Once again BMJ and its editor Fiona Godlee have demonstrated their high-handedness and double standards by refusing to allow full discussion of their non-disclosure of affiliations in the Wakefield affair. At least two letters responding to Godlee’s belated disclosure (HERE) have not been posted in the on-line edition, one of which documents undisclosed hospitality received by author Brian Deer a few weeks before publication of the articles attacking Wakefield. While BMJ have posted limited comments, they are evidently hiding from others by Dr Mark Struthers and myself which put their activities further under scrutiny. Even they have been forced to face the fact that as supposedly leading experts on Conflict of Interest they have been caught with their trousers down. Godlee and Marcovitch are both former chairs of COPE (Committee on Publication Ethics) (HERE ) so any claims at naivety fail. Marcovitch had even in an earlier article remarked on the double standards of the Journal of the American Medical Association, even if it is not quite the paradox that he claimed: "It is a paradox that the professional medical association that owns JAMA was less than open and transparent with Lundh and colleagues about potential financial conflicts (such as their income from industry sources) as they expect their authors to be." (HERE ).
Here are the missing letters.
"Re: In response to John Stone"
Thank you for responding . Unfortunately, as we know from the history of religion pious sentiments are not always accompanied by pious deeds: there can be no assurance from the finest words that the culture of a journal is not altered by its business associations. Moreover, we can base very little on the fact, bearing in mind the sequence of events, that BMJ discussed Vioxx in 2007 or Rosiglitazone in 2010 (a little after the horse had bolted in both cases?).
I wonder what we can deduce from the judgement that serial publication of Brian Deer's articles, full of familiar allegations for which many challenges exist , were of "high global importance" ? As it is, to my certain knowledge, several substantive letters questioning Deer's interpretations and findings have been blocked, and outside the traditions of academic and scientific publications the defence of them has been legalistic, technical and incomplete [3,4,5]. Most noticeably, Deer has never been required to return to BMJ's columns to meet any of the criticisms.
Further, I note with concern that while Harvey Marcovitch as a signatory of the editorial 'Wakefield's article linking MMR vaccine and autism was fraudulent'  and associate editor of BMJ may not have a problem with his role as head of GMC panels, he should as head of GMC panels have a problem with signing that article. He has also in that role failed to investigate or discipline the chair of the 'Wakefield hearing', Surendra Kumar, who failed to disclose that he sat on two licensing authority committees, owned shares in GSK , and after the hearing called for MMR to be made compulsory at the BMA  all in clear breach of the Nolan rules on standards in public life , although it may not have occured to him.
It also looks like it 'didn't occur' to Brian Deer when he accepted an invitation to address the American College of Toxicology in Baltimore last November  that the event was heavily endowed by the pharmaceutical companies, including GSK . And I recommend to him the seminal article on the subject by Ben Goldacre, 'Jounalists, anything to declare?' .
I trust that 'it didn't occur to us' will at least not be the resort of journal editors ever again after this misadventure.
 Fiona Godlee, 'In response to John Stone' BMJ Rapid Responses HERE
 Kimberly R Stagliano 'Re:BMJ response to emails from readers of Age of Autism', HERE
 Guardian UK
 Fiona Godlee 'BMJ response to emails from readers of Age of Autism', HERE
 Fiona Godlee, Jane Smith, Harvey Marcovitch, 'Wakefield's article linking MMR vaccine and autism was fraudulent', HERE
 John Stone 'Re: Financial conflicts -shock horror', HERE
 Lyndsay Moss'Doctors reject calls for compulsory pre-school immunisation' Scotsman 2 July 2010, HERE
 Summary of the Nolan Committee, HERE
 Ben Goldacre,'Journalists, anything to declare?', HERE
Competing interests: None declared
From Mark Struthers:
"Re:What about BMJ, Merck and GSK (and Andrew Wakefield)?"
Andrew Wakefield was accused and ultimately found guilty of serious professional misconduct for not disclosing in 'The Lancet' paper of February 1998 that he was a medical expert involved in assessing the merits of litigation against the manufacturers of MMR on behalf of children possibly damaged by the vaccine. However, the matter of litigation had no bearing on 'The Lancet' paper and Dr Wakefield had followed the 'subjective' Lancet disclosure rules in place in 1997 when the paper was submitted. 
In his report to the GMC of May 2007, Professor Sir Michael Rutter FRS, expert witness for the prosecution, declared that failure to disclose in 'The Lancet' was "quite unsatisfactory." At the subsequent GMC hearing, Professor Sir Michael, expert witness on behalf of the vaccine industry in the UK MMR litigation, confirmed that a researcher had an objective duty to disclose conflicting interests. The entirely laudable reason for the disclosure obligation was so that ...
... "the reader of the published research could judge for himself whether the quality of the reported science outweighs the potential for the conflict to bias the interpretation."
Of course, the disclosure rules for 'The Lancet' and other medical and scientific journals had changed in the intervening decade - but Sir Michael, an expert in conflicts disclosure, did not seem to feel the need to clarify the matter before the GMC.
It seems that the BMJ reader was not given the opportunity to judge the potential for the BMJ's conflicting interests to bias the editorial interpretation of Brian Deer's published research. The failure to disclose could quite justifiably be interpreted as "unsatisfactory".
 'Callous Disregard: Autism and Vaccines - the Truth behind a Tragedy' by Andrew Wakefield 2010. Chapter Eleven: Disclosure.
John Stone is UK Editor for Age of Autism.