PLOS Genetics updates flagged paper with expression of concern

PLOS Genetics has upgraded a notice on a paper to an expression of concern, raising the count for author chemist Ariel Fernandez to one retracted paper, and three expressions of concern.

The journal published “Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability” in 2008. In 2013, Fernandez corrected it, claiming that the work was not actually funded by the U.S. National Institutes of Health, as the original paper had said. The paper has been cited 33 times, according to Thomson Scientific’s Web of Knowledge.

Here’s the expression of concern in full, which was published on September 14:

Concerns have been raised with regard to some of the data and the conclusions of the PLOS Genetics article, “Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability”. The authors have been contacted and an investigation into these concerns is ongoing.

This Expression of Concern should not be considered as a statement regarding the validity of the work, but rather as a notification to readers. PLOS Genetics will provide additional information as it becomes available.

Here is the notice from January — which contains basically the same information — posted in the comment section of the article:

Please be advised that PLOS is working with the authors on an investigation regarding one or more issues that have been raised with respect to the content or authorship of this paper.

Commenters on PubPeer raised concerns about the data in the paper in 2013.

We asked PLOS Senior Editorial Manager Catherine Nancarrow why the previous notice was updated to an EoC. She said:

Concerns have been raised regarding some of the data and conclusions in this article and an ongoing investigation continues. We are unable to provide any further information or details at this time. Because a final resolution to this investigation may not be available for a considerable amount of time, PLOS Genetics has posted an Expression of Concern on this article. The issuing of an Expression of Concern under these circumstances is not only an appropriate and responsible course of action, as outlined in the guidelines set forth by the Committee on Publication Ethics (COPE; http://publicationethics.org/), but also is in keeping with accepted best practices for PLOS journals.

When we reported on the January notice, Fernandez told us:

All I know is that the challenger’s comments were made anonymously and were either not subject or did not pass peer review, so they have no scientific value. As a scientist I only address comments or challenges formulated in accord with scientific procedure, emanating from people versed in my subject.

We asked him if he had anything to say about the update to expression of concern:

I have little to say. The data is surely valid and reproducible and we don’t know what those concerns would be. As I recall, several years ago we were asked a few questions about the data by PLoS Genetics and we (Li, Liang and myself) answered them.

What were those questions? Fernandez told us:

I am traveling and have no access to the info, which dates back several years. As I recall, they were interested in the distribution of our data points and how our raw data was presented. We answered those questions.

Co-author Wen-Hsiung Li, a biologist at the University of Chicago, echoed Fernandez:

We the authors are not aware of what the concerns are. PLoS Genetics asked us questions about the work and we responded to those questions

Previously, Fernandez threatened us with legal action for reporting on an expression of concern.

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