An XMRV-related paper titled Identification of a Novel Gammaretrovirus in Prostate Tumors of Patients Homozygous for R462Q RNASEL Variant from Joe Derisi’s lab was pulled out by the journal PLOS Pathology. The journal explained its decision in a separate blog post.
Retractions have been rising lately and many are coming from reputed labs (Link, Link, Link). In the most high-profile case among those, Nobel-prize winner Linda Buck retracted two of her papers from Science and PNAS. In another highly visible case, famous chemist Peter Schultz retracted two high-profile papers related to ‘killer application’ for protein synthesis. Only half of those retractions were due to scientific misconduct according to a news feature published in Nature, whereas the remaining ones were had reasons ranging from irreproducible results to dumb mistakes. You can find the details in the following figure from Nature news feature:
As an established scientist as well as co-founder of an important journal, Mike Eisen should be the last person to be unaware of the above facts, yet he feigned surprise and accused the deciding PLoS editors of “expand(ing) the definition of retraction away from its common usage as a way to indicate misconduct to include all cases in which the findings of a paper should now be judged unreliable”. Is he writing from caves of Afghanistan, where Google is inaccessible? Paper after paper got retracted over the last few years from high-profile journals, because either the PI’s own group or other labs could not reproduce the results (see examples in second paragraph).
Dr. Eisen’s commentary does make a valid point or two on why the practice of retraction of papers is against preservation of ‘scientific truth’, but it would have helped up consider their merits, if he -
(i) refrained from calling names to Haldar and Barbour (‘deeply subversive’, ‘reactionary’, etc.) and explained how pervasive the practice of retracting papers to ‘correct the literature’ had been. The said editors were merely implementing PLoS retraction guidelines, which appears to be in line with other journals.
Journal editors should consider retracting a publication if:
• they have clear evidence that the findings are unreliable, either as a result of misconduct (e.g. data fabrication) or honest error (e.g. miscalculation or experimental error)
(ii) shown outrage about the practice of retracting to ‘correct literature’ before his own buddy got caught into the retraction net. Here is a 2008 quote from Linda Buck after her decision to retract papers of her post-doc.
Harvard Medical School has formed an ad hoc committee to review the retraction, and Buck has asked the Fred Hutchinson Cancer Research Center to review two later publications on which Zou was the lead author. “It’s disappointing of course,” says Buck. “The important thing is to correct the literature.” The retracted paper has been cited 138 times, according to Thomson Scientific’s ISI Web of Knowledge.
Did Dr. Eisen present any argument refuting her statement “the important thing is to correct the literature” between 2008-2012?
(iii) did his homework before writing this misleading sentence -
Rather than digging in their heals and defending their initial study – as many scientists do – the original authors accepted the newer results, and went to great lengths to figure out what had gone wrong.
In almost all non-fraudulent retractions, such as those linked in the second paragraph above, typically PI’s own lab pulled out the papers after finding out that the major conclusions were completely wrong. Amy Wagers’ case is a good example, where the researcher removed her own paper, when she could not confirm the results in further studies. The situation of Joe DeRisi is not as unique as Dr. Eisen presented.