Monday, May 26, 2008

New Meaning for the Term ‘Computer Bug’

Researchers in the US have created ‘living computers’ by using genetically altered bacteria. The findings of this research demonstrate that computing in living cells is feasible. It also opens the doors to a number of potential applications including data storage and as a tool in manipulating genes for genetic engineering.

The research team was from the biology and mathematics departments of Davidson College, North Carolina and Missouri Western State University, Missouri, USA. They achieved execution of DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP).

The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. The pancakes are of different sizes, each of which has a golden and a burnt side. The largest pancake must be on the bottom and all pancakes golden side up. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack.

A system was designed that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA. Inversions (or “flips”) of the DNA fragment pancakes were driven by genes added from the Salmonella typhimurium Hin/hix DNA recombinase system. The system used sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted. The time required to reach the mathematical solution reflects the minimum number of flips needed to solve the burnt pancake problem.

It is believed the system has the potential to be scaled up to larger and more complex problems and by exploiting the infinitesimally tiny scale of DNA and bacteria, ‘living computers’ could carry out complex parallel processing problems that would otherwise utilise very large and expensive electronic computing systems. Since bacteria multiply naturally and have their own repair mechanisms, ‘living computers’ could be less expensive and require less space compared with conventional devices. Additionally, ‘living computers’ could evolve through DNA mutations to solve new problems.

For further reading:

Malcolm Keth (41751819)

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