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Archive for the ‘Uncategorized’ Category

Protein folding is fun and games, and more

In Uncategorized on July 28, 2009 at 3:25 am

Despite the obvious advantage of having humongous amounts of computing power at one’s disposal, it seems that some problems’ solutions yet rely on humans’ puzzle-solving machinery, and our ability to recognize patterns that elude our hard drives. How our neural circuitry takes the leaps of logic that it does is another question, but since the capability is available, the win-win situation should be capitalized on–you get the satisfaction of solving a puzzle, and scientists get a candidate folded structure for a protein, for which the only available structural information is the primary sequence.

Gamers unravel the secret life of protein,” John Bohannon (Wired Science)


Learning: so easy a slime mold can do it!

In Uncategorized on April 19, 2009 at 7:44 pm

This is pretty amazing.  Single-celled slime molds have been shown to learn to anticipate events after repeated stimuli.  In this case:

As the cells crawled across an agar plate, the researchers subjected them to cold, dry conditions for the first 10 minutes of every hour. During these cool spells, the cells slowed down their motion. After three cold snaps the scientists stopped changing the temperature and humidity and watched to see whether the amoebas had learned the pattern. Sure enough, many of the cells throttled back right on the hour in anticipation of another bout of cold weather.

This sort of learning has been demonstrated before, in organisms as simple as earthworms and planarians.  But even then, these animals have at least a rudimentary “brain” consisting of specialized neurons.  Slime molds, on the other hand, are independent single-celled organisms.  They do, however, have the ability to aggregate to form complex systems, migrating as a single unit and forming a stalk to sporulate.  This new finding suggests that these emergent properties can also produce intelligent behavior, without the need for a nervous system.

For a bonus: detailed and colorful pictures of slime molds, with a focus on their fruiting bodies.

Smarter than most lower eukaryotes, including Congressmen.

Computer discovers the laws of physics

In Uncategorized on April 7, 2009 at 2:42 pm

In just over a day, a computer program at Cornell has extrapolated Newton’s laws of motions from a pendulum’s swings. The program starts with random combinations of addition, subtraction, multiplication, division and a few algebraic operators. Then, via a genetic algorithm, the program refines the formulae to pick out ones that fit the data better. It came up with the law of conservation of momentum and Newton’s second law of motion.

This raises some serious questions about the nature of science. It took physicists centuries to develop laws of nature to fit observed data; it took Hod Lipson’s program a day. We could worry about machines replacing human ingenuity. Or — a view I find more compelling — we see these algorithms as an aid to deriving the laws that explain other agglomerations of data, such as the genome or proteome. We don’t know the “laws of biology” in the way we know the laws of physics; and still less do we know the “laws of social science.” Maybe artificial intelligence is the best way to make progress on that.

Here’s Lipson giving a TED talk on robotics.

Kepler launches tonight

In Uncategorized on March 6, 2009 at 1:12 pm


At 10:48 PM EST Nasa’s Kepler telescope will launch. The Kepler mission focuses on finding other Earth-sized planets. It takes a very broad snapshot of the sky, compared to something like Hubble, and instead of taking pi ctures, it uses the transit method. How it works: watch a star for a very long time. If the starlight dims momentarily, we know a planet passed in front of it, and we’re able to measure that dip in brightness and find the size of the planet. This is the first time that photometry has ever been done on this scale, with this many stars. We may be able to learn whether planets like ours are rare or common in the galaxy — and how likely it is that some contain water, and, perhaps, life. Some webcasts here.

Obama administration nixes Yucca Mountain

In Policy, Uncategorized on March 6, 2009 at 5:41 am

From the AP:

Energy Secretary Steven Chu said Thursday the proposed Yucca Mountain site in Nevada no longer is an option for storing highly radioactive nuclear waste, brushing aside criticism from several Republican lawmakers.

To date about $13.5 billion has been spent on the project and last year the Bush administration submitted an application for a construction and operating license to the Nuclear Regulatory Commission….

Instead, Chu said the Obama administration believes the nearly 60,000 tons of waste in the form of used reactor fuel can remain at nuclear power plants while a new, comprehensive plan for waste disposal is developed.

But President Barack Obama’s first budget a week ago proposes scrapping all spending on Yucca Mountain except for what is needed to answer questions from the NRC on the license application “while the administration devises a new strategy toward nuclear waste disposal.”

The lack of a permanent storage site for nuclear waste has been a significant impediment to the expansion of nuclear power in the US.  Despite the vague talk of other options for waste disposal, this plan means that plants will have to continue to store their waste on-site, and above ground, making the construction of new power plants very difficult.  And given the amount of time and money required to prepare the Nevada site so far, it is unlikely that another solution will be forthcoming anytime soon.

While environmental advocates are usually the first to promote clean-energy subsidies, many have been lukewarm towards nuclear power.  Some of this aversion is due to safety – while there are 104 nuclear power plants operating in the US currently, the specter of Three Mile Island still haunts the industry.  Some of it is cultural, feeding off an aversion towards the “unnatural” in the environmental movement.

Yet of the various zero-emissions energy sources, nuclear power has been the most significant success, generating 80% of the electricity used by France.  (The only alternative energy that comes close is hydrothermal, which generates a similar proportion of Iceland’s energy.  But Iceland has both a smaller population and extraordinarily favorable geography for power generation.)  Because of this success, some within the environmental movement have been pushing for increased nuclear power as the best option to combat CO2 emissions.

But, like the majority of the environmental movement, Obama has a record of being less than wholehearted in supporting nuclear power, even as he pushes for subsidizing less quantitatively promising – but politically safer – sources of alternative energy.  The safety problem with nuclear power is a real and significant challenge, but by piling up waste at over a hundred discrete sites, this move will likely only exacerbate the problem in the short to medium run.  In the long run the risk may decrease, if only because nuclear power generation will stop altogether as old plants are shut down.

The cynic in me must note that the Senate Majority Leader, Harry Reid, is from…you guessed it, Nevada.