Let me recap. Six months ago I reviewed the latest bit of terrorism to emerge from the government’s Cobra bunker, courtesy of Alan Johnson, home secretary. Swine flu was allegedly ravaging the nation. The BBC was intoning nightly statistics on what “could” happen as “the deadly virus” took hold. The chief medical officer, Sir Liam Donaldson, bandied about any figure that came into his head, settling on “65,000 could die“, peaking at 350 corpses a day.

Donaldson knew exactly what would happen. The media went berserk. The World Health Organisation declared a “six-level alert” so as to “prepare the world for an imminent attack”. The happy-go-lucky virologist, John Oxford, said half the population could be infected, and that his lowest estimate was 6,000 dead.

The “Andromeda strain” was stalking the earth, and its first victims were clearly scientists. Drugs were frantically stockpiled and key workers identified as vital to be saved for humanity’s future. Cobra alerted the army. Morgues were told to stand ready. The Green party blamed intensive pig farming. The Guardian listed “the top 10 plague books”.

If anyone dared question this drivel, they were dismissed by Donaldson as “extremists”. When people started reporting swine flu to be even milder than ordinary flu, he accused them of complacency and told them to “wait for next winter”. He was already buying 32m masks and spending more than £1bn on Tamiflu and vaccines. Surgeries refused entry to those with flu symptoms, referring them to a government “hotline” where prescription drugs were ordered to be made available without examination or doctor’s note. Who knows how many died of undiagnosed illness as a result? Lines were instantly jammed. It was pure, systematic government-induced panic – in which I accept that the media played its joyful part.

This week the authorities admitted that, far from a winter upturn in swine flu, there has been a slump. From 100,000 a week at the peak, there were just 12,000 last week. After the coldest winter for decades, when deaths might be expected to rise, the rate is below that of seasonal flu. In the UK, 360 people have died under its influence, most with prior “non-flu” conditions. Swine flu is not nice – I have had it – but bears no ­relation to the government hysteria.

I accept that anyone can make a mistake, and authority has some duty to err on the side of caution. As Alastair Campbell implied on Tuesday, Iraq might have had weapons of mass destruction, so Blair was right to go to war just in case. But it is reasonable to ask, as the Chilcot inquiry is doing, why precaution on such a colossal and potentially ­destructive scale was justified when those who questioned the need for it have since been proved right. Is anyone asking about flu?

Swine flu is not the first time we have suffered this nonsense. I have a stack of predictions by senior scientists on BSE/CJD in 1995. It would “lead to 136,000 deaths” – a spurious exactitude used to convey plausibility – and “could infect up to 10 million Britons”. This led to an obscene £5bn campaign of cattle destruction and compensation. When the prediction proved wildly wrong, the government excused itself with a classic Rumsfeld-ism: “The absence of evidence is not the evidence of absence.”

This was followed by Sars 2003, a “panic gripping the world”. The World Health Organisation declared that “One in four Britons could die”. The medical doom-monger, Dr Patrick Dixon, said that Sars had “a 25% chance of killing tens of millions”, whatever that meant. The madcap Tory health spokesman, Liam Fox, demanded the arrest and quarantining of all recent travellers from Asia, including 30,000 Asian students.

In the event, some 800 people died with Sars worldwide, against 21,000 who died in Britain in the seasonal flu epidemic of 1999/2000.

Undaunted, within a year the same alarmists were at work on avian flu. With now habitual hyperbole, Donaldson predicted 50,000 deaths, with “an upper limit”, graciously conceded, of 750,000. When one dead swan slumped on a beach in Scotland, BBC reporters went crazy as inspectors stumbled through the seaweed, clad in anti-nuclear armour. Within a year the horror had passed. The global mortality was put at 262, with not one death in Britain. Another fiasco was brushed under the carpet.

The Blair government, and now Brown’s, have proved adept at using scare politics to divert attention from other troubles. During foot-and-mouth Blair was quick to don a yellow jumpsuit for photographers and intone as if he alone stood between an illness (that is in fact harmless to humans) and armageddon. This time the swine flu coincided with two other “mystery diseases”, MRSA and C-difficile, which killed 10,000 Britons in 2007 alone. But those deaths lay squarely at the doors of unclean NHS hospitals. Hence there were no scary stories or predictions about them from Donaldson.

Donaldson and his eager virologists will doubtless stick loyally to their predictions since it is “too early to be complacent”. His allies at the BBC did their bit on Wednesday with a Horizon programme that turned a serious study of virology into grotesque scaremongering, with solemn music and voices crying, “there’s no escape”, “this could take a devilish turn”, and “we don’t even know how many viruses there are!” Children writhed in agony from smallpox.

Mad scientist syndrome is rampant. Had these scares been disseminated by a private firm, a local authority or a newspaper (as was anti-MMR), they would be damned from on high with demands that heads roll. As it is, the government’s Scientific Advisory Group for Emergencies sails gaily on, still graced by the presence of Sir Roy Anderson, who ­happens also to draw a six-figure salary as a non-executive director of GlaxoSmithKline, which made hundreds of millions from the government’s panic. Anderson, and GSK, vigorously deny any conflict of interest.

The Council of Europe’s head of health, Wolfgang Wodarg, is one of the few who have dared blow the whistle on the links between “Big Pharma” and national and ­supranational agencies. He this week persuaded the council to stage a debate on the “enormous gains” made by GSK and others from the swine flu pandemic. He seeks details of relations between the companies and the WHO, given that stockpile contracts kick in the moment that ­organisation uses the word “pandemic”. It did so for the first time last year, with reckless alacrity.

I am not aware of the WHO or the General Medical Council or any of the medical colleges investigating these matters, or any check on conflicts of interest of government doctors who work for drugs companies. I am not aware of any Whitehall or Commons committee, any National Audit Office or competition inquiry into the supply of these drugs. All I know is that a huge amount of health money, time and effort was last year diverted from possibly critical therapies into what looked from the start to be yet more terror virology.

This is why people are ever more sceptical of scientists. Why should they believe what “experts” say when they can be so wrong and with such impunity? Weapons of mass destruction, lethal viruses, nuclear radiation, global warming … why should we believe a word of it? And it is a short step from don’t believe to don’t care.

Simon Jenkins’s distaste for scientists leads him to declare that they deliberately overstate risks, and make panic predictions (Swine flu was as elusive as WMD. The real threat is mad scientist syndrome, 15 January). In reality, scientists worked calmly – not “frantically” as Jenkins asserts – to predict the progress of the disease and to understand risk.

Jenkins says of the initial predictions about the spread of swine flu: “The chief medical officer, Sir Liam Donaldson, bandied about any figure that came into his head, settling on ’65,000 could die’, peaking at 350 corpses a day.”

Worst-case predictions are not figures plucked out the air “to convey plausibility”, but result from well-researched computer simulations. Margins of error are high; no one pretends otherwise. Yet Jenkins is delighted when a worst-case scenario isn’t met, as though he were right and everyone else wrong.

There is a genuine debate which we must not overlook. What should the government response be? Does the risk justify the expense of stockpiling vaccine? Is it right to divert funds away from other health matters? But Jenkins doesn’t ask such questions – instead he dismisses it all as “hysteria”. Reasonable advice – alerting morgues, identifying vital key workers – is denounced as “drivel”.

You could argue that media coverage of H1N1 was excessive and that editors think the biggest numbers make the best headlines. But the scientific process has been evidence-based and transparent throughout. At the Science Media Centre we have tried to ensure that responsible journalists have had access to the best scientists. We’ve seen lots of co-operation and very little hysteria.

Science moves by small steps, and as we learn more the picture becomes clearer. This is how official advice on Tamiflu for children was revised. Each time a risk comes along we are better prepared to characterise the next one. But decisions still need to be made early. Picture a beleaguered Simon Jenkins in the middle of a deadly pandemic, decrying the government’s woefully inadequate response and failure to order enough vaccine.

It’s embarrassingly straightforward. Viruses usually don’t mutate into major killers; that’s why there are still people left on the planet. But it has happened before and will happen again. We can’t predict when – that’s what risk is – but we can perform the analyses, educate ourselves and be prepared, all underpinned by evidence drawn from virology and epidemiology. Or we could shrug and say it’s all hype, and most of the time we’d be right. Similarly, most of the times I put on a seatbelt I don’t crash my car.

Jenkins’s logic goes as follows. Once there was a boy who cried wolf, but there wasn’t a wolf. Therefore not only do wolves not exist, but there must be a conspiracy between wolf experts, the lupine risk assessment board and the manufacturers of bite-proof trousers to convince the rest of us that they do.

With swine flu there wasn’t conspiracy and hype; just scientists, patiently performing the analyses, and explaining the possibilities.