Engineering Life

Written for Spring 2012 issue of I, Science magazine.

In May 2010, the J Craig Venter Institute held a press conference to announce the creation of a synthetic bacterial species. After 15 years of work, Craig Venter’s team, led by Nobel laureate Hamilton Smith, managed to synthesise the entire genome of a bacterium and insert it into a recipient cell. “This is the first self-replicating species we’ve had on the planet whose parent is a computer”, said Venter. “It’s also the first species to have its own website encoded in its genetic code.”

When Venter had described the sequence of technical breakthroughs leading to this result – transplanting a chromosome from one bacterium to another, synthesising the Mycoplasma genitalium genome, growing artificial chromosomes in yeast, adding ‘watermarks’ such as a web address to synthetic DNA to make it distinguishable from naturally-contaminated DNA – there was a single question from the crowd of reporters. “Could you explain, in laymen’s terms, how significant a breakthrough this is?”

It’s a question I put to Dr Tom Ellis, a synthetic biologist from Imperial College London’s Department of Bioengineering. For him, biological science and biotechnology are turning into an information science. “Think of the human genome as a vast amount of data”, he says. “Now we’re sequencing the genome of a new organism almost every day.” Admittedly, these are mostly bacteria with relatively small genomes, but the amount of data appearing is still staggering. “Biology is now an information-rich subject”, says Ellis. “Really information rich.”

Unsurprisingly, the common analogy is one of computation. “One of the major tenets of synthetic genomics”, says Smith in Creating Synthetic Life, a documentary made for the Discovery Channel, “is that the genome, the chromosome of the cell, is the software – the operating system of the cell – and the cytoplasm is simply the hardware that allows a genome to express itself.” The computational analogy can only be pushed so far, since DNA itself – the software – is physical: “You’ve got an operating system which is also part of the hardware”, Ellis notes. But it’s compelling, nonetheless.

“Synthetic biology is building new subroutines to run on the operating system”, he says. Slightly adapting Smith’s metaphor, we can put these subroutines in a more familiar context by thinking of them as apps, with the cell as a phone and the genome as an operating system such as iOS or Android. These apps are currently modest constructions, but researchers are “building up to entire programs that you can load and even subroutines that can then be engineered to run within those programs”, he says. “We’re getting up to that sort of complexity now.”

“The majority of synthetic biologists are working on the design of effectively small software apps that will boot up and run within the genome”, says Ellis. “What Venter showed is that all the materials are there to be able to write the entire operating system.” But, importantly, he didn’t rewrite it from scratch. Imagine a hacker copies the code for an operating system and adds something at the end – perhaps just a comment with her name. “That’s what Venter’s done – copied the entire genome and in just a few places put watermarks to say this isn’t the original one, this is the one with our change”, he says. “Do they understand the program, the operating system? Not really. Not yet. But they want to.”

Many institutions are working towards standardisation – in terms of data, how specific biological parts should be defined, and how parts are measured – that will bring an even greater level of engineering maturity to the field. “At the moment the computing analogies function to galvanise people into action,” says Dr Darren Nesbeth of University College London’s Biochemical Engineering Department. “Right now, most biological labs in the world pretty much do things in a bespoke manner. If people constructed biological devices using the same standardised language, then there are benefits to that in terms of what people can do.”

Standardisation will further support the establishment of repositories of biological components such as the BioBricks Foundation, which maintains a catalogue of parts and devices. “Hopefully, we’ll get to the stage where you can have an algorithm which tells you all of the rules for where things should go if you build up an entire genome from scratch”, Ellis says. “And then from that point, someone like Venter could sit down with the parts list he wants and create a cell that had a completely synthesised genome based just on parts.”

“The actual definition of synthetic biology is quite hard to pin down”, he tells me. “But the simplest way you could put it is that it’s about applying engineering principles to biology.” The more I think about what this prosaic statement actually means, the more I’m struck by its audacity.

See Your Favourite Acts, Discover New Ones

Interview with TEDxImperialCollege host Gareth Mitchell.

“This is turning out to be my fantasy dinner party,” says our TEDxImperialCollege host Gareth Mitchell as he looks through the list of speakers. “These have been an exciting few weeks. Every few days, the organising committee has been adding new speakers to the line up. Just look at the disciplines covered here: engineering, computing, art, green energy, entrepreneurship, development, neurotechnology, neuroscience (yes there IS a difference and I look forward to exploring that over a cup of tea!), music, fashion, design, and support for offenders.”

As well as being a lecturer in Science Communication at Imperial College, Gareth also presents Click – the BBC World Service radio show covering engineering and technology – and regularly contributes to BBC Focus magazine. As he puts it himself, his geek tendencies go back to a childhood spent playing with electronics, and as a science communicator he’s clearly relishing the prospect of hosting such an eclectic set of talks.

“There will be no ghettos here: just amazing, unexpected conversations both within and outside the sessions,” he says. “I am familiar with some of the speakers already but there are others who I’ll get to know for the first time. It reminds me of music festivals where the joy of seeing your favourite acts is matched only by that of discovering new ones for the first time.”

And just as the experience of seeing a band at Glastonbury is made richer by the atmosphere and heritage of the place, so too with TEDxImperialCollege: “One really feels the spirit of the Great Exhibition around these parts. South Kensington exudes the feeling of a place that’s been a home to science, culture and exploration for the last century and a half.”

“As for me, on the day I’ll do my thing: usher people on, usher them off, do the intros, make sure everyone’s happy and politely pester the speakers if they run over time. But most of all, I’m going to sit back, listen and soak it all in. See you there!”

Hello Game World

Feature written for February 2012 issue of Develop magazine.

I spoke to Mike Cook, from the Computational Creativity group at Imperial College London, about a future he’s bringing about in which games are designed by machines.

Angelina is a remarkable games designer. At only a year old, she’s designed several arcade-style games, a handful of platformers, and is to ready to tackle point-and-click adventures. She’s also not human. Half way through a chat over coffee in a university cafeteria, Mike Cook – gamer, computer scientist, and Angelina’s creator – stops himself. “I have to avoid calling it ‘she’ and ‘her’”, he laughs. “Slightly unhealthy, but there you go.”

Angelina is an AI system developed as an experiment in automated game design, part of a vision in which AI is not simply a source of increasingly sophisticated NPC behaviour, but has a hand in designing games themselves. “Almost everywhere has a bit of procedural content generation whether it’s narratives, music, whatever”, says Cook, “and all of that is backed up with what we would call AI.” Cook is part of Imperial College London’s Computational Creativity research group, which, as he puts it, “investigates processes we call creative when we see humans do them and tries to simulate them in AI”.

Download the (free) digital edition of Develop 124 (February 2012) to read the full interview (page 44).

Update [13.02.12] You can now read this online.

Uncontacted Tribes?

Written for Winter 2011 issue of I, Science magazine.

Update [04.02.12] Since this piece was written, The Observer has published videos apparently showing topless Jarawa women being made to dance for policemen and tourists on “human safari”.

Update [06.02.12] After Stephen Corry left his comments below, I invited him to put across his point of view more formally in an interview posted on the I, Science website.

In January 2006, two Indian fishermen were killed by indigenous tribesmen when their boat drifted too close to North Sentinel Island, a tiny outcrop in the Andaman archipelago between India and Burma. When an Indian coastguard helicopter later approached the island to investigate, Sentinelese warriors repelled it with spears and arrows – but not before the helicopter’s down-draft had revealed the fishermen’s bodies lying in shallow graves on the beach. This at least put paid to local rumours that the unfortunate men had been eaten by this uncontactable tribe, a people reportedly without the ability to work metal or use fire.

Keen to know more about these isolated Andaman Islanders, I contacted Dr. Michael Stewart, an anthropologist at University College London. “It’s all fantasy, the idea of an uncontacted tribe!” he interrupts, when I broach the subject. “It’s a total fantasy. And the Andaman Islanders are a wonderful example of that. The Andaman Islands are one of the major tourist destinations for South Asian tourists. Tens of thousands, if not hundreds of thousands go there every year”.

It is the Sentinelese who are at threat from an encroaching outside world. Their Andaman neighbours, the Jarawa, have suffered disruption, measles outbreaks, and unwanted tourist attention since the 300km-long Great Andaman Trunk Road was built through their forest homeland. Private companies operate illegal sightseeing tours for curious outsiders to take photographs, while dislocated Jarawa beg at the roadside. Legislation has been put in place to offer some protection but the fate of these people may still end up being similar to that of the Native Americans. “When the Andaman Islanders throw things at people it’s because they know them and they’ve had a bad experience with them”, Stewart wryly suggests. “It’s precisely the opposite of an uncontacted people”.

The fantasy of unknown peoples is a compelling part of popular culture and promoted by TV programs like BBC2′s Tribal Wives. “It’s more a kind of romantic fantasy that it would be possible to really get away and hide – it’s a humanized version of the yeti story”, Stewart says. He mentions an episode of Tribal Wives featuring the Huaorani – a remote Ecuadorian tribe – which doesn’t quite manage to keep the airstrip the Houarani have built to receive tourists out of shot. Similarly, in The Tribe That Hides From Man, a famous 1970 documentary film about ‘first contact’ with a Brazilian tribe: “If you watch it with a critical eye, it becomes quite clear that these people have steel axes – steel axes don’t grow in the Amazon jungle, they’ve got them through barter with other people”.

That’s not to say there aren’t pockets of truly isolated people, but it’s more accurate to think of them as reclusive than uncontacted. “There are Huaorani who are living in the Amazon who travel around in very small groups – just a family – a man, a woman, and some children – who really do avoid, as far as is possible, contact with other people. There are people who systematically avoid contact”. The Mbuti – an indigenous pygmy people from the Congo region of Africa – are another group who are “ambivalent about contact with outsiders”, as Stewart puts it. For the Mbuti a history of indebtedness and exploitation at the hands of neighbouring tribes led them to shun interaction.

If such people have deliberately sought isolation, there are obviously ethical questions about studying them. “It’s a constant source of self-questioning”, agrees Stewart. Generally, he believes social research is for the public good, noting parallels between much ethnographic research and journalism. As in the Leveson Inquiry, the issue is where to draw the lines. “Somebody who in some way betrays the secrets of a population they do research with – if that includes where they hide out, as it were – that would be universally condemned”.

But are there truly no unexplored peoples left in the world? “If people don’t want to be studied then they don’t get studied”, he says. “Famously, anthropologists don’t study the super rich of the Western world, who don’t want to have their lives exposed – there’s no ethnography of the Saudi royal family – these people stop you. Anthropologists have tried to do ethnography of the super rich and the super powerful but they don’t want to let anthropologists in”.

And the super rich are a lot better than indigenous tribes at keeping outsiders away.

///

Huaorani
Location: Ecuadorian Amazon
Population: 2500-4000

Mbuti
Location: Democratic Republic of the Congo
Population: 30000-50000

Sentinelese
Location: North Sentinel Island
Population: ~250 (incomplete but official census: 39)

Jarawa
Location: western side of South Andaman and Middle Andaman Islands
Population: 250-300

Spinifex
Population: ~150 in 1950s. So few that their lands were considered uninhabited and used as an atomic-bomb test site. They have since been allocated a protected conservation area.
Location: Great Victoria Desert, Western Australia.

Doggone Drunks

Written for Felix, Imperial College London’s student newspaper.

There’s undoubtedly a debate to be had about alcohol, but the Social Issues Research Centre ignores basic chemistry to push a click-bait message.

For all the millions it spends on cultivating an image of arch sophistication, Stella is still stuck with its “wife-beater” epithet – even more so now it’s become the tipple of choice for tosspot terriers. But the story of a Staffordshire Bull Terrier attacking a child after someone poured Stella down its throat isn’t the only piece about alcohol abuse that stood out recently.

A couple of weeks ago, the online BBC News Magazine ran an opinion piece (“Is the alcohol message all wrong?”) by Kate Fox, co-director of the Social Issues Research Centre (SIRC), a not-for-profit organisation based in Oxford that researches and monitors social and cultural trends. SIRC conducts most of its research by reviewing social-anthropological studies. In the BBC article, Fox seeks to put paid to “bizarre beliefs and weird customs” such as the notion that “heavy drinking causes promiscuity, violence and anti-social behaviour”. A key claim is that “[t]he effects of alcohol on behaviour are determined by cultural rules and norms, not by the chemical actions of ethanol”.

Now, I’m no expert on alcohol – not scientifically speaking – but that sounds odd to me. Having only just escaped the death penalty with a plea of diminished responsibility, I’m not sure that dog would be too pleased with the suggestion either. Looking for a second opinion, I contacted Dr. Robert Patton of King’s College London, who is the Health Services Research Coordinator for the South London and Maudsley NHS Trust Addictions Division, and who worked for the Home Office Drugs Prevention Initiative as a consultant in the 1990s.

“I had seen that article and did raise an eyebrow at those comments”, Patton said. I asked him about the idea that changes in behaviour were caused by cultural norms rather than chemicals. “While it is true to say that there is an expectation of the effect of alcohol that does to an extent modify behaviour”, he said, “the fact is that alcohol is a drug that does influence behavior in many ways, particularly those concerned with impulsivity (and restraint), aggression and coordination”.

Even judging by the comments Fox’s article received – over 1000 in half a day, many of them removed by moderators – SIRC’s position seems to be somewhat controversial. Helpfully, one of the commenters linked to a British Medical Journal editorial from way back in 1999 that expressed concern about SIRC’s close connections with MCM Research, a “commercial market research company” with several drinks companies as clients, including The Amsterdam Group, which numbers Bacardi-Martini, Bass Brewers, Carlsberg, Guinness, and Heineken among its members.

The BMJ also discussed SIRC’s criticism at the time of the media’s role in health scares (SIRC also apparently coined the word “riskfactorphobia” back then, but we’ll let that slide) and presciently asked, “how seriously should journalists take an attack from an organisation that is so closely linked to the drinks industry? If, for example, the centre attacked newspapers for exaggerating the effects of alcohol and thereby causing an unnecessary scare, could the centre put its hand on its heart and claim that it was totally neutral on the issue?”

Keen to get a clearer idea of where the organisation was coming from, and whether the BMJ’s concerns were still appropriate today, I spoke to Peter Marsh, SIRC’s other co-director. Marsh told me that MCM Research was “not actually trading in its own right very much these days” but that the work now goes through SIRC. SIRC’s website states that it is now the host for reports and materials of both groups. But on the question of how SIRC maintained independence in its research, Marsh was very keen to establish that the centre hasn’t done work for the drinks industry for several years, and that the last commission in this area “in a 5 year timeframe” was for Greene King on the role of the pub in the local community. That said, he also told me that Fox’s recent opinion piece is based on work begun 15 years ago.

But what of Fox’s assertion about the chemical effects of ethanol – or lack of them? Isn’t it dangerously misleading to suggest that drunken behaviour is simply a cultural norm that people conform to? “Except it happens to be true”, Marsh said, reiterating Fox’s observations, “in this country we expect [alcohol] to make us aggressive … You don’t get that in many other countries”. According to Marsh, “The only common chemical action is to make people go to sleep … the idea somehow that just consuming alcohol compels people to go and beat people up is not supported, certainly by our reading of the cross-cultural evidence”.

Whether or not SIRC have conflicts of interest, it seems irresponsible to draw such stark conclusions about the chemical effects of alcohol solely from anthropological evidence. SIRC’s overall position – that cultural aspects of alcohol abuse need addressing – is uncontroversial. The UK certainly has a problem with alcohol and fresh ideas are needed, but a debate that begins with an equivocation over what it is to be drunk in the first place is not the way to go.