Pulling on DNA’s bootstraps

Fifty years after the discovery of the structure of DNA, a new use has been found for the very molecule of life – as fuel for a molecular computer.

Ehud Shapiro of the Weizmann Institute of Science has, for many years, been working on developing the information technology inherent in DNA to power complex calculations. In the longer term, measured in decades, we might find autonomous, programmable molecular computers in vivo, sensing biochemical anomalies, consulting their programmed medical knowledge and synthesizing the appropriate drug molecules in response, Shapiro told Spotlight.

Ehud Shapiro

Ehud Shapiro

DNA provides one of the most compact and efficient digital information systems known. With just four basic building blocks it can represent the ingredients and blueprint for making a microscopic algae or an elephant in a molecule-sized space. A decade ago, researchers such as Leonard Adleman of the University of Southern California began to find ways to make laboratory-scale DNA manipulation solve mathematical puzzles, such as the travelling salesman problem. More recently, Shapiro demonstrated that a molecular-scale system that exploits the processing power of enzymes could carry out calculations without human intervention.

However, as with any electronic device, these molecular computers need a power supply. Obviously, connecting up a conventional power source, would be one option but Shapiro working with Yaakov Benenson, Rivka Adar, Tamar Paz-Elizur, and Zvi Livneh wanted a more frugal solution. They have now found that the single DNA molecule that encodes the input to the computation can provide all the power requirements too. In terms of speed and size, DNA computers may eventually surpass conventional computers that use silicon microchips.

DNA. Source: Proceedings of the National Academy of Sciences

DNA. (Source: Proceedings of the National Academy of Sciences)

Previously, the researchers had used the well-known energy molecule of living things – ATP, or adenosine triphosphate, as chemical energy for their DNA computers. In the new approach they have designed out this independent power supply so that the DNA input molecule spontaneously releases energy for the computational operations to take place. In each computational step, two complementary DNA molecules – an input molecule and a software molecule – spontaneously bond together. The software molecule then directs a DNA-cleaving enzyme to cut a piece of the input molecule. The enzyme, FokI, breaks two bonds in the DNA double helix, releasing the energy stored in these bonds as heat, sufficient to trigger the next step in the computation.

The Guinness seal of approval

The Guinness seal of approval

The computer itself is similar to the earlier system devised by the team. It is a special case of a Turing machine, a two-state, two-symbol finite automaton. It can answer simple questions about binary strings, which are encoded as DNA strings, such as Does a binary string of a’s and b’s contain an even number of a’s? or Is the length of the string even or odd?

This may seem trivial but such logical operations are at the heart of the computational process allowing much more sophisticated questions to be asked by linking many individual devices. Ultimately such computers could provide biological data analysis in vitro, without the need to convert the information to electronic format (i.e. sequence the DNA), Shapiro told us.

Astoundingly, a single teaspoon of Shapiro’s computer soup might contain 15000 trillion DNA computers, together performing 330 trillion operations per second with what he says is 99.9% accuracy per computation step. The overall process produces just 25 millionths of a Watt of waste energy. Shapiro’s work was recently awarded the Guinness World Record as the world’s smallest biological computing device.

Further reading

Proc Natl Acad Sci (USA), 2003, 100, (5), 2191-2196
http://www.pnas.org/cgi/doi/10.1073/pnas.0535624100

DOI: 10.1073/pnas.0535624100

Ehud Shapiro
http://www.wisdom.weizmann.ac.il/~udi/

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Molecular computers

An ethnic majority

A £2.5m Development Research Centre on Inequality, Ethnicity and Human Security is to be opened at Oxford University to look into the challenges facing multi-ethnic societies.

Queen Elizabeth House at the University of Oxford has won a £2.5m award from the Department for International Development (DfID) to establish the Centre. DFID instituted a competition for the establishment of Development Research Centres which would contribute to DGFID objectives, particularly the reduction of poverty, there were 100 applicants for the funding from around the world.

Frances Stewart (image courtesy Stewart family)

Frances Stewart (image courtesy Stewart family)

According to Frances Stewart, Director of Queen Elizabeth House, who will head the Centre, globalisation and mass migration are leading to more diverse national populations. She suggests that multicultural societies can bring increased potential for conflict, so It is vital to study and learn from those societies where different groups live together peacefully.

Religious and ethnic violence and how to tackle it will be high on the agenda at the new Centre. There are major economic and political causes of such violence, particularly arising from inequality between groups. Researchers in the Centre will explore why some multi-ethnic societies achieve peace and economic prosperity, while serious conflicts arise within other societies. Such conflicts almost invariably result in abysmal poverty. Researchers will also investigate sources of unequal access to economic and political resources between groups.

Religious and ethnic violence are high on the student agenda at the new QEH centre (image courtesy of QEH)

Religious and ethnic violence are high on the student agenda at the new QEH centre (image courtesy of QEH)

Stewart hopes that research to compare economic and political developments over several decades in both peaceful and violent multi-ethnic societies will ultimately shed light on why ethnicity becomes a salient factor in political developments in some societies but not in others. Researchers will also investigate sources of unequal access to economic and political resources between groups.

Image courtesy of QEH

Image courtesy of QEH

Scholarships will be available for four doctoral students who will work with overseas partners including institutions in Malaysia, Uganda, Nigeria, Peru and Bolivia. The other establishments involved are The Research Center for Society and Culture (PMB) at the Indonesian Institute of Sciences (LIPI), Jakarta, Indonesia. The Department of Political Science, University of Ibadan, Nigeria. The Department of Economics, Catholic University, Lima, Peru in collaboration with The Department of Public Policy, Catholic University, La Paz, Bolivia. The Centre for Basic Research, Kampala, Uganda.

It is hoped that in five years the Centre will have identified major economic policies and political systems likely to contribute to reduced group inequality and the promotion of peaceful multicultural societies. It will also have explored political obstacles to and opportunities for putting these policies into effect, Stewart told Spotlight.

Further reading

Queen Elizabeth House
http://www.qeh.ox.ac.uk/

Department for International Development
http://www2.dfid.gov.uk/

Frances Stewart
http://www.crise.ox.ac.uk/frances.shtml

Did the Earth move for you?

Just as a forensic scientist can find out what happened at a crime scene so a forensic seismologist can fingerprint the Earth to pinpoint unidentified explosions.

Geoscientist Terry Wallace of the University of Arizona is using data from some 3600 seismic stations – that normally look for volcanic and earthquake activity – to spot sinking submarines, industrial explosions, nuclear weapons testing, landslides, and other unidentified phenomena that make the Earth move.

Terry Wallace (image courtesy of Wallace)

Terry Wallace (image courtesy of Wallace)

Seismological tools and theory can be used as constraints to tell when an accident occurs or something that’s not accidental, like a nuclear explosion, explains Wallace, We can then put behind that some ideas of how big an explosion might be, or if it’s a landslide, how big the landslide might have been, or how far the rocks have fallen, for example.

He and his colleagues have confirmed, for instance, the when and where of Indian and Pakistani nuclear testing in the late 1990s. They have also studied the claim that Iraq tested a nuclear weapon in 1989. The alleged test was reported to have been carried out beneath Lake Rezazza, approximately 100 km southwest of Baghdad at 10:30h on 19 September. Wallace and his colleagues examined the global earthquake catalogues produced by the International Seismic Center and the US Geological Survey and say they reveal no seismic disturbances at all in Iraq that day. Moreover, they say there has been no seismicity within 50 km of the reported test site for the years 1980 to 1999. One problem with the assertion that no weapons testing took place, they point out, is that the detection threshold for these global catalogues was just magnitude 4.0 in 1989 so a smaller magnitude event may have not been picked up by the sensors. Thankfully, national catalogues for Israel, Jordan and Iran reported no seismic event in the region on that date either (19 September 1989).

Nuclear tests (image courtesy of Wallace)

Nuclear tests (image courtesy of Wallace)

The lower detection limit of modern seismic testing is only limited by the natural noises of the Earth. However, comparisons between results from different stations will reveal very fine detail. Explosions and earthquakes both generate seismic waves, but they have distinctive frequency signatures much like the tones of a voice, Wallace told Spotlight, Just as most children’s voices can be distinguished from adults, seismograms can be used to identify if a disturbance was caused by an earthquake or an explosion.

Two explosions (image courtesy of Wallace)

Two explosions (image courtesy of Wallace)

Wallace and his team have also analysed the seismic activity that occurred on the day the Russian submarine Kursk sank north of the Kola Peninsula. There were two explosions on 12th August 2000 associated with reports of this vessel sinking. There was a gap of two minutes between the explosions, the second of which was much bigger. Seismometers detected both up to 4500 km away. Calculations that compare results from different seismometers revealed that the second explosion was the equivalent of five tonnes of TNT exploding, which Wallace suggests was a warhead detonating. Our findings were corroborated when the Russians released their report in July this year, says Wallace.

The Kursk sank on 12th August 2000, in the Barents Sea

The Kursk sank on 12th August 2000, in the Barents Sea

Wallace revealed the latest details of his Earthly forensics investigations at the 2002 American Geophysical Union meeting in San Francisco in December. He revealed that he and his colleagues are investigating the sinking of the USS Scorpion submarine near the mid-Atlantic ridge in 1968, the sinking of another Russian sub in the Baltic in 1989, and the sinking of a large oil derrick in the North Sea that produced a 3.5-magnitude earthquake when it hit the ocean floor.

Water seismometers, or hydrophones, are even more sensitive to water rumblings than are the land-based versions. Using a hydrophone in the water, we can see the explosion of one stick of dynamite anywhere in the world. That’s how quiet the oceans are. So if you are going to hide something, don’t do it in the water, Wallace says.

The whole research effort for my group is to develop as big a portfolio as possible. This way, when we see an industrial accident where a fireworks factory blows up or a gasoline tank blows up, we have all the different kinds of seismic records we can get from that and we have characterized them. Then the next time something like that happens we have some experience to draw from. We’ve got some fingerprints left over to help us understand what is happening, Wallace adds.

Further reading

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Seismology
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