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Archive for March, 2009|Monthly archive page

“What we have [to avoid], is a failure to communicate”

In Physics on March 31, 2009 at 2:04 am

From SEED magazine:

Recently, a small group of American and Chinese scientists and engineers collaborated on a compendium of roughly a thousand terms and phrases related to nonproliferation, testing, and more. The latest edition of this “Nuclear Security Glossary” was made freely available online in November, though it remains a work in progress.

The need for such a nuclear glossary — a joint effort of the US Committee on International Security and Arms Control (CISAC) and the Chinese Scientists Group on Arms Control (CSGAC) — arose because accurate translations between English and Chinese can be tricky under the best of circumstances, and in the highly technical context of nuclear terminology, they are of fundamental importance. “Science rests as much on communication as discovery,” says Raymond Jeanloz, a physicist and CISAC member who helped craft the glossary.

While science is often an international collaboration, scientists remain the products of single nations and cultures.  They must therefore make a special effort to communicate with each other, particularly as science involves so many neologisms that complicate translations.  Many proteins, for example, have multiple names as they are first discovered in high-throughput assays (with little known about them) and then gradually characterized so they can be named based on function.

As a result, simply keeping up with and systematizing this torrent of new information is a task in itself – particularly, as the article notes, when there is a language barrier on top of it, and the science has political implications.


Just the science?

In Biology, Policy on March 17, 2009 at 6:51 pm

Last week, the Obama administration rolled back restrictions on federal funding for embryonic stem cell research on newly created embryos.  When he was in the Senate, Obama said the following:

…the promise that stem cells hold does not come from any particular ideology; it is the judgment of science, and we deserve a president who will put that judgment first.

A recurrent theme of this blog is that science policy is more than just science.  Like all policy decisions, it is informed by facts but fundamentally comes down to a question of priorities.  What is the value of a human embryo, and is it worth trading off X of these to develop Y therapies?  What is the cost of climate change, and how much are we willing to pay economically to mitigate the effects?  The “judgment of science” can tell us the characteristics of a blastocyst and vaguely sketch out possible benefits from stem cell research.  But the decision whether to have the government fund it is a political and ideological one, and to point to one side of the argument as “science trumping ideology” is disingenuous.

The Economist article goes on to point out that Obama opposes human cloning.  In his remarks on embryonic stem cell research he called human cloning “dangerous, profoundly wrong, and has no place in our society, or any society,” and promised that “we will ensure that our government never opens the door to the use of cloning for human reproduction.”  Now there are good reasons for this opposition: even on animals there is a very low success rate, and even for successful clones there are often lingering medical issues.  But notice how the reasoning has suddenly changed – he is morally opposed to human cloning based on these known risks, thus justifying at least defunding of the research and possibly (the wording is unclear) banning it altogether.  From science trumping ideology we now have ideology directing science.

Not that this makes these decisions necesarily wrong.  There are strong arguments for embryonic stem cell research, which become stronger or weaker depending on the value you place on a human blastocyst.  Likewise many (but not all) believe that the suffering attendant upon human cloning efforts is too great to justify scientific advance in that field.  But we need to be clear that these decisions are informed by science but ultimately based on personal beliefs and priorities, not solely on “the judgment of science.”

Politicians ought to appoint scientific advisors on a nonideological basis and listen to what they have to say, but it is ultimately their job to issue a judgment based on their value system.  However rhetorically convenient it may be, it is disingenuous for them to claim to follow science’s lead when approving of research, only to voice moral disapproval when they wish to hit the ideological brakes.

Nuclear Power: How it Works, What’s Next

In Physics on March 7, 2009 at 9:56 pm

Going back to Peter’s post on nuclear energy, I’d just like to link to Jonathan Golub’s great six-part series on nuclear power at his blog Dear Science.

What is radioactive waste, exactly? Well, nuclear fission works by knocking neutrons off the nuclei of uranium atoms, which releases energy in a chain reaction. In a nuclear reactor, the uranium rods are the fuel. Once the chain reaction has taken place, the rods are still radioactive — new elements have been created, which keep on undergoing radioactive decay. But these new reactions release neutrons too slowly to sustain a chain reaction, so they’re useless as fuel. These are called “spent” rods, and they’re what we mean when we talk about nuclear waste. We have to put them somewhere: we’ll next build some metal and concrete casks outside of the reactor building, next to the plant and store the rods there, at least for a few years. In the long term, you want them far underground and away from people — and that’s where Yucca Mountain comes in. How much risk remains, and how we evaluate costs and benefits, I honestly don’t know.

But we have another option: we can build better reactors. Normally nuclear power plants use lightly enriched uranium. Heavily enriched fuels (that release more neutrons) are typically used for bombs in the world’s nuclear arsenals. With better fuel, we can build a fast neutron reactor — no need for a moderator to slow down the neutrons and sustain the chain reaction. All those extra neutrons can smash up the radioactive decay products. This both boosts efficiency and burns off the radioactive waste.

Golub says:

Nuclear waste is the overwhelmingly major problem with nuclear power plants today. There is no plan, no strategy beyond burying it someplace for at least a million years. No technology exists that matches the problem. Fast neutron plants, that eat their own waste and potentially the waste of others, are an overwhelmingly better solution than Yucca mountain.

Where are these plants? The ideas here aren’t new ones. A pilot project, the Integral Fast Reactor (IFR) was to build a liquid sodium metal cooled, plutonium and U-235 fueled fast neutron reactor with an on-site waste processing center. The project’s budget was cut in 1994 by President Clinton’s energy secretary and thus languished before the project could be completed. The ideas from this project have been rejuvenated, with plans for a liquid sodium, liquid lead and gas cooled reactor variants based around the same general principles, called generation IV reactors, to be ready for commercial operation in 2030.

2030 is too far away. If we were smart, we would throw resources at these fourth generation technologies, pushing to have the pilot reactors and designs finalized within ten years. None of these are perfect. No source of power is without risk or environmental injury. None. Our planet hosts nearly seven billion people. Fossil fuel reserves are dwindling. The atmosphere and oceans are buckling under the carbon strain. Nuclear power, particularly responsibly applied with standardized plant designs and a real plan for dealing with the waste, remains our best hope. The physics and technology is available. We just need to do it. Now.

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.

Visa trouble keeps foreign scientists out

In Policy on March 4, 2009 at 5:44 pm

We should all be worried about this. Science and engineering students and postdocs from abroad are finding it more difficult to get visas, and experiencing longer delays. This is making researchers increasingly unwilling to study or schedule conferences in the US — we can no longer assume we’re the rest of the world’s first choice. As Danielle Guichard-Ashbrook of the Massachusetts Institute of Technology put it: “There are other countries that want these folks. They are the best of the best. They have other options.” Since Sept. 11, stricter security procedures have been hard on scientists trying to work here, especially in national labs that now have policies discriminating against some foreigners. If you’re unlucky enough to be a scientist from somewhere like Iran, you could be handcuffed, interrogated, mistreated, and detained in prison cells after you thought you’d obtained a visa. The UK has already started revising visa rules to help visiting scientists — will we follow suit?

The main cause of delays is a requirement, since Sept. 11, that each reviewing agency give a thumbs-up to the visa candidate. (Before 9/11, a visa could be granted if no agency objected within 10 days.) One remedy would be to hire more reviewers, or to rely more on the scientific community’s judgment by speeding the visa process if a U.S. university or scientific association can vouch for the foreign researcher.

Related: a miserably hilarious chart on the U.S. immigration process.

Something lovely: oscillography

In Delights, Math, Technology on March 3, 2009 at 4:06 am


Eric Archer, electronic media experimentor, has rigged up a vector art synthesizer with an oscilloscope, a digital pattern generator, and a set of identical cards called Quadrature Wavetable Oscillators, which convert digital information into analog voltages. The outputs are summed on a two-channel mix bus, with the two channels representing the X and Y coordinates in Cartesian space. The oscillations can make beautiful fine-line patterns reminiscent of the engravings on paper currency around the world.

Specialized lathes have been in use for hundreds of years to make complex patterns that are unreproduceable without directly copying them (i.e. photography or digital means). This is the historical art of guilloche (ghee-o-shay’) or Engine Turning. Remember the old 1970’s toy called Spirograph? It operates on a similar principle, producing mathematical curves called epitrochoids via revolving circular gears around each other while a stylus traces their motion. Other combinations of motion can be used, such as mounting the stylus to a rotating disc as it traverses a straight line. Watchmakers and jewelers have long used these techniques for ornamentation on their work. The famous Faberge eggs bear designs engraved by a similar technique.

Inside these sophisticated engraving machines, there are numerous settings to be made among the gears that revolve to cut the pattern. One doesn’t need many meshed revolving gears before it becomes possible to produce endless patterns that are practically impossible to replicate. Hence this technique was adopted very early by national governments to mint their paper currency, postage stamps, and other monetary certificates. The U.S. Treasury is rumored to maintain such a machine, known as a Geometric Lathe, containing ten interlocked pattern-generating discs. The settings of the discs would only be known to a select few, as this information must be guarded from the hands of counterfeiters… at least prior to the digital age we are in now.

More here.
Flickr stream here.
Also: Archer has a gadget that lets you listen to the modulations in visible light. The sun apparently sounds incredible — like “pink static.” Listen for yourself here.

Climate change and scientific objectivity

In Policy on March 2, 2009 at 10:38 pm

A continuation of our discussion of scientific input into policy debates:

The climate change debate is unusual in that scientists are understood as being almost monolithically on one side of the debate; in the public eye it is common to view it as The Scientists vs. The Politicians.  Part of this is because of the cognitive biases of scientists and the blurring between positive and normative positions, and these are effects we see in other debates, for instance about public health in third world countries.  But part of this phenomenon is structural: even under ideal cases, the debate about costs and benefits are split across disciplines.  One technocratic approach to evaluating climate change would be as follows:

1. Climate scientists estimate the extent of anthropogenic climate change, creating a graph of emitted greenhouse gases vs oC change in temperature, with nice error bars.

2. Economists calculate the costs of any arbitrary temperature change, along with the costs of an adjustment to any arbitrary CO2 emission level.  They find the point at which marginal cost equals marginal benefit.

3. Political scientists refine this estimate by calculating the probable public-choice inefficiencies of government policies.  They formulate the optimal policy, which will probably reduce emissions slightly less than the economists’ model proposes.

Even in this model, when everyone stays inside their disciplinary lines, scientists will be in the position of pointing out the costs of our current choices.  It is up to the social scientists to say yes, this is true, but the adjustment to lower emissions levels is not costless.

Given these roles, and given that scientists, politicians, and journalists all have their own axes to grind, it is not surprising that scientists are often presented as being monolithically on the interventionist side on the climate change debate.  The only way for their research not to be simplified into “Needs Action Now!” is if it claimed that either climate is static or that climate cannot be changed by man, both of which are almost certainly false.  But the sophisticated observer would note that their contribution is but one link on a long logical chain, a chain that needs to be viewed in its entirety to support an argument pro or con.  And honest (and modest!) scientists and journalists would do well to keep that framework in mind.

The Politics of Science

In Policy on March 2, 2009 at 4:19 am

Just a few points in response to Janice’s post.

The Tierney article is really about climate policy, at heart, so let’s talk climate. It seems to me that the situation is the following.

1.) Climate change can’t be faced without an understanding of science. Unless they want to be willfully blind, policymakers are going to have to listen to geologists, atmospheric physicists, engineers, ecologists, and so on, to make reasoned decisions.

2.) There’s significant and legitimate disagreement about our priorities, when it comes to climate change. These disagreements are more about values and politics than about science. How much do we care about the long run compared to the short run? How much do we want to sacrifice in present economic growth to protect against unlikely but catastrophic risks? How much do we care about the developing world compared to the rich world? How troubled are we by the prospect of government subsidies and mandates interfering with the market? How troubled are we by being required to consume less?

3.) The majority of climate researchers (at least, those who make their policy opinions known) favor strong emissions regulation. There are dissenters, but they are in the minority, and often affiliated with conservative think tanks.

Now, if your answers to the questions in 2.) lead you to oppose strict reductions in carbon emissions, then you’re in trouble. You have no choice but to listen to scientists — but the scientists are mostly lined up against you! If you’re Tierney, or Pielke, you rail against the “politicization of science.” But scientists — still more, scientists in Washington — are human. They can’t make themselves apolitical if they’re giving political advice.

Rather, I think we need to keep in mind that to some extent, science has its own political and philosophical slant. I’m going to hypothesize a little bit here, so bear with me. An academic scientist has dedicated years of her life to the study of nature, often forgoing a more lucrative career in the private sector, and frequently collaborating with colleagues from around the world. This suggests that scientists would be likely to
a.) be long-term thinkers
b.) have a sympathy for preserving the natural world, especially the particular subject of their research
c.) be inclined not to value financial ambition very highly
d.) not be very nationalistic; inclined to identify as closely with foreigners as with Americans

These are personal sympathies, or cognitive biases, that I think would make scientists favor different public policies than the average U.S. citizen. They’re also biases that would make scientists tend, on balance, to favor climate change legislation. (Confession: I’m an aspiring scientist, and I share all those biases to some extent.)

If we want to, as Pielke says, be honest brokers, we need to be honest about the fact that scientists have their own politics. It may be to some extent unavoidable that policy decisions advised by scientists will be scientists’ policies — technocratic and reliant on expert judgment. And there are limits even to expert knowledge; nobody in Washington is smart enough to really know which emerging clean technology promises the most success in thirty years. Maybe the challenge for policymakers is to know when to listen to scientists, and when not to.

Mammalian ancestor genome sequenced

In Biology on March 2, 2009 at 3:07 am

They’ve reconstructed the genomes for the woolly mammoth and the Neanderthal — now paleogeneticists led by Ian Holmes at UC Berkeley have sequenced the earliest mammal genome. How do you do that without a primitive mammal handy? It’s a statistics hack; they extrapolate from the genomes of living animals. Writes Holmes,

The cool thing is that you can get a lot of information about ancestral genomes just by crunching probabilities — even if you don’t have any fossils, or mosquitos-trapped-in-amber, or time machines, or whatever.

The even cooler thing (to my bioinformatics-geek mind) is that the algorithms used for this are almost exactly the same ones that linguists use to reconstruct ancient languages, like “Indo-European” or “Gondwanese”.

The problem here is to construct a phylogenetic tree (an evolutionary family tree), then deduce the amino acid sequences of the common ancestral proteins at the branches. So by looking at the DNA of present-day mammals, we can infer the shared genome of a common ancestor. This is reminiscent of the divergence of words from their original Indo-European ancestors: for example, the Proto-Indo-European word for snow (*sneigwh-) can be reconstructed from the descendant words for snow in the descendant Indoeuropean languages (German schnee, French neige, Irish sneachta, Russian sneg, Sanskrit snihyati, and so on).

The first scientists who proposed to reconstruct the genetic past from the present were Linus Pauling and Emile Zuckerkandl, who, in 1963, resurrected an ancient form of hemoglobin. They actually reconstructed the molecule in the lab. Which leads us to wonder, now that we have entire genomes of ancient organisms, whether some kind of Crightonesque resurrections might be possible. Would you want to meet a Neanderthal?
A velociraptor?

Much more here, in a book on ancestral sequence reconstruction.