In early 2004 the media campaign against Andrew Wakefield was gathering pace. In particular, the London Times and Guardian newspapers were increasingly peppered with sarcastic comments  about Wakefield and the MMR-autism theory, mostly coming from people with no direct knowledge of the science  – but who nevertheless felt the spontaneous need to offer an opinion. It was against this background that on Wednesday 18 February the Lancet editor, Dr Richard Horton, received a visit from freelance journalist Brian Deer and Liberal-Democrat MP, Dr Evan Harris, on behalf of the Sunday Times newspaper – also invited were Wakefield, Walker-Smith and Murch. According to Horton, giving evidence at the GMC, Deer and Harris had been dispatched by the newspaper in order to salvage a story which the newspaper had not considered strong enough to publish the previous week. Again, according to Horton in his book MMR Science and Fiction: Exploring the Vaccine Crisis Deer spoke at great length making allegations of unethical procedures used by the doctors, and of research fraud connected with the controversial Lancet study of 1998, in which Wakefield and colleagues and colleagues had defined a new condition 'ileal-lymphoid-nodular-hyperplasia' and posited, but did not confirm, links with a history of MMR vaccination and autism.

Most of the ethical issues were rapidly dismissed by the doctors, nor were they supported by the Lancet and the Royal Free Hospital where the doctors had worked and the investigations took place – though they were later revived by Evan Harris under privilege in Parliament and by the GMC. Agreement at the meeting, nevertheless, broke down over Deer's allegations about Wakefield's involvement in MMR litigation in which he had been commissioned to assess evidence by the Legal Aid Board (later the Legal Services Commission). In short, Horton denied he had known about this matter, and claimed that this alone undermined the study. This was what gave legs to Deer's apparently floundering investigation.

However, pre-empting Deer's Sunday newspaper scoop, Horton decided to go public on the issue, holding a news conference on Friday 20 February to denounce Wakefield. The following day he told BBC news: "If I knew then what we know now we would not have published that part of the paper which related to  MMR, although I do believe there was and remains validity to the connection between bowel disease and autism'. To many Horton's claim not to have known was a flabbergasting statement, but it was not immediately challenged – it may simply have been that definitive evidence that he was mistaken was lacking.

The immediate effect of all this was astonishing: for nearly four days Wakefield's alleged misdemeanours were principal item in the national media, led by BBC News. By Monday Wakefield was being condemned in news broadcasts by the Prime Minister, Tony Blair, and the Chief Medical Officer, Sir Liam Donaldson. At first sight the request of the Secretary of State for Health, John Reid, that the GMC investigate the matter looked more moderate, despite its long term repercussions. Effectively though, Wakefield's public reputation lay in tatters – blown apart by Horton, the media, Evan Harris and government politicians – over what was at the very worst a minor failure of disclosure by contemporaneous standards. It was only a week later (Friday 27 February 2004) that the Independent newspaper carried a report pointing out that Wakefield had acknowledged his involvement in the litigation in a letter to the Lancet published just a few weeks after the controversial paper in May 1998, thus apparently giving the lie to Horton's claim. However, no one was listening and the BBC refused to broadcast a correction. That very evening news came through that a High Court judge had upheld the Legal Service Commission's decision to withdraw funding for group litigation in the MMR case. Within the space of 8 days a double hammer blow had been delivered to those trying to establish the facts about MMR, bowel disorder and autism.

The GMC investigation, instigated by a government politician based on the complaint of a journalist, and supported by no parent took more than three years to prepare. By 2006, the medical and political establishment, were apparently getting cold feet. Editorials appeared in the Independent, New Scientist and British Medical Journal calling for the long delayed hearing to be abandoned. Nevertheless, it was clear by the end of that year that the GMC were determined to steam ahead, and the hearing was being scheduled for July 2007. However, in May 2007 after journalistic enquiries the GMC were at least forced to withdraw the panel chairman Prof Denis McDevitt, who by a strange coincidence had sat on the government committee that had originally passed MMR as safe for use in 1988 (not only that, the Urabe 9 version which had to be withdrawn across the globe because it gave rise to cases of mumps meningitis).

Then, on the eve of the hearing Brian Deer revealed a final item on the charge sheet. Following some facetious remarks by Wakefield at a seminar in 1999 he stood accused of taking blood samples from young children unethically at a birthparty for use in a study.

When the hearing sits it takes place in a large rectangular room in a modern office block, with a window down one side. Most of the space is taken by about 20 or so desks arranged in a quadrangle. At the near end as you go in there are about 20 seats for visitors (journalists, members of the public). The Fitness to Practice Panel, Chairman Dr Surendra Kumar, sit on the window side on the left, with their professional advisor, the legal assessor. The defence teams are on the left, the prosecution inhabit the far end, and the witness desk is centrally placed at the near end – witnesses give evidence facing away from the public.

As the hearing has wound on journalists have come and mainly gone. Supporters of the doctors come when they can, but even the 20 seats are generally sparsely inhabited – only two men (who are scarcely on speaking terms) attend regularly: Brian Deer and Martin J Walker. Over the first 16 months of the hearing, Walker has managed to report copiously – overwhelmingly the evidence and the incidents are such that they support the defence case – and very little has been heard from Deer, nothing in fact at all while the prosecution presented its case between July and October last year. No one knows who pays him, if anyone. This year occasional reports of peripheral incidents have appeared on his website: if there was anything more substantial there is no doubt he would tell the world.

There are many factual confusions in the prosecution case, but the most fundamental point that they have never grasped, or have tried to deny for their own purposes, is that the 12 children being examined in the Lancet study were ill, and had been referred to the paediatric gastro-enterology department of the Royal Free Hospital in London, which was the only service of its kind, because they were ill. Even the UK National Autistic Society, which has been no friend to Wakefield, warned prior to the hearing that there was a problem here:

The National Autistic Society (NAS) is keenly aware of the concerns of parents surrounding suggested links between autism and the MMR vaccine. The charity is concerned that the GMC hearing, and surrounding media coverage, will create further confusion and make it even more difficult for parents to access appropriate medical advice for their children.

It is particularly important that this case is not allowed to increase the lack of sympathy that some parents of children with autism have encountered from health professionals, particularly on suspected gut and bowel problems. Parents have reported to the NAS that in some cases their concerns have been dismissed as hysteria following previous publicity around the MMR vaccine. It is crucial that health professionals listen to parents' concerns and respect their views as the experts on their individual children.

There is an urgent need for further, authoritative research into the causes of autism, to improve our understanding of the condition, to respond to parents' concerns and to enable us to ensure that there are appropriate services and support in place to meet people's needs.

So far, the GMC have come up with no plausible reason why two experienced specialists like John Walker-Smith and Simon Murch would have ordered or carried out invasive tests into children who were in good health (Wakefield being a researcher who took no part in clinical decisions). Deliberately or otherwise, the GMC have confused the protocol for a study which was never conducted: 'A new paediatric syndrome: enteritis and disintegrative disorder following measles/rubella vaccination' with the small case series study 'Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children' (the Lancet study). Meanwhile, they have sought to maintain either that no ethical permission was obtained for the investigative procedures, or that the clinical ground on which ethical permission were granted for the investigative procedures on the children in the study were fabricated (though Walker-Smith, Murch and several people brought forward by the prosecution who were also involved in clinical decisions had no possible motive for this, even if ostensibly Wakefield did). By fancifully denying the very existence of the symptoms of the children the GMC are demonstrating how vulnerable the political and medical establishment is over MMR if they were ever properly confronted.

Unfortunately, the only real conclusion to be drawn from these events is that if you have a lazy, intimidated media, bullied and fed by the British government and pharmaceutical lobbyists, it does not really matter if the case does not hang together – the GMC can do anything it likes. Who, after all, is watching?

John Stone has an autistic son, and lives in London. Martin J Walker's continuing account of the GMC hearing can be read at: http://www.cryshame.org/