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 The Power of Plant Clock Computing

This story is from the category Computing Power
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Date posted: 05/03/2010

A newfound ability to model the complex feedback loops that control plant clocks could have important implications for computing. One of the limitations of conventional thinking in computation is that computable functions proceed in a sequential manner, one independent step after another. When computer scientists talk of parallelism, they usually mean carrying out more than one of these independent linear computations at the same time.

In the biological world, things are more complex because steps in biological computations may not be independent. Take, for example, the circadian rhythm in plants, the 24 hour cycle of biochemical processes that govern behaviour. The cycle has various important features such as the ability to synchronise with an external periodic light source and to continue to oscillate even in the absence of variations in illumination.

Biochemists have long known that these cycles are the result of various biochemical feedback loops in which the transcription of genes is boosted and damped.

Each feedback loop is part of a hugely complex biochemical network and is affected by many factors simultaneously, not least of which is the presence or absence of light and the state of the network with which it is most closely linked, which themselves may be interdependent feedback loops.

Of course, plant clocks have been studied for hundreds of years and a huge amount is known about how they work, particularly about Arabidopsis thaliana, a small flowering plant that is the standard object of study for plant biologists.

The trouble is that nobody has been able to accurately model the behaviour of these rhythms from first principles.
That's because these processes do not involve independent sequential steps, so conventional computational methods are just not up to the job. Biochemists need some other way of thinking about their problem.

As luck would have it, just such a system has been waiting in the wings. Process algebra is a form of computation that can handle multiple simultaneous interdependent steps and this makes it perfect for modelling these tricky biochemical networks and the feedback loops that drive them.

The trouble is putting it into practice: process algebra is not an easy toy to play with.

See the full Story via external site: www.technologyreview.com



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