October 8, 2010 11:39 pm

Rat’s the way to build a supercomputer

Computing

Rat’s the way to build a supercomputer

A simulated rat’s brain is beginning to take shape inside a Swiss supercomputer. The Blue Brain project at the École Polytechnique Fédérale de Lausanne combines painstaking biological investigation of neurones (brain cells) with one of the world’s most powerful computers, an IBM Blue Gene P.

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Henry Markram, the project leader, gave a progress report on “the first comprehensive attempt to reverse-engineer the mammalian brain” at last week’s ICT2010 conference organised by the European Commission in Brussels. Already, he said, Blue Brain is giving biologists valuable information about the way neurones grow and, conversely, providing clues for scientists and engineers about designing the next generations of computers. “There are beautiful organising principles in the brain that could show us a route to ICT [information and communications technology],” he says.

Just to be clear – Blue Brain is not a bionic hybrid of silicon and living cells. Though its data come from systematic micro-analysis of the anatomical, genetic and electrical properties of rat brains, Blue Brain exists solely in the electronic circuitry and memory chips of its host supercomputer.

Five years after the project started, Blue Brain has successfully simulated a small brain area containing tens of thousands of neurones within the neocortex. Over the next decade the project will move through species – on to cats, macaque monkeys and finally humans – and extend its reach eventually to the whole brain, with billions of neurones and trillions of connections between them.

A whole brain simulation will help neuroscientists understand how we interpret and store sensory information, and may even help us grasp how consciousness arises.

But that is for the long-term future. Meanwhile, Blue Brain is showing how neurones grow and interconnect; the rules by which the cells achieve the maximum diversity of connections – and therefore make the brain as resilient as possible – are different from those proposed by many neuroscientists, Markram says.

Blue Brain can help computer engineers overcome several barriers to the future development of supercomputers – such as cutting their energy consumption. “The brain saves energy by using very large numbers of relatively sluggish neurones and by ensuring that not too many neurones are active at a time,” he says. The brain is also far more efficient than computers at memory storage, internal data transfer and resilience when processors (neurones) fail.

But the most important lesson from the brain may be the way it visualises the results of its computations – the world we see or imagine – with the same neurones and synapses as those used for computation. Supercomputers, by contrast, produce huge amounts of data that then has to be visualised as a secondary process – often on another computer. “A new generation of brain-like machines would allow supercomputers to see what they are computing – not only in the physical world but in an infinite range of real and imagined worlds,” Markram says.

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A reed warbler feeding a cuckoo chick

A reed warbler feeding the cuckoo chick that was smuggled into its nest

We’ve all heard of the cuckoo in the nest, but how does the interloper come to monopolise its surrogate parent? Georgian scientists suspected internal incubation – and they were right

The cuckoo’s parasitic lifestyle depends on its eggs developing very fast. It lays into a nest that already contains the host’s eggs, but its chick must hatch first, so that it can eject the other eggs and claim the sole attention of its unwitting foster parents.

Researchers at Sheffield University have shown for the first time that the cuckoo achieves this rapid development by incubating its eggs internally for 24 hours before laying them.

The scientists first examined the newly laid eggs of eight European cuckoos and discovered that each had a markedly more developed embryo than other birds’ eggs. The researchers simulated the effects of internal incubation with eggs from another species, the zebra finch.

They kept newly laid finch eggs at 40°C – the body temperature of finches and cuckoos – for 24 hours. When eggs are incubated in the usual way by birds sitting on them in the nest, their temperature is usually around 36°C.

The zebra finch eggs did indeed mature more rapidly when incubated at body temperature. Further investigation confirmed that the cuckoo is capable of internal incubation – and that an egg incubated inside the bird hatches 31 hours ahead of any host egg laid at the same time.

“The idea of internal incubation in birds has until now been considered impossible,” says Tim Birkhead, the research leader.

“It was assumed that female birds could not hold on to a fully formed egg. In fact, the idea of internal incubation by cuckoos was suggested as early as 1800, but then ignored.

“Our results show that internal incubation gives cuckoo chicks that crucial head start in life, allowing them to dispose of their nest mates – a superb adaptation to being a brood parasite.”

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Chemistry

Why drinking fizzy pop can be a pain

The carbon dioxide in a fizzy drink triggers the same pain sensors in the nasal cavity as mustard and horseradish, say researchers at the University of Southern California.

“Carbonation evokes two distinct sensations,” says Emily Liman, senior author of a study published in the Journal of Neuroscience. “It makes things sour, and it makes them burn. We have all felt that noxious tingling sensation when soda goes down your throat too fast.”

It comes from nerves that respond to sensations of pain, skin pressure and temperature in the nose and mouth. The USC study has shown which ones are responsible.

The researchers found that when they put carbonated saline solution on to a dish of nerve cells from the sensory circuits in the nose and mouth the CO2 activated only a particular type of cell. The cells that responded were the ones that express a gene known as TRPA1 – the same ones that respond to mustard. Mice missing the TRPA1 gene showed “a greatly reduced response” to carbon dioxide. But adding the TRPA1 genetic code to CO2-insensitive cells made them responsive to the gas.

The pain-sensing TRPA1 provides only one aspect of carbonation’s sensory experience. Last year another US study showed that carbonation triggers cells in the tongue that convey sourness.

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Engineering

Tyre-mix concrete is road to the future

A European research team has developed a new type of concrete road that is energy efficient and ready for traffic immediately after laying. Its novel ingredient is steel fibre, recycled from waste tyres, which reinforces dry mix concrete.

The researchers, who were funded by Europe’s Framework programme, say use of the new material cuts the cost of road building by 12 per cent and construction time by 15 per cent.

And, because it is more durable and needs less maintenance, there is a 40 per cent reduction in long-term energy consumption.

The new mix uses a consolidation method, called roller compaction, that is quite different to that used on traditional roads.

While conventional concrete can take up to four weeks before being traffic-worthy, the new mix is stable enough for light traffic straight after being laid.

Professor Kypros Pilakoutas of Sheffield University, who coordinated the project, says: “The new material will provide a better infrastructure in the future: fewer potholes, less maintenance required and therefore less impact on the traffic.

“Furthermore, when the material is disused, it can be removed, crushed and recycled for a new pavement.”

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