How to engineer a system that fights back

Last week saw the release of a report on synthetic biology from the UK’s Royal Academy of Engineering. The headline call, as reflected in the coverage in the Financial Times, is for the government to develop a strategy for synthetic biology so that the country doesn’t “lose out in the next industrial revolution”. The report certainly plays up the likelihood of high impact applications in the short term – within five to ten years, we’re told, we’ll see synbio based biofuels, “artificial leaf technology” to fix atmospheric carbon dioxide, industrial scale production of materials like spider silk, and in medicine the realisation of personalised drugs. An intimation that progress towards these goals may not be entirely smooth can be found in this news piece from a couple of months ago – A synthetic-biology reality check – which described the abrupt winding up earlier this year of one of the most prominent synbio start-ups, Codon Devices, founded by some of the most prominent US players in the field.

There are a number of competing visions for what synthetic biology might be; this report concentrates on just one of these. This is the idea of identifying a set of modular components – biochemical analogues of simple electronic components – with the aim of creating a set of standard parts from which desired outcomes can be engineered. This way of thinking relies on a series of analogies and metaphors, relating the functions of cell biology with constructs of human-created engineering. Some of these analogies have a sound empirical (and mathematical) basis, like the biomolecular realisation of logic gates and positive and negative feedback.

There is one metaphor that is used a lot in the report which seems to me to be potentially problematic – that’s the idea of a chassis. What’s meant by this is a cell – for example, a bacteria like E.coli – into which the artificial genetic components are introduced in order to produce the desired products. This conjures up an image like the box into which one slots the circuit boards to make a piece of electronic equipment – something that supplies power and interconnections, but which doesn’t have any real intrinsic functionality of its own. It seems to me difficult to argue that any organism is ever going to provide such a neutral, predictable substrate for human engineering – these are complex systems which have their own agenda. To quote from the report on a Royal Society Discussion Meeting about synthetic biology, held last summer: “Perhaps one of the more significant challenges for synthetic biology is that living systems actively oppose engineering. They are robust and have evolved to be self-sustaining, responding to perturbations through adaptation, mutation, reproduction and self-repair. This presents a strong challenge to efforts to ‘redesign’ existing life.”

2 thoughts on “How to engineer a system that fights back”

  1. Would flu lab-on-a-chip sensors have a “soft” component? Does the part of a sensor that captures a pathogen need to mimic lung tissue closely?

    Before @home bioexperiments probably want to have a biosensor grid and administrative Rapid Response capabilities. I’m wondering if a biosensor stimulus package makes sense (microchips are product with longest supply chain says google).
    Wouldn’t the limitations of cell-based bioreactors be limited ranges of temperature, pressure, etc., vs. metal bioreactors? 95% of rare-Earth metals are mined in China, 80% of CNTs manufactured there. I’d say they’ve already won the race to spawn next IR unless Himalayas dry up (hockey countries would then rule).

  2. If I were to make a “chassis” for synthetic biology i would start real simple and more synthetic than biological-
    1. Start with a thin tube (~10 microns diameter)
    2. then put a lipid membrane
    3. work on making the membranes selectively permeable
    4. seal off a cross section of the tube with two selective membranes
    5. fill the zone between the membranes with the right kind of bio-kleptic machinery
    6. in order to take the reactants from one selective membrane and output products through the other membrane. No other functions.

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