A dismaying update: the paper in question contains a significant amount of outright plagiarism, and large chunks of text are taken literally from Butterï¬eld et al. 2006, "Oxidative stress in
Alzheimer's disease brain: New insights from
redox proteomics," European Journal of
Pharmacology 545: 39-50. I hope we hear from Han and Warda sometime; they've got a lot of 'splaining to do.
Mitochondria are fascinating organelles. They are the "powerhouses of the cell" (that phrase is required to be used in any discussion of their function) that generate small, energy rich molecules like ATP that are used in many cellular chemical reactions, but they also have important roles in cell signaling and cell death. They also have a peculiar evolutionary history, arising as endosymbionts; their ancestors were independent organisms that took up residence inside eukaryotic cells in a mutually happy and long-lasting relationship. They exhibit some interesting relics of that prior history, as mitochondria have their own private strand of DNA which encodes some of the genes needed for the chemical processes they execute. Other genes for those functions have migrated over evolutionary time into the nuclear genome, which means the mix of gene products operating in the organelle are from two sources, the mitochondrial and nuclear genome. It's a good subject for studies in proteomics.
Right now, there is a paper that is available as an Epub ahead of print in the journal Proteomics. It is not promising. In fact, all you have to do is read the title to make you wonder what the authors, Warda and Han, were smoking: "Mitochondria, the missing link between body and soul: Proteomic prospective evidence."
Attila Csordas asks, "Can you tell a good article from a bad based on the abstract and the title alone?", and I'm inclined to say yes. Sometimes you get pleasant surprises in the full paper that were not well described in the abstract, but when the abstract and title contain hints that the bridge is out and that somebody has switched the train to the wrong tracks, you can predict that there will be a train wreck if you read further. Here's the abstract. I've highlighted one provocative statement.
Mitochondria are the gatekeepers of the life and death of most cells that regulate signaling, metabolism, and energy production needed for cellular function. Therefore, unraveling of the genuine mitochondrial proteome, as the dynamic determinant of structural-functional integrity to the cellular framework, affords a better understanding of many still-hidden secrets of life behind the already known static genome. Given the critical mitochondrial role under different stress conditions, the aim of the current review is to merge the available scientific data related to mitochondrial proteomes and frame them into a reliable new agreement extending beyond the limited already accepted endosymbiotic hypothesis into broader fundamental mechanisms orchestrating cellular outcome on behalf of cell survival. The focus of this work is to cover first the mitochondrial proteome/genome interplay that is currently believed to be implicated in a range of human diseases. The mechanochemical coupling between mitochondria and different cytoskeleton proteins and the impact of the mitoskeleton on mitochondrial structure and function are then addressed. Further crosstalk between mitochondria and other cellular organelles, e.g., the ER and the nucleus is then discussed. Additionally, the role of mitochondria in apoptosis and the mitochondrial contribution in intercellular communication mediated by gap junctions are also described. These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative. Furthermore, the role of mitochondria in development of oxidative stress-based diseases, e.g., neurodegenerative and cardiovascular diseases is pointed out together with the prospective proteomics view as an alternative prognostic and diagnostic tool for interpreting many mitochondria-related anomalies. The insights generated by recent proteomic research that provide a rational impact on possible mitochondrial-targeted therapeutic interventions are also discussed.
My blog makes a career out of describing train wrecks, so how could I not continue on and read the paper?
It's a very strange paper. There is a core that is competently done; it's a review of the various functions of the mitochondrion, and 90% of it is useful, detailed stuff. It's a bit outside my field, but what I could follow seemed reasonable. But then…oh, man. Every once in a while, it just goes cockeyed and throws out these incredible non sequiturs, making bizarre assertions that are unjustified by the evidence. If Norman Bates were the author of this paper, I'd be able to tell you exactly which parts he wrote while wearing a dress. It's that freaky. In addition, the authors are not native English speakers, and occasionally, often at the same time the weird stuff is being trotted out, the language decays into incoherent babble.
I suspect the article has a very strange writing history, and wonder if there was a contest of wills somewhere between a real scientist and a flaming kook, and every once in a while the kook emerges. For instance, that promised disproof of the endosymbiotic origin of mitochondria? It's nowhere to be found. There's a lot of discussion of the diverse, overlapping functions of mitochondria, but I'm sorry, telling me something is really, really complicated is a tired creationist trick that does not in any way support a claim that that something required non-natural processes to form — known evolutionary mechanisms are quite good at generating huge amounts of complexity.
As for the promised "more realistic alternative" to endosymbiosis that was promised, here it is.
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.
Ah, the "mighty creator" argument. It's too bad the authors don't try to review the evidence for that, because it certainly doesn't emerge in their review of biochemistry. That evidence is probably lurking in the same place as the evidence for the other abrupt weird assertion they make in their conclusion.
Many controversial questions still need to be answered,
e.g., how signaling molecules and other proteomics candidates, with relative low abundance, precisely translocate
from or to mitochondria in a matter of milliseconds
while crossing a huge ocean of soluble and insoluble barriers. And more importantly, how such molecules further
selectively bind their targets to provoke their tidy streaming
cascades. The answer could be the contribution of cytoskeleton proteins or the presence of specific carriers or even pH
changes etc. This might be true, but we still need to know the
secret behind this disciplined organized wisdom. We realize
so far that mitochondria could be the link between the body
and this preserved wisdom of the soul devoted to guaranteeing life. We would probably be overjoyed by any mitochondrial-related scientific breakthrough, but the fact that cannot
be eluded is the knowledge that we have made only a few
breakthroughs so far.
I read the paper. I saw mentions of caspases, potassium channels, uniporters, chemical signaling, etc., but look as I might, there wasn't anything telling me how wisdom was encoded in the mitochondrion — the authors might as well have tried to justified the postulated Force in midichlorians. At least the context would have been more appropriate, because I sense a great disturbance in the institution of peer review, with a thousand reviewers crying out in agony.
I asked Ian Musgrave, who knows this subject better than I do, what he thought of the work. Here are some of his comments.
In the area I am familiar, oxidative stress, this seems a fairly ordinary review marred by the authors lack of English writing skills. The introduction, conclusion and "evolution" sections are near incomprehensible though. How could a competent reviewer let this through?
It doesn't help that several of the references in the section on the evolution of the mitochondrion seem to bear no relation to the statements
"Surprisingly, to date there is no supportive evidence demonstrating the presence of the proposed intermediate model that links
mitochondria and their alpha-proteobacteria ancestors in the frame of a basic concept of natural variation and selection with dynamic evolutionary ability toward possible future transformation [111]."What is the mitochondrion of Reclinomonas americana, chopped liver? It is the most genome rich of all the mitochondria, and is closest to the genome of the obligate intracellular parasite Rickettsia prowazekii (and the gene organisation is highly similar too) and you can find several intermediates between more highly reduced mitochondria and the Reclinomonas americana mitochondrion. (It doesn't help that ref 111 is about CD8 cells and viral infection, and has nothing to do with mitochondria). Not to mention the wide array of bacterial endosymbionts with a varying genome reduction and gene transfer to the host (eg Wolbachia), to the extent it is hard to decide if some things are endosymbionts or organelles (eg the intracellular cyanobacteria of Paulinella chromatophora). Then there is the amino-acid synthesizing endosymbiont, the gamma-proteobacterium Buchnera sp., with a vastly reduced genome that has all the characteristics of an organelle-in-waiting.
Attila Csordas and the commenters at PIMM have similarly noted the illogical leaps and odd misreadings of the citations that plague this paper, and we're all asking the same question: What happened in the peer review of this paper?
It should have been savaged by any competent reviewer. It's not to say it is a complete loss; there really is a substantial, knowledgeable core here, but it is pimpled with genuinely bizarre eruptions of unsupported lunacy that make no sense, are poorly written, and reveal that at least one person involved in the writing of the paper has an unscientific agenda that they were willing to interject into an otherwise sensible discussion. And it's glaringly obvious. The rotten bits leap out vividly, as if those sections were scrawled in crayon and dung, and I don't understand how a reviewer could have been unjarred by their inclusion, unless they were just rubber-stamping the whole paper unread.
It's a real shame, too. This is the kind of appallingly sloppy work that can taint the reputation of a whole journal, and I also have to wonder what the editors of Proteomics are thinking. Do they really want to go down that path pioneered by Rivista di Biologia?
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One possibility is that the authors suggested certain reviewers they knew would be sympathetic to their cause, and the editor(s) sent it to those reviewers.
I'm frequently asked for the names of individuals competent to review my work, and I provide them (making sure not to recommend my friends since they are a bit too happy to go off on one of my papers...what are friends for!). I also know of several people who work in my area who recommend me to the editors of journals - even though I'm something of a bastard when I review papers (I hate getting a review from someone like me, just hate it).
And there have been times when reviewers don't do their jobs, or the editor has to go off of one review in making his/her decision.
So it's not too surprising that something like this can slip through. Though I admit, this one seems pretty obvious and agregious.
Aaand the religious right are all about to cream their pants when they find out that there is a peer reviwed article that talks about a mighty creator. Imagine the stink they'll raise if Proteomics pulls it? Which they should do.
Is it possible that the bizarre non-sequiturs were inserted after review?- I could imagine a sufficiently dishonest author inserting all kinds of crap at the page-proof stage, which might only be handled by typesetters rather than the reviewers or editors. Which might explain why the weird claims don't connect to the rest of the paper.
"disciplined organized wisdom" sounds to me like "specified complex information" moved through a machine translator and back.
So, to summarize:
sciencey stuff
sciencey stuff
(ooh, real complex, goddidit)
sciencey stuff
sciencey stuff
(dung & crayon marks)
conclusion.
Will this count as a win for peer reviewed creationism?
Very good point!- this paper from Korean Babelfish by translated has been.
At first I thought this was an article from the new creationist journal referenced in the podcast discussed in the recent "Do You Like Your Science Snarky?" posting.
Could you provide some background on the Proteomics journal for non-scientists like me? Is this a normally reputable journal that somehow blew it?
--Tosser
This is so not good for another reason. The ID folks now have an answer to the challenge to find just one peer-reviewed article in a genuine scientific journal that supports ID and/or shows a failure in the ToE. Of course, pointing out that none of the evidence in this paper has anything to do with the sections that the lab monkey from down the hall inserted won't be a good enough counter. Even explaining that peer-review does fail sometimes will never be enough. There is going to be hell to pay for this one.
Absolutely baffling how this could get through.
The only things I can think of is that the comments were added after review was done. Or that they were inserted somewhere in the conversion of the manuscript into the formatted journal article.
A quick look at other articles the authors have written shows no other attempts at this.
I'm dumbfounded.
In some parts of the world, they are blissfully unaware there is a war going on. What might to them, seem an off the cuff inconsequential remark, is ammo for the soldiers of ignorance.
I think Aa is right on. I work for a journal and handle the peer review process. Our editor always asks the corresponding author for preferred and non-preferred reviewers. Often the names of only preferred reviewers are supplied. Generally, he tries to find other reviewers, but if he can't get anyone to review the manuscript, he'll use the preferred/non-preferred reviewers. The preferred reviewers are much more likely to give a good review. And sometimes, as Aa said, we only get back one review and have to base the decision on that.
It's a total embarassment that something like that got through the process, though I'm not entirely surprised.
I'm just a semi-naive observer of such topics, but I think it will have to be pretty compelling evidence to completely falsify the endosymbiotic hypothesis as it applies to mitochondia. It seems more likely to me that this statement is a slip of the pen that overstates the paper's conclusions -- or perhaps it is just wrong.
Do let us casual science-buffs know how it turns out. I would guess the work is either going to be immediately dismissed, or it is going to be a while before the smoke clears =)
Something weird happened for sure. No idea but lots of possibilities.
1. One of the editors of Proteomics might have been a Xian fundie.
2. The authors might have contrived to have the paper reviewed by someone as delusional as they were. It's been done before.
3. The journal Proteomics might have decided to start a controversy to wake up the readership. Nature does this occasionally.
Basically, it is a bad example of argument from ignorance and incredulity. Their conclusion doesn't even follow from their data and they ignore huge amounts of relevant data to come up with a lame conclusion.
The journal owes the scientific community an explanation. Otherwise, we will all know what to do. Relegate Proteomics to the minor journal with suspect articles category and not worry about paying much attention to it.
If they blow up their credibility, that is their problem.
Oh, silly me. I missed half the article. Never mind, I have my answer =)
As an aside:
Too... many... adjectives...
Even though I do get most of what the authors are saying in the quotes supplied by PZ, the article reads like treknobabble to me. Are all articles about cellular/molecular biology like this? I mean just look at this:
I swear there's a more efficient way of saying this. Are the authors paid per word?
Someone(s) need to inform the editors and/or publishers of this screwup. Three possibilities:
1. The editors are asleep at the wheel and let some wingnut nonsense slip through.
2. The editors are fundie Xians and promoting ID through their journal.
3. The editors deliberately set off some fireworks to see what would happen and wake up the readership.
This is so weird that an explanation is owed the scientific community.
I can already hear the insistent drone of the next 50 years of creationists:
"See?! See?! Intelligent design has PEER REVIEWED PAPERS PUBLISHED IN RESPECTED SCIENTIFIC JOURNALS!!! We're doing the research, and those damned Darwinists STILL won't admit they're wrong."
I suspect comment #3 may be correct - in many journals, it's possible to submit things after the reviews and acceptance, often to make a few remaining minor changes. I just did it myself (though for more noble reasons - the colors on that graph were f***ing awful).
Another possibility is that there was an layout screwup - someone got sent a rejected manuscript by accident or typo.
Anyhow, I agree that such a prestigious journal owes the community an explanation, and should promptly pull the paper.
Aren't you going to mark this post with the "Blogging on peer-reviewed research" icon?
Here's the contact information for the journal. I've already written to try to get some kind of explanation.
http://www.wiley-vch.de/publish/en/journals/alphabeticIndex/2120/?jURL=…
or
http://tinyurl.com/yvvsrl
Are reviews even generally peer-reviewed? I was under the impression that solicited reviews were just edited and published.
Does anybody think this sounds a little like our own version of the Sokal paper? (Except that we're calling bullshit?)
Oh man, this might be the single actually peer-reviewed article that the Id proponents have been waiting for. I can hear it now: they'll be trumpeting this article as the triumph of Intelligent Design and as heralding its mainstream acceptance by the scientific community.
Where's the wisdom?
The mitochondrian still is a source of problems for eukaryotes, as its DNA doesn't undergo recombination, and above all, lacks the repair mechanisms which exist in the nucleus (there may be some mitochondrial repair of DNA, but at best it's not very competent). That's why most of its DNA has undergone the ordeal of transfer to the nucleus.
If anything, the mitochondrian DNA provides a fairly good trail of gene transfers to the nucleus (visible by the differences in mitochondrial DNA across the taxa), which appear to be as non-teleoligical as is the rest of evolution. And it's another example of "poor design," which evolution has incompletely been correcting over hundreds of millions of years.
So the unsupported leaps to the wisdom of "the mighty creator" are not only anathema to the scientific method, they are contradicted by the evidence of "poor design" and of a long line of hit-or-miss evolutionary transfer of DNA out of the mitochondrian where it degrades rather badly, to the nucleus where it is both maintained and sexually recombined to further evolution.
Indeed, such IDiots have never once come up with a reason for sexual reproduction, while its evolutionary adoption by eukaryotes is completely in line with the pressures of selection. Mitochondria are thus not only great examples of "poor design," the contrast with nuclear DNA and sexual reproduction highlight that, probably most importantly, mitochondria are great examples of "poor design" for evolution, something that has been incompletely corrected by DNA transfers from the mitochondria to the nucleus.
Glen D
http://tinyurl.com/2kxyc7
I followed the link to the abstract, and from there, to the Wiley Interscience page, which has more information about the authors and their respective institutions.
That's an odd team to collaborate there, I think.
I was wondering if the article had been perhaps translated by... someone else. Although the title suggests that both authors approved the injection of superstition into the paper.
Wow, and I thought that there were some questionable articles that got through IEEE journals. I think Wiley will have a lot of 'asplainin' to do should this paper be published. All of the non-sequiturs make it look like Monty Python has taken up ID. My favorite passage is
Or, in other words, instead of using science, we should just assume that microevolution may occur, but there's no way that mitochondria could have evolved. And then let's go to church and praise Jebus for being so smart.
Hey, I'm not even a biologist, and I understood that paragraph. I didn't even take a biology class in college (sorry PZ, I needed chemistry and physics). It seems that unadulterated BS is universal.
In response to Tosser (comment #7)- it's not directly my field, but I have seen the journal name before. I would have thought of it as a reasonable journal if it had come up in another context.
In response to Felicia (comment #15)- that kind of wordiness is seen far too often in molecular biology papers. That is an especially egregious, but non-shocking example (content aside). Part of it is the large number of non-native English speakers, part of it is the volume some labs pump out papers at, part of it is simple laziness.
I really doubt this is the true explaination, but nobody has mentioned it... might it just be a joke? I mean, there are some classic doozies out there (random CS Paper Generator, anyone?). Here's hoping.
This is being passed around at my department right now. The general consensus involves an interrogatory ending with a word that rhymes with a common waterfowl.
Assuming that it is a review, I think you're right, and that it's a failure of editorial review, not a failure of peer review.
If they don't do something about this embarrassment, Proteomics deserves to be discarded by the scientific community. This junk is a travesty in any science publication, and it's up to that journal to decide if they're going to be a science journal, or a new age dispenser of woo.
Are we seeing the success of ID in foreign lands in this bullshit, perhaps a Muslim old earth creationist, and a Korean Christian of unspecified creationistic proclivities?
Glen D
http://tinyurl.com/2kxyc7
Hmm... I wonder how much this creationist paid to get his or her work printed in the journal?
The way I see it, Proteomics either lacks the academic integrity to filter these silly, supernatural pseudo-theories from its journal, or they lack the competence to understand what it is they are reviewing and publishing.
Either greedy or dumb, I suppose.
This will not further the creationists' case insofar as it will essentially destroy any and all credibility this journal once held.
In fact, I think it already has.
Glen D wrote:
Leave us not forget where the True Father, Rev. Sun Myung Moon, hails from.
fusilier
James 2:24
"Mitochondria, the missing link between body and soul: Proteomic prospective evidence."
Ward and Harn seemed to have watched a lot of Star Wars.
Mollie (#20):
Some journals do, some don't. I was invited to write a review recently and it still went out for peer review. There are good reasons for that: in areas where there are competing models and some healthy debate, a journal would want to make sure all models are represented fairly. The author is, of course, free to advance his own viewpoint in the review, but the peer reviewers are there to make sure you don't omit information and that you give your competitors a fair shake (even if they're obviously wrong ;) ).
Woo in mainstream science papers is a little more common than you might think, though it almost never hits the publication stage. In my duties reviewing and editing manuscripts, I've seen some fairly nutty stuff similar to this. The manuscript may be doing fine until the author inexplicably brings in "chi" or other such woo. Since it's often shoehorned in and has little to do with the experimental data, that stuff usually gets deleted at some stage in the review process, or just rejected outright.
There are usually multiple levels of review and editing, but I can imagine that given enough manuscripts like this, eventually you'd hit a "perfect storm" of incompetent or sympathetic reviewers without even trying. I think the more parsimonious explanation is that someone shepherded this in, a la Sternberg.
Would someone like to step forward and contact the journal? (I lack the credentials and knowledge to fully make the case that something went awry here.)
P.S. Becca, thanks for the response.
From the Instructions to Authors at the journal website:
Which means the guy to ask is the Editor-in-Chief.
This is he.
Whiskey....Tango..... Foxtrot....?!!!
This paper has got to be a joke. I can't believe those paragraphs could have been there when the paper was reviewed. No freaking way. It can't just be a language/translation issue....I cannot imagine any context in which that drivel could make sense.
It is not without any redeeming features though; "Tidy Streaming Cascades" is my new favorite name for a rock band.
Proteomics claims a respectable impact factor of 5.735.
Sneaking some paragraphs in is one thing, but is it that easy to sneak a title in? That alone should have caught peoples' attention.
Hrrm. Anyone know if Toxoplasma dembskii is a reportable disease?
Any competent reader should certainly greet this "review" with a "Tidy Streaming Cascade" of his/her own.
So has anyone notified the journal that published this article that it's just ID crap? You need to pull some chains & wake people up. Then you'll see if it was a mistake or intentional.
This phony crap should have been submitted to The Star
and all the other insane rags you see on the check-out
line in supermarkets. Right with the headlines of aliens
defecating their god in saint peter's square in Rome, and
proclaiming the chief moron to be the father. Shame on
Proteomics for publishing such deranged crap.
A coupla years ago a shared an office with a very kind, little German post-doc. One day she asked me "Jens, what do you think of this?" and showed me a paper she'd been sent for peer review. *artful pause* She was a co-author on that paper! I said she should just return it with the comment that it was the greatest paper she'd ever seen and that it could be published as were. She didn't.
I doubt, though, that that's the case here.
I'm leaning towards the suggestion that these comments might just conceivably have been inserted in the galleys. I certainly hope it's something like that. I guess that's one of the possible downsides to the increasing throughput and editing/typesetting done by the authors themselves.
As mentioned these authors sound like an odd couple. I'd put my money on the creationist being the Egyptian, but there are of course a strong showing for Christianity among Koreans. His institution sounds more respectable, though ...
Has anyone yet checked to see whether this might be plagiarised? I know that's a nasty charge, but from the disjoint style, and PZed's comment about the 'dress pieces', it doesn't sound altogether impossible that someone ... *ahegm* ... Dembskied a review from a lesser known journal/author/collaborator/&c and interspersed their own half-digested effluvia.
P.P.S "All your base are belong to us."
http://en.wikipedia.org/wiki/All_your_base_are_belong_to_us
I wonder (because I don't know):
Is it possible to hack a publisher's website and insert a paper, or even download a PDF, alter it and then replace it with the altered version?
I know nothing about the online publication software used by Wiley, but it occurred to me that it might at least be possible to do this. I'm trying to give the journal the benefit of the doubt for the moment.
Would anyone care to disabuse me of such hopes?
Mike @#38: Any competent reader should certainly greet this "review" with a "Tidy Streaming Cascade" of his/her own.
You mean, it should be pee-reviewed.
Excuse me, I have to go do some work now.
Eh, I still prefer "New Atheist Noise Machine".
Maybe the reviewers got confused and thought they were reading Madeline L'Engle?
Yes, it is a review. "Review" is the word on top of the pdf, and it also occurs in the abstract.
Here is the full text of the acknowledgments:
Does not explicitly thank any reviewers. "[A]ssisting the release of this work" is a phrase I've never seen before; it could mean anything.
However, the manuscript was first received on July 19th, while the revised manuscript (which was accepted on the next day) was received no sooner than October 2nd. Means, the first submission was rejected, and the authors spent months trying to fix it.
I've written a polite letter to the EIC asking what's up with the article. I vaguely know a handful of people on the editorial board, and if the EIC answer isn't helpful I'll write to them as well.
I very much doubt that this was peer-reviewed. Some review articles are peer-reviewed (e.g. Nature family of journals, etc) but most journals out of the top tier eitehr solicit reviews directly or take suggested review subjects, and don't send them for review. Either this slipped past a busy editor who skimmed it, or else the changes were made post-acceptance.
Eamon@#44: You mean, it should be pee-reviewed.
You sar, are the Winnar!
Seriously though, pee-review would be a great system for ID 'papers'. I mean, either urine or you're out.
I wonder how the authors would interpret plastids? Do they beleave plants have a soul or even two different souls because of the accompanying mitochondria?
Attila Csordás writes,
Let's see what comes back. . . .
""disciplined organized wisdom" sounds to me like "specified complex information" moved through a machine translator and back." Joshua Zelinsky |
I have not read the paper just the parts posted here but I have read other articles and web sites that have been translated by "machine" everyone of them has parts that are completely unintelligible, parts that are some what clear if you happen to know the subject, to parts that are comic in their language. In reading a web site discussing a Sterling engine it spoke of the duty of different parts of the machine to do what they did (as if they had a choice) though it was very hard to understand just what the parts were supposed to do without understanding how a Sterling engine worked in the first place.
Leaving aside the possibility that the writing was not very good in the original language to start with. The paper may or may not be as bad as it seems but Machine translation is not ready for prime time and needs to be proof read and edited as does OCR and not relied upon to work by itself.
I like this blog and wish I had the time to learn about all the details that make up the world keep it going
@ David Marjanovic -
I'd be *very* happy to get an accept/revise/reject notice within three months. Then tack on time for revisions. Three months is pretty *fast* (admittedly it varies with journals).
I think Sven Demilo might be on to something here regarding the editor in chief. He's based at UCD in Dublin which, unfortunately, has become a focus of Intelligent Design advocates in Ireland.
John Lynch did a story on it a few months back.
http://scienceblogs.com/strangerfruit/2007/09/id_in_ireland_say_it_aint…
Sounds like the paper is 95% legit. Maybe it passed peer review, and then a True Believer stuck his private views into the revised draft and submitted it without running it past his co-authors.
Though it would still be strange if the original title made it through peer review, or if the editors didn't notice that the revised submission had a change of title.
It would be nice to know which assholes approved this paper? They're either creationist/ID doops, or incompetant morons with their heads up their asses. How do you, as a scientist, granted if you're not a shill for these fucking creationists, allow a paper like this to press? Well, the journal's going to have a lot of explaining to do. Well, it's one more spike riddled path we'll have to travel through to fight these creationist morons.
Another oddity: Both authors use the abbreviation "Dr." in the author line of the e-pub. In another paper including both authors and appearing in the same journal, they omit this. Couldn't this technique be considered an appeal to authority?
Refs to both articles:
PROTEOMICS Published Online: 23 Jan 2008.
PROTEOMICS Volume 7, Issue 15 , Pages 2570 - 2590
Well, as Obi-Wan told us, mitochondrions are the very place The Force resides in, and the more you have, the stronger in the force you are. He just pronounced it wrong.
Sorry! I somehow interpreted this as the time between rejection and resubmission, which of course it isn't. I also seem unable to count to three...
#20:
After reading the abstract, that's exactly what I was thinking. Something to show that even the people who claim to be the experts can't tell nonsense from the real thing.
#47:
Sounds like you need more experience submitting papers! You generally figure an absolute minimum of one month for review, at least a week or two to deal with comments, and then another month for re-review. So I'd say it sounds suspicuously fast, because it means they didn't do much in the way of major changes.
PZ, you had me worried for a minute. It's another case of a review article rather than a research paper, just like Meyer's so-called ID paper. I am profoundly troubled that Proteomics was asleep at the wheel, however. I am wrapping up some proteomics research and I will be sure not to submit it there. Letters to the editor are definitely in order - there are other journals for philosophy and religion. I'm not a huge fan of "we the undersigned" letters, but I'll sign it and ask my mentors to sign it too if someone close to the subject pens one.
Actually, I guess I misread that and it wasn't re-reviewed, just accepted straight after the revision was sent. So maybe the authors spent that revision time adding in the sketchy stuff and the editor just checked it over to see that the comments were dealt with, and didn't notice the weirdness. Of course, that's assuming a best-case scenario where the editor isn't to blame, and given the title it's frankly hard to picture that.
Revised version received October 2nd, 2007; accepted October 3rd, 2007.
The false reference (to [111]) is a dead giveaway. Creationists will lie, cheat, and steal to support what they "think" (if you can use that word) to be "true".
Of course, when one believes in a god that doesnt follow its own rules, has already tried to destroy the earth (as it claims), requires a torture/murder to take place before forgiving anyone, and created a place of infinite misery, its tough to see how a believer could possilby be moral.
Its not "How can one be moral without a god?" it should be "How can one be moral with a god?"
Creationists are far more repellent than any hagfish, spider, snake, or nematoad could ever be. The world needs hagfish, spiders, snakes, and nematoads in order to have a healthy biosphere; we do not need creationists, and we may be better off without them.
I've written a polite letter to the EIC asking what's up with the article.
The editor-in-chief has replied to me and is clearly not happy with the paper. He's looking into it and says he'll get back to me.
I don't know why, but I blame the Moonies for this one.
Has anybody contacted Proteomics (or Wiley Interscience), requesting an explanation?
http://www3.interscience.wiley.com/journal/76510741/home/2120_kont.html
Uraniborg: That sounds like shoddy copyediting/typesetting to me. Someone's not sticking to the style guide.
Some of the edits authors submit at proof stage really do take the urine. I've had authors wanting to insert extra paragraphs that claim all kinds of interesting things not previously mentioned, figures with no relation to the original, suspiciously reworked equations... you name it. If the editorial office aren't seeing the proof corrections, then I can easily see this happening. I'll be very interested to hear what the editors has to say about this.
I want to be able to trust my authors, but there's a reason I'm bringing in plagiarism detection software, and making sure I see every paper at every stage.
Hi All,
As a professor of Cell Biology I felt qualified to inquire about this and here is the reply I received a few moments ago from Mike Dunn, Editor in Chief of Proteomics:
**************************************************
Dear Dr Farmer,
Thank you for your e-mail and for drawing my attention to the issues regarding the Review Article by Warda and Han (2008) Mitochondria, the missing link between body and soul: Proteomic prospective evidence. PROTEOMICS 8: EPub.
Clearly your e-mail raises very serious questions regarding the manuscript and our Editorial and Review Process which I am currently looking into together with my colleagues on the Editorial Board and at the Publishing House.
I will get back to you with our response as soon as possible.
Best regards,
Mike Dunn
What is [111]? I don't seem to have access to anything but the abstract.
Has anyone yet checked to see whether this might be plagiarised?
Good call.
Compare to McDonald T, Sheng S, Stanley B, Chen D, Ko Y, et al. (December 1, 2006) Expanding the Subproteome of the Inner Mitochondria Using Protein Separation Technologies: One- and Two-dimensional Liquid Chromatography and Two-dimensional Gel Electrophoresis. Mol Cell Proteomics 5:2392-2411 doi:10.1074/mcp.T500036-MCP200
"Due to the large number of unique protein species produced coupled with differences in their relative abundance, there is as of yet no single proteomics technology that has the analytical capacity or sensitivity to realize the goal of complete proteome coverage."
vs.
"due to the large number of unique protein species along with the difference in their relative abundance, there is no single proteomics technology yet that has the full analytical capacity or sensitivity to realize the goal of complete mitochondrial proteome coverage"
There may be more; that was the first phrase I checked.
Waitaminit.
So what we used to think of as 'mitochondrial disease' might actually be -- rapture of the mitochondria?
My mitochondria died and went to heaven?
"I am multitude." -- Scriabin
http://dresdencodak.com/images/stall15.jpg
Looks like some authors spent too much time watching Star Wars Episode I. "Metachlorions" on their minds.
Seriously, according to the Wedge document, the IDiots have now succeeded in their first goal.
Clearly the law of cause and effect indicates that this wasn't an accident. So, who dropped the ball and when?
My first guess was that the editor was a creo. From the above email, I guess it isn't too likely.
Still, it is interesting that all my cells have souls. Given the trillions of cells in the body, heaven must be a crowded place full of dimwitted unicellular entities. Raises all kinds of questions.
1. Do bacteria and plants/chloroplasts have souls?
2. If you drink too much or visit creo websites and kill a few million brain cells, is it murder?
3. If you baptize a body, do all the cells get baptized by proxy?
Got to hand it to whoever slipped this dreck in. They were either very lucky or very sneaky.
Hmmm, maybe miracles do occur? LOL
Peer review is not magic. It doesn't get any readers off the hook from reading and understanding the paper and the rest of the literature on their own.
There is lots and lots and lots of stuff in the peer review literature that is wrong. Most of that wrong stuff is a lot harder to figure out that it is wrong than this paper is.
Yes, the IDologists' quest for a peer reviewed article seems to rest on a tacit assumption that peer review is a seal of approval for whatever claims a paper makes. It's not; it's merely a filter for utter nonsense and a check that the authors did their homework. (And of course, this example and others illustrate that even that bit of filtering isn't always thorough.)
What they forget is that there is a second and perhaps more important stage of peer review, namely how peers react to a paper's claims once it is published and readily accessible in the marketplace of ideas.
In this case, though the first phase failed miserably, the second phase is working very admirably in terms of speed of response.
Of course, replication is the real test, not peer review.
Creo nonsense will no doubt sneak past peer review now and then, but if it's really about 'evidence for creation/intelligent design,' the replication step is highly improbable.
Not that letting junk get published as science is thereby excused.
Glen D
http://tinyurl.com/2kxyc7
Your example seems to narrow it down to either ID-style dishonesty or else another attempt at sokalization, on the submitters' side.
That still leaves the question of how it got through review.
I suspect it's a matter of mere hours before UD picks up on this (assuming they haven't already) and starts spinning it as another case of the Darwinist priesthood trying to expell some more honest scientists who came to an unauthorized conclusions.
I would like to point out to any guests that the problem isn't with *what* the conclusions were, but the fact that they don't actually follow from any evidence presented. We reject Lysenkoism as surely as we reject creationism, or any other attempt to establish a conclusion on the basis of preconceived ideology rather than evidence.
I, for one, will be happy to accept an inference of intelligent design, alien visitors, ghosts, bigfoot, CNF, flu-fell-from-the-sky, or anything else -- provided someone can actually support the inference with evidence, rather than the sort of handwaving the proponents of such ideas actually invoke.
They'd have to be pretty dumb to do that considering that the publication's editor-in-chief is sending out emails (I got one, too) stating that the paper "raises serious questions" about Proteomic's editorial and review practices. The EIC, in other words, doesn't seem thrilled that this junk not-close-to-science item ended up with his journal's banner on it.
Then again, it being a dumb thing to do likely increases the odds that they'll do it...
This reminds me of when I put my IQ at risk by reading that AiG "journal" article about geology for Phil. It was exactly the same thing. Reasonable, reasonable, reasonable, and then BAM out comes the crazy.
Ian,
Good work - inform the editor. Any paper that cribs from other authors is an automatic retraction, no matter what the subject is. The authors have some 'splaining to do.
Given the critical mitochondrial role under different stress conditions, the aim of the current review is to merge the available scientific data related to mitochondrial proteomes and frame them into a reliable new agreement extending beyond the limited already accepted endosymbiotic hypothesis into broader fundamental mechanisms orchestrating cellular outcome on behalf of cell survival.
Wait. I think they're onto something here...
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.
Yes! YES!!! What we need to do now is generate a quantum-phase singularity with an energy density of one-to-the-fourth power. If we re-route the warp engines through the starboard power coupling, bounce a graviton particle beam off the main deflector dish, and re-tune the shield frequencies we just might be able create a temporal decoherence field of sufficient magnitude to force an inverse-tachyon implosion. Geordi! Data! Assist PZ!
But remember to adjust for the phase variance...
Aw man! PZ always beats me! What are you doing reading Proteomics anyway?
drunkensci.blogspot.com
DS
Yes! YES!!! What we need to do now is generate a quantum-phase singularity with an energy density of one-to-the-fourth power. If we re-route the warp engines through the starboard power coupling, bounce a graviton particle beam off the main deflector dish, and re-tune the shield frequencies we just might be able create a temporal decoherence field of sufficient magnitude to force an inverse-tachyon implosion.
Pinky, are you contemplating what I'm contemplating?
Hey! Nobody should question the wisdom and power behind midichlorians. Nobody.
Pinky, are you contemplating what I'm contemplating?
I think so, Brain, but polypeptide cake puts my positronic pathways in such a twitter...
Uh, I think so, Brain, but we'll never get a monkey to use dental floss.
Hank @72,
no, it would mean your mitochondria were possessed by demons.
I urge researchers into mitochondrial disease to consider swine as a promising therapy (the mitochondria are put into them, you see, and then the swine run into the sea and drown).
someone already made a midi-chlorian reference, right? *checks* okay, good. how about a Trek-esque technobabble reference? *checks* outstanding! and people wonder why i love this blog ...
I've been in email contact with Dr. Mike Dunn about this, pointing out what's in this paper. So far, from the reasonably distressed nature of his response, my guess would be:
1. The editors are asleep at the wheel and let some wingnut nonsense slip through.
(raven, #13)
This...is going to be interesting.
Ah, late to the party. I see that Mike Farmer, Ian and Attila Csordás also did this. Good. He'll know people are paying attention.
Ian @ #71, have you passed on the plagiarised bit to him?
After seeing the plagiarism charge leveled on top of everything else, I am irresistibly reminded of this:
Heh.
Although I see now, after doing the research I ought to have done in the first place, the quote above is attributed to Samuel Johnson, but has not been found in his actual works.
Oh, the irony.
I suspect it really is all just a language problem.
"Metachlorines, the missing link between body and soul: Proteomic prospective evidence."
Is this the first instance of Jedi creationists?
I can haz jedi trix?
'In fact, all you have to do is read the title to make you wonder what the authors, Warda and Han, were smoking'
They were smoking the same as they were writing: bad shit, man.
Just thought I would interject about the quality of the journal. I am a proteomics guy by trade and I consider this one to be a middle-tier proteomics journal. It has a decent impact factor though, so it may be that the stuff they publish just doesn't totally jive with my particular interests in the field. In any case, I don't think it approaches a "prestigious journal".
DS
Dare I be the first to continue the Star Wars allegory?
"IT'S A TRAP!!"
Hokey religions and ancient weapons are no match for a good blaster at your side, kid.
Mollie (#20) asks,
A more exact comparison may be to the Bogdanov Affair, in which two French brothers (TV-show hosts, in fact) managed to publish in physics journals papers which were content-free nonsense wrapped in jargon. As in this situation, during that episode the informal network of scientists communicating online (on USENET, back in those days) caught the mistakes made by the formal peer-review system.
Many people compared the Bogdanov incident to Sokal's merry little prank, but as the story unfolded, the differences between the two became more evident. Paul Ginsparg, a physics professor at Cornell, wrote of the Bogdanovs:
As more information comes to light about the Proteomics paper, we should be able to tell which of these goals was in the authors' minds.
I feel compelled to interject a sliver of real science, actually a minor correction to a comment made by Glen Davidson (#22) when he says:
"The mitochondrian still is a source of problems for eukaryotes, as its DNA doesn't undergo recombination ..."
That may be true for mammals, vertebrates, presumably metazoans in general but it is definitely not true for mitochondria in general. Many flowering plant mitochondrial genomes have clearly (at least at some point) undergone extensive recombination and there are certainly protistan examples as well. In fact, in some or many or globally maybe most mitochondria, replication itself is initiated by recombinogenic processes which, in at least Euglena gracilis mito (which I have studied extensively, but I don't believe have a soul) continue at a very high rate throughout DNA replication.
Now back to the movie.
Is this the part where somebody says: "Damnit Kirk, I'm a Doctor, not a cell biologist" or something?
Clearly the article substitutes a biased teleology for analytical assessment. Someone pointed out a passage to me that reads
"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."
Riddle me this, what does "..more likely to be interpreted..." mean?
It isn't lack of precision in language where it should substitute simply for likely, or cleanly for likely. Likely might just mean it's all they can come up with and will stick their fingers in their ears and humm loudly if someone tries to offer an alternative explanation. And if that's what it does mean, then it all makes sense as an excercise in self-fullfilling teleological rationalization.
I am in the proteomics field and can only assume that this slipped either the editors review or it was changed after the peer-review.
I strongly hope that the editors will withdraw this article.
Nevertheless, quite embarrassing.
Ian @ #71, have you passed on the plagiarised bit to him?
Yes, and he's responded.
If anyone sees other examples of plagarism in this paper (or, of course, in any other papers in Proteomics), please pass them on to the editor-in-chief of Proteomics.
Now all we need is a Princess Bride quote.
"Inconceivable!"
My work here is done.
It's even worse. If the journal pulls the article, its evidence of the inquisitional tactics of the scientific thought-police. If the journal loses its reputation over this kind of thing, its the inquisition again.
If it can be pulled because of plagiarism, as seems possible, then the whole issue of content need never arise. I doubt even the ID folks want to make a stink about a paper rejected because it ripped off someone else's paper.
Shouldn't technobabble sound a bit more technical? Looks like regular babble to me.
looks like a good bit of plagarism by googling-here's another:
Mol Biol Cell. 2005 March; 16(3): 1543-1554.
Here, we demonstrate that mitofilin, a previously identified mitochondrial protein of unknown function, controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex.
Review:
Mitofilin is a previously identified mitochondrial protein intervening in the inner and outer mitochondrial membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex with the
assumed function of keeping mitochondrial cristae morphology
Mol Biol Cell. 2005 March; 16(3): 1543-1554.
Although the molecular basis for cristae morphogenesis is still unknown, there is increasing evidence that the mitochondrial fission and fusion machinery plays an important role in this process. OPA1/Mgm1, a large dynamin-like GTPase, is located in the intermembrane space (Wong et al., 2000 blue right-pointing triangle), the same submitochondrial compartment where mitofilin resides. In addition, down-regulation of OPA1 also resulted in altered cristae structure (Olichon et al., 2002 blue right-pointing triangle)
Review:
Although the molecular basis of cristae
morphogenesis is not completely understood, there is
increasing evidence that the mitochondrial fission and
fusion machinery plays an important role in this process.
OPA1/Mgm1, a large dynamin-like GTPase, is located in the
intermembrane space [33], where its down-regulation results
in altered cristae architecture and dissipation of the mitochondrial membrane potential structure [34].
Yep, it's heavily plagiarized. About 5% of the content is copied from Butterfield et al. 2006, "Oxidative stress in Alzheimer's disease brain: New insights from redox proteomics," European Journal of Pharmacology 545: 39-50.
See http://udel.edu/~mcdonald/wandahan.pdf for a side-by-side comparison.
Looks like this was rewritten without understanding -- "where" simply doesn't apply to "downregulation", or rather, gene regulation is something that happens in the nucleus or on free-swimming mRNA that could be anywhere.
Even the parts that are not original are not good, methinks.
Only makes me wonder how many other plagiarized papers never get detected because they don't add obvious bullshit in...
I just emailed Prof. Van Eyk about the first plagiarism...dammit, I knew there would be others. At least I have a template now....
Well...that should settle it....looks mostly plagiarized. Also, I think reviews are nothing ID types should get excited about-they aren't original work, and are often not really 'peer reviewed' (at least in my experience).
Anyone notice the 'revised' was accepted the day after it was submitted? I'm guessing the authors submitted a review-someone on the editorial board made suggestions, they fixed it up and added the hooey, resubmitted stating 'changes were made' and in it goes.
I have gotten frustrated about the trend in reviews lately, which summarize a few papers and references contained therein. They don't frame the field, introduce new hypotheses, or do anything particularly interesting. A decent Pubmed search could do the same. I'd settle for fewer, better reviews that are really peer reviewed, especially in 'hot' fields like RNAi or the Histone Code, where it seems like reviews and primary literature are too close to a 1:1 ratio.
OK...I've emailed Professors van Eyk, Butterfield, and Zha with the information. Thanks to everyone, especially John for that pdf - I gave Prof. Butterfield the link.
I have to say that this swift, collective smack-down by the informal web-based community makes me damn proud to be a scientist--and giddily hopeful for a more rational future.
Way to go, Paula! Way to go! (as long as we're on a classic movie binge, here)
So this paper wasn't intelligently designed --- it's a collage of bits and pieces picked up more or less randomly that stuck together, and that survived some winnowing process of random elimination, eh?
I sure hope they saved all the intermediate drafts and can figure out which of the participants are culpable and which merely incompetent.
By the Great Babelfish into the water goat the hydraulic ram was made. Has PZ the paper from the English into the German to and back from Russian translating tried?
They're just being God-like, since that's apparently how the "Designer" (or Crass Imitator) also designed all of life.
IOW, the "Designer" would be immediately dismissed for self-plagiarism if it tried to pass off all of its copies as works of science.
But religion is all about sympathetic magic, copying the divine, type and anti-type, so why shouldn't religionists be like God, copying with all of the defects while claiming to do something original? They're flattering God by doing nothing new or creative.
Glen D
http://tinyurl.com/2kxyc7
Oh, except that these plagiarizers at least know how to copy from disparate sources, unlike the narrow-minded idiot that is the IDists' "Designer." It can't even mix and match from unrelated vertebrates, unlike an uneducated child can.
Just to keep things straight, you understand, since I don't want anyone to see the great "God" of the IDists as being as intelligent in overall purpose (though it's fantastically good at the details) as a plagiarizer or a child.
Glen D
http://tinyurl.com/2kxyc7
Let's not let Mohamed Warda and Jin Han ("Solo"?) off the hook either. It's not like they haven't been published before...it might be interesting to scour some of their previous papers.
Since when is apoptosis a medical problem, let alone one of the top two medical problems?
"The proteomics prospective promises future dismantling of many life secrets that stand behind the mitochondrial border with the possible solution of the top two medical problems, namely, cancer and apoptosis."
I have a few questions and hopefully this won't sound too ignorant,
Since we know that there is significant plagiarism and the Ed. of the journal now has this information. What is the protocol in this type of situation? What kind of legal ramifications are there specifically for non-u.s. authors? I can't remember, but are they affiliated with an educational institution in any way (I hope not)?
Apoptosis is a medical problem? What? Apoptosis is the body's natural solution to cancer!
Man, the more we dig into this paper, the worse it stinks. Is anyone planning to do a journal club at their grad school with this one? Sometimes the most spectacularly fun trashings came out of those sessions with bad papers.
Against my better judgment, I pulled down a copy of the paper. Dear lord, that's brain rot. I think it's going on my lab's fridge for communal mocking.
I've been reading this blog for about two years now, and this is one of the most interesting thread I've read. Of course, I happen to work in the field of mitochondrial genomics, so this paper is of particular interest. My colleagues at work are all quite upset about the whole thing, like everyone here. But like DanioPhd said at #118, I'm proud to see how quickly you guys dismantled that paper. Proud to be a scientist.
The inclusion of apoptosis might not be that bad.
I remember reading something about how the sudden increase in oxygen levels in people who are resuscitated can cause the apoptosis mechanism in mitochondria to kick in.
This kills the heart muscle.
The increased oxygen level makes the cell think it might be cancerous.
Maybe this is what they were refering to?
I can't copy them now since I'm home and can't access the PDF, but someone who can should the last 3 sentences of the Conclusion - they're gems too.
If you click Warda's name on the PubMed abst, you get a bibliography of normal-sounding papers mostly in typical medical journals, as well as basic research jounals like BBActa and BBRC.
I can't take credit for finding the plagiarism, but I do want to pass along that Prof. van Eyk was VERY happy to see that it was caught and has alerted the other authors and the rest of her lab.
Yet would that be enough to have it be one of the "top two medical problems"?
I do not know how many people die from problems during resuscitation but I would guess it is not in the top two medical problems.
The main point I wanted to make was that mentioning apoptosis was not totally insane.
It seems a minor problem compared to the plagiarism and other idiotic statements anyway.
A nit-picking point, but the review article should have read: "frame them into a reliable new agreement extending beyond the limited already accepted endosymbiotic hypothesis into broader FUNDAMENTALIST mechanisms"...
To add to the list of appropriate TV/movie quotes already mentioned, here are a few more:
"I've got a bad feeling about this." (Star Wars)
"What do you get when you trace your butt onto paper?"
"Nothing anybody wants to see." -- 7th Heaven
"Welcome to the nether regions of the soul." -- Bart Simpson
"Staying with you (insert author's name here) requires a degree of stupidity of which I no longer feel capable." (Blake's 7)
"Don't think, Fingal. You're not propperly equipped for it." (Star Wars)
PZ, PLEASE let us know when this mega-turd gets retracted.
Spurge, #129 -
If the author's had an actual theory about apoptosis, or considered someone else's theory as worthwhile, they would have explained and referenced it. Please don't make excuses for this trash.
el-Hemp @ #130:
"This might be true, but we still need to know the
secret behind this disciplined organized wisdom. We realize
so far that mitochondria could be the link between the body
and this preserved wisdom of the soul devoted to guarantee-
ing life. We would probably be overjoyed by any mitochon-
drial-related scientific breakthrough, but the fact that cannot
be eluded is the knowledge that we have made only a few
breakthroughs so far."
And while we're at it, how about these guys:
"The authors are grateful to the effort of Dr. Nagwa Khafaga
and Mr. Mohamad Lebda in assisting the release of this work."
Oops...PZ already posted it. The acknowledgment is still worth checking, though.
Obviously the 'creator' claims in the paper are crap. However, it is critical to note that review articles are not subject to the same peer review process as original scientific works. Often authors are 'invited' by the journal to write a review. Thus, if an author is credible enough to be 'invited' and is writing a review of previously published work (all of which would have been peer reviewed) the need to peer review the review of previously peer reviewed work seems redundant- if you get what I'm saying. I have in the past been asked to peer review a particularly bad review, so it does happen, but it's not as likely that something this ridiculous could be published in an original scientific paper.
@ dkew
I did not intend to make excuses for the authors.
I was just commenting about why they might have included apoptosis.
It seemed to me that it was dismissed out of hand.
Your comment about including a reference and explaining what they meant makes sense.
It seems that I was wrong in thinking that it was dismissed out of hand.
I just emailed the corresponding author:
You guys are in trouble now!
See how fast you can get the retraction out, and post it at http://scienceblogs.com/pharyngula/2008/02/a_baffling_failure_of_peer_r…
I also suggest groveling apologies to the journal, HUPO, and everybody else.
See if you can save your career. It'll be a challenge!
Best of luck,
John
Isn't apoptosis a major cause of aging? It might be reasonable to consider senescence and death from old age as (in some sense) one of the biggest medical problems.
(For the avoidance of doubt: the paper is rubbish in oh so many different ways. But, y'know, maybe the bit about apoptosis is one of the parts they plagiarized, and I wouldn't want the original author to be maligned.)
"When Rapture comes, this protoplast will be unoccupied"
"Let's put the Almighty back in Mitochondrion"
"Let's put the Cristae back in Christmas"
Plagiarism may be common for these authors.
Compare phrases of Warda M et al. 2007. Glycoconjugate Journal [Epub ahead of print]. DOI: 10.1007/s10719-007-9090-8 (Han is also an author)
with phrases from: Chen C-P et al. 2007. Placenta 28: 97-106.
Warda et al:
"Detailed characterizations indicate the placental basement membrane tissue predominantly contains HS PGs, whereas CS/DS PGs are mainly located in the intervillous space of the ECM"
Chen et al:
"Detailed characterizations indicate the placental basement membrane tissue predominantly contains heparan sulfate proteoglycan (HSPG), whereas chondroitin sulfate and/or dermatan sulfate proteoglycans (CS/DS PGs) are mainly located in the intervillous space of the ECM"
or between the same paper and Tersariol ILS et al. 2002. Proteinase activity regulation by glycosaminoglycans. Brazilian Journal of Medical and Biological Research 35: 135-144.
Warda et al:
"HS, the constituent of up to 50% of the total expressed GAG in endothelial cells, is unique among GAGs in the ability to bind a large number of different proteins with complex role in the extracellular matrix, regulating a wide variety of biological process, including hemostasis, inflammation, angiogenesis, growth factors, cell adhesion
Tersariol et al:
"Heparan sulfate and heparin are particularly important among glycosaminoglycans in their ability to bind a large number of different proteins. Heparin-like glycosaminoglycans play a complex role in the extracellular matrix, regulating a wide variety of biological processes, including hemostasis, inflammation, angiogenesis, growth factors, cell adhesion, and others"
I should mention that the above quotes are taken from the first Warda paper that comes up in PubMed after the one mentioned in this blog.
DanioPHD (#118):
Ditto.
Sarah, If you haven't contacted the editor-in-chief of the Glycoconjugate Journal yet, please keep posting these and I'll write a letter. This is the sort of misconduct that deserves to be brought to light.
I am just a reader, not a scientist, but I found both names on that paper here: http://mitochondria.inje.ac.kr/03_publication/pub_03.php?year=2007
Hope this helps someone with more knowledge than I to find out more.
Re #80: Considering that UD is citing Rupert Sheldrake (indirectly, via people who are even more crackpot than RS is) it seems there is no limit to how hard Billy Dumbstruck will scrape the bottom of the barrel in his desperation to find quotable support for his own crackpottery. It's the classic bunch of drunks all leaning on each other schtick.
(See http://pandasthumb.org/archives/2008/02/the-double-edge-1.html for the details).
This whole thing began, apparently, with someone noticing the oddity of words like "soul" and "mighty creator" in a scientific paper. From there, the scent led to fairly large-scale plagiarism and who knows what other ethical violations. Funny how that works.
The initial post and all comments so far have neglected a crucial question bearing on the validity of this paper:
Does it, or does it not, include the phrase "powerhouses of the cell"?
Quite a few.
Excuse me, just of to poke around Déjà vu...
Bob
I've added passages that Warda and Han plagiarized from three other papers to my side-by-side comparison; see http://udel.edu/~mcdonald/wardahan.pdf. They copied from the following:
Butterfield, D.A., M. Perluigi, and R. Sultana. 2006. Oxidative stress in Alzheimer's disease brain: New insights from redox proteomics. European Journal of Pharmacology 545: 39-50.
Reddy, P.H. 2006. Mitochondrial oxidative damage in aging and Alzheimer's disease: implications for mitochondrially targeted antioxidant therapeutics. 2006. Journal of Biomedicine and Biotechnology, article 31372
John, G.B., Y. Shang, L. Li, C. Renken, C. A. Mannella, J. M.L. Selker, L. Rangell, M. J. Bennett, and J. Zha. 2005. The mitochondrial inner membrane protein mitofilin D controls cristae morphology. Molecular Biology of the Cell 16: 1543-1554.
[plagiarism first noticed by commenter RobertC]
McDonald, T., S. Sheng, B. Stanley, D. Chen, Y. Ko, R. N. Cole, P. Pedersen, and J. E. Van Eyk. 2006. Expanding the subproteome of the inner mitochondria using protein separation technologies: One- and two-dimensional liquid chromatography and two-dimensional gel electrophoresis. Molecular and Cellular Proteomics 5:2392-2411
[plagiarism first noticed by commenter Ian]
I'll e-mail the corresponding author of each paper, and the editor of Proteomics.
I am very impressed with what has been accomplished here in this thread, and these line are some of the funniest ever:
"Every once in a while, it just goes cockeyed and throws out these incredible non sequiturs, making bizarre assertions that are unjustified by the evidence. If Norman Bates were the author of this paper, I'd be able to tell you exactly which parts he wrote while wearing a dress. It's that freaky...
I suspect the article has a very strange writing history, and wonder if there was a contest of wills somewhere between a real scientist and a flaming kook, and every once in a while the kook emerges."
A fantastic blog.
The link to John McDonalds list of plagiarised passages accidentally includes a terminating full stop. This should work correctly:
http://udel.edu/~mcdonald/wardahan.pdf
Kudos to all for the great smackdown. It's starting to appear that the following excerpt, highlighted at the outset by PZ, is just about the only part that wasn't plagiarized:
...which makes me wonder, OK, was this the axis around which the whole series of ripoffs was supposed to gyre?
I haven't read the actual "paper" yet to come to a full judgment, but my ex-fundie spidey sense is tingling in one clear direction: they were driving toward trying to demonstrate that mitochondria were "added" into cells all at once after the Fall, to account for the way that original sin brought pain and death into the world.
Need to get to sleep and don't have time to try to prove it, but I bet these guys were seized by some ID-addled vision of expulsion from Eden as coterminous with a bacteriological attack by God... one of you with more patience for wading through this crap than I have can feel free to try to connect those dots, if you like.
--pr
Han, J. is apparently one of three in the Physiology Dept of the Faculty of Medicine,so far his creds seem to check out. The Warda, M. chap is another kettle of fish as he's not showing up having anythig to do with the University of Cairo which my sister happens to lecture at. My sister is fluent in Arabic so she's discreeetly checking things out. If they'll plagiarise you can't trust the paper their degrees are written on I say.
@118, 128: Yeah, but it makes me sad that us internet people do the work which should be up to reviewers or editors: checking for plagiarism, actually reading the paper and noticing such oddities... If the actual editors let so much pass unchecked, how many correct but plagiarized papers pass through? @149: Agree.
I fear though that once in a while the IDers will get a paper published in one or another way, given the enormous variety of journals around and the seemingly sloppy review practices at work on some of them.
Dammit, I've made myself a liar... I couldn't quite tear myself away after all.
Re my comments @155: check out these recent "creation microbiology" abstracts. I'd say that whatever looks bizarre or incomprehensible in this paper (which is probably to say, all the non-plagiarized bits) is "explainable" with reference to fundie concepts of the Edenic "natural world".
Sleep now... once again, good work, fact-checkers.
--pr
Ah, open source science. "Given enough eyes, all cases of scientific fraud are shallow."
I'm impressed by how fast you all turned up that evidence of plagiarisation. Wow.
But, for comments, it's Eric Saveau for the win.
I'm hugely impressed by the way this comments thread has produced a sort of science flashmob. Within 24 hours, the fraud is detected, deconstructed, and reduced to a few gleaming white bones.
But remember: There Is No Cabal.
Quis custodes ipsos custodiet? Pharyngula.
I have not yet gone through all of the paper I posted above (just googled a few sentences). J, if you want to start a letter, that's fine with me.
Perhaps others might wish to check other publications with both of these people as co-authors. Here's a list of the ten most recent publications by Wards since Oct 2006 (!), taken from PubMed, in case anyone wants to tackle these:
Warda M, Kim HK, Kim N, Youm JB, Kang SH, Park WS, Khoa TM, Kim YH, Han J. 2007. Simulated hyperglycemia in rat cardiomyocytes: a proteomics approach for improved analysis of cellular alterations. Proteomics 7(15):2570-90.
Cuong DV, Warda M, Kim N, Park WS, Ko JH, Kim E, Han J. 2007. Dynamic changes in nitric oxide and mitochondrial oxidative stress with site-dependent differential tissue response during anoxic preconditioning in rat heart.Am J Physiol Heart Circ Physiol. 293(3):H1457-65.
Kim HK, Park WS, Kang SH, Warda M, Kim N, Ko JH, Prince Ael-B, Han J. 2007. Mitochondrial alterations in human gastric carcinoma cell line. Am J Physiol Cell Physiol. 293(2):C761-71.
Park WS, Ko JH, Kim N, Son YK, Kang SH, Warda M, Jung ID, Park YM, Han J. 2007. Increased inhibition of inward rectifier K+ channels by angiotensin II in small-diameter coronary artery of isoproterenol-induced hypertrophied model. Arterioscler Thromb Vasc Biol. 27(8):1768-75.
Park WS, Son YK, Kim N, Ko JH, Kang SH, Warda M, Earm YE, Jung ID, Park YM, Han J. 2007. Acute hypoxia induces vasodilation and increases coronary blood flow by activating inward rectifier K(+) channels. Pflugers Arch. 454(6):1023-30.
Kang SH, Park WS, Kim N, Youm JB, Warda M, Ko JH, Ko EA, Han J. 2007. Mitochondrial Ca2+-activated K+ channels more efficiently reduce mitochondrial Ca2+ overload in rat ventricular myocytes. Am J Physiol Heart Circ Physiol. 2007 Jul;293(1):H307-13.
Park WS, Son YK, Kim N, Youm JB, Warda M, Ko JH, Ko EA, Kang SH, Kim E, Earm YE, Han J. 2007. Direct modulation of Ca(2+)-activated K(+) current by H-89 in rabbit coronary arterial smooth muscle cells. Vascul Pharmacol. 46(2):105-13.
Easom LR, Galatas S, Warda M.End-of-life care: an educational intervention for rural nurses in southeastern USA. 2006. Int J Palliat Nurs. 12(11):526-34.
Warda M, Toida T, Zhang F, Sun P, Munoz E, Xie J, Linhardt RJ. 2006. Isolation and characterization of heparan sulfate from various murine tissues. Glycoconj J. 23(7-8):555-63.
Kim N, Kim H, Youm JB, Park WS, Warda M, Ko JH, Han J.Site specific differential activation of ras/raf/ERK signaling in rabbit isoproterenol-induced left ventricular hypertrophy. 2006. Biochim Biophys Acta. 1763(10):1067-75.
Who wants to bet we find more instances of plagiarism?
Some of the apparent plagiarism looks like non-English speakers trying to cast someone else's argument in their own words. But the huge chunk from Butterfield (especially the MALDI Toff stuff), is pure, unadulterated plagiarism. I'm mortified I didn't notice at once, as Butterfield is a key player in my field (I did wonder why they hadn't cited Butterfield, now I know why).
It could be a Sokal style hoax still, but it's looking more like basic plagiarism.
It could be a Sokal style hoax still, but it's looking more like basic plagiarism.
But Sarah and others above have already identified plagiarism in other Warda/Jin papers!
I haven't been exhaustive, but this doesn't look plagiarised. But also, it is a very different kettle of fish to the mitochondrion travesty. The English usage is much, much better (although a few typos get in), and it is a serious, very science heavy paper. The logic and development of this paper is very different, even though there are lots of addition authors, it just doesn't have the feel of the mitochondrion paper. Perhaps Warda and Han were targets of a malicious prankster?
Molly nomination!
At the very least PZ should use this as a tagline for the blog!
I'm not not really convinced by those excerpts(very short sections with evidence of trying to rewrite in their own style). I'd need to see evidence of more extensive copying than that. Again, the papers feel different to the review. Then again, maybe they just finally went crazy with the review.
As someone who is publishing and is frequently asked to peer-review I can tell you that I never check for plagiarism unless there is something so peculiar in a paper as to raise my suspicions. (and yes, a reference to god would certainly do that). It is also very unlikely that I would detect outright fraud if it is committed well within the realm of what is at least theoretically possible and the documentation supports the findings and conclusion (and we all know what you can do with photoshop). And the editors ? In most (although not all) cases editors have academic assignments and do the editing of journals out of a sense of duty or to further their careers. So they're not fulltime editorial staff and probably have heaps of other obligations. The matter becomes if trickier if you author a paper and have a co-author who plagiarizes - truly those of you who publish, do you check all papers that list you as co-author ? Despite the fact that we all know that a paper retraction likely destroys the careers of all associated with it ? So yes, the peer review has its short comings, but to paraphrase Churchill "the peer-review system is the worst system - except for all the alternatives".
It's interesting that Warda is shown among the Mitochondrial Signalling Laboratory people, but the "CV download" button doesn't work and if you click on his picture (which for everyone else also goes to the CV), it goes to the CV of Jae Boum Youm, the person listed above. Very strange.
Peer-review isn't _for_ catching fraud. I review, and I generally do it on the assumption that the authors are honest. What I'm checking for is whether the paper is coherent and the conclusions follow from the argument and the data.
Fraud gets caught later, because it's not replicable or gets directly contradicted.
Is it possible Warda is a victim here? I doubt ID theft would be below such folks....
I found this bit on page 2:
It makes us sound so special, doesn't it? But then, the only other species actually mentioned is yeast.
I found this bit on page 2: "Moreover, there are significant differences in the spectrum of proteins associated with human mtDNA nucleoids when compared with that of other species, ..."
Looks like they borrowed that line from J. Biol. Chem., 281: 25791-25802, 2006. "Human Mitochondrial DNA Nucleoids Are Linked to Protein Folding Machinery and Metabolic Enzymes at the Mitochondrial Inner Membrane" Yousong Wang and Daniel F. Bogenhagen
http://www.jbc.org/cgi/content/full/281/35/25791
I agree with Ian Musgrave (#168) that the other instances Sarah quoted are at most venal sins. In technical literature and with the highly compressed format of an introduction it's sometimes really difficult to come up with completely novel phrases -- you have to get the same point across as everyone else, using the same technical words, and sometimes about the only thing you can do is rearrange the order of a list or something. It's not great, but it's forgiveable, especially with a non-English speaker.
Re. Umlik (#169) -- I do a reasonable amount of peer-reviewing and in the past year or so I have started to invariably check for plagarism -- even for people who I know personally and who I can't believe would ever plagarize, just so I don't feel like I'm picking on people (and as a sanity check, too). It's become trivial to grab a handful of phrases and through them at Google.
I agree with Stephen (#171) that peer review isn't for catching fraud, although it can happen at that stage.
I'm also wondering, like PennyBright (#172) if there's something strange going on with this paper. It looks nothing at all like these authors' previous papers or writing style. I am holding judgement of the authors (though not the paper itself) in reserve until we hear more.
Finally, as a general comment, the focus in these comments has been on the American ID and Fundamentalist movements. That seems rather parochial, and given the source of the paper seems to be barking up the wrong tree. Does Korea have any particular ID movement? (I know some Middle-Eastern countries do -- Turkey is notorious -- but that's not ostensibly the source of this paper.)
But, for comments, it's Eric Saveau for the win.
*bows toward Luna_the_cat*
Thank you. You are most gracious.
Ian commented (#175) "...the focus in these comments has been on the American ID and Fundamentalist movements. That seems rather parochial, and given the source of the paper seems to be barking up the wrong tree. Does Korea have any particular ID movement?"
Comments #29 and #66 mention the Moonies. Sun Myung Moon is from Korea, and is the inspiration for Jonathon Wells (see http://en.wikipedia.org/wiki/Jonathan_Wells_%28intelligent_design_advoc… ), one of the Discovery Institute's leading propagandists and the author of Icons of Evolution, a lifelong member of the Unification Church (the Moonies): "[The Reverend Moon's] words, my studies and my prayers convinced me that I should devote my life to destroying Darwinism..."
Thanks for the commenters unfolding the missing link between Warda and Han: Plagiarism prospective evidence.
This is real collective intelligence and is much more efficient than the formal editorial process at Proteomics.
ngong: "This whole thing began, apparently, with someone noticing the oddity of words like "soul" and "mighty creator" in a scientific paper."
What caught my attention was not really the title, which was an easy target (after all, there are so many stupid marketing titles out there, bad analogies and metaphors), but the meta statement in the abstract highlighted by PZ too: "These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative."
The term "realistic" was a the alarm. I wondered naively what other evolutionary hypothesis would be suggested by the authors.
Then came the "mighty" shortcut digged out by Alex Wild.
Also this story is a good excuse for reconsidering the role of reviews in general. As RobertC says in comment 116:
"I have gotten frustrated about the trend in reviews lately, which summarize a few papers and references contained therein. They don't frame the field, introduce new hypotheses, or do anything particularly interesting. A decent Pubmed search could do the same."
Finally, as a positive side effect, I am happy about the quick mitochondrial webinar triggered by this "review".
I suspect the main reason that plagiarism isn't picked up during peer review is because reviewers are reading for content. Changes in style, tense, or grammar - unless egregious - can be subtle. When you mix up cut-n-paste text with authors who clearly aren't native English speakers, all you have left is the overall impression of a poorly written paper, even if the science seems sound.
Many have commented about how the content of the paper reads as reasonable, reasonable, reasonable, CRAZY, reasonable, reasonable, etc. When I examine a paper, if I turn down the content filter and read for style, it'll read like voice, voice, voice, SCREAM, voice, voice, and if I google search phrases in the scream, I often find that the text was plagiarized, and the original source is the first hit.
As a grad student and postdoc, I never noticed the tone, voice, or style of scientific papers. As an editor, I've gotten in the habit of noticing it - these days, I often can tell when a section written by 1 coauthor ends and another coauthor's section begins, the voice changes so dramatically.
"1 ... and another" ?
Strikes me as a little odd. Maybe it's just my odd number numbness again. ;-)
Given that this appeared electronically Jan 23 and wasn't "appreciated" until Feb 6, it's entirely likely that it's already printed and in transit (in which case any hardcopies will become valuable collectors items). While we wait to hear from Proteomics, it might be interesting to learn from anyone with the time to sleuth further thru some of Proteomics' recent issues for their typical time differential between electronic and full release.
Plagiarism is not the only problem there...
Copying a short description of an experiment directly, but doing so with proper attribution, would be lame but hardly worth calling plagiarism (this is a review, after all). But here they even change the names of the authors around, and what does "same" refer to now? Very incompetent. It would be interesting to check for other false references, although the weirdness of ref [111] is hard to beat.
Of course, this all being a very interesting read, I would rather argue that the main failure is in the writing of the paper. The scientific 'review' is a hollow cover for most magazines. If an article is really too shocking, then the reviewers were wrong. However, the reviewers are never paid, so why would they even bother reading a paper in detail. So all in all, I would in this case blame a) the authors for accepting such a 'compromised' paper and b) the journal for their inability to pay reviewers and convince them to deliver proper work. Personally, I only review articles when I'm paid to do so, but then I will take sufficient time and effort to actually read the paper and not scan it !
http://analysis.yellowcouch.org/reviews.html
That's a really crappy attitude. If everyone shared it, the entire scientific enterprise would come to a screeching halt, at least in my field, in which most of the journals are sponsored by relatively small professional societies that are barely financially solvent as it is. I take pride in doing a good job in reviewing manuscripts, and in turn I expect conscientious reviews of my own work. If you're in science for the money, get the hell out.
Well done everyone. But I don't get #183. Who gets paid to do manuscript reviews? I restrict my reviewing to my own field when asked, served on only two editorial boards, and have done a total of around 3X the reviews as papers I've published (around 80 papers and around 200 reviews). I've never been paid.
What field pays you for manuscript reviews? Damn, I'd be making a good chunk of change. I agonize over my papers and manuscript reviews to make sure they're correct, clear, and well-informed. That's why this plagiarism - even apart from the irresponsible ID nonsense - really hits home for me. The perpetrators' careers should suffer.
In other news, Prof. Butterfield wrote back to me to express his gratitude, which I share with those who found and documented where his paper had been plagiarized. He's very upset and will write the editor-in-chief of Proteomics.
Sarah wrote:
Here's what I propose. The letter should be written or co-signed by:
1) The people who first suspected the validity of the review (PZ and others?)
2) Those who documented the instances of plagiarism (John McDonald, Ian Musgrave, RobertC, you, etc.
3) Others familiar with the specific field or proteomics in general and who can speak fluent facultese (Mark Farmer, me, etc.)
Thoughts?
In response to #185, I seem to have hit a note, but I don't see anything wrong with actually asking money to review something. My main argument is as follows: the journal earns money from the people who want to read it and earns money from people authoring the paper. So, journals basically sell their name and a 'quality peer review'. Thus, the value of a journal lies to a large extent in the quality of the review process. Therefore, asking money as a reviewer is certainly not inappropriate.
A sketch of the economics
a- authors _need_ to publish (so they pay 1500 EUR)
b- researchers _need_ to have access (so they pay to read it)
c- journals _need_ reviewers (but prefer not to pay for it)
You might not like this attitude, but I'm sure it will improve the quality of reviews
We ask again, what field are you in and what journal is paying you to review?
I review in mineral physics and condensed matter, and never met a journal that paid for it.
Werner,
Your point a) seems to indicate that you're in favor of pay-for-publish arrangements. Is that what you're advocating? I don't pay when I submit article submissions, and if a journal insisted on it, I'd look elsewhere.
Nothing wrong with advocating pay-for-publish arrangements like PLoS. But isn't the idea that a) author pays and then you skip b) paying for access? PLoS don't pay reviewers, or do they?
For what it's worth, I just emailed a staff writer at Science whom I met before with this story and copied the link to this thread. I gave him a 3-sentence run down and urged him to read this entire thread as well as the relevant links from people who found the plagiarized sources. Hopefully this will get bigger and the previous work of the authors will be scrutinized if they are indeed as dishonest as they appear to be.
I reviewed a ms for the Journal of Experimental Biology once and they sent me a CD with the whole year's run in pdf. I thought that was pretty cool. But it didn't help much with the mortgage.
I suspect that the Ward and Han Proteomics paper will be removed within a week. Editors work hard to improve and protect the Impact Factors of their journals (displayed on the home page of the Proteomics website). Dr. Dunn (Editor-in-Chief) is not so foolish as to let this go unrectified.
May I just interrupt this amazing dissection of this tissue of plagiarism and lunacy masquerading as a review to point out to sparc@#50 that the presence of trillions of souls may not be a problem. Ancient Egyptian mythology, after all, stated that every human contained seven souls (one of which died when the body did, and in a sense *was* the body).
So ten trillion souls is just, well, an upgrading for the modern era. :)
Sarah and J.
Still no word from Mike Dunn and the Editors of Proteomics but I imagine their plate is pretty full at the moment. Lots to think about.
My own two cents is: Too many journals each trying too hard for impact factors; too few reviewers and assistant editors with too little time (hell we do reviews as a volunteer service and honor to our profession) and too many IDers looking for opportunities to push forward their own agendas.
If Warda and Han are guilty of the third offense then they have earned what is coming to them. I'd be happy to be a co-signatory of any letter but I suspect that the wheels of true peer review are already in motion and will roll over the guilty with due haste.
I went thru the paper quickly today. I'm not a mitochondria expert, and can't comment on the specific examples, but I see that all of their work (assuming there really is some) is in cardiac tissue. As noted above, their only comparison for mitochondrial regulation is with yeast. From that, somehow, without a logic train, they conclude that the endo-symbiosis theory of mitochondrial evolution must be wrong.
The discussion of protein separation techniques on pp. 12-15 reads like a laundry list that a first-year cell biology grad student might know and use. And since part of the point of that section is to say how little is known about mitochondria, their conclusion of the death of the endo-symbiont theory seems premature and bizarre.
New theories are not typically proposed in reviews, by definition, but that would not itself disqualify one from consideration, of course. Nor would the atrocious English, altho the florid verbiage and the anthropomorphic characterization of mitochondria is disconcerting:
If there's anything new that is a killer problem for the standard theory, it isn't highlighted. Nor do they propose a new theory, or even resurrect an old one.
In reply to #196:
Very well said, Mark. My pen is at the ready if need be.
Because they volunteered. I've reviewed papers and done a thorough job. Never passed one without
1. minor problems fix this and this and it is OK.
or
2. major problems fix this and this and resubmit for review.
My papers have all been reviewed and almost always the reviews were done without mercy and competently. A few were pretty flakey. In general, the better the journal, the better the reviewers.
Strange. Proteomics has an impact factor of >6, which makes it a pretty influential journal in its field. I also thought the abstract was rather long and rambly, even for a review. Boy, it sure will be interesting to hear the explanation for this.
Ok, Han is from Korea, yes? Dembski recently linked to total wingnut writing for The Seoul Times,
"Understanding Intelligent Design Theory, Babu G. Ranganathan"
The excuse "DLH" gave for posting this tripe was "Posted to give glimpses of international interest in ID. Korea appears to allow significant freedom of speech and inquiry."
Click on this link to see it at UD
http://www.uncommondescent.com/intelligent-design/understanding-intelli…
Bot for a good time click on the article at the Seoul Times
http://theseoultimes.com/ST/?url=/ST/db/read.php?idx=6176
and at the bottom you get a long list of other articles Babu G. Ranganathan has written and also a brief bio. The man is a loon.
He's a Bob Jones graduate...
and at the bottom you get a long list of other articles Babu G. Ranganathan has written and also a brief bio. The man is a loon.
He's a Bob Jones graduate...
And from the name alone appears to be Thai and not Korean...but there's no direct link between group of ethnic origin and adherance to delusion.
As to Ranganathan, here's his site. Quack.
Here's something for our theistic friends: why should we accept theistic intervention with zero evidence for it? Seriously, methodological materialism has done pretty damned well. What value addition do you fools offer?
Beyond the "meaning" and "direction" that your silly fairly tale deity provides, I'm seriously left with a blank as to what y'all provide...in any terms.
In response to #190, I'm certainly not for 'pay-per-publish' type of arrangements. I'm entirely against it (see http://werner.yellowcouch.org/journals.html). But the truth is that in biology and life sciences one needs to pay to get something published. Which is certainly not healthy for the field.
This article seems to blame the peer review system but fails to take into account the economics of 'peer review' in biology.
http://exchristian.net/exchristian/2002/06/no-true-christians.php
Judaism gave the 10 commandments which the Christians stole - along with half of the Jewish Beliefs.
SALIVATION and BAPS.....FOR GOD's STEAK:
http://exchristian.net/exchristian/2008/01/entre-to-eternity.html
You may find this theory a bit tough to swallow, but the forensic evidence from Holy Scripture itself is damning. For starters, look at what Jesus himself said is necessary for eternal life:
"I am the living bread which came down from heaven; if any one eats of this bread, he will live for ever; and the bread which I shall give for the life of the world is my flesh." The Jews then disputed among themselves, saying, "How can this man give us his flesh to eat?" So Jesus said to them, "Truly, truly, I say to you, unless you eat the flesh of the Son of man and drink his blood, you have no life in you; he who eats my flesh and drinks my blood has eternal life, and I will raise him up at the last day. For my flesh is food indeed, and my blood is drink indeed. He who eats my flesh and drinks my blood abides in me, and I in him. As the living Father sent me, and I live because of the Father, so he who eats me will live because of me. This is the bread which came down from heaven, not such as the fathers ate and died; he who eats this bread will live for ever."
(John 6:51-58)
Apparently it takes a long time to say "bite me" in Aramaic, but the message from Jesus is absolutely clear and unequivocal. At least 6 times in this passage he says that the only way to live forever is to "eat his flesh" and "drink his blood." The Jews who were listening understood this to be a literal requirement. Picture how this must have struck the disciples. They were a roving band of semi-literate, unemployed, homeless men, hungering for a better life beyond this one. This Jesus, whom they followed and trusted, told them exactly what they had to do to achieve their life-after-life goal. And it would make perfect sense for them to take The Word at his word and do what he asked. Jesus would be their entrée, if you will, to eternity.
@205 J Cohen, isn't this a wee bit off topic here? Amusing as it may be as an example of kook, I can see no reference to the article(s) under debate. If you had explained the relevance of your links I might have explored them...
Rrr:
Maybe @205JCohen is comparing the poorly peer-reviewed journal article to a similarly poorly edited and fact-checked book. By comparison, they both waste people's time and attention for little value.
Anyone else here thinking "Sternberg shenanigans"?
What's the betting that when a proper investigation of this affair is conducted, it transpires that it was yet another piece of mendacity by someone on the creationist side trying to slip something under the radar?
Mind you, the plagiarism angle kills this paper stone dead full stop. Of course, that won't stop the the creo-morons bleating about "Darwinian thought police" or some other such excremental bilge, not least because unlike respectable academics, the Discovery Institute considers plagiarism legitimate. Harvard University cell video, anyone?
It's great to see how quickly this was picked up and dismantled right here.
OTOH, it would have also been nice to see UD and the rest of the creotards trumpet this high and low as the latest, greatest proof of goddidit, then see it dismantled. Because like someone said above, even if UD, etc., could have lied about the content all they wanted, the plagiarism would have forced them to drop it like it's hot and delete all references to having ever embraced it.
Ahhh, schadenfreude.
That brings back some memories. Anyone else here ever spend time at CF? There was a thread there asking if God was made of meat. Degenerated in pretty short order into a discussion of whether making Godburgers in Heaven would be considered blasphemous.
I would have expected the editors to give this paper intense scrutiny, since it claimed in the abstract to not only disprove the endosymbiotic theory, but also to provide a viable alternative.
These difficult theological questions must be confronted. For instance, does know how to relinquish his own omniscience?
According to the Bible, God isn't omniscient.
Genesis chapter 18:
20 Then the LORD said, "Because the outcry against Sodom and Gomor'rah is great and their sin is very grave, 21 I will go down to see whether they have done altogether according to the outcry which has come to me; and if not, I will know."
It says right there: God gets his information from hearsay, and has to go check for himself. Ergo, God is neither omniscient, nor omnipresent.
If, more recently, he's been getting his information from, say, Fox News, that might explain a great deal.
Who, when peer reviewing a long and technical paper, has not had the thought "Man, I wish I could skip this part... the other reviewers will cover it"?
But, you can't do that. You slog through it, because it is your job. I suppose it is possible that all 3/4 reviewers could have done the same thing, but it seems unlikely.
The nature of the text does lend support to the idea that material was added later on.
Bearing in mind the (presumably fairly remote) possibility that this wasn't actually their work, it might be a good idea to drop a line to one of the authors. As PZ says in the update, it would be good to hear from them. I don't see anyone having tried to contact them and it might at least be polite given the comprehensive and apparently justified slagging they have received in this thread.
Andy/#215: John Scanlon/#141 above did email one of them, saying "You guys are in trouble now."
Otherwise, a colleague tipped me to the notion that Korea has gone for proteomics in a big way. At least there is a Korean Human Proteomics Organization and the 7th Intl Conference was in Seoul last March: http://www.khupo.org/meeting/page.html?cid=4&lang=e&title=Symposia
Would that, then, possibly be a connecting dot to the other bizarre statement attributed to ref 111 (top RH, pg 8) that I don't think anyone else has specifically highlighted in this thread: "Therefore, the debates concerning the mitochondrial endosymbiotic hypothesis recently terminated with many questions still left unanswered [111 (sic)]." There's no evidence from the program that there was mitochondrial anything discussed at that meeting, but in their mind such debates might have taken place.
Astounding failure of the review system. This kind of thing will destroy the authors and perhaps take the journal itself into oblivion. WHAT WERE THEY THINKING?
I uncovered a case of 'plagiarism' once while reviewing a manuscript. I knew the field very, very well and something caught my eye.
But more often, I review stuff that I have only a general familiarity with.
Still, I doubt much slips under the radar.
I've scanned that Proteomics review. It seems like you can almost tell what stuff is not plagiarized, it has sections that are just written so poorly it clearly must be the work of the authors.
It has also been my experience that non-native english writing authors, especially from Asia, tend to be at their worse when they attempt the sort of metaphorical flourish evident in the abstract.
Unfortunately, nobody at Proteomics had the guts to put them out of their misery
....and I tend to be at my *worst* when I don't proof before post
I think its important to remember that often english is not the native language of the reviewers either. So they can check the science reasonably effectively because they are familiar with the technical language but will often simply switch off or assume they have misinterpreted some of the less technical language.
It looks like the science that the authors reviewed is sound so the reviewers of this article would have done their job there. If some of the verbiage is a bit odd maybe that wouldn't be enough to reject the paper or ask for corrections.
Its still a pretty poor showing, but kind of understandable.
Yeah, but...a good reviewer will at least acknowledge their limitations to let the editor know, if not the author.
I'm working on a major revision of my dissertation for journal publication right now; the review from the first reviewer stated flat out:
That way, the editor and I know that the observations made are tentative on that reviewer's part, which influences the revisions I'm currently making to get it accepted. Maybe in house, the reviewer and editor might not want to tell the authors that much--but to hide that information from the editor would expose the editor and the journal to just the kind of thing that's going on right now for Proteomics.
I can see how your scenario would happen, but really, if my whatever-language-it's-in were insufficient to understand something I'm asked to review, the editor ought to at least get a heads-up on that fact. It doesn't mean being ruled out as a reviewer, just not putting other members of the team at unnecessary and unexpected risk.
"Ooh, I knew we shouldn't have outsourced our word processing!"
I'm wondering the same thing, Stephen [Comment #3]. It reads like a document that someone has "fixed up" -- e.g., re-inserted their grammatical errors -- after it was edited.
And also,
Comment #196 explains where all those trillions of alien souls that advanced Scientologists are supposed to believe in got to.
I wonder how long the editorial staff at Proteomics will take to respond to this issue. It seems that a prompt statement on their website would have been a good idea.
But if mitochondria are supposed to be microorganisms that have adapted to symbiosis in our cells... why are there still BACTERIA and PROTISTA?!?
It would seem that Warda and Han have also plagiarized content from the Mitochondrial Research & Innovation Group at University of Rochester Medical Center (http://www.urmc.rochester.edu/mrig/).
The very first sentence of the abstract appears to have been copied verbatim from the introduction to the MRIG:
The entire first paragraph of "Impact of mitochondrial oxidative stress on proteome remodeling" except the last sentence has been copied from the same source:
Sadly, Warda and Han have not copied in the vision statement of MRIG - that would have been funny, though.
Are Warda and Han funded by the Reverend Moon?
Dave Wisker's Comment #211 must be addressed by Professor Dunn, after Dunn spins not noticing the fact the title contained the world "Soul," if Dunn is to retain a modicum of integrity here. I hope someone holds Dunn to answering Wisker's remarkably cogent and concise question.
The list of plagiarized sources just keeps growing. The following entire paragraph has been lifted from the paper "Peroxisome Proliferator-Activated Receptor {gamma} Coactivator-1 (PGC-1) Regulatory Cascade in Cardiac Physiology and Disease" by Brian N. Finck and Daniel P. Kelly:
As was the case for the paper by Butterfield et al., the authors do not even cite the source.
I was a bit too eager to submit the previous comment, so I had not yet noticed that the next paragraph had also been copied wholesale from Finck and Kelly:
"Aaand the religious right are all about to cream their pants when they find out that there is a peer reviwed article that talks about a mighty creator. Imagine the stink they'll raise if Proteomics pulls it? Which they should do."
To paraphrase Edmund Blackadder, I believe the reviewers' resignation and suicide are in order. It's just so bizarre. I look forward to the story behind the publication coming out.
Besides, everyone knows that mitochondria bears the mark of the beast.
HJ
I had a good laugh at this:
You almost have to stand gaping in dumbstruck awe before so impressive a display of sheer idiocy.
I've updated my side-by-side comparison of Warda and Han with their sources ( http://udel.edu/~mcdonald/wardahan.pdf ) to include the passages copied from Finck and Kelly and the MRIG web page, as uncovered by Lars Juhl Jensen above. I also found a passage Warda and Han copied from:
Modica-Napolitano, J.S., and K.K. Singh. 2004. Mitochondrial dysfunction in cancer. Mitochondrion 4: 755-762.
John and Lars,
So far I have written to the MRIG and to Profs. Kelly and Reddy. I have referred them to John's pdf file and to this blog, urging them to contact Prof. Dunn at Proteomics (Dunn also wrote back to me, saying in essence that he had to go through proper procedures to deal with this). I've already noted the replies I got from Van Eyk and Butterfield, and Kelly and Reddy just got back to me today expressing thanks and saying they would look into it ASAP.
I've never encountered such extensive plagiarism before. One wonders how much original material there is, aside from the mighty creator bit.
Regarding Warda's institutional affiliation/role here, something many have questioned, in the following paper from 2006:
http://ajpheart.physiology.org/cgi/content/abstract/293/3/H1457
Warda appears with Han's Korean institutional affiliation.
Perhaps it ought to be noted that Professor Lehrer, in his comments on one particular mathematician, implied a connection between belief in ID (or other creationist notions), and steal adapting the works of others and calling it your own:
_______________________________________
1: Note biological teleology!
I wonder who would play part of hypotenuse nowadays, since Brigitte Bardot has retired? Perhaps Paris Hilton?
Han is retracting the paper. He claims he mixed up an early and late draft of the paper and made "serious errors" in the final version. Hopefully, Dunn will be compelled to corroborate this easily verifiable claim.
In a civilized society, Science and Religion are well separated and each can enjoy the freedom to develop to its full blossom. This segregation between Science and Religion can ensure us enjoyment of the development of science and the soothing effects of religion to our lonely souls at the same time. Science is just like "Fire" and Religion as "Water". Human Beings need both to survive but any attempts trying to combine these two into ONE will be bound to fail, as Chinese saying goes, YOU CAN NEVER MINGLE FIRE WITH WATER.
"Honesty" is the personality any decent religion will value highly. "Evidence-based" is the foundation for real science. This Wanda and Han paper violated values and spirits of both Religion and Science. The publication of such paper in a decent science journal is a shame of Science; it is an even bigger shame of Religion.
The paper has been retracted (and see my blog on this too). The journal Proteomics is issuing a press release soon. Mike Dunn worked as quickly as he could and did the right thing. Too bad these authors slipped through the review system, but luckily it was fixed - thanks to blogs like this one!
A really big thank you to everyone who did something about this.
100 internet points each! :-)
No purpose for life but chance. Evolution is a strange religion.
"The journal Proteomics might have decided to start a controversy to wake up the readership. Nature does this occasionally."
I am at Nature, and can say "no we don't". We publish controversial opinion, yes, but all original scientific research papers and all Review articles are peer-reviewed by two to four peer-reviewers. We don't publish papers or reviews that have technical flaws identified by the peer-reviewers, until the reviewers are satisfied. And the editors here go to a lot of trouble to obtain decent advice, we would not give up and publish an article without it having gone through a thorough peer-review process. We do sometimes over-rule peer-reviewers (in both directions) on matters of opinion, eg how important and arresting the work is perceived to be - we make those judgements ourselves. But we very much are ruled by the external technical advice we receive. We are pretty hot on our language editing skills, also.
That's a very good point. I know that Nature is tough to break into (I have one paper published there, and it was many years ago), and everyone would be on the floor with shock if something this bad made it into Nature -- I can't even imagine this nonsense making it past the Nature shark tank.
Shouldn't we also be shocked that it made it past Proteomics reviewers? Is the Proteomics review process that much worse than Nature's?
Not buying your story. Not to disparage Nature which I read and enjoy but:
1. What about the cladistics arguments which raged a few decades ago. IIRC, there were accusations that the cladists were pushing their taxonomy scheme based on socialist viewpoints or the other way around. It was all amusing and went on for a long time.
2. How about that paper on homeopathy? I didn't pay much attention but IIRC, there was a paper a while ago about someone diluting a compound and discovering molecular memory in water or some such.
L'affaire Bienveniste? The guy was a respected, credible scientist who made specific, testable claims and could not just be dismissed lightly. Nature sponsored a team to visit the lab and get to the bottom of the claims -- I thought that was actually commendable.
@Maxine (post #243)...
Sorry but I have to agree with raven (post # 245) on this one. What you have written is a description of how the editorial process at Nature SHOULD work, but that is not necessary an accurate description of how it DOES work. There are several instances of papers in the Nature family of journals being shown later to be complete garbage, based on the lively discussions that ensue in your letters pages.
I think the bigger problem that Nature has, is the fact that its editorial board is paid. Most other journals use paid assistants and secretaries, but the people actually making the decisions are respected academics who are traceable via their institutions. Nature uses a paid editorial board that often includes people whom academics have never heard of. Many of these people have no publication record (on PubMed) and are not affiliated with any academic institution. I am not claiming they aren't qualified for the job, just saying that we are right to be suspicious when they make decisions that sometimes seem out of line with mainstream academia.
The power held by these editors is staggering. A colleague of mine once wrote a letter to nature protesting a paper published there. The letter was never sent to the original authors, and never sent to the original reviewers for comment. The editors just triaged the letter in 3 days claiming that they didn't have enough evidence and would basically have to prove that the experiments in the paper can't be repeated. Never mind the fact that the experiments were designed badly to begin with, it troubles me when an editor won't even enter into any kind of discussion about something published in their journal. The attitude of Nature et al. seems to be "its published, shut up and deal with it", rather than ever ever admit that something might be wrong.
You call that academic misconduct? This is academic misconduct!
Yes, it is a review. "Review" is the word on top of the pdf, and it also occurs in the abstract.
Here is the full text of the acknowledgments:
Does not explicitly thank any reviewers. "[A]ssisting the release of this work" is a phrase I've never seen before; it could mean anything.
However, the manuscript was first received on July 19th, while the revised manuscript (which was accepted on the next day) was received no sooner than October 2nd. Means, the first submission was rejected, and the authors spent months trying to fix it.
""disciplined organized wisdom" sounds to me like "specified complex information" moved through a machine translator and back." Joshua Zelinsky |
I have not read the paper just the parts posted here but I have read other articles and web sites that have been translated by "machine" everyone of them has parts that are completely unintelligible, parts that are some what clear if you happen to know the subject, to parts that are comic in their language. In reading a web site discussing a Sterling engine it spoke of the duty of different parts of the machine to do what they did (as if they had a choice) though it was very hard to understand just what the parts were supposed to do without understanding how a Sterling engine worked in the first place.
Leaving aside the possibility that the writing was not very good in the original language to start with. The paper may or may not be as bad as it seems but Machine translation is not ready for prime time and needs to be proof read and edited as does OCR and not relied upon to work by itself.
I like this blog and wish I had the time to learn about all the details that make up the world keep it going
Sorry! I somehow interpreted this as the time between rejection and resubmission, which of course it isn't. I also seem unable to count to three...
Revised version received October 2nd, 2007; accepted October 3rd, 2007.
Looks like this was rewritten without understanding -- "where" simply doesn't apply to "downregulation", or rather, gene regulation is something that happens in the nucleus or on free-swimming mRNA that could be anywhere.
Even the parts that are not original are not good, methinks.
I doubt very much that the more prolific/influential proponents of Creationism and ID will cite this paper either as an example of good peer-reviewed literature or as evidence of mainstream science's 'bigotry' (in having the paper pulled).
Both the implication in the announcement of withdrawal in Proteomics, and the evidence supplied in the PDF above would seem to indicate significant plagiarisation.
I am impressed with how this process works.
A question though. Is it possible that a third party submitted a paper under the names given ? I would assume there is some sort of verification done.
Phd.s Language is supposed to communicate.If you can't dazzle them with brilliance...
Language can also be used to baffle as in the murky field of politics. Generally those who use unnecessarily large words in excess are trying to hide something.
Oh do give me some good articles on the topic, a physiology book, a bible and a dart.
I think this spambot deserves to be tossed in the dungeon.
Well, it was an amusing read, and I think the product of automated translation.
But yes, clearly spam.
Yeah, we seem to be getting hit regularly on these old threads. Some just say a couple of words and have a link in their name.
Anyone know where I can get some Viagra?
You folks are awesome.
That is one world class smackdown. The very reason I stop by daily. I think this is one reason that the extremists would like to regulate the internet. We cummulatively represent a challenge to their power. They are being put on notice regularly that they can no longer get away with their shit
By this time nex month Warda will be frying falafels. While Han will be making Kim Chee. And the people behind this LIE should be made known as well.
When proof is asked regarding Intelligent Design this paper can be offered as proof. Proof that Intelligent Design is a lie and IDer's wilfully lie and plagiarize others work. As I claim to many that ask. The IDer's are people who do not have the discipline to do the real work. They do know how to copy and paste but continuously fail to discover anything new regardless of how many articles they hack apart.
Once again "FUKIN AWESOME"
JamesR:
"IDers...do know how to copy and paste..."
I don't think they can even do that - cf "cdesign proponentsists" in Of Pandas And People :)
*Applause*
(turns cartwheel)
*Applause*
10am - blog post
7pm - conclusive smackdown.
I am awed...and cross that I was at work and missed it all!
Now, did anyone archive the original paper because - strangely - it's vanished.