That ridiculous article on Biblical diagnosis has been officially retracted, and the editor left a comment at Aetiology:

As Editor-in-Chief of Virology Journal I wish to apologize for the publication of the article entitled ”Influenza or not influenza: Analysis of a case of high fever that happened 2000 years ago in Biblical time”, which clearly does not provide the type of robust supporting data required for a case report and does not meet the high standards expected of a peer-reviewed scientific journal. Virology Journal has always operated an exceptionally high standard of thorough peer review; this article has clearly not met these thresholds for balance and supporting data and as such, the article will be retracted. I should like to apologize for any confusion or concern that this article may have caused among our readership, or more widely.

Whilst only ever intended as an opinion piece and also a bit of relief from the ‘normal’ business of the journal, the speculations contained within this article clearly would be better expressed outside the confines of a peer-reviewed journal. Biomed Central does not support any views outlined in this article.

Oh, yes. The usual “We always operate with exceptionally high standards, except this one time” defense. Anyone remember the Warda and Han paper that was even more egregiously ridiculous, claiming that mitochondria were the “missing link between body and soul”? That was also blithely retracted, with no explanation from the journal Proteomics about how the mistake was made.

This is a serious concern, to my mind. Scientists are expected to be open and communicative about their work, explaining all the details about how we achieve our results. Yet then we hand that work over to a publisher (usually a for-profit organization), where it is subjected to an arcane process cloaked in mystery that they call peer review. And every once in a while, some strange fluke exposes the inherently arbitrary and chaotic nature of that process, everyone asks “how the hell did that get published?”, and some guy in a business suit steps out to unconvincingly tell us “oops” and reassure us that all is well in the machineries of their journal.

I don’t think it’s enough. If a publisher wants to manage this profitable business of publishing science journals, there ought to be an expectation of transparency — a fuller explanation of how submissions are handled, and when mistakes are made, a more thorough explanation of exactly how it happened. Without an open explanation of how such mistakes occur, I can’t have any confidence that efforts will be made to correct the process that led to them.

And it’s not just the journals. Scientists have to have some expectation of rigor. The author of the retracted Virology Journal has also tried to explain what he was doing.

I was astonished that our article, submitted initially in the debate section of the journal, had stirred up such negative publicity. As an article for debate, there was no absolute right or wrong answer, and the article was only meant for thought provocation. Neither was it meant to be a debate on the concept of miracles. My only focus at the time of writing was “what had caused the fever and debilitation” that was cured by Jesus. I was especially astonished that so many comments were made outside the scope of the journal. In medical writing, colleagues would usually make comments in the “letter to the editors” and the authors would respond in the subsequent correspondence.

He’s astonished? I’m astonished! It was an epically bad paper, using very poor data to draw a completely unjustified conclusion. If he’s going to waffle now about there being no right or wrong answer, then he shouldn’t use the pages of a peer-reviewed journal to conjure up an unsupportable answer. Can this man even think scientifically?

I am amused at the protest that comments were made outside the traditional protected filters of the journal itself. That’s such a genteel expectation: that one can screw up royally, and then because one is a member of a formal organization, all criticisms will be processed and massaged by an editorial staff, one will have an opportunity to restrict and reply to only those bits that are properly phrased in a mannerly mannered manner, and that everything will be officially published in a way to enhance one’s standing as a respected colleague. Thus can pompous twits find perpetual reinforcement of their status.

Well, screw that.

The world has got to change for science publishing. No more ivory tower isolation, no more confinement of ideas to a narrow set of mutually reinforcing academic cronies — write something really stupid, and we have ways to drag it out into the light of day, where a hundred thousand people will laugh at it and tear it apart.