Although I appreciated the humor with which Rick Trebino wrote about his effort to publish a comment, I also appreciate the underlying serious sentiments regarding the lack of scientific dialogue-debate in the scientific literature. My post last year about Rick’s tale of woe and intrigue generated a bit of discussion, and I thought it was time to revisit the issue of comments (or attempted comments) on journal articles to engage the scientific community.
I found a recent example in Cell instructive – both the comment itself and the manner in which article commentary is managed. Cell permits online comments, subject to Editor approval, but these are only posted on the journal page, not on ScienceDirect, Elsevier’s online full-text database through which most of their published material is accessed. One would think the best way to stimulate scientific discussion of an article would be to keep approved comments linked to the Websites through which most of the community will access the material.
For comparison, Science (AAAS) allows readers to submit E-letters in response to articles, and Nature invites comments directly, with no prior approval needed, though contributors must agree to the Community Guidelines. Nature also maintains a number of blogs, including Peer-to-Peer, which specifically solicits discussion about journal peer review.
Also, one would assume the involvement of the Editor in approving online comments would make them as rigorous yet more timely than printed letters. Cell does not indicate that comments will be held offline until the authors have had a chance to respond, but a recent case suggests otherwise.
In response to PcrA Helicase Dismantles RecA Filaments by Reeling in DNA in Uniform Steps by Park et al., Khan, Anand, and Leuba submitted a comment on August 23rd that was not displayed online until September 20th (simultaneously with author response). The Khan et al. comment focuses on science:
Dismantling of RecA filaments by PcrA was originally published in 2007 by our lab and collaborators
This paper from the Ha lab shows a “new” activity for the monomeric form of PcrA helicase at the ss/ds junction of DNA substrates. The authors show that PcrA helicase, which is bound to ss/ds junctions, can displace RecA under conditions in which PcrA helicase does not unwind the substrate. The thermophilic homolog of PcrA was used in these studies. Surprisingly, the authors of the current publication do not cite our paper published three years ago (Anand SP, Zheng H, Bianco PR, Leuba SH, Khan SA, J Bacteriol. 2007 Jun;189(12):4502-9. Epub 2007 Apr 20) which demonstrated the displacement of RecA from preformed RecA filaments by PcrA. Until the current publication from Ha and collaborators, our paper was the only one demonstrating the RecA displacement activity of PcrA. We had also presented our results at various international conferences, including the first Gordon Research Conference on Single Molecule Biology in 2006.
Our biochemical experiments on PcrA were prompted by genetic studies in Bacillus subtilis from the Ehrlich lab that showed suppression of a pcrA knock-out by mutations in the recFOR genes (Petit MA, Ehrlich D. EMBO J. 2002 Jun 17;21(12):3137-47). In our paper, we also showed the inhibition of RecA-mediated DNA strand exchange by three different homologs of PcrA (Staphylococcus aureus, Bacillus anthracis and Bacillus cereus). Moreover, using two different mutants of S. aureus PcrA, one of which was completely inactive for ATPase and helicase activities, we also showed that the ATPase and helicase activities are not required for the inhibition of RecA-mediated DNA strand exchange or for the displacement of RecA from either ssDNA or dsDNA. In addition, we showed that displacement of DNA-bound proteins by PcrA or its mutants was specific to RecA, as SSB or gp32 proteins were not displaced from the ssDNA. As a matter of record, ours was the first paper to show RecA displacement by PcrA using biochemical and spFRET-based assays. We believe that the broader implications of the mechanism reported by Park et al. in this publication would have been more thoroughly addressed in the context of our earlier findings.
The authors reply?
Apologies for our oversight
We thank Drs. Leuba, Khan and Anand for pointing out our failure to cite their 2007 paper in the Journal of Bacteriology. We apologize for this unfortunate oversight. Jeehae Park, Tim Lohman and Taekjip Ha
I am not sure a journal would print such an authors’ response.
In fact, the reply raises more questions than the comment. The authors couldn’t be bothered with a cursory literature search? (what about the reviewers?) A PubMed search for the Park et al. paper lists among its suggested Related Citations the earlier article by Anand et al. (and vice versa – search for the Anand paper, and Ha shows up as a Related Citation). Of course, the authors’ “unfortunate oversight” avoided the need to address the potential lack of novelty of their findings, which might have knocked their manuscript out of contention for Cell.
And, coincidentally, Ha was Vice Chair of the 2006 Single Molecule Gordon Research Conference at which the data by Anand et al. were presented.
So, Anand et al. data (biochemical & spFRET) presented at June 2006 Gordon Conference. Anand et al. paper received in March 2007 and accepted and published online in April (print publication in June). Park et al. paper submitted in December 2008, revised in February 2010, accepted in July 2010, and published in August 2010.
Aside from the authors’ economical reply and interesting chronology, there remain the unaddressed scientific issues raised … and the question of what journal article commentary is meant for, if not to launch thoughtful discussion of the underlying science.