As civil servants face the BSE inquiry, Fred Pearce reports that experts learned of the disease informally (below) and hears a frustrated, ignored researcher (right)

A sorry story of administrative neglect and politically compromised science is emerging from the continuing BSE inquiry. Over the past six weeks, civil servants and government scientists have been giving their side of the story. A detailed examination of their failings will follow in the autumn. But already enough has emerged for them to be fearful of those sessions. Indeed, some have engaged in pre-emptive strikes to neutralise criticism.

The epidemic of bovine spongiform encephalopathy among the nation's cattle became an international scandal in 1996 when a government advisory committee warned that it believed the disease had spread to humans in the form of a new type of Creutzfeldt-Jakob disease. The seeds of this crisis, however, were sown in the mid-1980s, when BSE took hold in British cattle herds and, in all probability, infected humans with CJD. Most evidence so far has concentrated on this period, with scientists accused of failing to recognise or act on evidence of a new epidemic.

Most alarming is the discovery that many top experts on cattle diseases and neuropathology heard of the disease only on the grapevine and after a long delay. It took 21 months for news to reach the government's chief veterinary epidemiologist, whose job it became to find BSE's cause and its pattern of spread.

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Carol Richardson, a junior female pathologist at the government's Central Veterinary Laboratory in Weybridge, Surrey, told the inquiry that she first saw the unusual brain damage characteristic of the group of diseases known as spongiform encephalopathies in a cow in the summer of 1985. She recognised its similarity to scrapie, the spongiform encephalopathy endemic in sheep for many years, and concluded that what she had seen was probably "scrapie in a cow". In September 1985, she reported this to her boss, Gerald Wells, head of neuropathology at the lab. To her surprise, she told the inquiry, her superiors did not act on her findings. Wells explained his apparent complacency. The diagnosis of "scrapie in a cow" was not conclusive, he said. The damage could have been caused by some toxin, such as a pesticide. Moreover, there had been other health problems in the herd from which the cow came. "In the light of these factors the case in September 1985 did not at that time suggest that a new disease had been identified," he said, although it had suggested precisely that to his junior.

It was 14 months before Wells began to revise his opinion and concluded that his assistant might indeed have uncovered a bovine spongiform encephalopathy. It was six months more before he shared his thoughts with colleagues at the laboratory and in the Ministry of Agriculture, Fisheries and Food. In May 1987, he broke the news to the government's chief veterinary officer, Howard Rees, and John Wilesmith, head of epidemiology at the laboratory. On June 5, junior agriculture minister Donald Thompson was notified. The threat was thought sufficiently important for him to interrupt the last week of a general election campaign.

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The delay did not go down well. Wilesmith told the inquiry he wished he had been consulted earlier. But once involved he worked fast to uncover the cause of the disease. By the end of 1987, he had deduced that it must have come from the meat and bone meal in cattle feed. He concluded from an analysis of the spread of the disease that the infectious agent had probably begun to reach the nation's cattle in the winter of 1981-82, shortly after feed-processing methods had changed in many rendering plants. The biggest changes were a reduction in the use of steam treatment and solvents used to extract the most tallow. Wilesmith concluded that these processes had previously killed the scrapie agent.

These conclusions, which remain the conventional wisdom of the BSE story, eventually led to stringent regulations on animal feed that are still in place today. Several witnesses commended the speed of Wilesmith's diagnosis. But there has also been harsh criticism of his later actions. In the absence of a defence from his superiors, he is in danger of becoming the scapegoat for the entire debacle.

One of Wilesmith's earliest steps was to try to model the outbreak statistically. His prognosis that there might be at most 20,000 cases of BSE proved hopelessly optimistic, as cases soared above 100,000. This work has been heavily criticised. Earlier in the inquiry, Roy Anderson, one of the country's top epidemiologists, attacked the secrecy and "amateur" approach of Wilesmith's unit. Anderson accused the unit of having caused a six-year delay in tackling the crisis. In particular, he said, its refusal to divulge raw data stopped him making calculations that would have revealed that cattle-feed regulations were being flouted - allowing BSE to continue to infect herds.

And Sir Richard Southwood, the zoology professor from Oxford who led the first inquiry into BSE in 1988, attacked Wilesmith's prognosis. He told of his frustration at a "marked tendency to be optimistic."

Wilesmith, he said, had assured his inquiry that there was no risk to human health. When Southwood produced his back-of-the-envelope calculation of the disease's likely progress, Wilesmith dismissed it as "much too high". Southwood was proved right. Wilesmith, to whom Southwood initially bowed on the matter, was proved badly wrong. In his evidence, Wilesmith has tried to defend his work. There was at the time, he said, a dearth of expertise in the field of veterinary epidemiology. It was barely taught in universities and not at all at postgraduate level. He now distinguishes between his simulation studies and his advice to Southwood. His analysis, he said, was a "simulation" not a prediction. It was "performed simply toI understand better the dynamics of what could have occurred in the exposure of the cattle population, and hopefully rule out at least the more extreme epidemiological scenariosI. The simulation was never designed to be a sophisticated mathematical model or a means of predicting the number of cattle that would develop BSE in the future". He added: "It is unfortunate that some appear to have misrepresented this simulation and the result arising from it."

There has been conjecture that Wilesmith may have suspected that BSE had emerged from a single cattle-feed rendering plant. He was pressed hard on this point by the inquiry, and in particular on whether he was "constrained by the sensitivity of all this" not to name names.

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Wilesmith responded that he had not wanted to become involved in a "witch-hunt". In any case, a single guilty renderer would have been hard to pin down. Calves routinely receive different feeds, often from different suppliers. Farmers regularly change suppliers as they shop around for cheap prices, and animals move around the country. Even from a single source, he said, the disease could have spread around the country in "less than a year". The track to a single renderer would have been very difficult to follow.

His laboratory only recently began systematic research to establish whether the source was a single geographical area or even a single renderer. This work, Wilesmith said, will parallel that by Anderson, who earlier told the inquiry that he could "produce a model to trace it back to a single source".

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The unease within the CVL and MAFF about the "sensitivity" of BSE in the mid-1980s was underlined by other witnesses. Sir Michael Franklin was permanent secretary at MAFF between May 1987, when CVL scientists first owned up to their concern about "scrapie in a cow", and October that year. He told the inquiry that there was "understandable" concern that "ill-informed" publicity could cause "public alarm" and generate "hysterical demands for immediate draconian measures".

In its approach, MAFF was largely reflecting the concerns and priorities of farmers. This community of interest was probably accentuated by the fact that junior minister Donald Thompson had been a farmer and butcher for 22 years before entering Parliament in 1979. Documents presented to the inquiry reveal that the National Farmers Union was adamantly opposed to the compulsory slaughter of BSE-infected cattle without full compensation from government. In June 1988, the NFU told the ministry it "would prefer to let the disease go through the national herd and hope to live with it" rather than accept uncompensated slaughter.

Both slaughter and compensation were unattractive ideas to a government committed to deregulation and reduced government expenditure in the food industry. As Franklin told the inquiry: "Two of the main features of government policy in the second half of the 1980s were the desire to reduce public expenditure and the belief that the agriculture and food industries ought to bear more of the cost of research and advisory work."

A big concern, supremely ironic given later events, was that government action against BSE might hit beef exports. A confidential memo from the ministry's head of animal health to Thompson in July 1987 said that such action "could alarm other countries and lead them to prohibit imports of cattle, semen and embryos from this country". The published minutes of a meeting with Thompson reveal that the prime concern was to manage publicity about BSE, not to tackle the disease.

The strategy proposed, and apparently adopted, was to acknowledge BSE's existence, announce research and sit tight until more was known. "It would be the concern of the chief veterinary officer not to arouse undue alarm and concern," Franklin said.

The strategy failed, even in its own terms. Efforts to avoid igniting public alarm simply stoked the fires for a bigger conflagration later. When draconian action was finally taken it had to be on a far larger scale - with a price-tag estimated by the National Audit Office at about Pounds 4 billion.

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