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Monday, 10 September, 2001, 15:39 GMT 16:39 UK
Processing power of single cells
The organisms are experts at sorting and shuffling DNA
By BBC News Online technology correspondent Mark Ward in Prague

One of the oldest forms of life on Earth has been revealed as a natural born computer programmer.

Scientists studying single-celled organisms called ciliates have found that the tiny animals are experts at sorting, shuffling and splicing DNA when they reproduce.

Some of the repertoire of tricks ciliates use to untangle their DNA resemble the techniques that computer programmers use to make software more elegant and robust.

The researchers believe that by using some of these techniques they can do a better job of harnessing the vast information processing power of DNA.

At least 2bn years old

Ciliates are known to be at least two billion years old, and are found almost everywhere on the planet and flourish even in the most hostile climates.

"They are one of the most successful organisms on Earth," said Gregorz Rozenberg, director of the Leiden Centre for Natural Computing in The Netherlands.

They are one of the most successful organisms on Earth

Gregorz Rozenberg
The best known ciliate is called Paramecium, and all members of this order get their name from the tiny hairs, or cilia, that all these single-celled organisms use to get around and trap food. Cilia means "eyelash" in Greek.

Dr Rozenberg believes that ciliates have been so successful because of what they do to DNA when they reproduce.

Uniquely, ciliates possess two nuclei. One large nucleus is used to keep the organism running on a day-to-day basis and is made up of separate strands of DNA, each one holding thousands of copies of the same gene.

The other, smaller nucleus contains a long, single strand of DNA that is swapped during reproduction.

After reproduction, the micro-nucleus is used to build a fresh large nucleus for the new organism. The micro-nucleus is shredded and the resulting segments are shuffled to ensure that each strand holds copies of a different gene.

Computational processes

Dr Rozenberg and his colleagues have found that the techniques used to create the strands of common genes bear a strong resemblance to the "linked lists" technique employed by many computer programmers since its first use in the late 1940s.

The technique is an economical way of searching and preserving the connections between lists of information.

While the reproductive strategy of ciliates is unique, Dr Rozenberg believes that the techniques they use to sort DNA, which includes methods of looping, folding, excising and inverting sequences, are common to many organisms.

"One of the fields of DNA computing is looking at the computational processes going on in living organisms and that's where ciliates fit very well," he said.

DNA: Attractive medium

The field of DNA computing was kicked off in 1994 when Leonard Adleman used strands of DNA to solve a simple example of a mathematical conundrum known as the Travelling Salesman Problem. This involves working out the shortest path that takes in all points on a given route.

By generating DNA sequences representing all possible routes and mixing them in a test tube, Dr Adleman was able to find the quickest route.

DNA is an attractive computational medium because it is small but can process lots of information at the same time.

Tackling a Travelling Salesman Problem that has lots of locations with a supercomputer can take years because even the most powerful supercomputers use only a few thousand processors.

Rather than find new techniques to carry out DNA computing, Dr Rozenberg believes that harnessing the information processing abilities of living organisms to tackle tricky computational problems could be more fruitful.

He is working with microbiologists from the University of Colorado, US, on ways to use ciliates for real DNA computing.

Dr Rozenberg unveiled his work at the 6th European Conference on Artificial Life being held in Prague this week.

See also:

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19 Feb 98 | Sci/Tech
Computers come to life
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