BioSysBio:abstracts/2007/iGEM2006 Imperial College
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Engineering a synthetic molecular oscillator based on the lotka volterra dynamic model
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Oscillators and oscillatory systems are ubiquitous in everyday life, from the alternating current electricity that we use to the circadian rhythms that control our sleep and wake cycle. Already, synthetic biology has begun to take on the challenge of creating the first biological computer, starting with ETH Zurich’s 2005 iGEM competition entry for creating a biological NOR logic gate and a two bit counter as well as Harvard’s BioWire design concept to transmit a signal down a length of bacteria. In computers, clocks are used to synchronise the components in order to prevent overflow of information within the system. On a broader scale, these clocks synchronise time around the world and are also used to determine the winner of eBay bids accurate to seconds, perhaps a more recognisable example to our modern life.
Why would we want to create a biological computer? Consider first the human brain, a complex network of cells intercommunicating to create our thoughts and conduct the human body symphoniously. If we can mimic this type of system in other non-neural type cells, we might be able to harness the massive scale parallel computing power inherent to biological systems.
Once we are able to create a biological oscillator, we can then move to synchronise several biological computers paving the way for an internet-like system controlled by bacteria. Further developments in biological to electrical interfacing could mean that communication between electrical devices and biological devices would be seamless. This can potentially integrate the existing infrastructure and novel biological approaches so the current technology would not be drastically displaced, but gradually replaced by biological machines. Moreover, the quest for self-reproducing machines has finally succeeded. Wouldn't it be great if our computers upgraded themselves? Made themselves faster every 30 mintutes? Genetically engineered bacteria indeed have this potential and are only limited by their lifespan and the biological reaction rates. Unfortunately, biological reaction rates are relatively slow when compared to electrical signals, but consider 100 years ago when we knew very little about electricity and how to harness the power of electricity. Biological engineering is at that stage now, and we cannot expect to surpass in a few years the engineering foundations that have been perfected throughout the ages.
Stable biological oscillations are seen to be produced with accuracy in predator-prey relationships, where we assume an exponential growth of prey and insatiable predators. The Lotka-Voltarra model for predator-prey interaction can be implemented given certain assumptions and given that we are able to find biological equivalents to predator and prey. Of course, a molecular predator-prey system would have different assumptions and thus different equations, but the fundamental predator-prey relationship can still hold. The assumptions and adaptations to the Lotka-Volterra system will be discussed further in the modelling document. Once we find molecules that can act similarly to predator-prey interactions, the next step is to successfully implement the system into bacteria!
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