Monday, February 11, 2008

Creating Mitochondria and a sign that we need open peer review

Well, since everyone else is posting about this I figured I should too (see for example Steven Salzberg's Blog, The Harvard Crimson, Pharyngula). If you have not heard yet, there is an article in the journal Proteomics that discussed how mitochondria must have been created by an intelligent designer.

For example on p8 the authors say:
"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."
Say what you want about the journal Proteomics but boy did they screw this one up. I think they probably should have caught this without much effort but who knows exactly what happened. In all fairness to them, it is possible for weird thin gs to slip through at any journal. Reviewers are busy. Editors are busy. Everyone is busy. How can we prevent this from happening again. There is a simple change we could make that would help. It is called Open Peer review. That is, if reviewers names were publicly attached to papers they reviewed, and their reviews were published, we would be less likely to see things like this happen. Then, if someone agrees to do paper review, they would be careful about it. Sure, we would probably have a harder time getting reviewers, but that would be better than publishing crap.

What are the risks with Open Peer review? Well, some people might feel afraid to criticize others especially people with power. Well, I find this sad. Scientists criticize our collaborators and friends ALL the time in private. Why not be public about it? Aren;t we supposed to be searching for the truth? If we are, shouldn't we be willing to give our opinions in public forums?


  1. I agree that there has been a serious lapse somewhere in the chain, but I note that we can't automatically assume that the reviewers are at fault. From what I can gather, the paper was mostly a decent review, with a couple of nonsensical statements stuffed into a few paragraphs. It is entirely possible that the reviewers did not receive a draft with those small sections, approved the review as it was, and then the authors snuck them in the final version. I have reviewed many papers that were acceptable pending changes but which did not require additional review and therefore which the reviewers would not see again before they appeared in print.

  2. Excellent point ... for a true Open Review system to work well, the original submission and each revision should be available. And the whole history of what got reviewed by whom should be available too. This is by the way, sort of what Biology Direct does.

    It may not be an ideal system but I think we need to experiment with new ways to do peer review for many many reasons. Preventing silliness like the statements in this paper is just one of the reasons.

  3. You know what else? I would like it if authors of rejected papers were obligated to provide any new journal with a history of submission and previous reviews. I find it incredibly frustrating to point out problems with a paper significant enough to cause its rejection from one publication, only to see it show up in print in another journal more or less unaltered. Requiring a submission of previous reviewer comments would improve that.

  4. Now that is a great idea ... this could be done through a centralized review system ... someone must have thought of this no? If not, it really would be great to have.

  5. Now this paper will be cited by creationists for at least the next 50 years.

  6. TR Gregory-

    The paper was not a 'decent review,' unless you consider cut-and-paste plagiarism of sources omitted from the citations to be 'decent.'

  7. Biology Direct system is great, the authors-reviewers ping-pong blabalabla section is sometimes very informative (especially for students I think) and gives a sense of responsibility to the reviewers. But i'm too bloody scared to submit a manuscript to those guys: it would be certainly reviewed by Koonin!

  8. The manuscript has been withdrawn. Apparently, the journal is conducting some serious investigations.

  9. The paper has been retracted and the journal will be issuing a press release tomorrow. The plagiarism was probably key in getting the authors to retract, rather than just editing out a few sentences.

  10. "Aren;t we supposed to be searching for the truth?"

    Truth? truth belongs in the humanities department. I prefer to build models based on testable hypotheses. The article should never have been published, but when scientists start talking about truth they sound more like preachers than teachers.

  11. Anonymous - I probably get your point but think you miss the forest for the trees. Sure - science is about hypothesis and models and theories and so on. But to say that science is not about the search for truth is inaccurate in my opinion. We may only be able to build and test theories. But many of us are in fact searching for something that we call "the truth." IOt may not be what philosophers call the truth, but that is OK with me.


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