What’s going to be the quickest way of achieving some kind of radical nanotechnology, in which sophisticated nanoscale machines carry out complex chemical tasks? Since nature has evolved sophisticated and effective nanomachines that are optimised for the nanoscale environment, an obvious approach is to take components from living systems and reassemble them to do the tasks you want. This is the approach of bionanotechnology. But we could take this logic further. Rather than rebuilding systems from individual biological components, we could take a complete organism, strip out the functions we don’t want, and patch in the genetic code for the components we need. This top-down approach to bionanotechnology is exactly what is being proposed by a new company, Synthetic Genomics Inc, founded in June by Craig Venter. Venter is, of course, the scientist behind the private sector venture to sequence the human genome. The initial focus will be on the use of these partly synthetic organisms to make alternative fuels such as hydrogen and ethanol.
The vehicle for these strange hybrids is likely to be the parasitic bacteria Mycoplasma genitalium, an unwelcome inhabitant of some people’s urinary tracts, which currently has the distinction of having the smallest known genome. This is contained on a mere 580,000 base pairs of DNA, coding for about 480 proteins and 40 RNA molecules. Venter’s group systematically knocked out genes from this organism in an attempt to find a so-called minimal genome. One can think of this as the simplest possible fully functioning life-form (of course, such an organism would be very restricted in the environment it can live in). In Venter’s 1999 paper in Science, Global transposon mutagenesis and a minimal mycoplasma genome, a further 100 proteins were eliminated without fatally compromising the organisms’ existence. Having stripped the organism down to a minimal level of complexity, the idea would be to reinsert synthetic genes coding for whatever machinery you require.
There are two questions to ask about this: will it work, and should it be done? It’s certainly a very bold commitment to a very reductionist view of life: in their words “using the genome as a bio-factory, a custom designed, modular cassette system will be developed so that the organism executes specific molecular functions”. As for the ethics of the enterprise, I’m sure even the most enthusiastic technophile would at least pause to think about the implications of attempting to re-engineer life on this scale. Indeed, Venter’s group commissioned their own bioethicists to think about the issues, and this ethical commentary accompanied their original Science article. This is just the beginning of a very big story.
I love it when people talk about the research I do. 😉
One of the big challenges in synthetic biology is to predict the intracellular dynamics of an organism, given that you are inserting some DNA sequence in a plasmid or in the organism’s chromosome. If you can do that, then you can determine what DNA sequences are necessary to get a certain type of dynamics…before you start the experiments. That’s the big difference between what ‘synthetic biologists’ and traditional molecular biologsts are doing: synthetic biology uses mathematics to engineer biological systems. Typically, molecular biologists use intuition and a lot of trial & error to identify useful mutations. (But I think that’s changing too.)
Actually, the mathematics used to describe biological systems at the single cell level will be very useful in other ‘small’ systems..such as describing polymers, crystals, ‘nanobots’, etc etc
For a bit of shameless self-promotion, here’s the url of the research (well, my advisor’s research):
http://www.cems.umn.edu/research/kaznessis/computational.htm
-Howard Salis
Thanks for leaving that URL, it’s very interesting and I absolutely agree with you that this kind of math is going to be extremely useful for understanding the operation of many nanodevices. You seem to have found a very good PhD topic… (a good department, too – I know quite a few of the faculty there).