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When JD Salinger's death was announced on Thursday evening, a three-minute item on public trust in science slipped out of the Newsnight running order. So here is what I was preparing to say:

The doctor whose research 12 years ago sparked the MMR vaccine controversy, Andrew Wakefield, faced what some called his "judgement day" at the (GMC) on Thursday afternoon.

The case raises far-reaching questions over how science is conducted, adding to those already swirling around over climate change research.

Science, how it is carried out and how it is reported, is under scrutiny. Some say it is about time.

Last year's e-mail release from the (UEA) raises questions about how open scientists are prepared to be when questioned by critics.

The information commissioner said this week that the unit had breached freedom of information laws by failing to respond to Freedom of Information requests, but says it is too late to prosecute.

The withholding of climate data is already being examined by an inquiry set up by the university, and chaired by Sir Muir Russell. There were calls on Thursday for this to be held in public.

And then there's "glaciergate" - evidence that the speed of Himalayan glacier melt has been seriously misrepresented in a report from the Intergovernmental Panel of Climate Change (IPCC).

It is profoundly worrying that it took three years for this issue to emerge, especially since the IPCC proudly proclaims its reports to be "peer reviewed", and therefore trustworthy.

The Wakefield case raises fresh questions. How rigorous are ethical checks on medical research? Who pays for the science we all read about? And again, questions over peer review, and just how robust this process is, given its aim of questioning new science before it is published.

The GMC panel looked into the circumstances surrounding research on 12 children, published in medical journal in 1998.

The liberal democrat MP Evan Harris is on the House of Commons' science and technology committee. He thinks the original Lancet paper should never have been published, and that the fact that it was means peer review failed.

"We need to look at peer review, because while it's far better than nothing, it is not perfect, and when it fails it gives claims made under peer review the imprimatur of being properly done, research being conducted properly, and there being sufficient oversight by other scientists of that work.

"So the stakes are very high and I think there's more that can be done to make sure that peer review is as fraud-proof or lazy-proof as possible. I just wish that either the science minister or one of the select committees would take this issue seriously, because it's in the interests of everyone, scientists and the journals and the public, that they can have faith in peer reviewed work."

It is hard to imagine how the GMC panel's findings could have been more damning.

It concluded that Dr Wakefield had carried out research without proper ethical approval, had shown "callous disregard" for the distress of children at a birthday party for his son, at which he had taken blood samples for his research, and that he had been "dishonest" in how he had presented his science to The Lancet.

The panel also found that his actions brought the medical profession into disrepute.

Having concluded, as it has, that Dr Wakefield's actions could constitute serious professional misconduct, the panel will now decide if his actions did constitute serious professional misconduct, and if so, what sanctions to impose.

The most serious of these is that he could be struck off.

Dr Wakefield made a brief statement: "Naturally I am extremely disappointed by the outcome of today's proceedings. The allegations against me and against my colleagues are both unfounded and unjust - I repeat, unfounded and unjust - and I invite anyone to examine the contents of these proceedings and come to their own conclusion...

"It remains for me to thank the parents, whose commitment and whose loyalty has been extraordinary, and I want to reassure them that the science will continue in earnest."

But Evan Harris thinks that the Wakefield case raises serious issues over the ethics of medical/scientific research:

"Even though it's 12 years after paper was published, I'm not sure we've learned all the lessons. I think that journals looking at studies done on human subjects should ask to see the research protocol - that's the plan giving ethical approval - and compare it to what actually happened as described in the paper.

"That way I think we will pick up on other people playing fast and loose with research ethics in this area. It does slow down researchers to make sure they get everything approved, but I think it's vital ethically and to keep the confidence of the patients that their wishes are being protected."

The GMC panel stressed that the Wakefield case is not a judgement on the MMR vaccine, and any supposed link with autism or bowel disorders. But both sides clearly see it that way.

There were extraordinary scenes outside the GMC, parents with anti-vaccine banners and a campaigner with a loudhailer suggesting the public look more critically at the role of the pharmaceutical industry in the UK's vaccine policy.

At the same time, many of the UK's major medical and scientific institutions re-issued a statement to coincide with the GMC announcement. It said that they believe that the MMR vaccine protects the health of children, and that "a large body of scientific evidence shows no link between the vaccine and autism".

Later, I spoke to David Thrower, a father of an autistic child he believes was damaged first by a single measles vaccine, and then by MMR. He has profound concerns about the state of science today:

"I think that whether there's confidence or not in the vaccine is not the point. The point is that people need to have confidence in science, and they need to be confident that the science is independently funded and independently reported and at the moment I just don't think we have that.

"I think scientific research has more or less now been colonised by the drugs manufacturers or it comes from government, there's no longer any independent money going into this issue and until we get that, we won't get any further forward."

at the (GMC) on Monday.

Dr Robert Trossel has already been suspended, so cannot practise as a doctor in the UK. He could be "struck off" if the GMC panel finds against him.

He faces allegations, read out at the hearing, of making false claims about stem cell treatments to nine patients suffering from multiple sclerosis, all of whom will give evidence over the coming weeks.

The GMC said on Monday that its witnesses will describe how Dr Trossel's treatments, costing thousands of pounds, left them with only short-lived improvement or no benefit whatsoever.

The GMC alleges that Dr Trossel's actions were not justifiable on the basis of available scientific or clinical medical evidence, inappropriate, not in the best interests of the patients, exploitative of vulnerable patients, false, misleading, dishonest, and an abuse of his position as a doctor.

FBI hunt

Dr Trossel admitted on Monday that in February of last year he was sentenced to five months imprisonment (which was suspended for three years), and fined 4,000 euros, after falling foul of Belgian law over a stem cell clinic there.

Newsnight uncovered Dr Trossel's link with this clinic as part of a series of investigations into his stem cell "treatments".

The GMC panel heard that a number of the patients reached Dr Trossel after contacting a company called Advanced Cell Therapeutics (ACT).

Newsnight established in that ACT was run by a couple called Stephen van Rooyen and Laura Brown, who are still wanted by the FBI for stem cell fraud under an extradition arrangement with South Africa.

Desperate

The GMC's witnesses, all of whom have agreed to be named, include Deborah Sandford, who suffers from multiple sclerosis (MS).

.

The couple had heard about the "treatment" in the New Pathways magazine for MS sufferers, and were desperate for help.

They saw the Newsnight item in August 2006, but decided to keep their scheduled September appointment.

They taped their conversation with Dr Trossel, and at that appointment he gave them a "certificate of analysis" for the stem cells he had intended to use in Mrs Sandford's treatment.

This certificate stated that the cells were not intended for use in humans.

Dr Trossel admits this, but denies that this stem cell treatment was unjustifiable on the basis of available scientific or clinical medical evidence, inappropriate, not in the best interests of the patient or exploitative of a vulnerable patient.

Checks and balances

The Newsnight team had already filmed a vial of stem cells at the PMC clinic with a label indicating that they came from a company called AllCells in the US, and established that they were intended only for research purposes.

They had not passed the usual checks and balances required before being injected into people.

Monday's hearing was told that another patient, Tracy Wagstaff, also saw the Newsnight item in August 2006 and contacted Dr Trossel's son who assured them that he was no longer involved with ACT, and that he was taking legal action against them.

The GMC said Ms Wagstaff had been left feeling "cheated and terribly upset".

In a slightly surreal twist, the hearing was also told that Dr Trossel was cautioned by police for making off without paying a parking bill at Stansted airport of £472.50 - a charge he admitted.

The hearing is expected to last until early March, with the defence beginning their case in early February.

I asked Dr Trossel for an interview at the hearing today, and he said he had received my request.

The head of his legal team also told me that they would "be in touch".