The BSE saga has provided the unseemly picture of a government hiding behind the white coats of science.

Scientists critical of the Government have been enjoying a field day over the latest BSE findings and the mad cow disease scare they unleashed. The row seems uncomfortably similar to previous official reluctance to accept the danger to people's health from radiation or lead in petrol, or, in the case of soldiers returning from the Gulf war, to acknowledge the existence of the disease that has afflicted them and cooperate with research into its origins.

The critics' case is easy to make. The Government makes a habit of ignoring early warning signals from independent scientists about hazards posed to humans, they say. And it chooses to take advice from a small group of hand-picked experts, particularly from those who think there is no problem. Otherwise, why was Harash Narang - a microbiologist with the Public Health Laboratory Service who linked Creutzfeldt-Jakob Disease, which destroys human brains, to BSE-infected meat back in 1990 - unable to secure government funding for his research? Why was Stephen Dealler, another microbiologist, dismissed as a scandalmonger? "Unfortunately you can pick the people who will tell you want you want to hear," says Dr Dealler, who works at Burnley General Hospital. "I'm afraid the people the Government picked were the people who were going to tell you 'Don't worry about it'."

The truth is probably less conspiratorial. John Webster, professor of animal husbandry at Bristol University, believes the reason the Government did not listen to critics about BSE was because no one knew anything for sure about the new disease. "It is perfectly simple to come up with hypotheses," says Webster. "The essence of a good scientist is not that you have bright ideas but that you can test them before throwing them out to an unsuspecting public."

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Sometimes scientists who want to do research find it hard to get the relevant information from the Government. Five years after the Gulf war began, Goran Jamal of the Institute of Neurological Studies at the Southern General Hospital in Glasgow went public last week with research on 14 Gulf war veterans with Gulf war syndrome. They have neural damage which control subjects did not have. Jamal suspects that a chemical they were given before the war, NAPS, may be to blame.

Jamal did not find out about the veterans from the Ministry of Defence: he had to go to the Gulf War Veterans Association. And his funding did not come from the MoD - it came from the Joseph Rowntree Charitable Trust and the Polden Peckham Charitable Trust. And he never managed to find out some crucial facts like the dose of NAPS that the soldiers received: "We have very little information. It is the sort of thing we all need to find out."

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He now wants to move beyond his pilot study to a large controlled trial. This will require the cooperation of the MoD, he says. "A lot of the data concerning the circumstances is in the hands of the official authorities." Whether the initiative goes ahead, he says, is in the MoD's hands.

It is another example of the vexed relationship between scientists and the Government. Even when the data is made available, uncertainty pervades science. Scientific answers are often couched in terms of statistical probability. The critical problem for government is translating such uncertainties into the certainties of public policy. At what point does a scientifically small risk to public health become unacceptable and why?

Robin Grove-White, director of the Centre for the Study of Environmental Change at Lancaster University, puts it another way. Science only gives one limited answer to each specific question asked, and there are no easy political answers. Advanced industrialised countries are entering a new phase in which the main actors, for example, the farmers or the animal feed industry, are constantly generating new risk, he says. Regulators and government are desperately trying to catch up with all this change.

In the case of BSE, there is concern among scientists that the public simply does not understand how tiny the risk is of becoming infected with mad cow disease. Fred Warner, who conducts research on nuclear weapons and is a visiting professor at Essex University's Scientific Committee on Problems of the Environment, says the Royal Society has been trying to do something about people's perception of risk for years. It has produced books, and met with social scientists and government - all to no avail. "We're in complete despair," he says. "If you look at the risks, you are more likely to be killed when you go out of your front door by a motor car than by mad cow disease."

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He might have added that at almost exactly the same time as the beef panic broke out the World Health Organisation warned of a new worldwide TB epidemic. Despite the much greater likelihood of contracting TB, nobody seems to have noticed.

Someone who has nothing to do with BSE but identifies with the researchers left out in the cold is John Cheshire, who works at the Science Policy Research Unit at Sussex University. His research into the economics of nuclear power was out of favour during the 1980s because it suggested nuclear power was expensive and therefore not viable. "We were seen as wild men, as oddballs," he explained. "The question was 'Are you one of us?' And in some ways we were not."

The marginalisation of his research had nothing to do with academic quality, according to Cheshire. It was simply that during the 1980s his perspective went against the grain. Sensibly, Cheshire did not take it personally, though he did feel excluded from committees.

Cheshire is phlegmatic about his experience and believes it is in the nature of scientific discovery and its relationship with the wider world. "There is a mainstream opinion and it changes by degrees," he says. "It can often change quite abruptly. Galileo could have given you some interesting quotes on that."

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Additional reporting by Aisling Irwin, Fred Pearce and Martin Ince.