Survival of the fittest for Ireland’s emerging bioinformatics sector

12 Feb 2009

The 200th anniversary of Darwin’s birth sees the dawn of Ireland’s bioinformatics sector.

Charles Darwin, born 200 years ago today on 12 February 1809, revolutionised science and modern thinking with the publication of The Origin of Species. His theories on evolution and natural selection are still hugely influential today.

However, whereas Darwin had to rely on observations of the external characteristics of animals, today his theories are being confirmed through bioinformatics. This new area of study is based on a marriage of biology and computer science, and Irish universities are leading the field.

Bioinformatics involves using computers to analyse molecular biology data, especially genome data. “Our genetic material is called

DNA. The genome is the unique sum total of all the DNA in each of us,” explains Professor Des Higgins from the Conway Institute of Biomolecular and Biomedical Research at University College Dublin (UCD).

Supercomputers known as genome sequencers are used to extract genetic information.

“To determine the genome sequence, you chemically extract the DNA from some biological material (eg cells). The DNA is then chopped up through a variety of procedures and run through machines that determine the sequence of small parts of it. That information is then assembled on a computer.

“When Darwin was looking for links between the species, he was only able to use what he could see in front of him. Using sequences, you can see what is related to what in unbelievable detail, and the amount of confirmation has been astonishing,” Higgins explains.

“The amount of detail means that we can look at the process of evolution – how evolution happens, mutation by mutation – and how natural selection acted to make evolution happen over the past four billion years. You can compare genes and genomes using computers to try to reconstruct the evolutionary events that have given rise to what you have today.”

The computers and programs used to sequence genomes have come a long way since bioinformatics was first developed in the Eighties. It took 13 years to sequence the first human genome, a project that involved huge international collaboration and ended with a positive result in 2003.

“DNA code is made up of four letters – a, c, g and t – and our entire human genome is three billion letters long – that’s enough data to fill a whole room. At UCD, we have recently taken charge of two brand-new, very high throughput sequencing machines worth a few hundred thousand euro each. Each one of those is capable of sequencing something like an entire human genome in a few days,” says Higgins, indicating the speed and extent of developments in bioinformatics.

Higgins is Ireland’s most cited scientist, thanks to his work in developing a computer program named Clustal in the Eighties, which is now used in almost every medical laboratory in the world. It is the most widely used bioinformatics program worldwide, and Higgins and his team continue to develop and update Clustal today, thanks to funding from Science Foundation Ireland.

At National University of Ireland, Maynooth (NUIM) bioinformatics has become so popular that the university has developed the first undergraduate degree in the subject in the country. Recently named University of the Year 2008, NUIM has established itself as one of the top centres of bioinformatics research in Ireland.

Dr James McInerney, principal investigator in the bioinformatics department, believes the discipline could yet play a part in bringing back to life species that are extinct due to natural selection and the survival of the fittest.

“I always thought that was the stuff of science fiction, until recently. Now I think it will happen. It’s quite possible that we could use bioinformatics to reconstruct extinct genomes on computers, make the DNA and then introduce this DNA into an appropriate recipient cell and induce the cell to grow. You could possibly bring back woolly mammoths, sabre-tooth tigers, and so on.”

The genome of the woolly mammoth has already been sequenced, and researchers are currently working on sequencing the Tasmanian tiger, but McInerney is most excited about the ‘missing link’ between man and apes. “The first Neanderthal genome is about to be published and that will be fascinating. We’re living in very interesting times in terms of our understanding of genomes and how organisms are put together.”

I wonder what Charles Darwin would make of it all.

By Deirdre Nolan