am much more harsh about writing quality in reviewing a review than in reviewing a paper containing original research. Reviews should be reasonably well written. Authors who cannot write in correct English (or find someone willing to proofread and edit, there are plenty of options to contract somene to do this) should not be invited to write reviews for journals in English.

OK, I realize that the authors are Korean, which presents some issues for translation into English (differences of tense, articles, etc. do add issues).

I'm fairly familiar with some of these issues because a few years ago I was hired by one of the labs at Harvard Med/Public Health to edit grad students papers--most of the students were from Korea or Taiwan. So, when I was editing papers, I was also including in my editorial marks why I was altering the text (i.e., redundancy, English idioms, active v. passive voice, etc.). I went above what was necessary in including why I was making certain changes. But, the head of the lab was actually somewhat appreciative of the extra labor I included.

I'm not saying everyone needs additional editors. However, if you'r publishing in a language not your own, it can't hurt to have a native speaker take a look at the paper....

That's just to deal with the language issues. Obviously, the issues of plagiarism are big problems.

However, one thing I'd like to add. It's been a day and a half. We shouldn't necessarily expect an immediate response from the editor. He's going to be chatting with the rest of the editorial folks, as well as the reviewers, etc. The early statement deals with the original issues brought up. As the issues of plagiarism come to the fore--out of this forum--one would (hopefully) expect different responses.

If I were to draw a lesson--get a good editor in the language you're going to publish in. And don't plagiarize (for some reason, I feel like that should go without mentioning, but obviously, it's not)

Seems like Prof. Dunn is in trouble indeed.
From the Editorial and Author Guidelines for Publication in PROTEOMICS

(ii) Review articles are normally invited by the Editor-in-Chief.
Authors wishing to submit a review article should send a brief outline of its contents to Prof. Dunn (eic.proteomics1@ucd.ie) before the manuscript is drafted.

Also, there have been many comments regarding the author's poor command of English (as a partial explanation/excuse). Although it pales in comparison to creationism and plagiarism, there is another point to be made about poorly (in this case very poorly indeed) written reviews. I am much more harsh about writing quality in reviewing a review than in reviewing a paper containing original research. Reviews should be reasonably well written. Authors who cannot write in correct English (or find someone willing to proofread and edit, there are plenty of options to contract somene to do this) should not be invited to write reviews for journals in English.

Protoeomics author page even has links for language assistance.

I heard back from Professor Dunn- a form-mail, I believe. What's interesting to me is he CCed Wiley's Corp HQ in Germany. I'm guessing he's been contacted by Wiley over the weekend. I'm going to predict he will soon not be the EIC of this journal. Good for science.

I've updated the side-by-side table of plagiarized passages in Warda and Han next to their sources, at http://udel.edu/~mcdonald/wardahan.pdf . Other commenters and I have now identified six papers and one web page that Warda and Han copied from.

I wouldn't be too harsh on Proteomics or its editor just yet. I don't know that any journal routinely checks for plagiarism, so they can't be blamed for being duped by that. As for the creationist passages, they could easily have been inserted in the revised version. I'm an associate editor of a journal, and when I say "This manuscript is acceptable if you make changes X, Y, and Z," and the authors send back a revised version with a cover letter that says "We made changes X, Y, and Z," I just check to make sure they really did make changes X, Y, and Z. I don't think to myself, "I better read again really closely through this whole boring manuscript, which was largely perfectly acceptable the first time I read it, in case the authors, who have a decent track record of publishing in reasonable journals, slipped in some crazytalk somewhere without telling me."

We should also keep in mind the legal issues. Plagiarism is a serious charge in the academic world, potentially career-ending for Warda and Han, and I'm sure the lawyers for Proteomics are involved at this point; they're not going let Proteomics say anything potentially libellous until they've got all the facts.

John:

I've glanced over those charts about the copied sentences, and at a glance it seems obvious that many sentences were copied. I'm just trying to enter the academic world, though, and I'm not clear where the boundary for acceptable behavior that they may have crossed is. The obvious bad thing to do is to copy the same ideas as a previous work, claiming that they are your own new ideas. I'm not quite sure how this might apply to a review article. The most obvious fault that a review article would contain in this direction is to copy an existing organization of a review of a field. I'm not sure exactly where the bad boundary would be there, since I've seen several reviews seeming to use a general outline from a previous source.

At the other end of the spectrum, every word I have read in nearly every review paper has been "borrowed" from other review papers. Most phrases, too, especially from papers in the same field.

Whole sentences are clearly a step beyond that, but if you're saying the same thing as in an existing excellent sentence, is there a good moral reason not to say it the same way? That's all that a table like that reveals in a case like this, without seeing how the sentences specifically and the ideas in general were organized in these papers. Some of the sentences in the table are rephrased, too, in a way that clearly shows at least a basic comprehension of the subject.

I don't want to distract from the clear enormity of the crimes of that paper against science, but I'm really unclear about any sort of boundary for plagiarism that would justify rejection or even a harsh judgement for a paper, especially a review paper. Is such a list sufficient as primary grounds, or would a panel just consider the sentence-comparison as a factor in a broader comparison?

to John (#41)

A "review" does not mean a direct copy-pasting from other sources without appropriate referencing... If Warga & Hun wanted to cite someone's text, then they had to enclose the whole citation within quotation marks, and specify from where it was taken from... it's kinda strict rule

Whole sentences are clearly a step beyond that, but if you're saying the same thing as in an existing excellent sentence, is there a good moral reason not to say it the same way?

This is what quotation marks and citations are for.