November 16th, 2012 | Category: Beginner's Guides, Blogs, iGEM, Synthetic Biology | Leave a comment

Guest post from Team Exeter’s blogger

As the dust settles on iGEM 2012, I have asked one of the Exeter 2012 team and iGEM blogger for her thoughts on a summer of iGEM.

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Synthetic biology is often automatically assumed to be genetic engineering (which is what I thought before iGEM) but actually it’s more genetics for engineers. At the start of iGEM the Parts Registry sends hundreds of freeze-dried genes to you, and then as if you’d been sent a mixed box of electronic components, you build a circuit and stick it in your prokaryotic circuit board. New genes and gene combinations (‘parts’) are encouraged, as well as characterising and categorising everything for future use – when you’ve made something you send it back to the registry and the whole field slowly grows this way. You could have accidentally massacred your E. coli with a gene that unexpectedly kills them, but you send it in and a few years later it’s the standard way to get rid of microorganisms which have been too lazy to pick up the right genes. Anything might be useful and can be utilised to create organisms that hopefully do something practical and world-saving, and it makes sense for it not just to be designed by biologists. Genes are not just genes, they are a computer program, or the blueprint for a set of interlacing cogs, or a circuit.

Fig. 1 Early days.

For me, the first few weeks of iGEM were a disorientating scramble, which in retrospect is not surprising. There were training days for lab and team work when professors would darkly mutter that cross-disciplinary collaboration was a big ask. When one of the physicists asked me if it were possible to make some calculating binary gated feedback malarky in a living system I said I didn’t know. I might have answered that if it could be done it was likely that nature already had an example of it, but frankly I had no idea what he was talking about. Somehow though, at some point in the first few weeks, we became an authentic team. The non-biologists spoke fluent biology and Freddie made a pretty stellar attempt at speaking physics (it involved swapping all adjectives for the word ‘quantum’). We decided, in short, to go for an authentic synthetic biology idea: getting E. coli to synthesise existing and new polysaccharides, which was a platform for everything from developments in medicine to allowing industry to design and engineer polymers based on specification.

Fig. 2 Physics demonstrating how cloning should be done, from first principles.

Lab work seemed to start a lot later than planned (there was a really weird issue with the synthesis of one of the new genes we wanted) but it was the highlight of the whole thing for me, which is good because it took up months. No undergrad should predict how they’ll cope in that sort of lab environment: first and second year lab sessions in bioscience are nothing like running your own project in a working lab. I found it easier than I expected when I got the hang of it, and it’s also worth mentioning that the three physicists who helped us took to it like ducks to water. Our lab work didn’t get as far as we wanted it to but it’s hard to predict at the start what’s realistic (although multiple professors told us we were barking mad, so we could have guessed). Despite spending every lab session prior to iGEM in a minimalist way before escaping as quickly as possible, I started, over the summer, to find lab work weirdly pleasing, to get as much crammed into a day as possible, and as the deadline drew closer we began seeing how long we could stay in the lab before someone came to shout at us or the building locked us into a random stairwell.

In a nutshell, iGEM work isn’t an academic assignment. There is no final percentage for each assignment and your creativity is as essential as knowing the facts and having drive. Teamwork is vital but finding your niche can be hard to start with (it was for me) and the whole thing to start with is like being thrown collectively into an ocean and finding that a biologist might know what a promoter is, but unless they remember to explain it to a mathematician the whole lot will sink. If you put effort in it’s unbelievably rewarding and if you’re feeling unenthusiastic about the lack of imagination in consecutive pieces of coursework it will give you what you want. My strengths and weaknesses became very obvious and I now see from the first interdisciplinary project I’ve worked on that one field of academia can’t be enough. I think finding this out was one of the best chances I’ve ever had.

Mary Beton.

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