What is Synthetic Biology?
Diana - So Jim, what do we mean by synthetic biology?
Jim - Well, synthetic biology has quite a broad, some might say ambiguous meaning, and if you'd look up synthetic in terms of the dictionary and its definition, you've got two accepted meanings for synthetic and that's mirrored in the activities in the field. So synthetic can mean artificial, something derived and unnatural, and there are many people looking at systems which are artificial and used in biology in the sense that they don't come from the natural world. But as well as this, you've got the original meaning of the word synthetic, derived from its root which is - that it's pertaining to construction and that's really, one would argue, is one of the primary efforts in synthetic biology is to build new techniques for constructing or rearranging biological systems.
Diana - So, if we're building things with biology, what kind of disciplines are involved in that?
Jim - Well it's highly interdisciplinary because you've got the understanding of the biological systems that's required, as well as these formalisms that come from engineering. So the idea that you can construct biological systems is based on the idea of modularity and having individual components that you can put together - in a crude sense, like Lego blocks, in that they're modular pieces that can be put together. But also, the complexity of biological systems which work in a very different way from normal man-made artefacts where a man-made artefact might be designed from the top down and things are connected from one to the other, but in a biological system, things are emergent, things have simple bases, but it's the interactions that build the kind of complexity that we see inside our biological systems, and that applies to artificial ones as well. It's there that computational science plays a major role in our understanding of these systems and is required not just for understanding but also design.
Diana - Can you give some examples of what synthetic biology has been used for so far?
Jim - Well it's a very nascent field, a very early field and in fact, in a way, the iGEM competition, this Genetically Engineered Machine competition that you'll be talking about in a minute is one of the major inputs into the field. It's unusual because it's essentially a student driven competition and it's driven by this conception of people coming together and sharing components or modules. The idea that you can take these simple functional elements and put them together into more complex systems is something that's quite new in biology. We've been doing genetic engineering of systems for something like 35 years now as a field and there's been this relative huge growth in our ability to manipulate the basic systems. An anecdotal way of looking at that, for example, is if you use the kind of understanding that we do have, you could ask any two biologists on the planet to put something together. Any two molecular biologists could assemble a system if you defined it for them. But they'd do it in a completely different way. Each individual would use bespoke techniques to construct this and that's quite unlike any other form of engineering at this point. And so, what synthetic biology is all about is putting in place the kind of rules and components that allow you to formally assemble systems in a regular routine way which every other form of engineering adopts.
Diana - So, this isn't just biochemicals. It's bio systems as well. You're combining lots of different systems to give one outcome.
Jim - Absolutely and I guess it's those lifelike properties that we take for granted, the fact that things can organise themselves and maintain themselves, and repair themselves. They're the kind of properties that people need to deal with the major challenges in sustainable resources and things like sustainable agriculture where you've got a biological basis. And to be able to re-engineer systems, you require this very different approach.
Diana - One thing that science fiction likes writing about are biological computers. How are computer scientists looking at this at the moment? What's been done so far?
Jim - The main approaches have been to take the idea that you can have simple components and there's this concept of emergence - you can take simple underpinnings and they don't just mean parts that you can put together, but also the interactions that underlie systems which might be comprised of simple elements. When it comes down to it, the kind of biology that we're talking about here, there are more similarities with social systems and economic systems. We have complex behaviour and complex phenomena coming out of local interactions. In the synthetic biology case, its interactions between genes and gene products in wider, say social situations - interactions between individuals. You have simple drivers like in a society if you're hungry, you go and get food, and someone fills that because they need to get food themselves so they will provide food for other people. And you have the kind of complex social systems you get around food and consuming food and society, which are driven by this very simple basic interactions. It's a crude analogy, but in biology, you need to be able to think of how you could assemble those kind of systems - these complex systems, from these simple interactions. Computer scientists have the tools which allow one to address these complex interactions and to look to engineer self organisation.
Diana - So, they can use these tools to look at the organisation, but has anyone actually built something that can store bits, data, binary information?
Jim - Well, there's a number of crude attempts to put together systems which will retain information, have genetic memory for example and information processing. So essentially, all genetic systems are based around this idea of taking inputs and providing outputs. So it's essentially like a cellular or genetic computer. There are many small examples - bio sensors for example, where one can take a simple input which might be the concentration of a chemical and produce a genetic response which produces some output, for example a pigment that you can see.
Diana - And what do you think is next?
Jim - The concept of synthetic biology and this idea of having more formal engineering approaches of manipulating genetic systems is not so much application oriented but it's a whole new process, a whole new way of looking at biological systems and being able to manipulate them. And those of us in the field see that it may all make a major contribution to the kinds of things that we're moving towards in terms of sustainable technologies which will be based on biological feed stocks and replacing some of the rather damaging ways that we deal with the environment at the moment and to move towards sustainable technologies.
Diana - Well, a little bit of plant fertiliser certainly sounds better than the 600-watt power unit that I've got on my computer at the moment!