The Great Beyond

by Heidi Ledford

So what does a swinging Nature reporter do on a Thursday night? Given yesterday’s news that there was an online protein folding game (Economist;MIT Technology Review), isn’t the answer obvious?

The game is called Foldit, and it lets users manipulate different parts of a protein (amino acid sidechains, beta sheets, and helices) to optimize its 3-D structure. A tutorial guided by a cartoon image of protein structure guru David Baker (University of Washington), complete with his trademark unruly ‘Einstein-the-early-years’ hair, teaches you a few basics: bring your sheets together to allow hydrogen bonding between them, and don’t let your amino acid sidechains bump into each other.

Wannabe structural biologists can download it here. Baker and his colleagues previously designed a program called Rosetta@home that harnesses idle computers to solve protein structures. But users who downloaded the program watched as their computers cranked away evaluating different structural possibilities and began to wonder: might a human do better? The Howard Hughes Medical Institute’s press release quotes Baker: “People were writing in, saying, `Hey! The computer is doing silly things! It would be great if we could help guide it.”

So now the skeptics get to try their hand. I gave the game a quick try, just enough to make it through the tutorial and take a stab at the first challenge puzzle: a beginner’s task based on a protein from a bacteria that can cause strep throat. (Somewhere around the sixth or seventh puzzle in the tutorial my mind started to wander and I turned on the webcast of the mock news program Colbert Report from the previous night. I finished the puzzle somewhere between when Stephen Colbert declared: “Scientists are so snooty” and when he shocked himself on a homemade electromagnet.)

Overall, I’m hooked. Not cancel-my-weekend-plans hooked, but I’ve definitely found a new way to procrastinate. I’d say you don’t necessarily learn a whole lot about protein structure, but really, did you want to? And if you did, they provide a separate tutorial that covers the details. Meanwhile, the game does give you that conceptual sense of how elegant (and frustratingly delicate) protein structure can be.

According to one press release, the high score could earn the winner a Nobel Prize for medicine. But I won’t hold my breath.

Posted by Nicola Jones
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How ‘green’ are you? Now there’s a very simple (and therefore surely inaccurate, but probably not too misleading) online questionaire you can take (from National Geographic), to make you feel smug or worried about your carbon footprint (most of us in the London office wound up with a smug, above-average Greendex score, though that’s probably because none of us own a car…).

Working out the environmental pros and cons of various activities is notoriously difficult and at times counterintuitive. A report in Nature once concluded, for example, that it’s better to use a styrofoam cup than a mug for your daily coffee, until you had used the same mug over a thousand times -- that’s thanks to the high-energy-use manufacture of ceramic, and the hot water and soap needed to wash your mug; in contrast styrofoam is easy to make, and causes no problems in landfill other than taking up space (Nature abstract, full text not online; New Scientist story). At least with carbon emissions there’s no need to quantify some amorphous ‘bad’ thing like ‘taking up space in landfill’ – carbon emissions are carbon emissions (well, the carbon could be in methane or carbon dioxide, with differing climate effects, but lets not be too picky). But it’s still hard to assess with simple questions like “Do you own a car” exactly what this means for your emissions.

Nonetheless, I’m all for raising awareness of carbon footprints – so long as it doesn’t make people who get a ‘good’ score think they don’t need to strive for improvement.

Here are some more, similar surveys:
Carbon offset survey, run by Environmental Economics MSc students at Imperial College, London.

Test your knowledge on environmental questions, with a quiz from Yale University, Forbes, and the BBC.

Tell us of your favourites…

Posted by Nicola Jones
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The audience at the 2008 Electric Aircraft Symposium in Silicon Valley late last month was given a “vision of the future” in which everyone has a personal car/plane that they can drive or fly (or read the paper while it drives/flies itself, actually), and which will be the “greenest form of transportation” (BBC; Wired). When will this future be? Oh, in 20 years or so they said.

Sounds great. But people have been predicting a helicopter-in-every-garage for decades; inventors have been working on flying cars, of the type intended for the masses, since at least the 1930s. Check out this cover of Popular Mechanics from 1951…

Is that vision now really going to come true? Technologies have improved of course, and companies offering up this vision seem to have abounded in recent years (eg Register, 2007; see a full list in the Roadable Times).

I’m not holding my breath yet. And I can’t help but wonder, if you can make self-flying battery-powered planes for everyone that are smart enough to avoid hitting each other in flight, why not just make smarter, self-driving, battery-powered cars? The main reason for gridlock is not so much the number of cars on the road, but delays in reaction time and other inefficiencies of the all-too-human drivers. Solve that and I don’t think you need to fly.

Posted by Nicola Jones
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Flowers have been found to have several tricks up their, um, sleeves when it comes to attracting pollinators, according to two reports we spied today.

First off, they wave at passing insects to attract their attention (BBC).

John Warren from the University of Aberystwyth was apparently inspired by watching flowers waving about in the wind at his daughter’s birthday, and wondering why they risked having their slender stems snapped by such movement. Not finding much in the literature, he set out to find an answer.

In a study of 300 specially grown flowers of varying stem lengths, tall wavy flowers attracted more pollinators, they found (Journal of Evolutionary Biology). Sadly the story doesn’t say by how much, nor is this mentioned in the freely available abstract… though the abstract does add that insects stayed on wobbly flowers less long than they did on stationary ones. (If only Wordsworth knew there was a reason for his host of daffodils "fluttering and dancing in the breeze" his poem might have been different).

Secondly, researchers have found just how effective orchids can be at mimicking female wasps, as a way to lure male wasps in to collect their pollen (Reuters). Not only do they attract the boys (which was already known), but they also seem to excite them enough to cause an ejaculation (releasing “copious sperm” according to the report). Obviously this is a waste of time and energy for the wasps, but apparently it helps the orchids, somehow – I guess by increasing stickiness? “Orchid species provoking such extreme pollinator behavior have the highest pollination success," they report in The American Naturalist.

Photo by Keith Weller, USDA

Posted by Nicola Jones
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How does a history of abuse leave its mark on the brain? A grim new study from PLoS ONE finds differences lurking in the brains of people who were abused as children and then committed suicide. The differences were epigenetic, meaning that rather than finding changes in the DNA sequence, there were differences in the frequency with which a chemical group, called a methyl group, is attached to certain regions of the DNA. This chemical modification can reduce expression of genes: in this case they looked at epigenetic changes to a gene that is critical for production of proteins and found that not only were there more methyl groups, but those methyl groups correlated with reduced gene expression. The implications are that abuse as a child may have led to these epigenetic changes which, in turn, could impact a critical function in the brain.

Reuters quotes Eric Nestler (University of Texas Southwestern Medical School in Dallas) as saying that drugs and psychotherapy might be able to reverse the epigenetic changes. Interestingly, the researchers found no correlation between these epigenetic changes and psychiatric diagnoses.

The researchers (Moshe Szyf of McGill University in Montreal and colleagues) compared 18 suicide victims with a history of childhood abuse to 12 patients who died from other causes. Overall, it strikes me as a complicated question to tackle, and one that might require more than a dozen samples to really pick apart. For example, New Scientist says that Szyf is now comparing his results with suicide victims who were not abused to determine whether the epigenetic changes were the result of abuse or suicide. Seems like an important control to do, and in fact it’s interesting how we’ve all homed in on the ‘child abuse’ angle when the paper stresses the ‘pathophysiology of suicide’ rather than abuse.

But it’s an interesting start, and follows on previous work in animals, including the fascinating study from several years back showing that mouse pups neglected by their mothers showed more stress later in life and harbored epigenetic changes in their brains.

Posted by Nicola Jones
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The birds are taking over. A crow patrol is scouring the streets of Kagoshima, Japan, according to a New York Times report. The birds' crime is not murder (the name for a group of crows) but instead causing blackouts by roosting among the power lines and reportedly “frightening away residents”. The patrol has been hired by Kyushu Electric, and tasked with looking for ways to reduce the city’s population of the noisy black birds.

Japan has apparently seen massive increases in the mythically (and to some extent experimentally) quick-witted birds, which have apparently been out-foxing the patrols by building dummy nests. (In a less quick-witted way, the blackouts happen when a peckish subject explores a high-voltage power line). This clash between Japanese city life and Corvus species parallels recent complaints by UK farmers that ravens have gone predatory on their herds; pecking lambs and calves to death in a black feathered frenzy. The Zooillogix blog gives the UK press a hard time for sexing up the story

Still the events do call to mind Alfred Hitcock’s 1963 classic The Birds, a remake of which, starring Naomi Watts, looks to be slated for 2009. Corvus species like crows, rooks, and ravens hold a special place in the scary bird category even if Hitchcock’s climax starred seagulls. Of course in the United States the only thing eerie about crows lately is their absence. Their susceptibility to west Nile virus has decimated US crow populations (Nature, sub required).

Posted by Nicola Jones
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Check out these maps highlighting where all the neurotic people live in the United States (and the extroverts, and the most agreeable people, etc), as published in Richard Florida's latest column (Boston Globe). The result is fascinating in a water-cooler kind of way. Look! All the neurotic people are in New York! Those open to new experiences cluster in California, etc. etc.

But we at Nature are left wondering exactly how these maps were made… It doesn’t say in the article how precisely how the data was collected, or if there might be a bias, for example, due to people living in cities being more involved in the study than others. It also doesn’t say whether the maps have been normalized for population density, though we hope they have. Okay, this is a column: you don't expect that kind of detail in a column. But then where can you get it? (I can't find a paper on the subject... Richard - help us out!)

The five personality traits highlighted are standard in psychology; you can take a test to assess your personal scores in these five traits online here (warning: you need to agree to a few conditions and it’ll take a while).

Florida is a regular columnist and “professor of business and creativity” at the Rotman School of Management, University of Toronto. The field he is exploring here is that of ‘psychogeography’, which seems to be an emerging trend in social sciences.

Posted by Nicola Jones
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As the death toll from the cyclone and resultant storm surge in Myanmar climbs (now some 22,000 according to the state media), aid efforts are still being hampered (LA Times).

The cyclone is being called the worst to hit Asia since 1991, when 143,000 died in Bangladesh (multiple sources). NASA has some satellite photos of the area taken before and after the storm, showing the extent of flooding (pictured here; NASA).

Why were things so bad? The storm was a severe one: peak wind speeds were 215 km/h (wikipedia), which makes it a category 4 storm in a scale of 1-5. But damage was exacerbated by the high density of people on the coast and the storm surge of up to 3.5 metres caused by the winds, said ASEAN secretary-general Surin Pitsuwan (BBC). Storm surges of up to 5.5 metres can be typical of category 4 storms. Warnings were issued by the Joint Typhoon Warning Center, which named the storm in late April (history of warnings linked to in wikipedia, initially targeted at Bangladesh more than Myanmar). But commentators on BBC radio complained there was only a few hours of warning for the people affected. For the moment it’s hard to tell exactly what happened on the ground.

Pitsuwan has also blamed a destruction of natural mangroves along the coast for the excessive damage (BBC again). There don’t seem to be any supporting claims from ecologists or storm specialists as yet, though mangroves were thought responsible, in part, for limiting damage in Sri Lanka from the Asian tsunami in December 2004.

The NY Times ‘dot earth’ blog highlights the trajectory of the storm as plotted on Google Earth, and puts in a shout to maintain Earth observation satellite systems, including systems to consolidate and use the data.

Posted by Nicola Jones
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As if China doesn't have enough to deal with ahead of the Olympics. Added to the problems of Beijing's polluted air, protests in support of Tibet, and the daft mission to take the Olympic torch up mount Everest being hampered by the weather, CNN is reporting an outbreak of the deadly enterovirus 71 in the city of Fuyang, south of the capital.

Continue reading "Paralysing virus strikes China ahead of Olympics" »

Posted by Mike Hopkin
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Canada is set to launch the first dedicated space satellite to watch for near-Earth objects (Vancouver Sun). The question is: do we really need one?

A number of Earth-bound telescopes are already used to spot and track near-Earth objects (NEO), including under the auspices of Nasa’s NEO Project. Commentators in New Scientist argue that the space-based telescope (called NEOSSat) will have better luck spotting asteroids that are within Earth orbit: these also tend to stay in line with the Sun, meaning they are only visible in the sky close to sunset or sunrise, when background light tends to drown them out. But they are also more likely to hit us, the article says.

But ground-based satellites can spot these too, even if it is a little harder. Alan Harris of the Space Science Institute in Boulder Colorado, US, told New Scientist he doesn’t think the project will add too much to what’s already available.

But hey, it’s only costing $10 million. And statistically Canada (the second largest country after Russia) has a lot of area sitting waiting to be struck by an asteroid, so maybe that makes them keen to get in on the game… even if there aren’t that many people actually living in most of it.

Posted by Nicola Jones
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