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Archive for February, 2009|Monthly archive page

Scientists need to keep their hats on in this political climate

In Finance and business, Policy on February 28, 2009 at 7:54 pm

A recent post by science writer John Tierney in the New York Times “Findings” column highlights Dr. Robert Pielke, Jr.’s book, The Honest Broker, which expresses a concern with scientists’ temptation to take advantage of their privileged position. Scientists in the company of non-scientists often overemphasize the credibility of their own models and speculations at the expense of politicians that don’t have the peer-reviewing ammunition that scientists do. Additionally, scientists who “enter the fray” find themselves having political debates, rather than scientific ones—Dr. Pielke wants the public, as well as the scientists, to recognize the distinction. The country is at a crucial juncture, and many will look to scientists for advice on investment options with regards to both the economy and climate change—in this light, the scrutiny is well-placed.

Although we shouldn’t jump the gun and become conspiracy theorists, it’s always prudent to revisit the important preface to critique of any science: scientists are human. It might seem like a trivial qualifier, but anyone who’s worked long enough in the sciences knows that they fight for credit, worry about their reputation, and navigate complex human networks like anyone else—most of us tend to forget this because we don’t often have the opportunity to share reflective conversations with science professors who have the honesty to look back their careers and laugh at themselves. I’m currently taking the course MOL 328 U.S. Medical Research and Researchers: Preeminence, Problems, Policies, and this post reminds me of the times that Prof. Rosenberg made polite remarks about arrogance and fiery temperaments (in reference to James Watson and Robert Gallo, respectively). Scientists’ personalities often make fascinating and amusing narratives, I assume because people so often take for granted the stereotype of scientists as disinterested, coldly intellectual fixtures that have better conversations with their computers and specimens than with other people. The strange juxtaposition of the objective reality we probe and our interpretation of it gives scientists this potentially awkward but uniquely endowed vantage point. Some make use of it, while others revel in their privacy and autonomy.

For those scientists (and academics in general) who have to defend their ideas in the public arena, debates that used to center on preliminary assumptions and gambles on plausible hypotheses are being transformed into debates that spill over from tiffs in academic journals to more personal political attacks in op-eds and press conferences. The emergence of the science blogosphere has made many scientists more accessible—by corollary, it has given contention a new place to thrive. The casual link between evolutionary theory and sociological and cultural history has encouraged people to interpret scientific results rather generously—while there are some who can thoughtfully articulate the interdisciplinary connections, it’s frightening how easily science and philosophy of science are confused.

The humanness of scientific research also introduces difficulties into collaborative projects that harbor potential for politicization. The relatively recent efforts in the last few decades to coordinate academia, government, and industry in the practice of medical research point to the impediments faced when groups with different goals and skill sets have to come to a consensus. The publication of the results of the Human Genome Project in two separate journals (Science and Nature) by two parties (at odds with one another over strategies for releasing the data), is one well-known example of the seeming irreconcilability of people’s (and scientists’) perspectives (reconciliation committees were unable to bridge the divide).

With this in mind, there are several problems with finding feasible environmental solutions that the government can pursue. For one, science advisers are inevitably going to have their own opinions on matters, and will steer funds and publicity how they see fit. I actually have very little idea how influential science advisers are, so if anyone would like to comment on this, please do. In any case, it’s problematic when scientists who’ve developed good tools and strategies are effectively ignored because the government has decided to back one public stance. Even if the government had a more multidimensional message to hash out, its inertia prevents it from reacting quickly enough to the innovations that periodically bubble up from scientists in academia and industry. Being a science major, I’m a bit lost on this one, because there are certainly times when the government primes the pump and energizes research in all sectors—what distinctions are there between the current environmental research movement and the booming medical research movement after WWII? The obvious factor is the economic fragility—post-war U.S. was the “last one standing,” but nowadays, we’re not even sure how many years it will take us to recover from the economic crisis. Even if we were to take into consideration the large wads of cash that are being handed to researchers as part of the astronomically large economic stimulus package, it’s a mystery to everyone whether stimulus money can actually be meaningfully utilized for research, which is a long-term endeavor. For more details on what the EPA plans to do with the money from the Recovery Act, look here. While it seems that the EPA is going to do a thorough clean-up job, there don’t seem to be any initiatives for creating technology for cleaner energy—something is missing the mark.

Not being an expert in policy, I am not surprised that the administration necessarily has to take a singular stance, but I am curious if there’s any way to make better use of the scientists who offer alternative (and often complementary) approaches to environmental problems. Is it a matter of freeing up regulation, federal funding, or large-scale implementation that makes the government’s role important in the furthering of these strategies, such as the air capture of carbon that Dr. Pielke feels is worth investing in? There is an incredibly palpable universal interest in environmental initiatives, but because of all the short-sighted projects and fire-lit hoops to jump through, we’re losing time while everyone lobbies for his own interests. The government lacks a systematic and diverse cooperative plan. Although the upcoming Power Shift Conference is certainly a step in the right direction, politicians’ willingness to establish effective clean energy policy has to start with a fair assessment of all the brands of environmental projects that are out there. Only then can young activists’ enthusiasm find a vehicle for realization. Tierney expresses a similar frustration when he writes, “Well, I suppose it never hurts to go on the record in opposition to a billion imaginary deaths. But I have a more immediate concern: Will Mr. Obama’s scientific counselors give him realistic plans for dealing with global warming and other threats?”

Stephen Colbert recently commented during his show (jokingly, but I suspect with some seriousness) on the parallel between the scare tactics of the Bush administration used to justify the Iraq War, and the apocalyptic grandeur of Democrats’ defense of the stimulus package. I think most people don’t care to be scared anymore–everyone knows there’s a lot at stake, even if you’re not sure what exactly the experts think it is. My feelings about expansive statements made by scientists seeking popular science sensationalism can be summed up by David Brooks’ worried remark in his recent New York Times op-ed column “The Uncertain Trumpet” on the many promises made in President Obama’s recent address: “Obama blew a mighty trumpet Tuesday night, but after you blow the trumpet, you actually have to charge.” Scientists can’t just capitalize on counting the ways that the world can end—they have a responsibility to bail us out when no one else knows how to. Along the way, the few pioneer scientist public figures are sure to blaze new trails, making the political machinery work for them, rather than working for the politics.


More efficient web storage for the developing world

In Technology on February 26, 2009 at 3:59 pm

As hard drive space becomes cheaper, RAM has remained expensive — meaning that internet access is still out of reach for most of the world. Vivek Pai, a CS professor here at Princeton, has developed an invention that may change that. HashCache is a highly efficient method of caching, or saving frequently accessed Web content on a hard drive instead of using precious bandwidth to to look it up every time. The RAM-hogging step in most caching methods is the index, a table that assigns each image or block of text on a website a number, which in turn is associated to a location on the hard disk. Pai’s breakthrough was eliminating the index; the number is the memory address. This significantly increases the efficiency of internet data transfer.

The development team has been working with Intel, which is “very keen on making technology affordable in developing regions,” according to CS department chair Larry Peterson. And the caching system is already being tested at the Kokrobitey Institute in Ghana and Obafemi Awolowo University in Nigeria. (HT

The interface between technology, altruism, and capitalism is an interesting one. Should inventors like Pai make an effort to make their products accessible at low cost to poor countries? Is that idealism, “creative capitalism,” or good business sense? Is it possible that inventors do more good for the world if instead they try to make as much money as they can?

Some very bright people discuss the question here. My take is roughly John Quiggin’s, which observes that technological creativity is not always — not at first, anyway — linked to profit.

Yet neither the Internet nor the Web was a product of the market economy, and even now the relationship between market incentives and the social contribution made by Internet-related activities is tenuous at best.

Both the Internet and the Web developed as non-commercial activities, outstripping or absorbing a variety of commercial competitors (Genie, Delphi, AOL and so on) before being opened up to commercial use in the mid-1990s. And even since large-scale commercial involvement began, most of the exciting innovation continues to come from noncommercial users (blogs and wikis, for example) or from non-commercial content producers (YouTube, Flickr and so on). By contrast, heavily funded commercial innovations such as push technology and portals have failed or declined into insignificance.

Of course, corporations still have a large role to play in the economy of the Internet. A company like Google, for example, provides services that cannot easily be replicated by users acting either individually or collectively. But Google depends crucially and directly on the content created by users and more generally on the goodwill of the Internet community.

If these assets were lost, Google would be vulnerable to displacement; Microsoft’s loss of its seemingly unassailable dominance of both personal computing and the Internet software market is an illustration. Google’s slogan ‘don’t be evil’ and its sensitivity to criticism, for example over its compliance with Chinese censorship laws, illustrates the point. Equally, so do the many products Google creates and gives away, with no obvious path to future profit.

Paradoxically, the most profitable ideas were often not invented to be profitable. The Twitter guys invented a new form of human communication (communicagion?) and they’re not worried that they still don’t make a dime off it. Somehow, they’re sure, they will — and we believe them. People come up with ideas, especially scientific and technological ideas, more out of curiosity than either altruism or greed. Humanitarian and financial benefits usually follow a project that some guy just thought was intellectually cool. Maybe making it possible for a few billion more people to go online will, in the long run, make greater profits than commercial licensing in developed countries ever will. The techie’s ethic of compulsive sharing — reminiscent of Joseph Priestley’s fevered scientific correspondence — doesn’t look very businesslike, but it makes useful ideas happen faster.

Don’t be evil?

In Delights, Technology on February 26, 2009 at 3:07 am

Google Street View, which tries to present car-eye-views of the landscape in addition to Google Maps’s satellite images, has managed to turn up some interesting artefacts, including a creepy guy with a sniper rifle and a marriage proposal.  But as it turns out, one of the Street View cars, which carry the cameras used to make these composites, hit a deer in upstate New York, and the accident was captured on camera.  Google has since published an official response to the incident (apparently the deer was able to leave the scene on its own), and removed the incriminating photos.

Bambi survived

Bambi survived

Fish with transparent head

In Biology, Delights on February 25, 2009 at 5:55 pm


The barreleye fish Macropinna microstoma lives at the bottom of the ocean off the coast of central California — and Monterey Bay Aquarium researchers have discovered that its head is transparent. Its eyes are surrounded by a transparent, fluid-filled shield that covers the top of the fish’s head, and they are free to rotate in any direction. Normally the shield is destroyed when the fish is dredged up to the surface — this is the first time it has been seen intact.

A new phase of boron

In Chemistry on February 25, 2009 at 12:51 pm

This may be the first appearance of a chemical discovery on the Conan O’Brien show. A team of researchers led by Artem Oganov of Stony Brook University has discovered a new form of boron — a crystal structure that includes, for the first time ever seen, ionic bonds within a single element. Boron is a “schizophrenic element,” says Oganov — it was already known to have three forms, one dark red, one coal-like, and one hideously complicated structure called T-192.

All previous forms of boron have had B_12 clusters of 13 boron atoms — what makes this structure remarkable is that it also has B_2 pairs, which produce a faint but perceptible ionic character as charge is transferred from the structure to the pairs.

How was the new form discovered? Not by a lab accident but by an algorithm. The researchers used a computational technique known as evolutionary structure prediction that encodes parameters of the crystal structure; starting with a number of trial configurations for the atoms, it discards the high-energy (unstable) patterns, and tries again, eventually converging on a stable configuration. The algorithm may come up with stable configurations not yet observed in nature, which leads chemists to go looking for temperature and pressure conditions that can create them.

The article is here. More on evolutionary crystal structure prediction here — it actually gives a pretty intuitive sense of the algorithm. It’s modeled on biological evolution: different molecular configurations are produced by “heredity,” “mutation,” and “permutation” (that is, two crystal lattices may be averaged to get a new one, one lattice may be warped a random amount, or two atoms may be exchanged within a lattice.) Then, the individuals are selected to survive or die based on “fitness” — in this case, fitness means low chemical potential energy. The surviving configurations then have “descendants” which are further pruned. Eventually the algorithm finds local minima for potential energy: the stable configurations.

Stop Math Now!

In Finance and business, Math on February 25, 2009 at 4:47 am

Or so it would seem…
This article by Felix Salmon, pinpoints the Gaussian Copula formula, an advance in financial mathematics pioneered by David X. Li, as the source of our financial collapse.

With his brilliant spark of mathematical legerdemain, Li made it possible for traders to sell vast quantities of new securities, expanding financial markets to unimaginable levels.

His method was adopted by everybody from bond investors and Wall Street banks to ratings agencies and regulators. And it became so deeply entrenched—and was making people so much money—that warnings about its limitations were largely ignored.

Then the model fell apart. Cracks started appearing early on, when financial markets began behaving in ways that users of Li’s formula hadn’t expected. The cracks became full-fledged canyons in 2008—when ruptures in the financial system’s foundation swallowed up trillions of dollars and put the survival of the global banking system in serious peril.

So what is a copula? It’s a statistical model for determining correlation between different random distributions. Correlation is at the heart of the business of financial engineering — if you’re going to construct a CDO out of mortgage obligations, you’d better know the probability that all of them will default at once. Pricing risky assets — the problem the market got horribly wrong — rests on computing the correlation between rare events. Li’s formula had a deadly simplicity. Correlation was reduced to one parameter — it didn’t take into account the relationships between various loans that make up a pool. The correlation between two stocks may not be constant over time, but the copula formula treated it as if it were.

So is financial math evil? I’m inclined to think we need more of it, not less. A simple model was applied too enthusiastically by bankers who didn’t understand the quants — maybe we’d have been spared the current credit crisis if asset managers had more mathematical sophistication.

But read Salmon’s whole article; it’s very smart and very accessible.

New Plumbing for the Internet

In Policy, Technology on February 16, 2009 at 5:49 am

For those of you who didn’t catch it, the NYT had an article yesterday titled, quite simply, “Do We Need a New Internet?“. It’s worth a few minutes of your time on the Old Internet to take a look at it.

The article’s premise is that the Internet was never created for the requirements we’re now asking of it. It was meant to be a network for the military and professors in their ivory towers. From the hardware and TCP/IP upward, the idea was to let a close knit community more easily share papers and mail.

But then a funny thing happened: the rest of the world moved in. All of a sudden, you’re not sure who your next door neighbor is. Is he the innocent server he says he is, or does he have more malicious designs? Ideally, when you can’t see the dude or dudette you’re communicating with, you’d like your network to help you out, by either limiting who can join or or limiting anonymity of the participants. Unfortunately, because academics made it, nodes on the Internet, by default, trust other nodes, and because it was commissioned by the military to be resilient in the face of Soviet attack, there’s no central control area on the Internet.

The only thing growing faster than our dependence to the Internet, it seems, is the number of ways to exploit Internet security flaws. The article does a good job of talking about the state of Int

ernet security today, describing a sort of patchwork solution to the holes we find every day. Particularly striking was the warning about the impending calamity if we continue down this increasingly futile road: “If you’re looking for a digital Pearl Harbor, we now have the Japanese ships streaming toward us on the horizon.”

This struck a chord with me because it’s not the first time I’ve head someone talk about a concerned Internet attack:

Lawrence Lessig, a respected Law Professor from Stanford University told an audience at this years Fortune’s Brainstorm Tech conference in Half Moon Bay, California, that “There’s going to be an i-9/11 event” which will act as a catalyst for a radical reworking of the law pertaining to the internet.

The article goes on to mention that…

Lessig also revealed that he had learned, during a dinner with former government Counter Terrorism Czar Richard Clarke, that there is already in existence a cyber equivalent of the Patriot Act, an “i-Patriot Act” if you will, and that the Justice Department is waiting for a cyber terrorism event in order to implement its provisions.

So far, we’ve talked about technology; now come the policy issues.

What the NYT doesn’t really bring up is what, if we were have a New Internet, it would look like. It surely wouldn’t be just about the technology: unlike during the 1970’s, governments and businesses are a lot more aware of the power of the Internet, and you can bet they’re going to want to have a say in designing this New Internet. Privacy becomes one important concern. We’ll surely be giving up some of it (a necessary cost), but who determines what’s too much? Would we give the American government be too much of our information? Are we granting the Chinese filters their wet dream?

What of companies? Do they have access to our data so they can better target their advertisements (and “enhance our Online experience”)? If ISPs get too much of a say (or if we yearn for central authority), can we say goodbye to Net Neutrality? Does doing so mean we say goodbye to YouTube?

The point is not so much to scare people (or spew anti-government, anti-corporate hate) as to remind everyone that the prospect of a New Internet designed by special interest groups is almost as scary as the prospect of living with the current Internet. The free and natural evolution of the Internet is, after all, the thing that’s allowed to the Internet to be the base for so much great innovation. But then, if we don’t do anything, we risk “cyber 9/11” and may have to live with the Government’s version of the Internet.

It’s not clear what path we’ll venture down, but either way, it looks treacherous. Welcome to the future.

The INternet

The Internet

Geeks just wanna have fun

In Delights, History on February 15, 2009 at 9:00 pm

In connection with Sarah’s post on scientific clubs in the 18th century, it bears repeating that the majority of these scientists were hobbyists.  While this meant that there was a broader base of interested tinkerers, this system was not without its drawbacks:

“…Not long after the establishment of the Academy of Natural Sciences of Philadelphia, Mr. Say was prevailed with to become one of its members. Of the origin of this highly respectable and useful institution, I shall at this time merely assert, that its founders had any thing in view but the advancement of science. Strange as this may appear, it is nevertheless true, that the club of humourists, which subsequently dignified the association under the imposing title of Academy, held its weekly meetings merely for the purpose of amusement; and, consequently, confined itself to those objects which it was thought would be most conducive to that end.

…great was his surprise, on being inducted into the temple of science, to find that the whole collection consisted of some half a dozen common insects, a few madrepores and shells, a dried toad fish and a stuffed monkey: a display of objects of science calculated rather to excite merriment than to procure respect, but which, in the end, proved to be the nucleus of one of the most beautiful and valuable collections in the United States.”

-Say, Thomas and John L. Le Conte, ed. American Entomology: A description of the insects of North America v.1. Boston: Estes & Lauriat, 1859 (?). vii-x.

AcademyAcademy of Natural Sciences
Animal House

Animal House

The Lunar Society: citizen geeks of the 18th century

In Delights, History, Technology on February 15, 2009 at 5:55 am

Boulton, Watt, and Murdoch, members of the Lunatic Society, in Birmingham, England.

Boulton, Watt, and Murdoch, members of the Lunatic Society, in Birmingham, England.

Science before the twentieth century wasn’t done by “scientists.” There was no such word. There were educated amateurs and self-taught tinkerers, building their own labs in search of discovery or a patent. And so there wasn’t such a distinction between science and culture — the smart set went to “electrical parties” to see demonstrations of the newly discovered force. Ben Franklin wrote,

A turkey is to be killed for dinner by the electric shock, and roasted by the electric jack, before a fire kindled by the electrified bottle; when the healths of all the famous electricians of England, France, Holland, and Germany are to be drunk in electrified bumpers, under the discharge of guns from the electrified battery.

The best example of the public nature of science in Enlightenment England was the Lunar Society, a club of industrialists, natural philosophers, and intellectuals that met in Birmingham at the full moon between 1765 and 1813. The port and talk flowed. Joseph Priestley was a regular member: a self-taught chemist, political radical and Unitarian minister, he discovered oxygen and its necessity for animal life, invented seltzer water, and supported the American and French revolutions. Also a “Lunatick” was Josiah Wedgwood, the great ceramics industrialist and founding member of the Society for the Abolition of the Slave Trade. James Watt, the inventor of the modern steam engine, attended meetings regularly. Thomas Jefferson and Benjamin Franklin visited occasionally; Antoine Lavoisier corresponded with Society members; John Smeaton, the father of civil engineering, and Joseph Wright, the painter of the Industrial Revolution, were also regulars.

It must have been a thrill. Something like TEDTalks with Stilton. Writes Adam Hart-Davis:

The Lunar Society believed in argument and cooperation. They had long discussions about why thunder rumbles and decided the best way to test their various theories was by experiment. Boulton made a 5-foot-diameter balloon from varnished paper, and they filled it with a terrifying mixture of air and hydrogen (“inflammable air from iron”). They lit a fuse underneath, released the balloon into the night sky on a calm, clear evening and waited for the bang. Unfortunately, the fuse was rather long, and they all assumed it must have gone out; so they began to talk among themselves, when there was a colossal explosion, and they all said, “There it goes!” and forgot to listen for the rumble! Watt was at home 3 miles away and wrote that the bang was “instantaneous, and lasted about one second.” This seems self-contradictory, but in any case, the experiment failed to produce a simple answer to the original question.

There you have it: science, explosions, debate, optimism, politics, technology, curiosity. The future started more than two hundred years ago.

Darwin zen

In Biology, Delights, History on February 15, 2009 at 3:33 am

In honor of Charles Darwin’s 200th anniversary: the best and oddest of the web.
Darwin’s complete published and unpublished works.

Convergent evolution could reflect molecular constraints: “Things don’t just happen in chemistry.”

Adam Gopnik talks Darwin and Lincoln.

Swimbladders and humble-bees.

Darwinian animation.

Chuck’s daily routine.

Darwin has a posse.

Read aloud from the Origin of Species.

Darwin’s London.

Darwin and Adam Smith.

Darwin’s grant proposal is turned down.