Monthly Archives: August 2010

Why I made my PhD thesis look pretty

Posted on by
1

In the summer of 1988 I was finishing my PhD thesis at Cambridge University’s Institute of Astronomy. Then—and maybe now, too—the rules stipulating the physical appearance of an astronomer’s thesis were pleasingly light in number and exactitude: The book had to be hardbound, the paper acid-free, and the total number of words below 60 000.

Taking those stipulations as an opportunity to relieve the toil of describing my research, I decided to design a good-looking thesis. Fortunately, the typesetting program TeX had arrived at the institute. Even more fortunately, one of my grad student predecessors, Sterl Phinney, had bequeathed a set of TeX macros. I had the tools to implement my decision.

A trip to the institute’s venerable library revealed that most theses were typewritten, double-spaced, and printed on one side of each page. Consequently, a typical thesis was as thick as Martin Chuzzlewit.

I don’t know about you, but if I’m to read 60 000 words, I’d rather they were arranged on pages like a published, typeset novel, rather than like an author’s prepublication manuscript. I can’t remember which novel I was reading at the time, but I measured its mean number of words per line and its number of lines per page. My thesis would have the same.

Using both sides of a page doesn’t make a book or thesis easier to read, but it does make it thinner. Paul Dirac’s 1926 Cambridge thesis was famously short—just 17 pages. My thesis, which analyzed x-ray observations of two neutron-star binaries, could never match Dirac’s terse profundity, but if it was double-sided, it would be among the slimmest in the institute library.

ThesisSpread340.jpg

The photo shows a two-page spread from chapter 3. You can see some of my design elements: running heads for the thesis (left) and chapter (right); generous margins to avoid overlong lines and pages; figures and tables embedded in the text.

Besides displaying my vanity, I’m not sure what my attention to graphical design accomplished. But I like to think that my goal of enhancing readability was appreciated by my examiners and by the small number of other people who read the thesis.

My thesis popped back into my mind yesterday when I was browsing through the latest issues of the two magazines I contribute to, Physics Today and Computing in Science & Engineering. Articles in both magazines can be somewhat tough and technical, but they look good, thanks to the professionals who lay them out: Elliot Plotkin and Rita Wehrenberg at PT and Monette Velasco at CiSE.

I have no doubt that their attention to graphical design is appreciated—and not just by me.

Charles Day

Physics and the fight against cancer

Posted on by
Reply

At first glance, cancer might seem defenseless against the weapons devised by physicists or built from their discoveries.

The resolution of magnetic resonance imaging scanners, for instance, is a few cubic millimeters. Nascent tumors can in principle be detected when they’re small, isolated, and easiest to treat. And when a tumor is found, high-energy x rays, gamma rays, protons, and other forms of radiation can be directed at tumors in beam patterns of increasing sophistication and effectiveness.

But having written about cancer over the years, I’ve learned that there’s more to beating the disease than locating and zapping tumors.

One of the biggest challenges arises from the nature of cancer. Ironically, given that the disease is characterized by rampant cell division, tumors grow slowly and, for the most part, stealthily. The ability to resolve a lentil-sized tumor is little help if you don’t know where to look.

And that ability is even less help if you don’t know whether to look in the first place. In rich countries, cancer ranks below heart disease and noncancerous respiratory diseases as a leading cause of death. Most people don’t die of cancer. Routine, image-based screening for the general population would reveal too few tumors to offset its huge cost.

Compounding the detection problem, especially for breast cancer, is the number of false positives. Five years ago, in the course of looking for research to write about, I came across a paper in the Proceedings of the National Academy of Sciences by MIT’s Michael Feld and his collaborators. Its introduction began with this striking and somewhat depressing paragraph (with my emphasis added):

In the United States, ≈216 000 new cases of breast cancer are diagnosed each year, and 40 000 women die from the disease. Mammography, the most common technique for detecting nonpalpable, highly curable breast cancer, employs x-rays to quantitatively probe density changes in breast tissue. Because these density changes are not uniquely correlated with breast cancer, mammography serves as a screening technique rather than a diagnostic tool. Thus, a lesion found through either clinical breast examination or mammography is always biopsied. Because of current limitations, 70–90% of mammographically detected lesions are found to be benign upon biopsy. Breast biopsy is most often performed by surgical excision that removes the entire lesion or by core needle biopsy that removes 5–12 cores of tissue, typically 1 mm in diameter and several centimeters long, to ensure proper sampling. The complete diagnostic process, from start to finish, may take months and may include multiple biopsies.

But if you can detect cancer early, the prognosis following prompt treatment is good. Table 8-2 in The Biological Basis of Cancer (Cambridge U. Press) compiles three-, five-, and ten-year survival rates for seven malignancies. All except the ten-year survival rate for breast cancer are above 57%.

How could physics help to achieve a survival rate of 100%? As a former astronomer, I’m not qualified to answer, but as a writer, I can imagine what an ideal treatment might look like.

Early detection would be carried out through a noninvasive, nonimaging method. A blood test would be ideal. To kill the tumor, the patient would ingest an agent that would make its way to the tumor, stick to it, then inject a cancer-killing drug into the tumor cells. A blood test after the treatment could confirm its success.

How fanciful is that scenario? And where does physics fit in? I’m not sure about the first question, but the second is easier to answer because physicists are already working with scientists in other disciplines to solve it.

A blood test might arise from the statistical analysis of the cancer genome. Nanoparticles that can adhere to tumor cells have already been developed. Research that seeks to discover how viruses inject their RNA or DNA into cells could point to how artificial viruses could accomplish the same thing with anticancer drugs. Physicists are also working on how to repair p53, a key, cancer-fighting protein that fails to protect cells when it suffers certain mutations.

But before that research bears fruit, physicists are improving current therapies and diagnostics. The latest innovation that I’ve come across, stereotactic body radiation therapy, entails treating tumors with short, intense bursts of radiation.

From my inexpert perspective, the prospects for defeating cancer look good.

Charles Day

This collection makes me want to walk around Prague and bite somebody!

Posted on by
3

The title is a quote from yesterday’s New York Times. In “My Must-Have Looks for This Fall,” a fashion designer called Zaldy described with wit and relish the clothes he wants to own this coming season. The one-named designer continued: “And I know they’re crazy, but some pieces from Bernhard Willhelm—you never know when you’ll need a color-blocked crotchless Lycra wrestling suit!”

When I encountered Zaldy’s remarks, my reaction—after choosing purple and chartreuse for my crotchless wrestling suit—was how utterly unlike a physicist Zaldy is when it comes to clothes. The massed physicists I saw last March at the American Physical Society’s meeting in Portland, Oregon, were not badly dressed. Rather, in their jeans, sneakers, and T-shirts, they dressed with attention to comfort and indifference to fashion.

There are, and were, exceptions. Every photo I’ve ever come across of J. Robert Oppenheimer, including the one below, shows a man who chose clothes that fitted and flattered him. And some physicists take the trouble to develop a signature look. Four come to mind who habitually wear all black.

jro.jpg

But most physicists don’t follow Oppenheimer’s example. The most extreme example of sartorial insouciance I’ve witnessed was that of James Heath, a pioneer of molecular computing (and who would probably call himself a chemist, I should point out).

One November, Heath flew from Los Angeles to Boston to give an invited talk at the Materials Research Society meeting. He showed up in the convention center wearing a brightly colored short-sleeved shirt, shorts, and, if I remember correctly, sandals. Not only had he forgotten to dress for Boston’s weather, he’d also left his laptop in California.

Did those mental slips matter? Hardly. Using hastily prepared, hand-written viewgraphs, he gave one of the best talks of the meeting. Indeed, it’s conceivable that in creating his viewgraphs, Heath was forced to focus more on his message than on its presentation.

And it’s also conceivable that the trust physicists and other scientists enjoy in the eyes of the public arises in part from their being above looking nice for TV cameras. After all, one of the most credible physicists of all, Richard Feynman, titled one of his books What Do You Care What Other People Think? Further Adventures of a Curious Character.

Charles Day

Read some history of science this week!

Posted on by
Reply

Every now and again, I walk from my office at the American Center for Physics to visit the Niels Bohr Library, which is on the same floor. There, arrayed on racks that cover a wall, is the library’s collection of current journals, magazines, and newsletters. The journals I always browse first are the ones devoted to the history of science and technology.

My interest in history, not just the history of science, has two sources. First, like most physicists, I want to understand the workings of nature; that quest for understanding also extends to societies, past and present.

Second, in researching their works, historians strive to discover the significance and meaning of past events; in writing their works, historians—the good ones, that is—tell compelling tales. I read history for pleasure.

Today’s library browsing yielded a prize. The current issue of Isis, the journal of the History of Science Society, has a focus section of essays about the cold war, a period of grim fascination for me. I was born during the Cuban missile crisis of 1962. When the revolutions of 1989 ended the war, I was halfway through my first postdoc.

isis.jpg

Among the essays is one I was especially pleased to find: “Transnational Science during the Cold War: The Case of Chinese/American Scientists” by Zuoyue Wang of California State Polytechnic University in Pomona. I’d heard Zuoyue present an earlier version of the essay last November at the National Air and Space Museum’s series of colloquia on contemporary history. The full article is available for free on the Isis website. As a foretaste, here’s the abstract:

This essay examines the experiences of about five thousand Chinese students/scientists in the United States after the Communist takeover of mainland China in 1949. These experiences illustrate the often hidden transnational movements of people, instruments, and ideas in science and technology across the Iron Curtain during the Cold War. I argue that those hundreds who returned to China represented a partial “Americanization” of Chinese science and technology, while the rest of the group staying in the United States contributed to a transnationalization of the American scientific community.

Now it’s quite understandable if you don’t share my enthusiasm for learning about NSC-68, Charter 77, SS-20s, and other icons of the cold war. Still, I urge you to read some history of science this week. Zuoyue and his fellow historians don’t merely recount what happened. They explain what those events meant and mean.

Charles Day

ArXiv, a cornucopia of general-interest papers

Posted on by
1

About twice a week I trawl the arXiv preprint server in search of papers to post on Physics Today‘s Facebook site.

When I first started the practice, I worried it wasn’t sustainable. The magazine’s Facebook fans are enthusiastic about physics, but a lot of them aren’t practicing physicists. And even if they were, most arXiv preprints are written by specialists for specialists. Having found one or two papers of general interest, I wondered if they’d keep appearing.

But to my delight and surprise, it’s turned out to be fairly easy to find appealing papers. Granted, they tend to appear in a small subset of categories, but there’s enough variety to spice the Facebook site.

For today’s post, I found “The Entropy of Morbidity Trauma and Mortality” in the quantitative biology category. In the paper, Clive Neal-Sturgess, a professor emeritus of mechanical engineering at the University of Birmingham in the UK, tackles the problem of evaluating the severity of multiple injuries using entropy. The paper’s abstract begins:

In this paper it is shown that statistical mechanics in the form of thermodynamic entropy can be used as a measure of the severity of individual injuries (AIS), and that the correct way to account for multiple injuries is to sum the entropies. It is further shown that summing entropies according to the Planck-Boltzmann (P-B) definition of entropy is formally the same as ISS [Injury Severity Score], which is why ISS works.

The thermodynamical approach isn’t far-fetched. Injuries entail the fracture, shearing, tearing, or rupture of biological tissue, whose ordered structures constitute a human’s stored entropy.

I’m not sure what motivated Neal-Sturgess to post his paper on arXiv—his first on the site as far as I can tell. The paper’s formatting doesn’t evince the use of a journal’s style sheet or LaTeX template. It might not be destined for formal publication.

But I like to think that he shares with Physics Today‘s Facebook fans an enthusiasm for talking and learning about physics.

Charles Day

Promoting the LHC with a New Age video

Posted on by
Reply

Last Friday I received an e-mail entitled “LHC video by Bob Dylan’s son.” When I clicked on the link inside, I thought the link was out of date. What appeared on my screen was not the Large Hadron Collider, its mammoth detectors, nor anything obviously to do with particle physics.

Instead, the five-minute video opens with shots of a little boy wandering about in a forest, as an unknown narrator talks about the names of birds in different languages. So far, so New Agey, I thought, but the video soon shifts its attention scienceward to the 19th-century naturalist Alfred Russel Wallace, whose dogged study of Earth’s animals and plants led him to propose a theory of evolution independent of Charles Darwin’s.

Next comes Brian Cox, a member of the collider’s ATLAS team, who discusses links between art and science. Pictures by William Blake, Leonardo da Vinci, and other artists flash by.

Collider for CERN from MadeByFreeForm on Vimeo.

The images of the LHC that fill most of the remainder of the piece are eye-catching, even beautiful. Aesthetically, they hold their own against the photos and drawings of nature and the works of art that precede them. The instruments of particle physics, if not perhaps the science itself, are beautiful, the video seemed to say.

But the video offers another, possibly contradictory point of view—that of Richard Feynman, who appears in extracts from archival interviews. Feynman says that nature is what it is. We might want to find a single ultimate theory but, he warns us, reality could consist of millions of onionlike layers.

That nature at its most fundamental level should be as beautiful as nature at its highest level is a prejudice, a hope, and possibly a mistake.

Charles Day

Is a warmer Earth a greener Earth? Remote sensing says no

Posted on by
Reply

As the vast tall jungles of the Amazon evince, plants thrive in warm wet environments. Global warming, by promoting evaporation, should make some parts of the world wetter as well as warmer. Could our climate-changed world become greener? Would those extra plants, by sequestering carbon dioxide, help mitigate global warming?

Maybe. Rising temperatures also promote desertification. And if it gets too hot, the enzymes that catalyze photosynthesis stop working. Earth could become browner, not greener. In a paper published today in Science, Maosheng Zhao and Steven Running of the University of Montana in Missoula have tackled the green-versus-brown question in what I think is the only way possible: They analyzed remotely sensed data.

Amazon.jpg

The Moderate Resolution Imaging Spectrometer has been mapping Earth’s vegetation from space since 1999, when NASA launched Terra, the spacecraft that carries MODIS and four other environment sensors. The picture above is a MODIS image of the Amazon basin.

Unless you work in the field of remote sensing or, like me, have friends who do, you might not appreciate the science behind Terra and other Earth monitoring missions. MODIS is just as sophisticated as any imaging spectrometer built for astronomy. Its 36 wavelength bands span the range from 400 nm to 14.4 μm. Every day, Terra beams down a terabyte of data, a rate comparable to that generated by Higgs-hunting particle accelerators. And to extract useful data, you need to solve and apply radiation transfer formulas that Subrahmanyan Chandrasekhar and others developed for stellar atmospheres.

Zhao and Running used a decade’s worth of MODIS data to evaluate Earth’s net primary production (NPP) of carbon—that is, the mass of carbon from atmospheric carbon dioxide to terrestrial biomass. The decade 2000–09 was the warmest ever recorded. During that time, NPP rose in the Northern Hemisphere but it fell in the Southern Hemisphere in response to extensive droughts.

Unfortunately, the global balance turned out to be negative. Zhao and Running found that NPP decreased by 0.55 petagrams. Earth is getting browner, not greener.

Charles Day

Scarcity amid abundance in reporting science

Posted on by
2

My local newspaper, the Washington Post, like others in the US, has been reducing its coverage of science for years. Granted, stories about astronomy, health, and the environment continue to appear, but not in a science section and not written by a reporter whose expertise, experience, and beat is science.

Science’s lowly status at the Post is reflected by the paper’s website, where you’ll find neither a tab nor a link labeled “Science.” Anyone who browses the website for science needs to know in advance that stories about biology, chemistry, or physics are collected under national news—even when the newsworthy research is carried out abroad.

Now it’s quite possible that the Post, CNN, the Dallas Morning News, and other outlets that cut their science coverage did so because news about science isn’t as popular as other fare. The hypothesis isn’t fanciful. Thanks to the web, it’s easy for editors and publishers to discover what kinds of stories people click on the most. Maybe science stories are like green vegetables served to children: edifying, but unloved.

On the other hand, US newspapers—far more than their counterparts in the UK and Japan, the two other countries I’ve lived in—rely on advertising revenue. If a section doesn’t attract ads, its popularity won’t save it from the axe, as last year’s demise of the Post’s standalone Books section evinced.

But whatever the plight of science reporting, one thing stands out in blunt, ironic contrast: It’s never been easier for journalists to find science stories. Every day, public information officers at universities, journals, funding agencies, national labs, and professional societies issue press releases. To get a sense of the PR cornucopia, visit the Breaking News section of EurekAlert!, an online clearinghouse for press releases run by the American Association for the Advancement of Science.

At least one online outlet, Science Daily, exploits the flood of press releases to the hilt. There, you’ll find the same press releases as on EurekAlert!, identified by their sources but not flagged as PR.

What to make of the scarcity of science reporting amid the abundance of press releases? Although I’m in the news business, and although I respect and value the work of public information officers, I think scientists should redouble their efforts to reach the public directly.

The public could indeed have a limited appetite for daily science news. But as the growing popularity of New York’s annual World Science Festival and other science fairs attests, the public is still hungry.

Charles Day

Leprosy of tin

Posted on by
1

I first heard about tin pest (lèpre d’étain, “leprosy of tin,” in French) yesterday in the midst of reading a history of Singapore.

By the late 19th century, Singapore’s prosperity had risen dramatically, thanks in part to the opening of the Suez Canal, the extension of the telegraph from Europe, and the development of Malaya’s tin industry. Wondering why tin became a hot commodity, I turned to Wikipedia, where I encountered tin pest.

Tin is a soft, shiny metal that resists tarnishing and is nontoxic, which is why it has been used for more than a century to line steel food containers. The Wikipedia entry also told me about tin’s principal allotropes (structural forms). The useful metal, known as white or β tin, is the stable allotrope above 13.2 °C. Below that transition temperature, a brittle, fragile insulator called gray or α tin is the more stable.

The modest transition temperature might seem to rule out many practical uses for tin, including food storage. Fortunately, the α–β transition has a high activation barrier. Still, when the ambient temperature is low, objects made of white tin will transform readily, if slowly, into gray tin and disintegrate. You can hasten the transformation. In this video, where 1 second of screen time corresponds to 1 hour of real time, a tin ingot is chilled to −40 °C.

Organ pipes in Northern European churches fell victim to this tin pest; so, perhaps, did the tin buttons on the uniforms of Napoleon’s soldiers as they retreated from Moscow in the frigid winter of 1812 (the buttons story isn’t confirmed).

My former ignorance of tin pest brought to mind a 1956 short story by the science fiction writer Philip K. Dick. In Pay for the Printer, the residents of a future, war-torn Earth rely on docile alien beasts called Biltongs to make copies, in a chicken-laying-eggs way, of cars, TVs, and other otherwise unobtainable consumer items. The replicated goods don’t last, but that’s not a problem—until the Biltongs start dying off. Then, humanity realizes that it must shed its dependence on the Biltongs and recover its former ability to fend for itself.

I hope Earth is not ravaged by a war that wipes out our knowledge of how tin and other materials fare under not-so-extreme conditions. But as the world’s supply of hydrocarbons runs out, we could find ourselves relying more on traditional, sustainable materials like sisal and gutta-percha. And if that happens, we may need to relearn what our forebears knew of those materials’ natural vulnerabilities.

Charles Day

Let’s hunt for M-class planets!

Posted on by
Reply

This morning I went to the National Academy of Sciences’ Keck building in Washington, DC, to attend a briefing about the latest decadal survey of astronomy and astrophysics.

Like its six predecessors, the current survey, which covers 2012–21, ranks future ground- and space-based missions in order of scientific priority. Unlike those predecessors, the survey identified a new quest in addition to astronomers’ prime directive of understanding the universe and its contents. Now, astronomers really want to find habitable worlds outside our solar system.

Technology is one reason for this newfound enthusiasm for what Mr Spock calls M-class planets. NASA launched its newest planet surveyor Kepler last March. So far, the mission has found more than 300 new extrasolar planets. None has an Earth-like mass and orbit, but Kepler‘s instruments are working well enough to identify one. Followup missions, of the kind envisioned by the decadal survey, could determine whether those Earths have terrains, atmospheres, and oceans that can sustain life as we know it.

There’s another reason—and it surprised me. When the briefing was over, I chatted with the survey’s chair, Roger Blandford of Stanford University. He told me that incoming graduate students want to work on problems to do with finding and understanding planets. “It used to be cosmology that inspired them,” he said.

Star Trek, whose M-class planets notoriously looked like the uninhabited parts of Southern California, has probably been around for too long to have caused the newest generation of astronomers to seek and study new Earths. The discovery of extrasolar Jupiters in the early 1990s might be responsible.

But whatever the source of their inspiration, the new planet hunters are in a sense returning to a style of exploratory science practiced in previous centuries. When Meriwether Lewis and William Clark left Pittsburgh in August 1804, their main goal was to survey the lands acquired by the US in the Louisiana Purchase. Lewis and Clark also found and documented 178 new plants and 122 species and subspecies of animals.

Being a Vulcan and having seen and visited scores of M-class planets, Mr Spock would hardly raise one of his upswept eyebrows if he came across another one. But imagine the thrill that one of today’s graduate students will feel if he or she finds the first extrasolar Earth.

Charles Day