A baffling failure of peer review

| 28 Comments

A dismaying update: the paper in question contains a significant amount of outright plagiarism, and large chunks of text are taken literally from Butterfield 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?

Continue reading "A baffling failure of peer review" (on Pharyngula)

28 Comments

”…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…”

Well, that’s one theory. Hardly fact though.

Actually, ss, it is an hypothesis, and there has yet to be any evidence against it. It is an appealing hypothesis because of its explanatory power. No other explanation has yet been proposed that explains so many of the facts about mitochondria.

Now, I cannot access Pharyngula from work, so I cannot read PZ’s comments at this time. However, the phrase that he highlights:

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

is rather ominous.

For one thing, it is hard to envisage a “more realistic” alternative, because there is nothing unrealistic about the endosymbiosis idea. The very fact that the authors implicitly describe it as “unrealistic” suggests that they are prejudiced, which is unlikely to lead to good science.

Crosspost from PZ board:

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.

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.

This is so weird that an explanation is owed the scientific community.

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.

What evidence did the authors give for a human soul? I’ve never even seen one but they sound cool.

I’m going to crosspost a post of mine from Pharyngula like raven did, because the fact that the mitochondria are, above all, counter-evidence to the “design hypothesis”:

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/3yyvfg

raven:

3. The editors deliberately set off some fireworks to see what would happen and wake up the readership.

It’s not April 1st yet, is it?

There are multiple lines of evidence that strongly suggest that the mitochondria was derived by endosymbiosis. In order to replace this “accepted theory” one has to come up with a better explanation for all of the evidence, including: the fact that endosymbiosis can be observed in the laboratory; the prokaryotic nature of the inner mitochondrial membrane; the sensitivity of mitochondria to antibiotics that affect prokaryotes; the prokaryotic nature of the mitochondrial genome (circular molecule, lack of introns, few intergenic spacers, polycistronic transcripts); the sequence similarity between mitochondria and bacterial genomes; the lack of proofreading and repair mechanisms in mitochondrial DNA replication; ribosomal DNA similarity to prokaryotes; distinct genetic code; and the evidence for transfer of mitochondrial genes to the nucleus. Simply finding something difficult to explain in the nuclear genome won’t even come close.

And what is all this nonsense about a soul anyway? Having found no evidence of a soul in the nuclear genome, now they turn to the mitochondria? News flash, we had complete mitochondrial sequences from humans long before the human genome project was finished. If there were evidence for a soul gene in there, it would have been found long ago. And what about the chimpanzee for which the mitochondrial sequence and much of the nuclear sequence is known? It’s sequence is very similar to humans. Do chimps have the soul gene as well?

P.S. Oh yea, I forgot, lack of recombination as well.

I’m not too surprised that something like this can slip through. Terrible papers slip through in physics as well. It’s a sign of an overloaded system of review and the intense specialization that occurs as the number of fields expands.

Here is a true story that physicists will appreciate.

I remember a talk given by Victor Weiskopf at an April meeting of the American Physical Society in Washington DC many years ago. He was commenting on the growth in physics and the increasing number of journals and pages along with the problems it presents in quality control and sorting through it all to get at the good stuff. But the way he did it was unforgettable (for a physicist anyway).

He had calculated the rate of increase of the number of pages of publications in just the Physical Review over just his lifetime. He then figured out how this would appear as the Physical Review was stacked on a huge shelf. As time progressed, the right-hand edge of the journal would be moving toward the right at a certain velocity as pages accumulated. This velocity would be constant if there were no increase in the rate of publication, and he figured out how many meters per second this would be, given the rate of publication at that time.

However, given that the rate of publication was increasing, the right hand edge of the accumulating Physical Review would no longer be moving at a constant velocity but would be accelerating. Weiskopf had also calculated the acceleration.

He then estimated the date in the future when the right hand edge of the accumulating Physical Review would be traveling faster than the speed of light.

He concluded, “But that will not be a problem because the journal will no longer contain any information.”

Keep in mind that is a review, not a research paper. It’s still ridiculous that a religion paper got into Proteomics. I won’t be publishing there.

Does this mean that the soul has maternal but not paternal inheritance?

What would conservative Christians think of that?

Oh my goodness, HDX, you’ve opened a can of worms. They won’t like the implications regarding their virgin-born savior, that’s for sure.

On the other hand, they’re awfully good at compartmentalization. They haven’t really proven willing to address Behe’s belief that monkeys-to-man could be undirected, but HIV and malaria require the Loving Touch of a Merciful Designer…

Victor Weiskopf

Oops! It’s Victor Weisskopf, not Weiskopf.

OK, I’ve just read PZ’s article on Pharyngula, and I am starting to think that the paper is a joke.

HDX:

Does this mean that the soul has maternal but not paternal inheritance?

What would conservative Christians think of that?

Wouldn’t matter - according to the story, Joseph wasn’t His father anyway. ;)

Henry J: Wouldn’t matter - according to the story, Joseph wasn’t His father anyway. ;)

Somewhere in the Good Book it states He is the Son of David.

(Us Davids keep track of things like that. :-))

To note this here, there’s a suggestion with some evidence in comments on Pharyngula that the paper also includes some plagiarism.

Well if it is a review paper, it should contain significant portions of other papers. Of course, they should all be properly identified and credit given where credit is due.

I really can’t understand how someone could expect to get away with something like this. Unless of course they are creationists. Many creationists apparently feel that there is no problem with plagarizing whenever they choose, even if they are lawyers who should supposedly know better. Oh well, if you don’t do any research what else have you got?

Then again, if this whole thing is some kind of sick joke, why plagarize a respectable scientific source?

Mike Elzinga Wrote:

… He then estimated the date in the future when the right hand edge of the accumulating Physical Review would be traveling faster than the speed of light.

He concluded, “But that will not be a problem because the journal will no longer contain any information.

LOL

David Stanton Wrote:

Well if it is a review paper, it should contain significant portions of other papers. Of course, they should all be properly identified and credit given where credit is due.

I think, though, that even a review paper should not contain verbatim quotes. Sure, it summarises the ideas, results, concepts and explanations of other papers, with appropriate referencing, but it should do so in the authors’ own words, not by verbatim quotation, even if correctly referenced.

I’m assuming someone has contacted Proteomics about this. Is it, or not really?

Nigel D: I’m assuming someone has contacted Proteomics about this.

Yes - several of us have notified the Editor-In-Chief, Michael Dunn, and gotten back a polite response that they’re looking into it. See comment #69 at http://scienceblogs.com/pharyngula/[…]peer_rev.php

Oh man are you telling me the first peer-reviewed paper supporting IDC is plagerized bunk?

I guess WADerloo is postponed once again. Sigh…

Paul Burnett:

Nigel D: I’m assuming someone has contacted Proteomics about this.

Yes - several of us have notified the Editor-In-Chief, Michael Dunn, and gotten back a polite response that they’re looking into it. See comment #69 at http://scienceblogs.com/pharyngula/[…]peer_rev.php

Thanks, Paul. I cannot access the scienceblogs.com domain from work, and didn’t get online from home last night.

I think it is quite unfortunate that this BS paper has been uncovered before Denyse O’Leary could discuss it as an example of “non-materialistic science” aka BS.

I sent a quick email off to evolutionnews.com letting them know that ID got a peer reviewed article published and seeing if they were going to write an article on it :-)

Shouldn’t they be happy?

Has this paper been officially retracted yet?

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This page contains a single entry by PZ Myers published on February 6, 2008 9:14 AM.

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