“This situation left me ashamed and infuriated with myself:” Scientist retracts two papers

A Portuguese group has retracted two papers in the Journal of Bacteriology after mislabeled computer files led to the wrong images being used.

And, we’ve learned in a heartfelt email, the first author was devastated.

Here’s the notice for “MtvR Is a Global Small Noncoding Regulatory RNA in Burkholderia cenocepacia”:

A number of problems related to images published in this paper have been brought to our attention. Figure 1D contains duplicated images in lanes S and LE, and Fig. 4D and 6B contain images previously published in articles in this journal and in Microbiology and Microbial Pathogenesis, i.e., the following:

C. G. Ramos, S. A. Sousa, A. M. Grilo, J. R. Feliciano, and J. H. Leitão, J. Bacteriol.193:1515–1526, 2011. doi:10.1128/JB.01374-11.

S. A. Sousa, C. G. Ramos, L. M. Moreira, and J. H. Leitão, Microbiology 156:896–908, 2010. doi:10.1099/mic.0.035139-0.

C. G. Ramos, S. A. Sousa, A. M. Grilo, L. Eberl, and J. H. Leitão, Microb. Pathog. 48:168–177, 2010. doi:10.1016/j.micpath.2010.02.006.

Therefore, we retract the paper. We deeply regret this situation and apologize for any inconvenience to the editors and readers of Journal of Bacteriology, Microbial Pathogenesis, and Microbiology.

The paper has been cited twice, according to Thomson Scientific’s Web of Knowledge.

Here’s the notice for “The Second RNA Chaperone, Hfq2, Is Also Required for Survival under Stress and Full Virulence of Burkholderia cenocepaciaJ2315″:

Problems related to images published in this paper have been brought to our attention. Figure 8 contains duplicated images as well as images previously published in articles in Microbiology and Microbial Pathogenesis, i.e., the following:

S. A. Sousa, C. G. Ramos, L. M. Moreira, and J. H. Leitão, Microbiology 156:896–908, 2010. http://dx.doi.org/10.1099/mic.0.035139-0.

C. G. Ramos, S. A. Sousa, A. M. Grilo, L. Eberl, and J. H. Leitão, Microb. Pathog. 48:168–177, 2010. http://dx.doi.org/10.1016/j.micpath.2010.02.006.

Therefore, we retract the paper. We deeply regret this situation and apologize for any inconvenience to the editors and readers of Journal of Bacteriology, Microbial Pathogenesis, and Microbiology.

The paper has been cited 14 times.

Principal investigator Jorge Leitão gave us a quick recap:

A problem with a malfunctioning  computer and image storage and mislabeling led to the assembling by one of the co-authors of images that were previously published by our research group. I didn’t detect the problem when the manuscript was sent for publication. Although the conclusions were not compromised in any of the two papers, we retract the papers precisely because some images were wrongly used.

First author Christian Ramos was chattier when we spoke to him via email:

First of all, the problem was pointed out by a reader of the journal, otherwise, we would never detect it, because it have reproduced the experiments several times for other pieces of work, and always got the same results.

I the 2011 paper (http://jb.asm.org/content/196/22/3980), it was first submitted to other 2 journal (JBC and RNA Biology), whom requested a lot of modifications, and therefore, we accumulated a lot of processed data files. In between the process, the hard-drive of the computer that was used to store the data files (which is shared by 5 research groups) stopped working due data overloading. Nonetheless, we were able to retrieve the original data, or so we thought. At the time, I was responsible for composing the final figures of each paper that we produced, and asked the team members to give me the files. In Figure 8 of this paper, it seemed that there has been a labeling error in the source files, and I did not realize that some images where duplicated in the experiment that was being represented, neither that parts of the image had already been published. I should stress that that the images were produced in our lab and represent our data.

…

Although it is no excuse, this was a genuine naïve error, which was not detected by any of our team members, nor the referees in 3 journals (including J. Bacteriol) or the editor which handled the paper. In fact, Prof. Thomas J. Silhavy, which currently is the editor in chief of the journal (and with whom we discussed the course of action regarding these 2 papers), was the editor which handled the paper. We discussed with Prof. Thomas J. Silhavy the possibility of publishing a “Author’s Correction” (please see attached file), but he was unreceptive, and therefore, we retracted the paper.

I the 2013 paper (http://jb.asm.org/content/196/22/3981), it might sound strange, (and probably was the main reason of the editor in chief decision), the reasons for the problems with figures was quite identical. This has a reasonable explanation: Part of the paper was performed at the same time of the 2011 paper, and in fact the sRNA described in the 2013 paper appeared in the 2001 paper in EMSA experiments. We wanted to label it as LhdR (for Large Hfq dependent RNA), but a referee suggested that we remove all that data from the paper and prepare a new one, and rename the sRNA for MtvR. I followed the suggestion. Most phenotypes were already done, but we needed to perform a few more experiments. The draft was the sent to NAR, who rejected based of lack of mechanistic data. Molecular Cell rejected it based on lack of ground-breaking novelty. Cellular Microbiology recommended the paper for Molecular Microbiology, which after 4 round of review, rejected the paper. We knew that it was rock solid science, and that the results shown were really important, so we sent it to mBio (ASM). They recommended it to J. Bacteriol, and the paper was accepted with minor changes.

…

If in the 2001 paper, we felt that it was a serious scientific breach, but could be corrected, in this case, besides the naïve errors, we were sloppy in revising the manuscript, for which there are no excuses, and the paper must be retracted.

This situation left me ashamed and infuriated with myself, and disappointed with the team members. Ashamed because I did not perform my job well and failed to see such mistakes, infuriated because I believed that I could trust in the team members, when I should have known better. Disappointed because only myself and the PI made any effort to deal with this situation.

We have the clear notion that this will make publishing much more difficult, but for the sake of science and scientist, it was required. From this came one very big lesson: We should trust no one, not even ourselves, and always verify everything at least 5 times.

Update, 10 a.m. Eastern, 10/29/14: Ramos asked us to add a statement clarifying what he wrote above:

The errors that were published result from lack of self-verification, and therefore are my responsibility, and all co-authors were completely unaware of them. I wish to publicly apologize to my co-authors, to all the scientists in the lab, to J. Bacteriol, the referees, editors, editorial and production staff that handled the papers, the readers, and especially to all members of the scientific community for this naïve error.

Hat tip: Kerry Grens