Monthly Archives: December 2012

Standards rule OK

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My title comes from the chorus of a song on the Jam’s second album, This Is the Modern World (1977). Written by the band’s singer and guitarist Paul Weller, the song is a bombastically ironic attack on the enforcers of social conformity.

But if Weller were not a socially conscious rock musician and instead were a computational scientist, he might have still chanted, “Standards rule OK!” For without standards in hardware, software, and data formats, our work would be less efficient and less effective.

I first appreciated the importance of computer standards when I worked at NASA’s Goddard Space Flight Center in Greenbelt, Maryland, in the early 1990s. My field, x-ray astronomy, was just three decades old at the time. The first pioneering missions could detect only a handful of bright objects. But their successors—among them the European Space Agency’s European X-ray Observatory Satellite (EXOSAT; 1983–86) and NASA’s Einstein Observatory (1978−82)—observed thousands of x-ray emitting stars, galaxies, and other cosmic objects. Then came Germany’s Röntgen Satellite (ROSAT; 1990−99) and Japan’s Ginga (1987−91), which added to that swelling collection.

Because spacecraft telemetry is limited by bandwidth, the data gathered and beamed to Earth by satellite observatories are packaged in efficient, instrument-specific formats—15 altogether for the instruments carried by the four spacecraft listed above. In contrast with the diversity of telemetry formats, the figures that embody the data’s scientific content (and ultimately appear in research papers) typically come in a smaller set of generic flavors: images, spectra, and light curves.

Creating those figures entails background subtraction, binning, filtering, and other generic tasks. In principle, the software that, say, Fourier-transforms a data stream from EXOSAT‘s Medium Energy instrument could do the same for a data stream from Ginga‘s Large-Area Counter. But the raw formats are as different as Dutch and Japanese. If the same software is to work with data from those and other missions, the data must be translated into a common format. And that format must be flexible enough to accommodate new instruments.

My former colleagues at GSFC duly picked such a format: flexible image transport system (FITS). Originally developed for optical and radio data, FITS makes extensive use of headers and keywords. Like XML, FITS is extensible. Whenever a new detector technology comes online, new keywords and data structures are defined within the FITS framework. Granted, someone has to write an instrument-specific program that translates telemetry into FITS, but no one has to take on the more onerous job of rewriting data analysis software.

When I left GSFC in 1997, astronomers there and elsewhere used three software programs to analyze their data: Xspec (for spectra), Xronos (for light curves), and Ximage (for images). Now, 14 years later, they’re still using the same three programs for data from observatories that launched years after my departure.

FITS made its public debut in 1981 in a paper in Astronomy and Astrophysics. On 30 November of that same year, the Swedish pop group ABBA’s eighth and final album The Visitors became the first recording available on a new format, the compact disc. Although CD sales are waning, it remains a durable standard—at least I hope so. I have six Jam CDs.

This essay by Charles Day first appeared on page 96 of the September/October 2011 issue of Computing in Science & Engineering, a bimonthly magazine published jointly by the American Institute of Physics and IEEE Computer Society.

Earthquakes, soft bombs, and internet vulnerability

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Once I’d taken in the devastation wrought by the Tohoku earthquake and tsunami, my thoughts went to the physicists I knew at Tohoku University. The university is located in the city of Sendai, 81 miles from the earthquake’s epicenter and just 10 miles from where the tsunami hit land.

News was frustratingly difficult to obtain at first. Tohoku University’s website was down; emails were either not get­ting through or not being answered. On 16 March, five days after the earthquake struck, a friend of mine posted on Physics Today’s Facebook page that he’d heard from an old classmate of his, a nuclear physicist at Tohoku Univer­sity. Some campus buildings were damaged, but there were no casualties.

I learned later that the earthquake had damaged power lines and telecommunications cables. What’s more, the shutdown of Fukushima I and other nuclear power sta­tions in northeastern Japan had created a power shortage. Even if telecommunications cables or cellphone towers had remained operational, information would have stopped flowing on the internet due to a lack of electro­motive power.

That information is intrinsically physical and requires energy to store, process, and transmit is a familiar con­cept to physicists. But I was still surprised that an earth­quake had shut down, or at least slowed down, Sendai’s internet. After all, the internet’s message protocols and network structures were designed to survive nuclear attacks.

Given the nature of warfare, you can presume that if one group of military thinkers has devised a new weapon, another group will try to devise a countermeasure. I don’t know whether the US Pentagon’s ­BLU-114/B “soft bomb” was designed to take out an enemy’s internet, but, by targeting power plants, it could achieve that goal, too.

The soft bomb is a remarkable weapon. Within the bomb’s casing are a classified number of bomblets that contain a classified number of chemically treated graphite filaments. When detonated over a power plant, the bomb­lets release the filaments, which spread and fall in a dense cloud. Because graphite is a conductor, the filaments short­-circuit transformers on contact, leading to damaging lightning­-like discharges.

During the 1999 Kosovo War, the US Air Force’s F­-117 stealth fighters dropped soft bombs to temporarily disrupt or knock out 70% of Serbia’s electricity­-generating capacity. According to a timeline of the war published by Rasmus Ole Rasmussen, Bent C. Jørgensen, and Bernhelm Booss-Bavnbek, Belgrade’s power was cut off on day 66 of the war. Six days later, on 6 June, Slobodan Milošević accepted NATO’s peace plan.

I hope military thinkers are devising ways to protect the internet’s physical infrastructure—if not from soft bombs, then at least from earthquakes and tsunamis.

This essay by Charles Day first appeared on page 104 of the July/August 2011 issue of Computing in Science & Engineering, a bimonthly magazine published jointly by the American Institute of Physics and IEEE Computer Society.

When the pie shrinks

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When I read the title of James Langer’s editorial in the 12 October issue of Science—”Enabling scientific innovation”—I expected a generic exhortation for the US to invest more money in basic research. What Langer wrote, however, was a despairing indictment of how the US evaluates and funds scientific proposals in these times of tight budgets.

According to Langer, just when advances in experimental and computational techniques have opened up new areas of research, opportunities to fund such research are contracting. Worse, the shrunken funding pie has made peer reviewers and proposal writers averse to risk. As Langer puts it:

In my area of condensed-matter and materials physics, the U.S. National Science Foundation (NSF) can fund only about 10% of the individual-investigator proposals it receives. [The Department of Energy (DOE) has similar difficulties.] Each proposal is sent to a group of peer reviewers, who rank it on a scale ranging from “excellent” to “poor.” NSF then funds only those proposals that receive the uniformly highest reviews. One less-than-“excellent” review, no matter how misguided, is usually enough to doom a proposal. Any proposal that is truly innovative, interdisciplinary, or otherwise unusual is almost certain to be sent to at least one reviewer who will be less than enthusiastic about it. Sensible investigators know not to submit such proposals; as a result, some of the most urgent research areas are disappearing.

Evidence to justify Langer’s fears appeared this week in the form of a commentary in Nature entitled “Research grants: Conform and be funded.” The authors, Joshua Nicholson of Virginia Tech and John Ioannidis of Stanford University, looked at the relationship between a biomedical researcher’s citations (a rough measure of scientific significance) and the level of his or her funding from the National Institutes of Health (NIH).

In particular, Nicholson and Ioannidis examined authors of papers that have garnered more than 1000 citations since 2001. The pair found that

three out of five authors of these influential papers do not currently have NIH funding as principal investigators. Conversely, we found that a large majority of the current members of NIH study sections—the people who recommend which grants to fund—do have NIH funding for their work irrespective of their citation impact, which is typically modest.

Such correlations don’t prove that review panels aren’t funding high-risk, high-reward proposals. But at least to Nicholson and Ioannidis, the correlations suggest that NIH is failing to fulfill its mandate of funding “the best science, by the best scientists.”

In his Science editorial, Langer struggled to come up with a more effective way of funding the best science. He even entertained—but dismissed—the idea of disbursing money through a lottery, which could well do less damage, he wrote, than the current system does.

But there is no more effective way than peer review. When funds are limited, it’s hardly surprising that reviewers become more cautious. Investors do so too. The solution to the review problem is both simple and hard: Increase the size of the funding pie so that reviewers are emboldened to take risks.