The publishing house Elsevier no doubt hoped to put a major embarrassment behind itself Thursday by retracting one of the most controversial papers of recent times. Instead, it has created further contention over peer-review practices in the for-profit scientific publishing world.

The paper, by French researcher Gilles-Eric Seralini and his colleagues, created an instant uproar when it appeared in Elsevier’s journal Food and Chemical Toxicology last year. The paper’s explosive finding was that laboratory rats fed for up to two years on genetically modified corn of a type widely used in the United States developed huge, grotesque tumors.

Numerous researchers, however, pointed to what they said were glaring shortcomings in Seralini’s methodology, analysis and conclusions. (We outlined those criticisms here; a digest of the critiques published by London’s Science Media Centre is here.) Seralini’s background as a long-time critic of genetically modified foods lent credibility to critics’ assertions that his study was designed from the first to support a predetermined conclusion.

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Seralini’s study also became fodder for the campaign promoting California’s Proposition 37, which would have required labeling for genetically-modified foods at the supermarket. (The initiative failed.)

Elsevier’s action, which has been challenged by Seralini, has already shifted the debate from the adequacy of the original paper to the process of peer review in scientific publishing and the politics of this particular retraction. The European Network of Scientists for Social and Environmental Responsibility responded within a day with a statement calling the retraction “a travesty of science” that appears to be “a bow to industry.”

Other commenters noted that the retraction statement specifically states that the editors “found no evidence of fraud or intentional misrepresentation of the data.” That raises the question of whether the retraction was an overreaction, since the article, once published, had been subjected to vigorous reexamination. The website Retraction Watch points out that many in the scientific community believe a retraction should be reserved for cases of “fraud and serious error.”

What remains unresolved is how a paper ultimately judged to warrant retraction got passed by peer review and reached print in the first place. Publishing standards are coming under intense scrutiny these days, especially in the life sciences, as we recently reported. The withdrawal of a paper with political implications, like Seralini’s, will only intensify that debate. Stay tuned.