All posts by Simon Makin

Simon Makin is an ex-post-doc researcher in auditory perception turned journalist. Follow him on twitter @SimonMakin.

Could we be releasing a smallpox superbug?

Smallpox SuperbugIn early July, scientists at the National Institute of Health in Maryland, USA, discovered a stash of vials containing the deadly (and thankfully all but extinct) disease smallpox. They had been sitting, forgotten in a storage room since the 1950s. So, if the smallpox in the vial was infected with another microbe, could the mix result in a new infectious disease?

Thankfully, the short answer is no. Viruses change in two main ways. The first way is mutation. It sounds like the stuff of an X-Men movie, but mutations happen all the time – although they cause change relatively slowly. The second way is called “recombination”. This occurs when two separate, but related, viruses infect the same cell. During the process of multiplying within the host, the genetic coding from both viruses can get mixed together, making a new virus. This wouldn’t necessarily make it a “superbug”, but it could give it new abilities. It may mean that people who were previously immune are now vulnerable, or the virus could become more contagious.

To multiply and spread, most viruses hijack the infected person’s cells’ own replication machinery inside the cell nucleus. Smallpox works a little bit differently – it has its own copying apparatus and so can replicate outside the nucleus. (Even so, it still needs to infect a cell – but just doesn’t need to burrow into the central nucleus of the cell.) The upshot is that just mixing two viruses in a test tube, away from any living cells, won’t produce anything new. Without something to infect, a virus can do nothing. Therefore smallpox virus would have to get out into the world and start infecting people before it would have any chance of combining with other viruses. Even then, recombination is unlikely because the smallpox would have to infect somebody at the same time as another virus similar enough to recombine with it.

Fortunately, there’s not much chance of the virus escaping out into the wide world, as the Centers for Disease Control and Prevention (CDC) pledged to destroy the sample once they’ve run a few tests. That still leaves samples of smallpox in two labs: one at CDC HQ in Atlanta and one in Moscow. Debate continues over whether to destroy these final two samples, potentially making smallpox extinct once and for all, or continue using them for research, with the risk of the virus breaking free and sweeping through the world once again.

Answer by Simon Makin. Question sent via Twitter: If smallpox in that vial was infected with another microbe could it mutate […] in 50 years?

Footnote: Interestingly, the tool that was instrumental in eradicating smallpox was a virus of the same poxvirus family, vaccinia. This has the same “antigen” (the part that triggers an immune response) as smallpox, but it’s a fairly minor infection, so it could be used as a “live” vaccine, conferring immunity to smallpox without doing much harm. Researchers are still using vaccinia today, by using recombination to create vaccines with the antigens of the virus the vaccine is made for, but which cause mild infections. It’s also being used in gene therapy, but that’s a story for another day…

Image credit: Vincent Racaniello on flickr

Article by Simon Makin

July 22, 2014

Simon Makin is an ex-post-doc researcher in auditory perception turned journalist. Follow him on twitter @SimonMakin.


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Review: Richard Wiseman dispels the paranormal in a magic show!

Richard Wiseman closed this year’s Brighton Science Festival, on Sunday 3rd March, with a spectacular show of magic, jokes, illusions, and psychology. Although he is now Professor of the Public Understanding of Psychology at the University of Hertfordshire, he wasn’t always a psychologist. He started out as a stage magician and so he kicked off the evening with the first magic trick he ever performed – a simple handkerchief manipulation.

Richard Wiseman in BrightonIt might seem off-topic for a show supposedly about the paranormal, but the methods employed by magicians actually exploit the same kind of psychological phenomena that lead people to believe they’ve experienced the supernatural. When a visual illusion brought the realisation that our senses “construct the world” he got excited by the idea that “experience may not be a wonderful guide to reality”. This sparked his interest in psychology and he now conducts research as well as communicating to the public what modern psychology has revealed about the workings of the human mind.

A simple but effective demonstration of how misdirection is the essence of magic involved revealing how a common sleight-of-hand trick works. In the ‘French drop’ a coin is apparently passed from one hand to another, but is actually dropped into the palm of the original hand. We follow the direction of the magician’s gaze as he looks pointedly at his other hand, far from where the coin really is. Despite showing us exactly how this is done, we all still failed to spot it – time and time again – because it “exploits the normal rules of social attention” and we look where he looks without being conscious of what we’re doing.

The same ‘spotlight of attention’ is responsible for the phenomenon of ‘change blindness’, which Richard exploited in his viral video, the ‘colour-changing card trick’.  Our eyes take quick snapshots of parts of the world to build up a scene. Our brain then assumes things that weren’t changing continue unchanged when our attention is focussed – giving the illusion we’re seeing a lot more than we really are. This is only exposed when a scene is suddenly restored to an earlier state, revealing how much changed without us noticing.

Prof Richard Wiseman (source: Wikimedia)He also assaulted our minds with some of the strangest and most effective perceptual illusions around, because they reveal the mind working in even more subtle ways than attention tricks. There was a demonstration of ‘perceptual constancy’ where the context surrounding part of a picture changes what we see, and ‘closure’, where our mind ‘fills in the gaps’, so we see a picture of a scantily-clad woman with the clothing in the picture covered up as completely naked, and so on.

It was a very visual show overall as illusions and magic make for spectacular theatre. At one point however, we were also treated to an auditory illusion in which lyrics on a screen dictated what we heard – with hilarious results. It all goes to show, that in certain circumstances, to a certain extent, we perceive what we expect to perceive. This is especially true when it comes to faces. Many psychologists believe our brains are ‘hard-wired’ for recognising faces and as a result we’re prone to seeing them even when they’re not there. This explains both how often ‘ghostly’ faces appear in photographs and the tendency to see faces in funny photos of inanimate objects.

Richard is a master showman, competent at working a crowd and the evening was very much a show, brimming with audience participation, wonder, guffaws and gasps. Personally though, I would have liked to see some deeper explanation: he never really went into depth as to why many of the visual illusions work or what they tell us about how our senses work.

I should probably come clean and admit that I was a perceptual researcher for years, and so maybe not the best person to review a gig like this – I’d seen many of the illusions before and know how and why they work. Friends I went with also made comments along the lines of it being “science-light” however, so I obviously wasn’t the only one. That being said, the audience was thoroughly entertained, and I’m sure virtually everyone was convinced by his central point: that some of our strangest experiences are probably just the consequences of our even stranger minds…

Article by Simon Makin

March 15, 2013

Simon Makin is an ex-post-doc researcher in auditory perception turned journalist. Follow him on twitter @SimonMakin.


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Ben Goldacre’s Bad Pharma – Live! Reviewed

Ben Goldacre is a self-proclaimed “nerd evangelist”. He’s probably best known for his Guardian column and first book, Bad Science, which managed to be belly-laugh funny as he skewered pseudoscience, quackery, and more, with compelling logic and calm, sardonic, reasonableness. He’s a doctor, academic, and journalist, and you only have to listen to him speak to be convinced he cares deeply about the things he writes about. He makes as much noise about them as he can because he passionately believes somebody has to.

Ben Goldacre at lecternHe was at the Brighton Science Festival on 2nd March to talk about the topic of his new book Bad Pharma. Unlike Ben’s previous writing, it is not particularly funny. There’s an occasional smirk to be had, sure, but you get the feeling it’s not trying to be funny, simply because he doesn’t think it’s a laughing matter. It is one thing when some quack is depriving a handful of idiots of their pocket money, but quite another when it is literally a matter of life and death – on an industrial scale.

He lost no time driving this point home by leading with the story of lorcainide. This is one of a class of drugs widely prescribed in the 1980s to people who had suffered heart attacks, as it was thought they saved lives by supressing irregular heart rhythms. But when a large trial was conducted to establish whether they really did reduce deaths (the Cardiac Arrhythmia Suppression Trial (CAST), which published results in 1991), it turned out they actually increased the risk of death. It’s estimated the drug’s popularity may have led to what he called “a biblical death toll” – of between 100 and 150 thousand Americans. This was all down to people acting with the best intentions, according to plausible beliefs.

We were then told about a 1980 study on lorcainide, in which nine out of 49 participants on the drug had died compared to one out of 46 given a placebo. Nobody knew about this. Why? The drug’s development was “abandoned for commercial reasons” and the research hadn’t been published. In an article published after the CAST trial, the researchers described these results and suggested they “might have provided an early warning of trouble ahead.” That’s a euphemism for the deaths of tens of thousands of people. Regarding the fact it wasn’t published at the time, they wrote: “it now provides an interesting example of publication bias.”

This is the heart of the matter. Published research has shown that not all research gets published. The majority of clinical trials are conducted, or at least financed, by pharmaceutical companies. Results that show their drugs in a good light are far more likely to be published than those that don’t – and they are perfectly entitled to withhold information like this. Ben explained: “We know from the best currently available estimate […] that about half of the trials that have been completed don’t go on to be published, and that trials with positive results are about twice as likely to be published.”

Think about that for a second. We like to think doctors make decisions based on a complete picture of all the scientific evidence. Not only is that not true, but the evidence they’re using is systematically biased to overestimate benefits or underestimate harms. Because of this we can’t know what the true benefit/risk balance is for many drugs (and all drugs have side-effects) and we can’t compare the relative benefits of different drugs to decide which is best. Imagine there’s one drug that saves six lives out of 10 and another that saves eight – but we don’t know that because we don’t have all the evidence. That’s a potential net cost of 2 human lives out of every ten people needing that kind of treatment. Apparently some drug company employees have a hard time understanding that point.

Are all drug companies evil?

Of course, not all ‘pharma’ is ‘bad pharma’. Drug companies have developed some of the most beneficial science mankind has ever known, saving countless lives. Ben was quick to point this out, but he doesn’t believe this gives them free license to distort evidence in ways which demonstrably harm people. Nor is he saying that all people working for drug companies are “bad, evil, people”. It’s more a case of “misaligned incentives” and a broken system.

Ben Goldacre lecturingAnd although big pharmaceutical companies take the brunt of the attack, it’s really a critique of the whole edifice of medicine: researchers who agree to be gagged by contracts, journals who fail to check proper methodology, editors who fail to enforce trial registers, regulators who maintain the culture of secrecy (and suffer from the same “revolving-door politics” as any other industry-related government structures). Even the doctors simply too busy to read past industry marketing – all must shoulder part of the blame for letting them get away with it.

Although this is weighty, important stuff, he didn’t forget people were there, at least in part, to be entertained. One of the highlights was a great explanation of funnel plot graphs – just so he could show us you can look for “evidence of publication bias – in studies of publication bias!” Explaining statistics to a lay audience is an achievement in itself, but managing to make it funny puts Goldacre in a different league. Never talking down to the audience, he’s like a likeable, articulate nerd, explaining something to less informed but intelligent pals. Without dumbing down, he led us through understanding and realisation to shock and anger – which, of course, was the object of the exercise.

The second half of the show was a Q&A session hosted by Sile Lane from Sense About Science. Dr Goldacre teamed up with SAS (and a few other organisations) to launch AllTrials.net. This is a campaign calling for all trials to be registered and all trial data to be released, including full clinical study reports, for all currently used treatments. It’s supported by over 200 organisations, including over a hundred patient groups, NICE, IQWiG (the German equivalent of NICE), the Royal Society of Medicine, the Medical Research Council, the Cochrane Collaboration, and the Wellcome Trust. Most excitingly, one of the biggest drug companies in the world, GSK, who were fined $3bn last year for “acts of criminal and civil fraud, including hiding data”, has recently signed up – which will hopefully open the gate for more to follow.

You can read more about the campaign, and sign the petition, on the website, or keep up to date with progress on Ben’s blog. If you want to know all the grimy details of specific companies’ bad behaviour, I recommend picking up Ben’s book.

Article by Simon Makin

March 11, 2013

Simon Makin is an ex-post-doc researcher in auditory perception turned journalist. Follow him on twitter @SimonMakin.


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‘The Catalyst Club’ – Review (Brighton Sci-Fest)

The Catalyst is a monthly Brighton club harking back to the debating societies and gentlemen’s clubs of yore, where three speakers each step up to a lectern for 15 minutes apiece. Last Thursday’s line-up at the Brighton Science Festival was originally conceived as a sex, love and happiness-themed Valentine’s special. However, the speakers couldn’t make that date so it was rescheduled and brought under the banner of Brighton Science Festival. The venue, the Latest Music Bar, was a great spot for it, with a cosy jazz club atmosphere downstairs, and a screen relaying the action upstairs for those who couldn’t get hold of a ticket.

In addition to introducing each speaker, regular MC, David Bramwell, had conscientiously dug out some appropriate stories. Apparently, in a survey of 10,000 Japanese 16 – 19 year-old males, 35% said they had no interest in sex. Whereas the same study in England didn’t give a percentage – it just said there was one bloke called James from Peterborough! I don’t claim to know how true this is…

The Catalyst Club at BrightonAlso in keeping with the theme, we were all asked to play guinea pigs for a smartphone dating app. The idea being to discover who might want to get to know you in the room you’re presently in – to help you meet people wherever you go. But between the app seemingly still early in development (there was ‘no gay option yet’, despite being in Brighton), and the WiFi cutting out repeatedly, I think it’s safe to say no iMatches were made on the night. Interestingly though, the exercise did get me and two nearby girls talking to each other, proving you don’t need an app to grease the wheels of sociability – you just need beer and a talking point.

The first speaker, writer and editor Vanessa Austin-Locke, talked about how, “our minds, our chemistry, our history,” lead to, and colour, extreme sexual experiences.  She told the story of an interviewee referred to as “snorkel”, who had an early sexual experience on a family trip to the beach, and who now gets his rocks off in a bathtub with a dominatrix, some seaweed and a snorkel, “without so much as the touch of a hand”. She sees a connection between fetishism and post-traumatic stress disorder: both have the effect of “trapping the mind and causing it to fixate”.  Quoting extensively from Nabokov and Anaïs Nin, she delivered a sociological essay which, although light on science, was poetic and literate suggesting that all such experience is part of the search for “the little death, the big death, and – ultimately – life”.

Next up was Prof Elaine Fox, talking about the psychology of optimism and pessimism. She’s an experimental psychologist and an expert in the area, having recently published a book, Rainy Brain, Sunny Brain. She told us about the ancient fear and pleasure systems in the brain, which ensure that our brains automatically tune into things that are either dangerous, or good for us. These are the physical circuits that underlie how optimistic, or otherwise, we each are. She continued to explain that although there is evidence for benefits of optimism – it is not as simple as positive thinking. Other components such as positive actions and persistence seem to have a greater impact on our lives. Finally, she spoke about the interaction of genetics and environment in determining our psychological destiny. A study looking at a gene linked to anxiety and depression, and the number of nasty incidents in the participants’ lives found that neither the gene nor the life experiences alone predicted risk of depression – but both taken together did. Prof Fox said this shows: “the gene itself is not our destiny,” and neither are the things that happen to us.

Bringing up the rear, as it were, professor of experimental psychology at Sussex University, Zoltan Dienes, told us all about “the secret logic of sexual fantasy”. He described some categories of female fantasies such as “beloved”, “victim”, “dominatrix” and “wild-woman” and a school of psychoanalysis that proposed the purpose of such fantasies is to counteract anxieties. So a woman with a fear of men being weak would be turned on by a fantasy in which she was dominated or even abused – i.e. a victim fantasy. A fear of being unloved would be counteracted by a beloved fantasy, and so on. He then described an ingenious experiment involving a device called a “vaginal photoplethysmograph”, stories about “being in the frozen peas section in Tesco’s” as a “neutral condition”, and a number of other anxiety-inducing stories, in order to turn this into “a testable hypothesis”. Unfortunately, the arousal caused by each fantasy went in the opposite direction to that predicted by the theory, even though the match between each anxiety and fantasy was the same. So – it was all a bit confusing really. But as he got by far the biggest giggle count of all the speakers, no-one was really complaining. Prof Dienes also offered his own thoughts on what it might all mean in the Q&A session afterwards.

All-in-all, this was an interesting and unusual Thursday night out, and one I’d recommend the next time the Catalyst Club convenes.

Links:

Catalyst Club
Brighton Science Festival

Article by Simon Makin

March 7, 2013

Simon Makin is an ex-post-doc researcher in auditory perception turned journalist. Follow him on twitter @SimonMakin.


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