January 18, 2013 6:41 pm

This rare GEM can model our world

Computer modelling of the world’s ecosystems could help predict climate change
A hyena eyes flamingos in a South African lake©Corbis

A hyena eyes flamingos in a South African lake: ecosystem models simulate feeding, reproduction and death

Scientists in Cambridge are developing the first general-purpose computer model of the biosphere, which will allow researchers and policy makers to simulate any system of living organisms on Earth, big or small. A general ecosystem model, or GEM, is the biological counterpart of global climate models, which capture the physics and chemistry of land, oceans and atmosphere – and have been crucial for making predictions about climate change.

The original GEM’s creators at Microsoft Research Cambridge unveiled the model in the journal Nature, ahead of next week’s inaugural plenary meeting in Bonn of the Intergovernmental Platform on Biodiversity and Ecosystem Services, a new body affiliated with the UN. At present, decisions about conservation are based on limited and specific studies, showing for example that the diversity of birds declines in deforested landscapes. GEMs could capture the broad-brush structure of any ecosystem by simulating processes such as feeding, reproduction and death. Applied to the African savannah, for instance, it would model the total biomass of all the plants, the grazing animals that feed on them, the carnivores that eat the grazers, and so on – mapping the flows of energy and nutrients down the food chain.

“As recently as five years ago people were saying it would be impossible to build a global ecosystem model because there were too many complexities and uncertainties,” says Stephen Emmott, head of the Cambridge lab. “But now we have done it, and we are about to publish scientific papers giving our results.”

Though modelling every organism within an ecosystem is impossible – it would require too much computing power – the researchers say they can obtain valid results by applying rules about the way individuals behave in groups.

But the biggest stumbling block to building good GEMs is obtaining enough good data for them. For example, almost no data have been collected on the distribution of body sizes in the oceans, from plankton to whales. The Microsoft scientists plead for more governments to devote more funding to gathering GEM data. Costs could be reduced by “harnessing the power of citizen science”, crowd-sourcing information through websites such as iNaturalist and eBird.

The Microsoft scientists are collaborating with the UN Environment Programme World Conservation Monitoring Centre in Cambridge. Although it has so far been funded by the computer software company, to the tune of a few million pounds, Emmott says everything about the model will be open to the scientific community.

“We hope that this will have a similar effect to the first climate model 40 years ago,” he adds.

. . .

Why antioxidants may not be anti-cancer

As James Watson prepares for the 60th anniversary this spring of his discovery of the DNA double helix with Francis Crick, he is throwing himself into cancer research. He calls his latest paper about the role of oxidation in late-stage cancer, “among my most important work since the double helix.”

Many people see antioxidants, which occur plentifully in fruit and vegetables and in nutritional supplements, as healthy because they destroy “reactive oxygen species” that can destroy DNA and proteins.

Sunny side up

egg

British eggs have become more nutritious, says the Institute of Food Research. On average they contain twice as much selenium, 20 per cent less fat and 10 per cent less cholesterol than in the early 1980s.

But reactive oxygen species are not always harmful. Indeed, in his paper in the journal Open Biology, Watson calls them “a positive force for life” because they play a key role in apoptosis – the biological process in which unhealthy cells commit suicide.

Watson’s hypothesis is that this oxidative destruction of cancer cells is an important mechanism for fighting tumours, both naturally and using chemotherapy. Excessive consumption of antioxidants can therefore promote the progression of cancer by suppressing oxidation.

The balance between oxidants and antioxidants is important for health. People with neurological diseases such as Parkinson’s suffer less cancer than the general population, he says, because their oxidation system is unusually active. The opposite applies to people prone to cancer.

“My approach to treating late-stage metastatic cancer, which is currently incurable, is to find a way of getting rid of antioxidants selectively in cancer cells while maintaining their activity elsewhere in the body,” says Watson.

At 84, he still works at Cold Spring Harbor Laboratory where he was director for many years. “I started cancer research in the 1950s and have probably been working in the field for longer than anyone else in the world,” he says.

Meanwhile Watson has firm advice for people thinking of taking antioxidant supplements as a way of warding off cancer: don’t.

. . .

Artist’s reconstruction of the toothed bird Sulcavis geeorum©Stephanie Abramowicz

Artist’s reconstruction of the toothed bird Sulcavis geeorum

Beak with a bite: the birds with teeth

As birds evolved from dinosaurs, they usually lost their teeth and instead developed specialised beaks to manipulate food. But Sulcavis geeorum, a toothed bird that thrived 120 million years ago, shows dental evolution moving temporarily in the opposite direction.

An international study of fossils newly discovered in China’s Liaoning province reveals Sulcavis as the first bird known to have had “dental ornamentation” – special features such as ridges, serrations or striations to cope with a particular diet – rather than simple teeth. The research appears in the Journal of Vertebrate Paleontology.

The fossils have robust teeth with grooves on the inside surface, which would have strengthened them for eating harder food items. The researchers believe Sulcavis had a durophagous diet, meaning it devoured prey with exoskeletons such as crustaceans. The teeth of the new specimens increase the known variety of tooth shape in early birds, suggesting previously unrecognised ecological diversity in the enantiornithines, the group of birds to which Sulcavis belonged. During the early Cretaceous period they were the most numerous birds on Earth. “While other birds were losing their teeth, enantiornithines were evolving new morphologies and dental specialisations. We still don’t understand why [they] were so successful in the Cretaceous but then died out ...” says Jingmai O’Connor of the Institute of Vertebrate Paleontology and Paleoanthropology, Beijing.

. . .

On target: genes that know their place

For many years after genetic engineering started in the 1970s, scientists had no way of directing where the added genes would end up in the genome of the host organism – whether microbe, plant or animal. The technology inserted new DNA randomly into the genome. Sometimes it worked, sometimes it didn’t and sometimes it had the unfortunate byproduct of disrupting existing genes.

Now, however, targeting techniques are being developed for precisely altering genomes by adding or deleting genes in specific places. The latest, from Harvard University and Massachusetts Institute of Technology, is adapted from naturally occurring proteins that bacteria use to defend against viral infection. The system incorporates a bacterial DNA-cutting enzyme called Cas9, which is linked to short stretches of RNA designed to target specific locations in the host genome. Details appear in the journal Science.

The approach – called CRISPR for “clustered regularly interspaced short palindromic repeats” – can be used either to disrupt the function of a gene or to replace it with a new one. For replacement, a template for the new gene must be added too; this is copied into the genome after the DNA has been cut. “Anything that requires engineering of an organism to put in new genes or to modify what’s in the genome will be able to benefit from this,” says Feng Zhang, lead author.

Although the potential applications are very wide, the researchers are interested first in using CRISPR to study and then treat inherited brain diseases.

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