The Best Australian Science Writing 2012 (24 page)

Think about that next time you're selecting a surgeon.

Gaming is a billion-dollar industry, and with games moving from the console and PC to the smartphone, the number of gamers is likely approaching the billions. Video games are here to stay and even non-gamers can benefit from helping to direct the rules of future games: akin to the way the Red Cross recently suggested the rules of war games be revised according to international humanitarian law.

As well as the many positives already stated, video games can also be an invaluable, yet indirect, source of learning. Although educational games are often boring, numerous games successfully incorporate educational information.

Such games include the Assassins' Creed series, which combines actual historical events with gameplay, and the Professor
Layton series, which involves solving brain teasers to progress the story. Similarly, a new action game currently under development claims to teach gamers how to code.

Games and gamers can also be viewed as an untapped problem-solving resource. Researchers interested in solving complex protein-folding problems created an online game, Foldit, which led gamers to provide valuable contributions to AIDS research.

What if we take this another step forward and use games and virtual worlds to help individuals with social problems? In many games – such as World of Warcraft or the Call of Duty: Modern Warfare series – players are required to interact with others to finish quests or progress the storyline. Some individuals can find it easier to adopt a more confident personality in the virtual world. Could this be used to treat depression in teens?

I'm a gamer and have no problem in letting my kids play video games (in moderation, of course). I also look forward to the day when I'll be able to play co-op first-person shooters with my sons (to my wife's chagrin).

Just like any other technology, gaming has a place in society. And, if managed appropriately, games could provide even greater physical and psychological benefits than already demonstrated. It's up to society to shape this technology towards a beneficial end.

Until then, I'll be happy taking Earth back from the Reapers in Mass Effect 3.

Myth-busting

Eyesight

Licence to heal

Nick Miller

In late 2008, a travel agent (and regular polo player) fell ill in Lusaka, Zambia. She had a high fever and her gums were bleeding. It looked a lot like Ebola, a fierce virus that kills four in five of those it infects.

The patient was flown to Johannesburg in South Africa for treatment but the virus ravaged her system, sweeping through her body, ripping apart the lining of her blood vessels until they were unable to transport oxygen. She died.

A few days later, a Lusaka paramedic from the flight fell ill with the same symptoms, and died. Then the nurse who had received the patient in South Africa became ill with the same symptoms. As did a worker who cleaned the room in which the patient was received. And then another nurse at the Johannesburg hospital, again with the same symptoms.

By now the hospital knew it had something dangerous on its hands. It wasn't Ebola, but it was something like it. This kind of haemorrhagic fever virus is so lethal that the military fears it may one day be turned into a weapon.

Tight precautions were put in place. Doctors and nurses treating the infected patients wore gloves over their gloves, covered their legs and shoes and wore face shields and goggles. Anyone
coming within 2 metres of the patients wore respirators. Both nurses and the cleaner died.

Then another person became sick, a nurse who treated one of the secondary cases. Considering the virus's progress so far, her prognosis was worrying.

As before, the virus swept through her system. She was soon comatose with a high fever, her liver failing, her blood pressure falling, her whole body in shock. But by now Dr Ian Lipkin was on the case.

Lipkin has been called a ‘disease sleuth', the world's leading ‘virus hunter'. From his laboratory at Columbia University's school of public health, in the northwest corner of Manhattan, New York, he fields samples from around the world, flown to him sometimes with desperate speed, from cases where sickness and death have mystified the locals. And using the latest tools, he works against the clock to contain the plague.

‘We were called in the middle of the outbreak,' Lipkin remembers about the South African case. ‘Nobody really wants to admit that they can't sort it out, there are sensitivities, so it takes a while.'

His team at the Centre for Infection and Immunity swung into action. They get two or three calls a day, and occasionally lives are immediately at risk, in which case it's all hands on deck.

They tore the samples they had been sent into genetic shreds, using a barrage of cutting-edge hardware and software. They were looking for recognisable patterns, a process Lipkin says is like putting back together ‘one book in a library that a gale has gone through'.

Soon they had it. It was a new member of the arenavirus family, a type that infects rats and occasionally humans, a relative of the virus behind Lassa fever. They sent the news back to South Africa. Armed with this knowledge, doctors tried the drug Ribavirin, the standard treatment for Lassa fever.

It worked and the nurse recovered. But it was almost a year before she could return to her job.

* * * * *

I meet Lipkin in his corner office in Upper Manhattan, which has sweeping views over the Hudson River. He holds out his hand and I move to shake it, but he withdraws it slightly. After a moment of embarrassing confusion I realise he was just motioning for me to take a seat. The virus hunter doesn't shake hands – whether for his safety or mine is never made clear.

He has a professorial air, a supreme scientific confidence, the bearing and manner of a kind of medical Sherlock Holmes. He's not exactly scary, but there's the slight sense, as he looks at you through his glasses, that he's mentally taking you apart to study your genes. His confidence isn't undeserved. Usually, scientists are proud and lucky to identify one new virus in their lives. Lipkin's team has clocked up 400 in the past decade.

Lipkin fervently believes that we are not doing enough to protect ourselves from the potential of a deadly outbreak. Furthermore, he suspects that many conditions such as mental illnesses, cancers or chronic fatigue syndrome may have a biological agent behind them, the discovery of which would revolutionise treatment and prevention.

About 10,000 samples come to his lab every year, from fish, fowl, man and beast, and on any day his team is working on 100 or more. One day it is a worrying new strain of Ebola in Spanish bats, the next day a new hepatitis virus that has just broken out in British dogs, the next a mystery infection that is wiping out fish farm stocks in Scandinavia. His workers look at a new New York flu, an African cold, some ‘bush meat' seized by customs inspectors.

The dangerous ones, where people have died of an unknown agent, are examined in a ‘biosafety level 3' room that you need
FBI clearance to enter. It is constantly monitored by cameras, and the researchers wear full body suits with their own oxygen supply (‘It's exciting the first time, but it quickly gets annoying,' says one of the workers).

In earlier days the techniques were slower, as scientists had to ‘culture' (grow) a virus before it could be studied. They still make cultures, but new genetic techniques make them less vital. They now have slides, and electronic chips that bind to parts of DNA they recognise and light up to signal the discovery. There are also ‘mass throughput' genetic sequencers that can untangle the code of a mystery sample in less than a day, studying more than 100,000 different parts of the DNA sequence simultaneously.

One of the first cases to benefit from the centre's new technology was a series of mysterious deaths in Melbourne in 2006. Jovo Vranjesevic, 57, died from a stroke soon after returning from a holiday in Europe, and his organs were donated to save other lives.

A 63-year-old grandmother received one of his kidneys, and a Monash University lecturer got the liver, both operations taking place at the Austin Hospital. A third person received the other kidney at the Royal Melbourne Hospital.

All three recipients died a month after receiving the transplants. But in all three cases, there was no identifiable cause. If it had been a common infection hidden in the donated organs, it was one unknown to medical science.

An inquest is still to officially give a verdict as to the cause of the deaths. But the hospitals had to move fast, to make sure that whatever was behind the deaths did not have the potential to claim more victims.

After being stumped initially, the teams in Melbourne called on Lipkin. He emphasises that it was a team effort, and that vital work was done by the Melbourne experts in identifying the link between the cases.

Lipkin's team analysed samples and found a novel virus, an arenavirus like the one later found in South Africa. ‘We used all the different tools that we have here, and eventually found this agent using high-throughput sequencing,' Lipkin says. Having identified the virus, doctors can now decide whether it is common enough, and dangerous enough, to screen for in future transplants.

* * * * *

Lipkin didn't see himself becoming a virus expert. At university he studied cultural anthropology. ‘It was a classic liberal arts education,' he says. He went on to medicine, but his aim was to go back to medical anthropology, to travel the world and care for indigenous people, to study shamanism and bring back ‘biomedicals' from the jungle that might have use in Western medicine – almost the mirror image of his current job.

But while working as a doctor in San Francisco in the early 1980s, HIV came onto the scene. ‘I was intrigued by the observation that people couldn't figure out why people were getting sick,' he said. ‘I was not the best scientist in the group, but I was the only person who was willing to work with these patients at the time, so I started figuring out why they were ill.' Along the way he discovered and described new neurologic diseases associated with autoimmunity and the nervous system.

Then came the Borna virus, in the late 1980s, an obscure virus linked to psychiatric diseases in humans. It took him three years to unravel its genome and he began to get a reputation as a virus hunter.

His career got another boost with an outbreak of encephalitis in New York in 1999. Health officials thought the culprit was the St Louis encephalitis virus, but Lipkin showed it was actually a West Nile virus, previously unseen in the US and closely related
to a virus called Kunjin that is endemic in Australia – it is spread by mosquitoes and infects humans, waterbirds and horses.

As a result of this breakthrough he was invited to give a talk at Columbia, and while there he was offered a job. ‘This changed things dramatically. Suddenly I had the ability to start collecting samples from all over the world, not only from people but from animals, and to look at the connection between human and animal diseases,' Lipkin says.

It is this interface between humans and animals that poses the biggest threat to humanity. Bacteria or viruses that an animal tolerates may, if transmitted or mutated, be deadly to an unwary human system.

While most viruses that cause acute disease in humans have been found, there are at least a million more viruses in the vertebrate animals alone, and far fewer than 1 per cent have been characterised.

The sprawling, fast-moving modern world makes it ever more likely that new infectious agents will appear, jump from animals to humans, and spread quickly. One of Lipkin's favourite quotes is that ‘the greatest threats to human beings on the planet are viruses'.

He hopes that people will get over the sense that there was an overreaction to swine flu in 2009. There were worrying lessons from that, he says, exposing the limited capacity for a country to develop a vaccine for mass distribution in a hurry. ‘That was a situation where that particular virus was not a major threat to humankind. But the next one may be,' he says.

A new infectious agent might not directly hit humans but it could change our world. A new disease that hit wheat, or corn, or poultry could be devastating.

Lipkin is also intrigued by the possibility that viruses may be the hidden culprit behind many chronic diseases.

‘Most people think of infectious agents as causing pneumonia,
diarrhoea, encephalitis,' he says. ‘They don't think of them as really causing things like cancer or mental illness. I think there's at least decent data to suggest that some forms of mental illness and cancer, and other immune diseases, like rheumatoid arthritis and so on, can be attributed at least in part to infections in a genetically susceptible host.

‘If you have a disease that's chronic, and you can ascribe it to an infectious cause and you can develop a vaccine that can prevent mental illness or cancer or what have you, that's a very heady concept, isn't it? It means you can have a huge impact,' he says. It is a theory that has started coming into vogue.