November 2008 Archives

The European Science Foundation is gearing up for its own synthetic biology research programme. EuroSynbio will become a theme under the foundation's Eurocores scheme assuming ten or so national funding agencies come up with the necessary promises of money by December 10. If that happens, the first calls for proposals will be published on December 20, with the first projects expected to get underway at the beginning of 2010.

Funding levels for Eurocores programmes typically run at around €5m to €10m. If it goes ahead, EuroSynbio will run for four years and will cover three main areas. One marks a key difference with the approach to synthetic biology that we could call the "MIT school" and the "European school". The MIT school tends to work on the basis that biology can be made so modular that you can assemble parts into a living system and they will work as is. The European school assumes that evolution is always there and will attempt to modify whatever system you build. Researching into the problems raised by evolution is not isolated to Europe but I've heard it discussed more here than in the US.

The first research focus in EuroSynbio then will be to look at "system assembly and molecular and cellular complexity in the context of Darwinian evolution".

The second focus concentrates on computational design tools and the third on the "social context", just in case you didn't think there were enough studies on ethics, governance and public dialogue in this business already.

Teams taking part in this year's International Genetically Engineered Machine (iGEM) came up against an inadvertent initiative test. And it was one that set a lot of teams back weeks or even months as they vied for the top prizes.

One of the big promises of synthetic biology in the world of iGEM is that you can glue off-the-shelf bits of DNA together to make new 'circuits' that effectively reprogram a microbe such as Escherichia coli. Most of the time, people use a mixture of readymade parts and bits they assemble themselves. The student teams who take part have to provide the DNA components they build to a registry of parts that can be used by future teams. That way, the registry of 'Biobrick' parts keeps growing.

But there's a scaling problem. As more Biobricks are made and more teams take part, it gets trickier to send out the DNA. In the previous year's competition, the Biobricks were sealed in 96-well plates before being delivered. If you multiply a couple of thousand parts by 80-odd teams, that's a whole stack of well plates. So, the organisers decided to try sending out DNA spotted onto books of filter paper and then dried. It was a much cheaper and, apparently, more practical option.

Unfortunately, there was a snag: it didn't work. The phrase of the competition this year was "we tried to extract the DNA for this part from the Biobrick book but we couldn't". Teams ended up cadging DNA from each other - often from the samples delivered the previous year that they had kept in the fridge.

When iGEM organiser Randy Rettberg asked for a show of hands on who had trouble extracting the DNA, I don't think a single hand stayed down. When asked who did succeed, only the members of one team - Caltech - thrust their hands into the air.

I asked Josh Michener of the Caltech how they managed it. The approach they took was to ignore the protocol published in the book and use some super-competent cells from a commercial supplier to get enough DNA to work with. The trouble, as Rettberg said later, was that the ordinary cells recommended for iGEM work would work but deliver less than one colony of active bacteria. For most people, that meant no positive result. This is one of the factors that is likely to lead to a shift in the way that the DNA in the Biobrick registry is delivered and, ultimately, stored.

Splitting the winners up regionally isn't ideal considering the organisers are trying hard to keep iGEM as a single, global event. But I was compiling this list in the iGEM Europe workshop late this afternoon after the competition closed. In the meeting, Sven Panke of ETH Zurich said he tried to compile a list of European winners but could not get them all down. Score one for shorthand, although I didn't try to record the bronze, silver and gold winners: those are on long lists sitting on photos that are currently importing into Lightroom.

I've split the teams into non-US and US. And it shows how well universities outside the US are now doing in spite of being later to get into synthetic biology and, in some cases, having the disadvantage of comparatively short summer breaks – the time when teams get to do most of their lab work.

A special mention needs to go to IIT Madras who fell foul of the US visa system. They won two prizes including one potentially powerful technique: "Took simple idea of hybridising promoters and pushed it all the way," said Stanford's Drew Endy. But the US government would not give them visas to actually attend the event.

I missed one award - experimental measurement - because I was changing the lens on the camera to get ready for the final awards (this one reason is why journalist multi-skilling doesn't really work in practice). But I'll pick those up from the recording later or just crib it from the iGEM site if that gets updated before I get the final list together. Update: It's now in place and it's another European team: Bologna.

Non-US
Grand prize: Slovenia
First runner-up: Freiburg
Other finalist: Taipei

Health: Slovenia
Manufacturing: Imperial
Foundational advance: IIT Madras
New BioBrick part, natural: Imperial
New BioBrick part, engineered: IIT Madras
Human practices: Heidelberg. Honourable mention for Valencia
Experimental measurement: Bologna
Modelling: BCCS Bristol
Wiki: TU Delft
Poster: Heidelberg
Presentation: Heidelberg

US
Second runner-up: Caltech
Other finalists: UC Berkeley, Harvard

Food and energy: Harvard
Environment: Brown
Software: UC Berkeley Tools
New application area: UCSF
Poster: UCSF (Honourable mention)
Presentation: Washington (Honourable mention)

The iGEM competition has now reached such a size that, if it grows anymore, it might be too big for even the sprawling MIT campus to host. With 800 participants split across some 80 or so teams, the Kresge Auditorium is almost full and the presentations sessions needed to be spread around the wonky architecture of the Stata Center.

The competition probably won't grow the way it has over the past four years - the first one in 2004 had just five teams and seven people. But the organisers are working on the basis that the 2009 competition could be half as big again. In 2010, the organisers think there could be 180 teams and no less than 1800 students.

MIT's Randy Rettberg said the organisers are now looking at whether to move the jamboree, the focus of the competition, to a larger, dedicated convention centre and away from MIT. The growth may also mean the created of a more formal structure for the competition - hosted possibly by a not-for-profit organisation.

One of the early concerns seems to have gone away, said Rettberg in his speech as the judges deliberated over who would win the grand prize underneath the Kresge Auditorium.

"For several years, I have been explaining synthetic biology by saying we have a question to answer. Can simple biological systems be built from standard interchangeable parts and operated in living cells? Or is biology so complex that each case is unique? People, said: 'Randy, this won't work.'

"Now," Rettberg added. "The question is starting to look a little silly. It is obvious you can do this, or least the undergraduates can."

Now it's a question of scaling. Rettberg says a good size for a competition like this is 55 teams - so it might make sense to divide the contest into four main groups, perhaps picking an ultimate winner out of that. It would allow relatively easy scaling to 220 teams overall. Rettberg said he prefers that approach to regionalising iGEM. As it stands, however, the aim is to keep everything together, although the projects are already grouped into seven classifications: environment; food or energy; foundational advances; health or medicine; manufacturing; new applications; and software.

However, this is the kind of problem a lot of people would like to have. There are conference organisers who would kill for a 50 per cent annual growth rate.

It's the end of the first day of the International Genetically Engineered Machine (iGEM) competition. Thanks to American Airlines, I wound up missing the first of the four main sessions. But I've almost managed to catch up on what I missed through the poster session that rounded off my time at the Stata Center today.

In the five years since competition first got underway, iGEM has not just grown in terms of numbers - there were just five teams who entered the 2004 competition; this year 77 teams from around the world presented their work in Cambridge, MA. Although it started as a competition for undergraduates, the age range has increased with some teams, such as the University of California at San Francisco, bringing high-school students onboard. Other than the advisors, the Lethbridge Calvin Christian School (CCS) team started off as all high-school students.

This evening, the judges had the unenviable task of whittling the 77 final entries down to six finalists. They get a second chance to describe their work tomorrow in the Kresge Auditorium at MIT in a bid to win the top prize.

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