Here's another complicated story that came to light (no pun intended) when some people noted that an entire issue of the Harvard Health Policy Review seemed to have disappeared from the web. One article in that issue was by Donald W. Light and Rebecca N. Warburton and accused the Harvard-based editors of the Journal of Health Economics (JHE) of bias in handling an earlier paper of theirs on the true costs of drug industry research. (Disclosure: I am currently involved with Don Light in co-authoring a couple of manuscripts.)
You can read the Light-Warburton paper in the Harvard Health Policy Review (the disappearing paper) at http://healthyskepticism.internetkeep.net/share/JHE-HHPR-Ethical%20Standards-9-08.pdf Meanwhile, here's a brief summary.
One of the most widely cited pair of papers, published in the JHE in 1991 and 2003, was by DiMasi et al. of the Tufts Center for the Study of Drug Development. The second paper reached the widely quoted conclusion that it costs the drug industry $800M to develop one new drug, when you count all the failed drugs that have to be investigated along the way. The Tufts center is well known to be funded almost entirely by the drug industry, and the $800M figure has been much repeated in industry-friendly sources.
Light and Warburton wrote a paper criticizing the methods used by DiMasi and colleagues, and also calling atention to how the funding of their center created a conflict of interest in relation to their research. They chose to submit the paper to JHE, on the natural assumption that the journal would find controversy about a previously published paper interesting to their readers.
The editorial board assigned editor Thomas McGuire to the Light-Warburton manuscript. Light and Warburton describe this as an editorial conflict of interest as McGuire had also edited the DiMasi papers and could view the Light-Warburton critique as an attack on his own editorial judgment. (I demur here and wonder if the paper was assigned to McGuire because drug company research might have been his own special area of expertise.)
There then followed a long soap opera of disputes between the authors and McGuire, which is painstakingly detailed in the second Light-Warburton article. Suffice it to say here that McGuire seemed more interested in excising from the manuscript any passage that might offend DiMasi and his Center, than in protecting the intellectual integrity of the exchange of ideas. McGuire also appeared to have sent the Light-Warburton manuscript to DiMasi for comment without notifying the authors of that fact. JHE accepted from DiMasi a long and tangential reply to the charges raised by Light and Warburton, and when the latter two tried to rebut statements in the reply, they found their own rebuttal severely restricted both in length and in content. Finally, when the paper was published on the web, Light and Warburton discovered for the first time that DiMasi and his colleagues had been allowed to append a further response, which they had never seen and to which they had no opportunity to reply. In short, rather than dealing seriously with the charges from Light and Warburton that DiMasi et al. had used inferior methods, JHE gave DiMasi et al. every possible opportunity to restate their own case and to impugn Light and Warburton in the process.
Irked by this evidence of extremely one-sided editorial management, Light and Warburton proceeded to write their paper #2 exposing the conduct of the JHE editors, contrasting their behavior unfavorably to several published codes of ethics for journal editors, and making recommendations for further reforms based on their own sad experience. Their paper #2 was published in the Harvard Health Policy Review, Spring 2008 issue. That entire issue has recently disappeared with no explanation from the periodical's website (according to several fellow Pharma bloggers--see for example the Oct. 20 post on http://www.gooznews.com/).
ADDENDUM 10/22: Ed Silverman on the Pharmalot blog has provided us with both additional background and a useful update (it turns out the missing issue is back up on the web, with an apology)-- see http://www.pharmalot.com/2008/10/the-case-of-the-disappearing-journal-article/