Category: PLoS Biology

Dear journals: Clean up your act. Regards, Concerned Biostatistician

Romain-Daniel Gosselin

Recently, a biostatistician sent an open letter to editors of 10 major science journals, urging them to pay more attention to common statistical problems with papers. Specifically, Romain-Daniel Gosselin, Founder and CEO of Biotelligences, which trains researchers in biostatistics, counted how many of 10 recent papers in each of the 10 journals contained two common problems: omitting the sample size used in experiments, as well as the tests used as part of the statistical analyses. (Short answer: Too many.) Below, we have reproduced his letter.

Dear Editors and Colleagues,

I write this letter as a biologist and instructor of biostatistics, concerned about the disregard for statistical reporting that is threatening scientific reproducibility. I hereby urge you to spearhead the strict application of existing guidelines on statistical reporting. Continue reading Dear journals: Clean up your act. Regards, Concerned Biostatistician

Judge tosses case, saying that court-ordered retractions are not part of scientific publication

“Retractions are part and parcel of academic and scientific publication. Court ordered retractions are not.”

So ends a judge’s September 30, 2016 opinion dismissing a case brought in 2014 by Andrew Mallon, a former Brown University postdoc, alleging that his advisor and former business partner, John Marshall, had published a paper in 2013 in PLOS Biology that should have listed him as a co-author.

As with most court cases, this one had a long backstory: An earlier version of the paper had listed Mallon as a co-author, but was rejected by Neuron in 2011; after the authors had a dispute over the data, a different version of the manuscript was submitted to PLOS Biology in 2012, leaving Mallon off the co-author list. So Mallon had sued to have the paper retracted.

In communications with Retraction Watch and other media, as well as during depositions of the plaintiffs, Mallon referred frequently to allegations of scientific misconduct, including the fact that the first author of the PLOS Biology paper had an unrelated paper retracted in 2010 for duplicated data. However, this case was brought under the Copyright Act, which focused on the authorship dispute.

Kevin Tottis, who represented Marshall and co-defendant Dennis Goebel, told Retraction Watch his clients “are delighted with the judge’s decision.” Massachusetts District Court Judge Timothy Hillman, he said, Continue reading Judge tosses case, saying that court-ordered retractions are not part of scientific publication

Researcher who sued to stop retractions gets his sixth

Mario Saad
Mario Saad

A sixth retraction has appeared for a diabetes researcher who previously sued a publisher to try to stop his papers from being retracted.

Mario Saad‘s latest retraction, in PLOS Biology, stems from inadvertent duplications, according to the authors.  Though an investigation at Saad’s institution — the University of Campinas in Brazil — found no evidence of misconduct, a critic of the paper told The Scientist he does not believe that the issues with blots were inadvertent.

Previously, Saad sued the American Diabetes Association to remove four expressions of concern from his papers; they were later retracted, even though Unicamp recommended keeping three of them published.

Here’s the new retraction notice, for “Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice:” Continue reading Researcher who sued to stop retractions gets his sixth

“I shared:” Can tagging papers that share data boost the practice?

Psychological Science

After a journal began tagging papers that adopted open science practices — such as sharing data and materials — a few other scientists may have been nudged into doing the same.

In January 2014, Psychological Science began rewarding digital badges to authors who committed to open science practices such as sharing the data and materials. A study published today in PLOS Biology looks at whether publicizing such behavior helps encourage others to follow their leads. 

The authors summarize their main findings in the paper:
Continue reading “I shared:” Can tagging papers that share data boost the practice?

Authors retract striking circadian clock finding after failing to replicate

Screen Shot 2016-03-02 at 9.29.28 AMThe authors of a paper showing a “striking and unanticipated” relationship between light and temperature in regulating circadian rhythms are retracting it when the results couldn’t be replicated.

After being contacted by another group who couldn’t reproduce the data, the authors failed to, as well. They “have absolutely no explanation for the discrepancies with the original results,” according to the note in PLOS Biology.

It’s an unfortunate turn of events, but Continue reading Authors retract striking circadian clock finding after failing to replicate

Popular paper by famous longevity researcher gets mega-correction

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Leonard Guarente

A highly cited paper by a well-known scientist at the Massachusetts Institute of Technology who studies longevity could have aged better: The ten-year-old paper has earned its second correction.

It’s one of multiple papers by lead author Leonard Guarente that have been questioned on PubPeer. Guarente has already retracted one, and plans to address another. Continue reading Popular paper by famous longevity researcher gets mega-correction

Mol bio paper pulled by PLOS following investigation into figures

Screen Shot 2015-11-17 at 11.58.47 AMPLOS Biology has retracted a paper about the molecular details of β-catenin expression following an investigation by the first author’s institution in Italy.

The investigation, by the Istituto Nazionale per la Ricerca sul Cancro, found that there were multiple “figure anomalies.” According to the note:

An explanation of inadvertent error was given for some of the issues identified, while for two issues, a satisfactory explanation could not be provided.

First author Roberto Gherzi says none of his co-authors helped prepare the figures. The authors maintain that the conclusions are unaffected, but that assurance wasn’t enough for the journal. Here’s more from the lengthy retraction note, which provides some backstory on the “serious concerns” regarding the data:

Continue reading Mol bio paper pulled by PLOS following investigation into figures

Investigation triggers retraction for biochem paper

PLOS BiologyA paper has been retracted from PLOS Biology for duplicating lanes and incorporating others that “came from an unrelated experiment that had already been published.”

According to the retraction notice, first author Laura Cerchia says that the mistakes came “as a consequence of incorrect incorporation of representative blots.” Cerchia — along with her supervisor, study author Vittorio de Franciscis — “apologizes for this.” None of the other authors were “involved in the preparation of these figures, and there is no concern about the results that they contributed.”

Cerchia maintains that the paper’s conclusions are still valid, but the remaining authors write that the issues undermines their confidence in the results. According to the notice, the retraction is a result of “an institutional inquiry” at the Consiglio Nazionale delle Ricerche (CNR) in Rome, where Cerchia and de Franciscis are both based.

The notice tells the rest of the story:

Continue reading Investigation triggers retraction for biochem paper

Former postdoc suing lab head for publishing paper he says he wrote, without his name

plos biologyA pharmaceutical researcher is suing his postdoctoral advisor and former business partner, accusing him of publishing a paper in PLoS Biology they wrote together, and removing him as an author.

According to the complaint, Andrew Mallon and John Marshall co-founded a company, Ardane Therapeutic, to commercialize a potential therapy that Mallon discovered for Angelman Sydrome, a developmental disorder characterized by cognitive impairment and autism.

In 2011, the two, along with several other members of Marshall’s lab at Brown University, wrote and submitted a paper to Neuron (listing Mallon as the first author), which was not accepted. Shortly after submission, “Mallon and Marshall had a falling out,” the complaint says — specifically, they “disagreed about how Ardane should be operated and about the required standards of legal and ethical conduct.” Mallon left the lab and founded his own company, Calista Therapeutics.

In 2013, Marshall and his team published a paper in PLoS Biology, “Impairment of TrkB-PSD-95 Signaling in Angelman Syndrome,” that had some passages taken almost verbatim from the Neuron submission, the complaint says, but Mallon was not included as an author. According to the lawsuit:

Continue reading Former postdoc suing lab head for publishing paper he says he wrote, without his name