Hugh Pennington

Joe Biden’s great-great-great-grandfather, Edward Blewitt, was overseer at the Ballina Union Workhouse in County Mayo from 1848 to 1850 during the Great Irish Famine. Many died in the workhouse and others perished in the temporary fever hospital built against one of its walls. With his family, Blewitt emigrated to Pennsylvania in 1851. He did well, despite the political power of the anti-Catholic, anti-Irish Know Nothing movement, a nationalist and Protestant political party, which in the 1850s had a hundred congressmen, eight state governors, and a controlling position in half-a-dozen state legislatures. Before his job at the workhouse, Blewitt had been an engineer for the Irish Ordnance Survey; in Pennsylvania he helped to lay out the new mining town of Scranton.

Student halls of residence have now joined cruise liners, care homes, meat plants, giant evangelical church gatherings and migrant worker dormitories as Covid-19 transmission hot spots. The US is top of the league table so far. A New York Times survey found that by 25 September, 1300 colleges had been affected and 130,000 students had tested positive. Universities in Scotland start teaching earlier than in the rest of the UK, so here they have led the way, with cases and outbreaks at St Andrews, Aberdeen, Glasgow and Edinburgh. Many other universities in England, Wales and Northern Ireland have followed since.

In 1964 there was a typhoid outbreak in Aberdeen caused by contaminated corned beef from Argentina. Opinion among older Aberdonians is sharply divided about Ian MacQueen, the local medical officer of health. Some say he saved the city. Others say he did more damage than good. Dr MacQueen ran daily press conferences. At the beginning he said the outbreak was under control and the number of cases would be small. Then, as case numbers continued to rise, he started doom-laden talk about a second wave, and predicted as many as 40,000 possible cases. But as case numbers fell, his waves turned into a series of wavelets. At the end of the outbreak, 507 cases had been diagnosed. There were no waves, or even wavelets. Three people died, none of typhoid.

Pharmacopoeia raiders are busy, looking for Covid-19 remedies that might be hiding in the long list of tried, tested and safe drugs. I did this for smallpox a long time ago, when it was discovered that the antibiotic rifampicin blocked its growth. It turned out that the effective dose was far too high to be useful. The smallpox strain I used in this work was called Butler. It had been isolated in Rochdale during a big outbreak in 1952. Most of the 138 cases had never been vaccinated. Nobody died, because the causative virus was variola minor, very closely related genetically to classical smallpox – variola major – but very different in its clinical effects: v. minor with a case fatality rate in the unvaccinated of less than 1 per cent and v. major with a rate higher than 20 per cent. 

Covid-19 has made A&E departments very quiet. I worked in the one at St Thomas’s Hospital when it was called Casualty. Undressing a homeless patient once caused the centrifugal escape from his clothes of a shimmering sheen of lice, hundreds of them. Sister Cas was called. She rolled up her sleeves and said: ‘This reminds me of Dunkirk!’ Most lousy people have only a handful. The best quantitative study of lousiness was done by Alexander Peacock, an RAMC entomologist, in the trenches on the Western Front in the First World War. He found that 95 per cent of the soldiers were infested, more than 60 per cent with 20 lice or fewer, but 2.8 per cent – he called them ‘horrible examples’ – had more than 350 on their trousers and shirts. This pattern of distribution, in which most of a human population’s parasites are concentrated in only a few individuals, is very common. Statisticians call it ‘overdispersion’.

More than sixty years ago, puffing on an untipped Senior Service (we were allowed to smoke in those days) to cover up the reek in a dissecting room at St Thomas’s Hospital, I was struck down by a pandemic virus that had recently evolved in China. By the time I fell ill (its onset was very sudden) the virus had already killed more than 20,000 people in the UK, with 1150 dying every week at its peak, and 80,000 in the US. In the first UK wave, more than half the deaths occurred in the under-55s. It went for the elderly later, in its second wave. It killed quickly: nearly 20 per cent of its younger victims died before getting to hospital and two-thirds were dead within 48 hours of admission. But it has been airbrushed out of history, despite being by far the most lethal pandemic to affect Britain at any time in the hundred years after the ‘Spanish’ flu pandemic at the end of the First World War.

The emergence of a new coronavirus in Wuhan at the end of 2019 has not been a virological surprise. New coronaviruses causing respiratory infections have been detected from time to time since SARS (which was a surprise) in 2002-3; MERS came in 2012. How ‘new’ these viruses are is debatable.

In 2004 I described the basis of attacks on the MMR vaccine as ‘unsubstantiated speculation masquerading as science’, and finished the piece: ‘I despair.’ Measles is now busier in Europe than it was fifteen years ago.

‘Chlorinated chicken’ is pejorative. Chlorine gas doesn’t come into it. The meat isn’t bleached. Poultry carcasses are washed with dissolved antimicrobials such as sodium chlorite, chlorine dioxide and trisodium phosphate. The EU banned it in 1997, not because the washes leave the meat dangerous to eat but because it might incentivise poultry producers and processors to give hygiene a lower priority. This argument was used in the 1930s by opponents of milk pasteurisation.

A recent review by scientists in Australia of 73 historical studies of insect decline concluded that insect biodiversity is threatened worldwide, and 40 per cent of insect species are threatened with extinction over the next few decades. But there is a puzzle. The classes that are declining fastest are butterflies, bees and dung beetles. No one is going out of their way to eliminate them. Other insects that we attack deliberately and for which extinction would be a cause for celebration are doing well.

Romaine lettuce in the US is currently under the cosh of a Food Safety Alert: don’t eat it, whether head or heart or baby; don’t sell it; and don’t eat ready-mixed Caesar salad, which contains it. Contamination with E. coli O157:H7 is the reason. An outbreak started in October, with 50 cases across 11 states, as well as in Ontario and Quebec, with 13 in the US admitted to hospital. The lettuce may have been grown in California, unlike the produce that caused the first romaine outbreak this year, which was grown in Yuma, Arizona. That outbreak lasted from March to June, and was the biggest E. coli O157:H7 outbreak in the US for many years, with 201 cases (96 hospitalised) and five deaths.

The UK has the highest incidence in the world of poisonings caused by the toxins produced by E.coli O157:H7. It killed 17 people in the outbreak centred on Wishaw in central Scotland in 1996, still a world record for lethality. My involvement in attempts to stop a repeat led to an invitation to visit the Defence Science and Technology Laboratory at Porton Down. Security was impressive. The heavily armed welcome at the gate left an abiding memory. It is reasonable to guess that the Russian chemical warfare facility at Shikhany is as well guarded. The notion that nasty substances of high purity could leave it without some kind of authorisation seems highly unlikely.

Oxfam is in serious difficulties. It is reasonable to speculate that the hard time it is being given by the international development secretary, Penny Mordaunt, is due to the workings of Miles’s law - 'Where you stand depends on where you sit' – in that it reflects forces in the British government and the Tory party hostile to the foreign aid programme. I sit as a microbiologist, and see the harmful events in Haiti following the arrival of foreigners after the 2010 Port-au-Prince earthquake very differently, both from a quantitative and from a political point of view.

Some reviewers of the film Goodbye Christopher Robin are saying that A.A. Milne had post-traumatic stress disorder. Yes, he was at the front during the Battle of the Somme; in August 1916 he was a signals officer there, and worked in no man’s land. But PTSD didn’t send him home. He was brought down by trench fever (bartonellosis). A bacterial infection spread by body lice (not those of the head or pubes), it causes a high fever, which repeats itself a few times every five days. It doesn’t kill, but sometimes leaves its victims feeling weak for many months. This happened to Milne. After being invalided home, he lost weight and developed fatigue, said to be caused by ‘overwork’, but much more likely due to the persistent effects of Bartonella quintana. In the early autumn of 1917 he spent three weeks at Osborne House on the Isle of Wight, then a convalescent hospital for officers.

I lived for several years on the 10th floor of a tower block in Cumbernauld. It swayed a bit in the wind, but had been strengthened after the Ronan Point disaster. Ronan Point in Canning Town was built from large prefabricated concrete panels. Ivy Hodge was one of its first tenants, moving into a corner flat on the 18th floor on 15 April 1968. At 5.45 a.m. on 16 May, she struck a match to light her gas cooker. A friend had fitted the cooker. He tested for leaks using a lighted match, but had used a substandard nut, and there was a leak. The explosion blew out the external load-bearing walls of her living room and bedroom. The corner walls of the flats above collapsed and fell. Their weight took out all the corners of the flats below. Four people were crushed to death.

The ‘much loved’ status of red squirrels in Britain probably won’t be damaged by the discovery that some of them are lepers. The finding that individuals on Brownsea Island are infected with a leprosy bacterium with a DNA sequence close to that of one circulating in medieval England seems unlikely to provoke significant concerns for public health, either. We don’t hunt, skin, eat or cuddle red squirrels so the opportunities for transmission are remote.

The announcement on 26 October that the Wellcome Trust, the Gates Foundation and the UK, US and Brazilian governments will spend $21.7 million over the next two years releasing Aedes aegypti mosquitoes infected with Wolbachia in Rio de Janeiro and Medellín is excellent news. Wolbachia, a bacterium that lives in the reproductive systems of insects and worms, is one of the commonest parasites in the world. In some of its invertebrate hosts it either kills males or feminises them. For others, infection with it is essential for fertility. Discovered in 1923 in the ovaries and testes of mosquitoes from Boston and Minneapolis, it remained an entomological curiosity for half a century before its importance began to be realised. Now it has its own website, and the Anti-Wolbachia Consortium, A-WOL, is funded by the Gates Foundation.

When a war goes wrong, a longstanding British political habit is to establish an official inquiry. They take many forms. Florence Nightingale used the Royal Commission on the Health of the Army (1858-62) to promulgate her views after Crimea. The Second Boer War engendered nearly as many fat volumes as Chilcot. Several covered ‘The Military Preparations … the supply of Men, Ammunition, Equipment and Transport … and Military Operations’, others ‘The Care and Treatment of the Sick and Wounded’. The Elgin Commission took evidence from the military commanders, and the secretary of state for war set up an expert commission to investigate dysentery and enteric fever.

Since I wrote about Zika in February, genome sequencing has shown that the virus has three lineages: West African, East African and Asian. Analysis of a 1966 Malaysian strain and a 1968 Nigerian one point to an Asian origin for the Brazilian viruses; it is likely that Zika has been circulating in Brazil since 2013. The virus has been evolving in expected ways (its RNA genome has a high mutation rate); no change that could account for an enhanced ability to damage the brain has yet been found. None of these findings has hit the headlines.

In 2014 the prime minister commissioned Jim O’Neill to conduct a review and make recommendations to ‘defeat the rising threat of superbugs’. O’Neill’s final report, published on 19 May, predicted that superbugs could kill 10 million people a year by 2050, the equivalent of one person every three seconds, more than cancer, with a cumulative cost of around $100 trillion.

In its last week in print, the Independent carried a piece under the headline: ‘One more thing imperialism has to answer for: dysentery.’ It’s a striking statement, but is it true?

The persistence of Ebola virus transmission in Sierra Leone, Liberia and Guinea took everyone by surprise. Previous outbreaks had lasted only weeks. The World Health Organisation’s response to Zika in South America has been significantly influenced by criticisms of the speed of its response to the events in West Africa. But a recent note in the Morbidity and Mortality Weekly Report from the US Centers for Communicable Disease Control and Prevention is a reminder that the absence of virologists, public health doctors and nurses wasn’t the only reason for the size of the Ebola epidemic.

‘It is too early to say whether those responsible for Alexander Litvinenko’s end intended its cause to be discovered,’ I wrote in the LRB nine years ago. ‘A lingering death caused by a painful poison unknown to science sends out a powerful message.’ The evidence presented to Sir Robert Owen’s Public Inquiry Report, published on 21 January, is clear. The plotters of Litvinenko’s death intended its cause to remain a mystery.

On 18 April 1947 in a cage on a tree platform in the Zika Forest in Uganda, rhesus monkey number 766 developed a fever. Its serum was inoculated into the brains of mice. They fell ill. Zika virus had been discovered. The sentinel monkey researchers were the virologist George Dick and the entomologist Alexander Haddow, based at the Rockefeller Foundation Yellow Fever Laboratories in Entebbe. Haddow went on to build a 120-foot steel tower in the forest to study high-flying mosquitoes and their viruses. The best time and place to find Zika virus was in the evening, 80 to 100 feet above the forest floor.

Shares in the Nahl Group, part of the ‘no win no fee’ legal industry, fell by 25 per cent overnight after the chancellor of the exchequer announced in his autumn statement that the government ‘intends to introduce measures to end the right to cash compensation for minor whiplash injuries’. He also said that the government would be consulting on the details and expected average savings of £40 to £50 per motor insurance policy to accrue. In 2012, the Ministry of Justice characterised the UK as ‘whiplash capital of the world’. In 2012-13 there were 476,938 claims for whiplash, making up 58.2 per cent of all road traffic accident personal injury claims. The quick jerk of the head caused by the sudden stop of a vehicle can cause real injury. But in cases of minor whiplash the diagnosis relies on symptoms alone. This is the problem.

A police helicopter crashed into the Clutha Vaults Bar in Glasgow on 29 November 2013. The pilot, two police officer passengers and seven in the bar were killed. The Air Accidents Investigation Branch published its final report last week. Relatives of those who died had been briefed in advance. They said that they were doubly disappointed.

With the exception of the novels he serialised in them – Hard Times, A Tale of Two Cities, Great Expectations – the contents of Charles Dickens’s weeklies Household Words and All the Year Round have mostly been forgotten. But the lucky purchase by the book dealer Jeremy Parrott of a bound set of All the Year Round with handwritten marginalia identifying nearly all the anonymous contributors of its 2500 articles, stories and poems has generatedmuchexcitement. The handwriting seems mostly to be Dickens’s own, and names Elizabeth Gaskell, Wilkie Collins and Lewis Carroll among many others: the speculation is that the bound set was Dickens’s file copy, which he kept in the flat above the office. Whether the number of general readers will increase – in spite of the complete availability of both weeklies’ contents online – is hard to say. It would be a great pity if it didn’t. Although the articles were written a century and a half ago, they covered many issues that still trouble us, and show that what we tend to think of as new and malignant manifestations of modernity are anything but new.

The Morecambe Bay Investigation, chaired by Bill Kirkup, published its report on 3 March. ‘The name of Morecambe Bay,’ it says, ‘has been added to a roll of dishonoured NHS names that stretch from Ely Hospital to Mid-Staffordshire.’ The report isn’t about the town of Morecambe, but deals with the dreadful things that happened for nearly a decade across the bay at Furness General Hospital (FGH) in Barrow, part of the University Hospitals of Morecambe Bay Trust.

There’s been excitement this week at the announcement of a new antibiotic. Called teixobactin by its discoverers, it is produced by a soil bacterium, also new to science because it needed the development of a novel system to enable it to grow and be tested in the laboratory for antibiotic production.

The Vale of Leven Hospital Public Inquiry report was published on 24 November. At least 34 patients had been killed by Clostridium difficile in 2007 and 2008 in the hospital in Alexandria, a small town at the foot of Loch Lomond. The report tells one horror story after another about bad nursing, ignorance about infection and management incompetence. The failings beggar belief.

The current Ebola virus outbreak in Guinea, Sierra Leone and Liberia is the biggest ever in terms of fatalities, geographical distribution and duration. A person sick with it flew from Liberia to Nigeria, the most populous country in Africa, from which many travellers arrive in the UK every day. So it was no surprise to hear that COBRA has met. Announcing that it has met is in itself crisis management: ‘We are aware of the problem and something is being done.’

Sooner or later the Brazilian football team will be treated like lepers, or perceive themselves to be so. Unfair to lepers, but appropriate for an off-pitch reason. The official World Cup mascot, Fuleco, is a Brazilian three-banded armadillo. Humans apart, the armadillo is the only animal that gets leprosy. Admittedly, the evidence refers to the nine-banded kind; it is not known whether the three-banded armadillo is susceptible. It would be very hard to find out, because the Brazilian species is very rare and in danger of extinction. Fuleco's name is a portmanteau of ‘Futebol’ and ‘Ecologia’.

Bacillus cereus has infected premature babies in London, Brighton, Peterborough, Cambridge, Luton and, possibly, Southend and Basildon. One has died. Contaminated intravenous nutritional food was the route of transmission. Bacillus cereus is everywhere. Its natural home is soil, water and vegetation, and it is found in most raw foods, particularly cereals. It produces tough spores, which are heat resistant (they survive boiling), and toxins.

A cluster of nine cases of tuberculosis in cats in Newbury at the end of 2012 and early 2013 spread to their human owners, causing serious lung disease in two of them and infection without disease in another two. Unsurprisingly, when the results of the investigation were published, it became a top news story. It would have been an even bigger one if it hadn’t had to compete with Ebola in Guinea. TB in domestic cats is not new.

The government blame game about the floods is in full spate. Eric Pickles is a penitent convert to dredging. ‘For every complex problem there is an answer that is clear, simple and wrong,’ H.L. Mencken said. The Somerset Levels have been flooding regularly since well before the Domesday Book. Pumping has been going on for almost 200 years. But once the media have got a grip, scapegoats must be found. I expect that a Public Inquiry will be announced soon, ostensibly ‘to get to the truth’ but really to kick everything into touch.

Rukshar Khatoon, from Sahapara, Howrah District, West Bengal, has joined Saiban Bibi, a Bangladeshi beggar living on a platform of the railway station at Karimganj, Assam, and an unnamed cow grazing in Tamil Nadu, as markers of the success of vaccination programmes in India, successes which confounded all the critics. Rukshar was 18 months old when she developed paralytic polio in January 2011. Saiban was 30 when she developed smallpox on 24 May 1975. The Tamil Nadu cow developed rinderpest in September 1995. All three diseases are now extinct in India.

Horse sold as beef led to Chris Elliott’s review into the integrity and assurance of food supply networks. His interim report was published on 12 December. The proposed ‘food crime unit’ gripped the media. It’s a good idea. But not as good as the idea for a ‘legally privileged information gathering facility’ run by industry, separate from government. Elliott could have called it a ‘clype unit’ if he’d used his Ulster Scots. A clype is a tell-tale. The facility would be a safe haven for industry to share suspicions, even gossip, while protecting commercial confidentiality.

The UK fossil fuel extraction industry has always been dangerous for its workers, even if things are orders of magnitude safer today than they used to be. In 1938, 858 coal miners were killed in accidents, including 90 in explosions, 408 by roof falls, 194 in haulage and transport accidents underground, and 76 on the surface. Others died from Weil’s disease caught by contact with rat urine. Thousands developed pneumoconiosis, and paraplegia from roof falls was common.

Late in the evening of 6 July 1988, the Piper Alpha oil platform 110 miles north-east of Aberdeen was destroyed by two big explosions; 167 men were killed. The Cullen Inquiry found that the platform had been inspected 12 days before the disaster to check on progress following a fatal accident nine months before. The inspector had spent ten hours on the platform and concluded that ‘lessons appear to have been learned’. Lord Cullen was not impressed: 'the inspection... was superficial to the point of being little use as a test of safety on the platform. It did not reveal any one of a number of clear-cut and readily ascertainable deficiencies.’ Recent events surrounding the Care Quality Commission and the University Hospitals of Morecambe Bay NHS Foundation Trust seem little different in principle. Whatever transpires regarding the alleged cover-ups, there is agreement that the CQC should have done better as an inspectorate.

The virus in eastern China that since late February has killed 26 out of 128 confirmed cases has been officially named ‘avian influenza A (H7N9)’. Analysis of its genes shows a mixture derived from several bird flu viruses, and that the virus has been evolving for some time.

The despair I expressed nine years ago in a piece for the LRB on the MMR disaster – ‘Why can’t doctors be more scientific?’ – persists. Anti-vaccination proponents still peddle junk science with vigour. So it’s a relief to see on TV the families in South Wales queuing to get the MMR vaccine for their children. The last time citizens there queued like this was during the smallpox outbreak that started in Cardiff in January 1962; 47 people fell ill and 19 died.

The discovery of the Crossrail 13 – the skeletons found buried 2.4 metres under the road round Charterhouse Square – came as no surprise. John Stow’s 1598 Survey of London said that on account of the pestilence ‘the churchyards were not sufficient... The Bishop of London, in the year 1348, bought a piece of ground, called “No mans land”... for the burial of the dead.’ It was close to Charterhouse. Plague had arrived in England from France that summer, and came to London in the autumn.

When Sally Davies, the chief medical officer for England, said that antibiotic resistance is a ‘ticking time-bomb’, that it could mean a return to 19th-century treatments for infection, and that as a threat it ranks alongside terrorism, she made sure her message was heeded and that Volume Two of her Annual Report would be noticed. Her saying that a hip replacement operation could be lethal helped propel the issue to the top of the news. But it was unfair to orthopaedic surgeons. Ever since the surgery was developed they have been obsessed with preventing infection. They count an infection rate greater than 1 per cent as a failure; and antibiotics on their own don’t work at all well when metalwork is there. But it is easy to guess why Davies used this example. She was speaking to politicians and Treasury officials, many of whom will need new hips and knees fairly soon.

The British aversion to eating horse is strong and longstanding. ‘Horse-Eating’, the lead piece in Charles Dicken’s Household Words for 19 April 1856, explains why: Prejudice, and nothing else! the same prejudice which makes the English refuse to taste frogs and escargots, though both are esteemed and expensive dishes on the continent; which makes the Orientals reject the flesh of the hog, though here we know how good it is; which causes, in short, nearly one-half the world to loathe nutriment which is greedily consumed by the other half; which has given rise to the true, but unreasonable fact, that one man’s meat is another man’s poison. The problem isn’t taste. On his last march, Captain Scott’s diary entry for 18 February 1913 read: ‘Temp -5.50. At Shambles Camp.’ Captain Oates’s ponies had been shot there on the way to the Pole. ‘Here with plenty of horsemeat we have had a fine supper... new life seems to come with greater food immediately.’ On the next day: ‘To-night we had a sort of stew fry of pemmican and horseflesh, and voted it the best hoosh we ever had on a sledge journey.’

Eliminating an infectious disease by deliberately eradicating the causative agent has happened only twice: smallpox fell in 1977 and rinderpest – cattle plague – in 2011. Polio should be next, but the murders in the last week of vaccinators in Pakistan – one in Charsadda, two in Peshawar, five in Karachi – have stopped the eradication programme. Nothing new for the Taliban, who blocked polio immunisation in Waziristan earlier this year. Things haven’t been helped by the disclosure that Dr Shakil Afridi, whose activities helped to locate Osama bin Laden in Abottabad, operated under the cover of a bogus immunisation programme run by the CIA.

With two million cases in the UK every year, norovirus exceeds all other causes of diarrhoea and vomiting by many orders of magnitude. If a malevolent person had set out to create it as the nastiest virus known, their only disappointment would be a lethality failure; the vast majority of victims get better after two or three days without specific treatment. Just as well, because there isn’t one.

A coronavirus particle has spikes on its surface with knobs on the ends, making it look a bit like the sun and its corona. Hence the family name. Human ones were first seen in the 1960s by the electron microscopist June Almeida, in collaborative common cold research with the virologist David Tyrrell. Growing the viruses was very difficult. Almeida and Tyrell were enthusiasts for organ culture (I am reminded of it daily; I worked with June and have a scar on my forearm where skin was taken in a vain attempt to grow wart viruses). Bits of tissue kept alive in test tubes were infected with sneezings from common cold sufferers. It turned out that a quarter of colds are caused by coronaviruses.

Legionnaire's disease got its name in a blaze of publicity when attendees at the 1976 Philadelphia State Convention of the American Legion were struck down with severe pneumonia. They had stayed at the Bellevue-Stratford Hotel from 21 to 24 June: 182 fell ill and 29 died; 39 passers-by were also affected, five fatally. Funerals and marching legionnaires made good television. The story was top of the news for five nights. But the cause was a mystery until a cold review of samples from victims was conducted six months later. It turned out to be a bacterium. This was unexpected. The pathology didn’t fit a bacterial cause, and it was widely believed that bacteria did not spread on the wind.

The influenza season draws to a close. But the virus isn’t going quietly. Monday 2 April started early for me with an interview on the Today programme about the sensible decision by the US National Science Advisory Board for Biosecurity to give up trying to censor papers describing the enhancement of bird flu infectivity in ferrets. I covered the same story for Good Morning Scotland. The benefits of knowing about potentially nasty mutations before they take us by surprise far outweigh any risks from al-Qaida virologists.

Lambing is just starting. But the pictures on TV in the last few days have been of stillborns, and of newborns with bent legs, seized-up joints and crooked necks. Their mothers had been infected during pregnancy with the Schmallenberg virus, called after the German town where it was discovered last year. It belongs to a family – the bunyaviruses – that are mostly spread by insect bites.

The big question for virologists in recent years is why H5N1 influenza hasn’t mutated to cause a pandemic. It is as feeble today at spreading from person to person as it was in 1997, when it first drew attention to itself through a dramatic chicken-to-human outbreak in Hong Kong. H5N1 human infections are very nasty with a high mortality, But they are very hard to catch. To start growing, the virus has to get deep into the lungs. The surest way for this to happen is to be a South East Asian cockfighter. They stimulate the birds by spitting down their throats; the birds spit back.

Cell suicide by a programmed process – apoptosis – is necessary for human health. It starts long before birth, sculpting us as embryos. It is essential for the proper functioning of our immune systems and of organs that continually produce new cells, like the intestines and bone marrow. When it goes wrong, it can lead to strokes, heart attacks and cancer. Its subversion by microbes plays a crucial role in Aids and many lethal infections. Todd Rider and his colleagues at MIT's Lincoln Laboratory may have found a way to use the enzymes that make it happen – caspases – as antiviral agents.

Don’t think that because your salad sprouts are organic, grown on your window sill, and supposedly good for you, that they haven’t accumulated many food miles or are safe to eat raw. Compelling evidence published by the European Food Safety Authority yesterday points to fenugreek sprouts as the vector of the E. coli that caused the enormous German outbreak in May and June (more than 3000 cases, with 47 deaths) and a French outbreak at Bègles, near Bordeaux, in June. The only common factors in the outbreaks were genetically identical E. coli O104:H4 – and fenugreek from the same Egyptian source.

'It's the sprouts,' the head of the Federal Robert Koch Institute in Berlin, Reinhard Burger, announced on 10 June. No surprise. Bean-sprout food-poisoning outbreaks occur regularly. The first big one was caused by Salmonella in the UK in 1988, when 143 people fell ill after eating contaminated mung bean sprouts. The outbreak in Sakai City in Japan in 1996 was caused by radish sprouts contaminated with E.coli O157. In the UK last year 231 people were infected with Salmonella from bean sprouts.

The E. coli outbreak in Germany is enormous. In case numbers (so far) it falls short of the 1996 outbreak in Sakai City in Japan, but the number of those in Germany going on to develop haemolytic uraemic syndrome (HUS), the main complication, which affects blood cells and kidney function, is far greater than in any previous outbreak – 520 on 2 June – and the proportion of those infected that have gone on to develop HUS is also much greater. Germany usually sees about 65 HUS cases every year. In Sakai City only 106 out of 2764 microbiologically confirmed cases developed HUS. The number of deaths in Germany already exceeds the 17 in central Scotland in 1996.

The media are giving as much attention to the Fukushima I nuclear power plant as they are to the impact of the tsunami, even though the likelihood of measurable health effects from the former is small, and the number of deaths caused by the latter is certain to be very large. This isn’t surprising: nuclear fear, founded on Hiroshima and Nagasaki and reinforced by Three Mile Island and Chernobyl, is not irrational, though it’s worth noting that many more people have been saved by X-rays and radiotherapy than have been killed by radiation of any kind. What’s happening at Fukushima Dai-ichi Units 1 and 2 is similar to what happened at Three Mile Island Unit 2 in 1979.

The prime minister admitted last week that supplies of seasonal three-component influenza vaccine in some English general practices had run out. The health minister, Andrew Lansley, had to appear on Newsnight to defend using old stocks of the single swine flu vaccine to meet demand. Leaving the ordering of vaccine to individual GP practices instead of maintaining a central stock was clearly a flawed policy.

The swine flu virus – Influenza A (H1N1) 2009 – is behaving as expected: it’s back as the dominant seasonal flu. Maybe a little early, but so is the winter. It’s also behaving like all previous influenza-A strains in that some infections have been fatal; usually, but not exclusively, in people with pre-existing health problems. We’re much better at handling flu than we used to be. Severe infections can be treated in intensive care units; the last pandemic before swine flu was in 1968-69 when ICUs hardly existed, and the development of extracorporeal membrane oxygenation (ECMO) machines was a long way off. Essentially, ECMO does the work of patients’ lungs for them; most of the 14 machines in England are currently being used to treat flu cases. We have effective anti-virals. And vaccine development and delivery is now very quick: six million doses were given in response to swine flu without significant safety issues. But vaccine uptake in those who need it most has been disappointing.

Many infections kill slowly. Hardly any are lethal within 24 hours of the onset of symptoms. Bubonic plague takes days to kill and haemorrhagic smallpox takes a week. Cholera and inhalation anthrax are about the only diseases whose victims can wake up feeling fit but be dead by nightfall.

The revelation that meat from the bulls Dundee Paratrooper and Parable has been eaten by people created a media storm this week. It happened because the animals were the offspring of the cloned product Vandyk-K Integ Paradise 2, a Holstein cow in Wisconsin. Particular outrage has been expressed by Compassion in World Farming, the RSPCA and the Soil Association. They have said that the cloning process causes animals to suffer, and have raised food safety concerns. The Food Standards Agency is the main regulator; it has pointed out that milk and meat from clones and their progeny is a 'novel food' and requires authorisation from them before it can be marketed. They say that this was never sought. I have no doubt that the milk and meat from these animals was safe to consume.

Deirdre Hine’s ‘independent review of the UK response to the 2009 influenza pandemic’ was published yesterday. Her team was based in the Cabinet Office, which played a central role in the implementation of the pandemic plan. That’s one reason the word independent had to be in the title of her review. But there’s no doubting Hine’s independence. As the chief medical officer for Wales, she got into trouble during the BSE crisis for criticising the work of officials above her pay grade at the Department of Health in London. She was right then, and she has got it just about right this time too.

Good to hear that the Prince's Foundation for Integrated Health has stopped its operations with immediate effect. Disappointing, though, that the reason is not because its founder has taken on board Oliver Wendell Holmes's views on homeopathy – 'a mingled mass of perverse ingenuity, of tinsel erudition, of imbecile credulity, and of artful misrepresentation, too often mingled in practice, if we may trust the authority of its founder, with heartless and shameful imposition' – but because of a more mundane alleged deceit: two people have been arrested on suspicion of fraud and money laundering. When Holmes wrote his essay in 1842 he believed that homeopathy would soon go the way of touching for the scrofula – another Royal Cure – and Bishop Berkeley's Tar Water ('good for so many things').

In recent times the usual response to scientific uncertainties about risk has been to apply the precautionary principle. Action is taken to prevent potentially dangerous events when there is no robust evidence about their likely magnitude, or sometimes even about the likelihood of their occurrence. With both Eyjafjallajökull's eruption and swine flu, pessimism and a heavy reliance on a very small number of historical events drove the policy response. It is on record that major damage has occurred on the few occasions when planes have flown through thick volcanic eruptions. In the century before swine flu there were only three flu pandemics, in 1918, 1957 and 1968. So when the precautionary principle led to the roll out of planned policies – zero tolerance for ash and very vigorous controls for the newish flu virus – the science was very imperfect.

'H1N1: now entering the recrimination phase,' a recent 'Editor's Choice' in theBritish Medical Journal was headlined. The piece began: 'If influenza was a rock band how would it rate its latest release, H1N1? Not too well, I suspect, despite the greatest prepublicity since – well, its previous release.' A nice summary. People have died – but in far fewer numbers than even the most optimistic official estimates predicted. Absenteeism has not stopped the trains or planes or threatened food supplies. The second wave came, but the virus had not mutated. We have been lucky, so far. The virus has been no nastier than seasonal flu, and the usual target for lethal infections, the elderly, have been largely spared, probably because of immunity conferred by H1N1 infections suffered by them 60 and more years ago.

Charles Haddon-Cave's Nimrod Review: An Independent Review into the Broader Issues Surrounding the Loss of the RAF Nimrod MR2 Aircraft XV230 in Afghanistan in 2006 was laid before Parliament and published by the Stationery Office on 28 October. Two days later it was out of print. The Review was not a Public Inquiry with statutory powers. It sat in Ministry of Defence premises. Some staff were seconded from the ministry. But its conclusions, and its naming of the incompetent, leave no doubts about its independence. The accident to XV230 was avoidable. My report identifies manifold shortcomings in the UK airworthiness and in-service support regime, and reveals matters which are as surprising as they are disturbing.

Swine flu has been spreading in Britain for three months. The virus has got about quite well, although the great majority of infections have been mild. Until two weeks ago reassurance about our preparedness for a pandemic was the order of the day. But the media tone changed with the reporting of the deaths of six-year old Chloe Buckley and Dr Michael Day. Chloe was said to have been infected with the virus but didn’t have the ‘underlying health conditions’ usually present in fatal cases, and Day was the first healthcare worker to have a lethal infection. Coincidentally, the tenor of official public pronouncements altered too. The chief medical officer for England mentioned the possibility of 65,000 deaths. On television he was quick to qualify: that figure was a worst-case scenario, necessary for planning, not a prediction. But the number, not the caveat, got the publicity. There was also a change in the way that case statistics were announced, with a shift from laboratory confirmation to estimates based on GP consultation rates and clinical diagnoses. The overnight five-fold increase in ‘cases’ was inevitable. Lab tests tend to underestimate, and consultation rates increase because of the media coverage.

The first death caused by swine flu virus outside the Americas occurred in Scotland on Sunday. The announcement generated more media interest than the declaration three days before by the World Health Organisation that the spread of the virus had moved into pandemic mode. But the declaration was expected and generated less fear than anticipated. The public can see that in Britain the virus is doing well – which is all that was needed to meet the pandemic criterion of sustained community spread in a region outside the Americas – and the message that the virus is mild is also well established, tempering the notion that the word 'pandemic' carries lethal overtones. But this means that a death requires explanation. There is no such thing as a naturally avirulent influenza virus. Even the mildest ones that infect humans can kill. They do it routinely every winter.

The spread of the novel influenza A(H1N1) virus through North America is nearly complete. Only three continental US jurisdictions (Wyoming, West Virginia and Alaska) and three Canadian provinces or territories (Newfoundland, Nunavut and the Northwest Territories) haven't reported cases. Its progress elsewhere is still slow, however. Japan (163 cases), Spain (103), the UK (102) and Panama (54) lead; vigorous containment is still the order of the day in the UK. But unless the North American epidemic slows soon, the continued export of the virus – in the coughs and sneezes of infected travellers returning home (particularly to the southern hemisphere, which is just entering its flu season) – has a good chance of defeating all best-laid plans. And it is doing well in Japan.

Influenza virus has only eight genes. The molecular structure of the most important proteins they code for is known in intimate detail. The coming and going of its epidemics have been studied by statisticians continually since the 1840s. But predicting pandemics remains a fools’ game. It falls into the category of Alvin Weinberg's 'trans-science' – a question of fact that can be stated in the language of science but is unanswerable by it. Weinberg’s examples focused on the impossibility of predicting the probability of extremely improbable events. There have only been three influenza pandemics in the last century: in 1918, 1957 and 1964. The uncertainty is massively amplified by evolution – the random and frequent genetic mutations and the swapping of genes between bird, pig and human viruses.