Cocktail Party Physics

swing shift

It don't mean a thing if it ain't got that swing, or so the classic song lyric goes. Which means that I must lack meaning, since when it comes to dance, I am best described as "athletic" rather than artful. It's not that I can't feel the beat, but that I lack that certain je ne sais quois that makes something "dance" as opposed to mere rhythmic movement.

Remember that scene in Miss Congeniality, where Sandra Bullock's character is trying to learn a dance routine for the beauty pageant, and resorts to martial arts moves when she can't remember the steps? Ahem. That would be me. Endurance? Check. Timing? Check. Enthusiasm? No problem. Actual fluidity and grace? Not so much. And yet I thrill to films like Strictly Ballroom and Idlewild, imagining myself capable of those frenzied yet artfully timed dance moves. In my mind, I am Ginger Rogers and Shakira ("Hips Don't Lie") combined -- with just a hint of the Dancing Pipecleaner Man (hat tip: Angela Gunn, who reminds us all that "F is for Footloose"). Not even this handy Website Jen-Luc Piquant unearthed, with tips on how to dance specific styles, would be much help, I fear.

Physics might not be able to explain my sad lack of swing-y rhythm (and self-delusional fantasies to the contrary), but it definitely has something to say about the accompanying music, according to Kenneth Lindsay, an acoustician and Brazilian percussion player who has created a computer program to visually analyze the musical stylings of swing. I missed Lindsey's presentation at last December's Acoustical Society of America meeting (held in Honolulu, Hawaii), because it conflicted with another session on animal bioacoustics, and I just had to see the excised Siberian tiger larynx in action. But by all accounts, Lindsay's talk was quite the jazzy hoedown, complete with some Brazilian drumming to demonstrate different swingy styles.

Yes, there are a wide variety of swing styles, part of the reason it's difficult to pinpoint exactly what constitutes "swing" from a musical standpoint. Its history dates back to the 1920s and the advent of the Charleston and the Lindy Hop. The swing dance craze really took off when the Savoy Ballroom opened in New York City in 1926, where some of best dancers and bands found a home. The next decade saw the creation of the Jitterbug, a bouncy six-beat variant, inspired by the eponymous tune by Cab Calloway. Add in the influence of swing/jazz giants like Benny Goodman, and my friends, you had a movement, as tap and jazz steps made their way even to the more hallowed halls of professional dance.

Purists would limit their definition of swing dance to things like the Charleston -- usually danced to 2/4 ragtime -- the Balboa (an 8-count dance featuring quick footwork), and the Lindy Hop, characterized by an emphasis on improvisation. (The Lindy Hop was so adaptable, it easily incorporated steps from other 8-count and 6-count swing styles.) Over time, the list has extended to incorporate American jazz, Caribbean beats, reggae, samba, and more bluesy styles like "dirty dancing."  Lindsay's work is more concerned with the accompanying music, specifically its ability to get people to move their bodies in such an energetic and rhythmic way. "If you're tapping your feet, that's swing," says Lindsay.

Why human beings react this way to swing music is a question for other sciences, but Lindsay thinks there are clues in the math -- specifically, the unique rhythms of this kind of music. Most notably, swing has lots of triplets, irregular notes -- those that are 2/3 the length of a regular note -- and relies heavily on micro-timing of pulses and meter. Or, as Wikipedia prefers to describe the syncopated timing of swinging jazz music: "a combination of crotchets and quavers which many swing dancers interpret as 'triple steps' and 'steps' -- yet [it] also introduces changes in the way these rhythms were played -- a distinct delay or 'relaxed' approach to timing." This contrasts rather sharply to certain other styles, like syncopation, which plays a note when a pause is expected, or doesn't play a note when it is expected.

The trick is figuring out how to visualize sound in order to analyze it scientifically. Acousticians do this by turning sound waves into spectrograms. Wikipedia tells me that "the spectrogram is the result of calculating the frequency spectrum of windowed frames of a compound signal. It is a three-dimensional plot of the energy of the frequency content of a signal as it changes over time." Whatevs. We prefer to think of it as a live-action visual depiction of a sound wave traveling through space over time. It's basically the aural equivalent of a telltale fingerprint of any given signal, whether it be an animal's cry, speech processing, or -- in the case of the image shown -- a violin.

There's different ways to plot a spectrogram, but in general, the horizontal axis denotes time, and the vertical axis denotes frequency. That's two dimensions. The third plot point is the amplitude of the sound wave (which roughly corresponds to decibel level), or intensity. In the above spectrogram, intensity changes are depicted by using changes in color, but there are computer modeling programs that can create truly 3D visual representations of a sound wave.

Even better: it's a two-way process.There are also a plethora of computer programs capable of turning a digital image into sound, including (for all the hard-core geeks out there, these are for Mac, Windows and Linux, respectively) MetaSynth, Coagula, and Enscribe, as well as JavOICe (a Java applet). So those who create electronic music can "hide" images in their tunes.

We're mostly talking relatively obscure electronic artists who do this, but Internet rumor has it that a leaked MP3 version of "My Violent Heart" -- a track from an upcoming Nine Inch Nails album, Year Zero -- ends with a few seconds of static. Analyze that static in a spectrogram and you'll end up with the image of a hand reaching down from the sky. Spooooky. The cerebral wags in the band might also have included an MP3 of crickets chirping on a second track, "Me, I'm Not," that reveals the number 216-333-1810 when fed through a spectrogram.  Trent Reznor's home phone number, perhaps? Who knows? This the 21st century technological equivalent of back-masking, or the Beatles' hiding "Paul is Dead" in a track off one of their later albums.The NIN album comes out April 17th, and it'll be interesting to see if there's any basis to the rumor. (Jen-Luc has her Cyber-Spectrograph fired up and ready to roll!)

But this post isn't about Nine Inch Nails' spectrogramic shenanigans, it's about the serious study of swing. Lindsay had his own fun with spectrograms. He took digital versions of famous swing songs, like Ray Charles' "Fever," and broke them down into their most basic components: notes, even single pulses, to within 3-10 seconds per unit. In some cases, he was able to fine-tune the differences between the sounds to half a millisecond. Why bother? Because the resulting spectrogram allowed him to separate out the sounds of instruments, voices and drums according to their pitch and note. This in turn provides a fuller profile that tracks critical distinctions between the rhythmic patterns in different musical genres -- say, swing versus "Riverdance" or a militaristic Sousa march.

Lindsay learned some interesting tidbits from his experiments, such as the fact that Ray Charles was one tight snapper: his snaps on his famed duet with Natalie Cole are timed so well, he is never more than 5 milliseconds off the beat. Sure, any truly talented musician keep an amazingly precise steady tempo; Lindsay's analysis adds some scientific credence to that ability. He's also now in the process of developing his own (Mac-compatible!) software to make it easier for solo composers and garage bands to modify and get the right timing in their pieces, thereby avoiding the dreaded tinny, over-precise mechanical sound that generally plagues such endeavors.

Rhythmic music is also integral to Capoeira, a Brazilian martial art noted for its acrobatic movements and kicks. In recent years, the style has become hugely popular in North America and Europe, in large part due to its unique blend of music, dance, athleticism, and martial arts strikes and dodges. It's no accident that a scene in Idlewild depicts some Capoeira choreography. Halle Berry trained with a Brazilian Capoeira mestre for some of the fight scenes in the Raspberry-honored movie Catwoman (c'mon, you know you saw it, if only to snicker at the bad dialogue and ogle Berry's skin-tight outfits); so did Charlize Theron for her role in Aeon Flux. Wesley Snipes is fond of incorporating Capoeira moves in his action flicks, including Blade, and the martial art formed the basis for the fighting style of the Jaffa people in Stargate SG-1. Add to that cameo appearances in music videos by Ricky Martin and Christina Aguilera, not to mention Mazda's use of a traditional Capoeira tune in one of their TV advertisements (Zum Zum Zum), and Brazil's national martial art is practically mainstream.

Capoeira has its origins in the Portuguese slave trade. From the 16th to 19th centuries, slaves from all over Africa were shipped to Brazil -- then a Portuguese colony -- bringing their cultural traditions with them. Capoeira developed as a secret art, to resist oppression, keep the culture alive and lift the spirits of the unfairly subjugated. Following the abolition of slavery, it soon became associated with criminal gangs, causing Brazil to outlaw its practice in 1890. But eventually Capoeira moved back into the mainstream; in 1937, then-president Getulio Vargas declared the discipline to be the national sport of Brazil. Capoeira schools have proliferated ever since, spreading around the world, particularly in North America.

There was a Capoeira school across the street from my NYC gym in the late 1990s, and on Friday nights, classes would spill out onto the sidewalk for an impromptu "demonstration" of the style. It was quite a party, and never failed to draw an enthusiastic crowd. Participants form a circle -- called a roda -- and take turns playing instruments, singing, and sparring in pairs in the center of the circle. The music sets the tempo and style of the game (jogo) to be played within the roda -- and it is more of a game than a fight in its modern incarnation; practitioners rarely make contact; it's considered a sign of lack of control and technical expertise to actually strike one's opponent. (Nor is it the only fighting style out there that incorporates elements of music and dance: Batuque and Maculele are two lesser-known styles closely connected to Capoeira, and old writings and engravings in Cuba depict a since-lost fighting dance called baile del mani, showing two men moving to the rhythm of yuka drums.)

Instruments used include berimbaus, resembling an archer's bow, with a steel string stretched across a gourd for resonance. Striking the string with a stick produces the tone, and the pitch of that tone is regulated by a stone. The berimbaus set the rhythm, but the music is also augmented with tambourines (pandeiros), a rasp (Reco-Reco), and a double gong bell (Agogo). Sometimes the musicians might add a conga drum (Atabaque), but this is considered optional. There are three basic kinds of songs: a ladainha (litany) is a narrative solo usually sung at the opening of a roda. This is followed by a chula or louvacao, basically a call-and-response format giving thanks to god and one's mestre (teacher). But the real action happens during the corridos, the songs performed while a game is being played, which also employs call and response, except the responses to each call are not set, but can be changed at the whims of the people in the roda.

All movement starts with the ginga, which literally means to rock back and forth, or to swing. The martial aspect can be seen in the attack moves: kicks, sweeps, and occasional head strikes. There are evasive ducks and rolls for defensive maneuvers, cartwheels (with and without hands), hand spins, hand springs, sitting movements, jumps, turns, and flips. (Modern breakdancing owes quite a bit to Capoeira.) One signature move, called the au batido, combines elements of both attack and defense. It starts with an evasive cartwheel, which leads into a block/kick -- in fact, it usually combines two kicks, creating a double spinning kick. Powerful upper body strength is critical to pulling off many of the more advanced moves.

The music dictates the action. Slow music is used for slower (albeit complex) ground moves and handstands; the slower games are all about showing off one's control and finesse, subtleties that are frequently lost on less knowledgeable audiences. The real crowd-pleasers are the faster games, because the faster rhythm means the dancers move more quickly and can generate greater circular momentum -- the key to gaining "big air" for the flashier acrobatic maneuvers. (See? There's some science there! Plus, we eagerly await Lindsay's spectral analysis of the corridos.)

Clearly, that song lyric has it right: it all comes down to that telltale swing (or ginga), whether we're talking jazzy dance halls or musical martial arts. Maybe I can't dance, but at least I can fight. So I do have my own sense of swing.

a girl's best friend

One of the first things that a newly betrothed woman must do is get her shiny engagement ring properly sized, I discovered last November. I'd never been one to wear rings of any sort, but really, how hard could it be? I figured I'd just find a local jeweler to do the job, since I believe in supporting small neighborhood businesses whenever possible. Alas, it turns out the road to re-sizing is fraught with peril if one lacks a knowledgeable guide. And I picked the wrong local jeweler.

He seemed competent and nice enough when I inquired about sizing the ring, and the price was reasonable, so I dropped off my ring and returned a week later to pick it up. The size was correct, but the color seemed a bit off, and the metal (white gold) had lost its sheen. When I checked the back of the ring, I noticed that the jeweler had pretty much just cut away the excess metal and soldered it back together with a new plain white gold double band -- which might have been less noticeable if the original bands weren't carved with a decorative motif that was absent from the new ones. Examining the ring more closely under better light once I got home, I noticed that the new metal didn't even match the original ring in color.

I'll spare you the account of my ugly confrontation the next day with said local jeweler, when I complained about his shoddy work, except to say that he tried the oldest argument in the book: "You know nothing about gold! How dare you come in here and complain about my work?" That's not a very good argument to present to a woman who writes about science for a living, with a particular interest in materials physics, because I actually do know a little something about gold -- certainly more than his average customer. His point was that he'd had to use gold (i.e., a compatible metal) rather than something closer in color, like silver, to solder the ring back together and therefore wasn't able to match the color. Also, the heat from the soldering reacted with the chemicals in the air and dulled the original finish, which he claimed was beyond his power to prevent. I countered by arguing that this wasn't the point of contention: my objection was to the finish work -- more precisely, the complete lack thereof.

A brief recap of the various types of gold used in jewelry might be in order here, especially for other newly engaged persons, because what happened to me is not uncommon. Yellow gold will always be the, er, "gold standard," particularly the 24-carat variety, which has a higher purity than, say, 18 carat gold, which is made of 25% other metals, such as copper or zinc. But for things like engagement and wedding rings, white gold has become hugely popular in recent years. It's basically a gold alloy containing at least one white metal to "bleach" the pure gold and lighten the color -- usually palladium, nickel, and occasionally silver; cheaper alloys may also contain copper, compromising the color a bit more. Most plain rings (simple wedding bands, for example) use a nickel alloy, which is both hard and strong, while the more malleable palladium variety is favored when gemstones are involved. The quality can range from 9 carats to 21 carats, but the most common is 18 carat white gold, made by mixing 75% gold with 25% other metals.

However, most people don't realize that white gold jewelry is often electro-plated with rhodium to improve the color and make it more shiny and silvery, and therefore more appealing to the customer. Eventually the coating starts to wear off and the ring becomes more off-white and dull in appearance, but a good rhodium plating should last at least three years before this happens. Exposure to harsh household chemicals can exacerbate the wear and tear, and so can soldering -- which is what happened in my case. That's what I meant by the lack of finish work. I could have forgiven the sloppy soldering job, since  that's just the back of the ring, which doesn't show. But to not bother with re-applying a new rhodium coating after the sizing demonstrates --among other things -- a lack of thoroughness, not to mention pride in one's handiwork. I cut my losses and took the ring to a more reputable jeweler, who re-coated it so it looked good as new.

The small diamonds in my ring weren't affected at all by the sizing fiasco, diamonds being among the hardest naturally occurring substances known to man.  Jen-Luc did a bit of nosing around the Internets and found that "diamond" derives from the ancient Greek adamas, meaning "invincible" (thank you, Wikipedia). The online consensus is that diamonds were first mined in India; there are references to the gems in a Sanskrit text, the Arthashastra, circa 296 BC, as well as a Buddhist text known as the Anguttara Nikaya. They soon became associated with divinity, which is why they were used to decorate religious icons.

Diamonds were also popular in ancient Greek, Roman and Chinese culture. The Greeks poetically believed them to be tears from the gods, while the more pragmatic Romans believed they were splinters of fallen stars. Europe caught onto the fad rather late in the game, circa 1300 AD, in part because (a) Arabic traders restricted the flow of trade between Europe and India in earlier centuries, and (b) the Christianized Western culture was suspicious of the popularity of diamonds for decorating images of "false gods." (I'm sure we'll hear from commenters debating the relative merits of "BCE/CE" versus the traditional "BC/AD"  nomenclature, but I'm sticking with tradition in this instance.)

The modern world is even more pragmatic in its attitude towards diamonds than the ancient Romans; there's a huge global market for industrial grade diamonds (those deemed unsuitable in clarity or color for being cut into gemstones). Some 80% of mined diamonds find industrial applications: cutting, grinding, drilling and polishing, mostly. For instance, they're embedded in drill tips or saw blades, or ground into a fine powder for grinding and polishing applications. But these uses aren't unique to modern times. I happen to have a set of diamond-tip drill bits, thanks to having a father and a brother in construction, but similar tools were apparently used in Yemen as early as the 4th century BC. And in 2005, a team of US and Chinese archaeologists discovered four stone ceremonial burial axes dating back to the Liangzhu and Sanxingcun eras (4000 BC - 2500 BC), which they believe to have been polished using diamond powder.

Materials derive their various properties from molecular structure. In the case of diamonds, the hardness factor is due to the fact that each carbon atom is connected to four other atoms by strong covalent bonds. Chemists figured that much out in 1797, subsequently embarking on a centuries-long quest to make diamond out of baser forms of carbon (allotropes) or carbon compounds. Scientists didn't succeed until the 1950s; General Electric is usually credited with developing the first commercial process for synthesizing diamonds. Note that these are not "synthetic" gems, like cubic zirconia; they're actual diamonds, just made in a lab rather than being mined from volcanic pipes deep in the earth where high pressure and temperatures fosters the formation of crystals out of carbon deposits; the resulting gems eventually reach the surface with volcanic activity. The preferable term for the manmade gems is "cultured" diamonds. (As yet, there is no "acceptable" term for the practice of converting the carbonized remains of loved ones into "memorial diamonds," a la the LifeGem Company.)

GE has since invented another process for improving the color of certain natural diamonds -- those that are somewhat brownish-tinged and therefore less expensive -- by heating them in a special furnace.  Yes, diamonds come in many colors, the result of impurities (such as the presence of nitrogen) or structural defects; yellow and brown are the most common, although the famed Hope Diamond was known as the "French blue," deriving its deep rich hue from the presence of boron. The GE process uses high heat (more than 1800 degrees Celsius) and pressure (between 50,000 to 70,000 atmospheres) to essentially redistribute the defects in the carbon lattice within the rest of the crystal. The resulting diamond resembles its pricier, colorless cousins once the process is completed.

That's just for mildly colored imperfect diamonds. Apparently so-called "fancy colored diamonds" are quite desirable if the color is intense and brilliant enough. (Jen-Luc is reminded of one of her favorite scenes in the musical Gigi, when the young title coquette-in-training is asked by her grandmother to identify various gemstones, and when presented with a yellow stone, guesses, "Um... topaz?" The grandmother, once the courtesan of minor kings, is horrified: "A topaz?!? In my jewels?" It turns out to be a rare yellow diamond.) Combining neutron or electron irradiation with annealing can turn more rare brownish natural diamonds into green-blue and orange-red shades, further increasing their value to the gem trade.

More recently, Gemesis Corporation has entered the commercial market for manufacturing atomically, structurally and chemically pure diamonds so well that it takes some pretty fancy lab equipment to distinguish the manmade stones from nature's handiwork. Similar high-temperature treatments with beryllium have been used to improve the qualities of rubies and sapphires -- in fact, similar techniques were used even in ancient times, according to this article in Chemical and Engineering News. And certain Thai gem dealers have been chemically diffusing beryllium into low-quality sapphire and rubies by heating the stones in the presence of chrysoberyl, a mineral commonly mined along with pink sapphires in Madagascar. The result: gemstones of very rare colors.

So how do you know if your gemstone is "natural" or an artificially enhanced version (assuming you care about such things)? Unless you have access to high-tech spectroscopic instruments, you might just be out of luck. Even the Gemological Institute of America (GIA) has had to resort to expensive techniques like secondary ion ass spectrometry and laser ablation-inductively coupled mass spectrometry to quantify the various trace elements down to levels of parts-per-million.

In 2005, a team of German physicists at the University of Bayreuth created a material even harder than diamond by subjecting C-60 molecules to even more immense pressures -- nearly 200,000 times atmospheric pressure -- combined with very high heat (2500 degrees Kelvin). They call their new material "aggregated diamond nanorods," because unlike regular diamond, this carbon form is made of tiny interlocking diamond rods. If you've never heard of them, perhaps it's because the moniker just lacks the oomph of, say, buckyballs, or even carbon nanotubes. But once the manufacturing process is scaled up, aggregated diamond nanorods (ADNs for short) are expected to find loads of useful industrial applications, just like their other carbon siblings.

The German scientists were able to achieve the intense pressures to create ADNs thanks to 5000-tonne multianvil press. We had a nice conversation about diamond anvil cells here last fall -- scientists routinely use such devices to squeeze materials between two opposing cone-shaped diamonds. They've also been used to simulate the extreme pressures existing in the centers of planets, creating new materials at the same time, such as metallic hydrogen and perovskite.

Speaking of intense pressures and temperatures, supernovae might well be the origin of carbonado diamonds,  so hard they can't even be polished or cut, making them useless as gemstones. They're composed of millions of small diamonds arranged in varying orientations. First discovered in Brazil by Portuguese explorers in the 16th century, carbonado diamonds were used to drill the rocks for the Panama Canal in 1905, and to polish Brazilian hardwood before shipping it off to Europe. They're only found in Brazil and the Central African Republic (although some geologists claim to have found it in Russia as well), which were once part of the same land mass.

Carbonado deposits are also much older than conventional diamond mines: 3.8 billion years or so, compared to 1 billion and 100 million years for diamond mines. That's what prompted scientists at the Florida International University -- Stephen Haggerty and Jozsef Garai, along with Case Western Research University researchers Sandeep Rekhi and Mark Chance -- to hypothesize that carbonados came from outer space, specifically, via a diamond-bearing asteroid that crashed to earth billions of years ago. That asteroid, in turn, was propelled into space as the result of a stellar supernova explosion.  The researchers used Brookhaven's infrared synchrotron radiation equipment to identify trace elements in carbonado, notably nitrogen and hydrogen. The presence of the latter in sufficiently high levels, per Haggerty, indicates the stuff came from interstellar space, which is especially rich in hydrogen.

Their online paper  on the subject appeared last December in Astrophysical Journal Letters. The NSF press release generated a huge amount of media coverage (there's an extensive list of links here), but the supernova-origin hypothesis is not without controversy: many diamond experts are skeptical. So is fellow blogger (and frequent commenter at the cocktail party) LabLemming, who asserted in a January post that the AJL paper "misrepresents the literature, fails to describe its samples and analyses well enough to allow an objective interpretation, and overstates the quality of the data." He also bemoans the utter lack of media coverage for a paper by Kagi et al. in American Mineralogist he deems to be "a contender for the best paper on the subject in the last five years."

LabLemming's specialty is, apparently, carbonado diamond, so we'll assume he knows his stuff from a technical standpoint. We can comment -- albeit somewhat cynically -- on the media angle: "it came from outer space" is just so much cooler than a standard dry materials paper, however careful and technically accurate the latter. Like it or not, spin sells. And "spinning" science doesn't necessarily make it "wrong." ("Ooh! Shiny!") Also, did Kagi et al. issue any sort of press release countering the hypothesis, thereby generating more media interest in their own work? (Does anybody even know Kagi's first name and research affiliation? This is vital information for journalists seeking to track down outside experts!) Even LabLemming has yet to post a detailed account of his critique of the Garai et al. paper, and reasons for preferring the Kagi et al. paper.

As a result, any journalist doing some preliminary Google research isn't likely to find much in the way of countering hypotheses. (If we all link to LabLemming's posts, maybe the Google ranking will skyrocket on that particular search. I try to do my part!) If they're experienced enough to have built up a network of scientific experts in various fields, they'll be okay, but many daily newspapers simply foist the science beat on Average Joe Reporter, who might not have those kinds of contacts.

I guess my point is that, while LabLemming's gripes are valid, it's very easy to grumble and point fingers at the mainstream media when it comes to science coverage -- even more so when they muck up your favored research topic. But the problem is far more wide-ranging than mere ignorance/laziness on the part of reporters. Scientists need to be more media-savvy -- where was the press release for the Kagi et al paper? Reporters at mainstream media outlets need to foster better ties with the research community and build up their own network of outside experts.

It would help if newspapers cared enough about science coverage to give reporters "beats" in specific subfields of science, but considering most no longer even have science sections -- and what little science is reported tends to be health and nutrition related -- that's purely wishful thinking. Still, sometimes the system works, and you end up with a well-written, accurate yet artistic article about a fascinating topic in science -- as rare as a deep blue diamond, and just as valuable.

lateral moves

We're back on our home turf, after making our way across all three US time zones (some more than once) in the past two-and-a-half weeks. My internal clock has no idea what time it's supposed to be. And there's been nonexistent blogging here at the cocktail party over the last week as I've struggled to catch up with everything that piled up in my absence.

Among other news, I returned to find that Frink Tank has declared itself suspended in a persistent vegetative state, hinting at some deep dark conspiracy. Jen-Luc Piquant is tres desole at the loss of one of the most irreverent science-minded blogs out there. Yet she is ecstatic to note the return to the blogosphere of that unrepentant miscreant, professor of dangeral studies Michael Berube (our fellow French-Canadian), who retired his eponymous blog earlier this year, and is now hanging his hat at Crooked Timber. (Hah! Future Spouse predicted Berube wouldn't be able to stay away!) Such a mishmash of conflicting feelings -- Jen-Luc's Cyber-Gallic soul doesn't know quite what to make of all the happy/sad permutations, ergo, she has taken refuge in the cool, emotionally detached objectivity of her crackpot scientific research.

While we're all eagerly awaiting Berube's first pithy offering at his new bloggy home, check out this intriguing article by Lindsay Borthwick in the current issue of Seed about a serious challenge to long-held assumptions about "silent" genetic mutations. Basically, silent gene mutations, while plentiful throughout the human genome, have long been believed to have no impact on the amino acid sequence of proteins -- since the late 1960s. Amino acids, for those like me who don't regularly follow genetic research, are the fundamental building blocks of proteins. Adding amino acids one by one to a growing protein chain causes it to elongate, until the protein begins folding. And how it folds determines its biologically active function. (I think.) 

However, last December, a team of scientists at the National Institutes of Health -- led by Chava Kimchi-Sarfaty -- published a paper in Science reporting that the silent mutations occurred more frequently than usual in one particular gene (multidrug resistance, or MDR1), commonly found in human cancer cells; in fact, it's what makes cancer cells resistant to chemotherapy drugs. The gene variant that had a particular kind of silent mutation enhanced this resistance even more. Further investigation revealed that these mutations were slowing down the process of protein manufacturing.

This is relevant because, per Borthwick's article: "[T]he folding of a protein into its three-dimensional shape is partially speed-dependent, [so] these mutations were able to alter the structure -- and biological function -- of the protein without changing its basic building blocks." They call the mechanism "translational pausing." The upshot is that the long-accepted theory of neutral molecular evolution is likely wrong. The mutations in question might be "silent" to the casual scientific observer, but they are potentially quite deadly. Furthermore, the NIH researchers also found some 40 other examples of silent mutations that can change the way a gene is spliced, thereby causing diseases like cystic fibrosis or connective-tissue disorders.

The SEED article ties in nicely with some belated news from the APS March Meeting held in Denver a couple of weeks ago, namely, the role that something called horizontal gene transfer might play in the evolutionary process. One of the things that puzzles scientists is that, per that all-important fossil record, single-celled life forms first appeared about 3.5 billion years ago, with another 2.5 billion years passing before multi-celled organisms finally made their debut on the scene. Here's the thing: it took just 1 billion years -- give or take a few -- for every other conceivable form of life to evolve: plants, mammals, birds, insects, reptiles and any other terrestrial species.

That's a pretty significant increase in the rate of evolutionary development, and scientists have been baffled about why this is so. The standard mechanisms are point mutations -- "random changes in single nucleotides on the DNA chain, or genome" -- and recombination, which occurs when the genetic sequences of a set of parents are recombined ("sexual selection"). But models that simply take into account these two common mechanisms really don't explain the sudden rapid acceleration of evolutionary rates indicated by the fossil record.

Enter Rice University physicist-turned-bioengineer Michael Deem, who has a penchant for adapting mathematical models from physics to the mutation and evolution of the flu virus, among other research. Lateral moves across the traditional boundaries between scientific disciplines can be difficult, since different fields use widely different terminology, and often employ vastly different approaches, but the potential payoffs are huge. For instance, Deem says he has now developed "the first exact solution of a mathematical model of evolution that accounts for this cross-species genetic exchange." He attributes the phenomenon to horizontal gene transfer (HGT), in which the DNA from one species is introduced into another.

The notion was first broached some 50 years, but only recently have scientists started taking it seriously, particularly in light of the increase in drug-resistant bacteria, and the surfacing of evidence of a specific protein used by bacteria to trade genes. And Deem found that by accounting for HGT -- in addition to point mutations and sexual recombination -- his model can demonstrate how HGT increases the rate of evolution by spreading favorable mutations across populations.

So it is indeed possible to swap entire sets of genetic code, including the genes that allow bacteria to develop resistance to antibiotics -- and, in fairness, for the human immune system to continually adapt to invasive species, an attribute Deem has traced to an HGT insertion that occurred some 400 million years ago. In fact, he thinks a significant portion of our DNA was donated by viruses and bacteria that infected our ancestors over lots and lots of generations.  "Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species," says Deem.

I wrote about Deem's prior work on flu vaccines -- notably, the use of nuclear spin glass modeling to better predict which strain of the flu virus was likely to dominate in any given year -- a few months ago here, particularly the notion of "original antigenic sin." See, the antibodies produced by the body's immune system to fight exposure to the flu virus become part of the body's "memory" so that it can fight off future exposure the same flu strain. The problem is, those same antibodies end up suppressing the creation of new antibodies when the body is exposed to a new strain of the flu. The phenomenon has also been observed in dengue fever and HIV, among other viruses, and the latter was the topic of the second paper Deem presented at the Denver meeting.

HIV is an especially difficult virus to eradicate, in part because the thing mutates so quickly after initial infection, producing several different virus strains. It's an ingenious "divide and conquer" strategy, according to Deem: the human immune system responds to viral infection by producing antibodies to ward off any given strain, but it tends to only focus on a single strain; the rest just run rampant. So the body defeats itself thanks to in-fighting among its own T-cells, and the end result is full-blown AIDS.

T-cell competition takes two forms, per Deem's computer models: original antigenic sin (described above, and also known as "deceptive imprinting"), and something called immunudominance, which occurs when several viral strains simultaneously infect a single person. The cells that respond to each strain compete until one emerges the victor. "Once the immune system chooses a winning set of T-cells, it has a natural tendency to go with those cells when it's confronted  by new strains of the same disease in the future," Deem is quoted in the Rice press release. "For HIV, which mutates rapidly, this is an Achilles' heel. We found a direct correlation between the level of competition among T-cells and the rate at which the virus escaped."

That's what makes the HIV virus so deadly. But Deem thinks it also suggests a potential new strategy for a more effective HIV vaccine. It's been difficult to develop such a thing because of how quickly the virus mutates. Deem thinks that inoculating someone at various points on the body against different strains simultaneously could all but eliminate competition among T-cells, so that the HIV will be trapped in a permanently latent state, never raging out of control to develop into full-blown AIDS.

How is this possible? You may well ask. There are lymph nodes scattered throughout the body, responsible for producing those all-important T-cells, but it takes four or five days before any T-cells produced therein to leave the node and spread throughout the body. Simultaneous inoculation would mean that each different node would select for a different strain, with no single T-cell emerging as dominant, because immunodominance doesn't have time to kick in. It's ingenious; now we just need to develop effective HIV vaccines. In the meantime, Deem hopes to test his multi-vaccination scheme on the spread of dengue fever.

Many years ago, I lost a close friend to AIDS, one among millions of gay men who died in droves in the first wave of infections that hit the US. If only we'd had access to an HIV vaccine then; alas, he didn't even have access to some of the better drug therapies available today to keep the disease under control. And the pain of watching a loved one slowly waste away with disease isn't limited to those with full-blown AIDS; we are mortal beings, so death and dying is universal; our mortality is the ultimate incurable disease, an inescapable fact of the human condition. The only variant is how we shuffle off this mortal coil. One of my oldest and dearest friends is currently holding vigil at her mother's bedside as cancer practically eats the unfortunate woman alive. Listening to her describe what her mother and family are going through, I find that words -- usually my trustiest allies -- fail me. There is simply no way to respond to this kind of pain, except silent commiseration and support; anything else just comes off seeming trite and insincere.

I bring up the unwelcome specter of human mortality not to end on a "downer" note, but because it's on my mind at present, and because it's a very real, brutal reminder of why the work of Deem and others like him is so damned important. It's easy to forget that the seemingly cold, objective realm of science also has a profoundly human face -- perhaps more visible when it comes to human health, but  no less present even in something as abstract as computer modeling. Like genes that move horizontally across species, scientists like Deem who move across traditional disciplinary boundaries can bring useful ideas and mechanisms to bear on well-worn knotty problems. Ideally, that lateral "cross-species" exchange leads to better survival strategies, and longer, healthier human lives.

a cabinet of curiosities

I've long held an arguably unhealthy fascination with the 17th century proliferation of so-called "cabinets of curiosities," a.k.a. wunderkammers ("wonder-rooms"). Unhealthy in the eyes of various pals over the years who didn't share my somewhat morbid interests, that is. Historically, the cabinets were pretty much random collections of strange-yet-fascinating stuff, combining collected specimens from natural history (it must be said that sometimes these were faked, but heck, it's all in fun), archaeological artifacts, religious or historical relics, the odd work of art, and any other quirky item that caught the cabinet-creator's fancy. Those doubting Thomases aside, lots of people share my fascination with idiosyncratic collections.

Initially, the term "cabinet" referred to entire rooms, not large pieces of furniture, so such cabinets are actually the precursors to the modern concept of museums. That early eccentric eclecticism is still evident in such places as the Mutter Museum in Philadelphia, for example, or Seattle's Olde Curiosity Shop -- one of my favorite childhood destinations. Given my love for that hodge-podge approach, and given the fact that I'm still (still!) traveling, and finding it difficult to write coherent blog posts, I thought I'd assemble my own bloggy version of a cabinet of curiosities (or, as Jen-Luc Piquant uncharitably calls it, "lazy linkage"). Besides, I've collected all manner of fascinating little links over the last couple of weeks -- "Ooh! Shiny!" -- and this lets me clear the fodder files a bit by highlighting the following octet of Cyber-curiosities (like the historical cabinets, an odd mix of fact and fiction).

1. There's one question that keeps getting asked every time I show up for a talk or reading for the Buffyverse book. (Other than, "So, exactly what kind of hallucinogens were you taking when you decided to write this book?") I thought I'd lay the matter to rest once and for all here: I am not writing a book on the physics of Firefly The Series So Cool We Must Not Speak Its Name (TSSCWMNSIN). I know, I know, it's a nifty idea, and I'm definitely a fan of Firefly TSSCWMNSIN. But there's already an incredibly useful online Wiki devoted to the series, including the scientific and technological aspects. Really. Here's a little discussion arguing that the series honors, for the most part, Einstein's light speed limit. There's also extensive discussions of the weaponry ("Mmmm, weapons," Jen-Luc murmurs appreciatively), and diagrams of the various types of aircraft/spaceships. Someone give these folks a book deal already! They've pretty much done all the preliminary research.

2. It's been a good week for pop culture physics, actually. Chad over at Uncertain Principles points us to the blog of Terence Tao, the young mathematician who won the Fields Medal last year, but is still hip enough to (a) have a blog, and (b) write killer posts like this one, providing his take on quantum theory, illustrated via Tomb Raider. (Lara Croft's impressive mammaries would be another fascinating subject for a future post on anti-gravity.)

3. As for my beloved Buffyverse, allow me to direct your attention to a podcast of a panel discussion at the 2007 South by Southwest Festival, exploring the real-world possibilities of building a "pleasurebot." (Hat tip to the folks at SuicideBots, bringing you daily doses of "hot bot on bot action!") Notably absent from the proceedings was Warren Meers, head of The Trio in Buffy Season 6, who built April the perfect girlfriend, and the much beloved and mourned Buffybot, with her latent Spike adoration and fondness for silly knock-knock jokes. Jen-Luc shrewdly points out that Warren's absence was probably due to the fact that (a) he was flayed alive in the season finale, and (b) he's, um, entirely fictional.

4. Since we're on the Buffy bandwagon, whenever I give a talk someplace that has A/V capabilities, I love to open by showing the pivotal scene in the Emmy-nominated Season 4 episode, "Hush," in which Buffy's scream causes the monsters' heads to explode. I use it as an example of forced oscillation resonance -- which most of us would recognize instantly as what's happening in those old Memorex commercials when Ella Fitzgerald shatters a crystal wine glass with her voice. But I was surprised to learn this week that there's also a medical phenomenon called "Exploding Head Syndrome." Great name, but a bit misleading for literal-minded types like me. The patients' heads don't actually explode; the condition causes them to awaken frequently in the middle of night by the sound of a very loud bang -- painless, but weird, in that it seems to occur only in the sufferer's head. And it's still something of a mystery, since neither patient cited in a 1988 Lancet study had anything physically wrong with them at the time. Hindsight is golden: it would have been fun to include mention of that in the Buffyverse book. If I had only known....

5. Another inadvertent omission: a discussion of the physics behind the crossbow, a common weapon used by Slayers and their Watchers throughout Buffyverse history. (Confession: I covet my very own wooden crossbow -- illogically, because really, there's no place in Los Angeles where it would be safe enough to fire one. And I doubt Future Spouse is keen on having one around the home.) It's a fascinating cross between a bow-and-arrow and a rifle (it has a trigger and stock). While it operates on similar mechanical principles as the former, it's easier for a smaller person (like Buffy) to use, because it doesn't require nearly as much upper body strength. Once the string has been drawn taut, you can hold it in place indefinitely by cocking the weapon, storing all that potential energy until you need to shoot the pointy wooden stake at an approaching vampire.

6. If hardcore Whedon fans are puzzling over what to get the Series-Creator-Who-Has-Everything for his birthday (there's still a few months left for shopping, people, at least according to the IMDB!), perhaps they can pool their resources and bid on this handy-dandy 19th century Vampire Hunting Kit, offered by a Swedish dude named Thomas Sandberg, who's created his own online Cabinet of Scientific Curiosities. (Behold, the tenuous connection!) These things don't come cheap: a similar kit apparently sold at Sotheby's a couple of years ago for something on the order of $18,000. For that price, you get a revolver with silver bullets, garlic powder, a silver dagger, an ivory cross, a mirror, a wooden stake, and a bottle of Professor Ernst Blomberg's Vampire Serum (Jen-Luc suspects it's common holy water), all stored in a handsome mahogany box. Did we mention the helpful pamphlet (circa 1851) on how to hunt and kill those pesky bloodsuckers?

7. Both the exploding head syndrome and the vampire hunting kit items came to my attention via The Proceedings of the Athanasius Kircher Society, whose entire reason for being is to "perpetuate the spirit and sensibilities of the late Athanasius Kircher. Our interests extend to the wondrous, the curious, the singular, the esoteric, and the sometimes hazy frontier between the plausible and the implausible." The Society held its inaugural meeting just this January at the CUNY Graduate Center in New York. (There's a "highlights reel" of those inaugural proceedings at the Society's Website, for those who are interested.)

Kircher was indeed a fascinating historical personage, who has only quite recently begun to be unearthed from relative obscurity. Not only does this humble 17th century Jesuit scholar/priest now have his very own eponymous society, but in 2002, New York University sponsored an entire symposium in his honor. There's also a permanent exhibit on Kircher at the Los Angeles-based Museum of Jurassic Technology -- very much in the spirit of a cabinet of curiosities.

Why do people love Kircher so much? His scientific reputation was a bit sketchy, in that he had a tendency to blend "traditional Biblical historicism and the emerging secular scientific theory of knowledge." For instance, while he published on magnetism, astronomy, optics, archaeology and linguistics (including Egyptian hieroglyphics), he also wrote treatises on the Tower of Babel and Noah's Ark. Sure, he conducted scientifically sound experiments , including one that essentially disproved Johannes Kepler's speculation that the sun was a giant magnet whose rotation around its axis caused the earth and planets to stay in their orbits. But he also took what he learned from that investigation and used it to invent a "magnetic oracle," a divination device that he dubbed "magnetic hydromancy."

Still, one certainly can't doubt the man's passion for scientific inquiry, nor his boundless curiosity about how the world works. Even while tending to the sick when the bubonic plague hit Rome in 1656, he still took time to observe micro-organisms under a microscope in hopes of finding a cure. He didn't find one, but he did advance the germ theory of disease that was way ahead of the medical orthodoxy of his day. Fans of Charles Babbage, take note: Kircher came up with his own machine for answering mathematical problems, although it was far from perfect, in that it required memorizing long poems in Latin in order to perform the most elementary functions, according to Michael John Gorman of Stanford University, one of the emerging scholars who are studying this fascinating personage. Fortunately there was also a cheat sheet for those with faulty memories: an 850-page instruction manual that makes the average Microsoft User's Manual seem like a model of concise clarity by comparison.

And what an adventurous life the man had -- a regular Indiana Jones of the 1600s. He skirted death on numerous occasions, beginning with a boyhood leg injury that turned gangrenous -- which he claimed, was miraculously healed by the Virgin Mary when he visited one of her shrines while at seminary. (She also threw in healing of a herniated disc for no extra charge.) He was shipwrecked on an island while traveling to Austria, and was nearly hung by overly-ardent Protestant cavalrymen on another of his many travels. Just before Adolph, the Protestant king of Sweden, invaded Franconia and Wurzburg, Kircher fled his teaching post at a college in the latter town and eventually landed in Rome. For his last great adventure, he traveled to southern Italy, Sicily and Malta, where he witnessed the eruption of Aetna and Stromboli, and even had himself lowered into the active crater at Vesuvius. Lowered... himself... into... an... active... volcano. The A-Man had some serious cojones. Naturally, the experience reminded him of eternal damnation:

"The whole area was lit up by the fires, and the glowing sulphur and bitumen produced a intolerable vapor. It was just like hell, only lacking the demons to complete the picture."

Perhaps realizing he'd never top that experience, Kircher soon retired to a quieter life of scholarly contemplation, but he was just as prolific in his writing as his wandering, producing 11 full-length books in 20 years. Oh yes, he also established his own museum of strange artifacts (including a stuffed aardvark and an automaton) in Rome, one of the earliest recorded cabinets of curiosities. He died in 1680, and we're delighted that, more than 400 years later, he's finally getting the recognition he deserves. Athanasius Kircher -- don't let the sissy first name fool you, he was a manly man of science, and just enough of a mystic to keep things interesting.

8. Finally, I spent most of yesterday en route from Los Angeles to Chicago, where I'm appearing tonight at the Women and Children First Bookstore. (Chicago residents, feel free to stop by! It starts at 7:30 PM.) As such, I missed a couple of wonderfully quirky occasions. First, it was Pi Day, celebrating that most irrational of numbers -- usually by eating pie (duh). Second, it was Albert Einstein's birthday, which I'd planned on officially making an annual "Talk Like a Physicist" Day. Alas, I was remiss in following up on that. But there were so many other birthday wishes for Albert floating about the blogosphere, that I didn't worry too much about my dereliction of duty; with or without my birthday wishes, Al was definitely feeling the love. There's always next year. And in case you missed it, as one final curiosity, let me direct you to BuzzSkyline's most excellent poem celebrating Einstein's "miracle year" in 1905. Happy belated birthday, Al! At least I posted in time for the Ides of March, bane of Julius Caesar.

ready for their close-up

Hollywood celebrities relish their photo ops, and exert a great deal of effort in putting their best face forward. But while biological entities like cancer cells and protein molecules aren't camera shy, they're not exactly photogenic either. It's tough to image such things in sufficient detail for meaningful scientific analysis, because they're so darn tiny to begin with. Fortunately for any spotlight-hungry biological molecules out there yearning for their 15 minutes of fame, physicists are constantly developing new and improved methods to get better pictures of these tiny objects that are so critical to human health. Even in biophysics, image counts, you see.

It helps to have a bit of sparkle, and it turns out that healthy (from the disease's perspective) cancer cells do shimmer impressively for the cameras -- CCD cameras, specifically -- with a new technique called digital holographic imaging that produces time-lapsed, dynamic speckled images that "shimmer" in response to cellular motion. Recent work at Purdue University marks the first time holography has been used to study the effects of a drug on living tissue, according to David Nolte, the Purdue University physics professor who headed up the research. (For tons of great links and handy tips on creating your own holograms, go here.)

Back in 2002, Nolte's group was the first to use holography to image the internal structure of tissue. Conventional microscopy techniques use 2D slides and therefore don't delve very deeply into tissue, which is essentially a 3D construct; Nolte wanted to get a peek inside the tissue itself, preferably at a depth of about 1 millimeter, to gain a better understanding of its structure. (Yes, it's not much, but that should give you an idea of how little conventional microscopy penetrates the surface of tissue.) Now he's combined holographic imaging with laser ranging -- a technique similar to radar, in that it measures how long it takes for a laser pulse to travel to an object and be reflected back. "The holography gives us the peaks and valleys and detailed depth information, while the laser ranging allows us to control how deep we are looking," he said in a recent press release.

Nolte had more to say about his work in person at the APS March Meeting in Denver (yes, we are still here, but not for long!). He began by provocatively asking, "What is life," and concluded that life is basically motion. One might quibble philosophically (or atomically-physically) with that statement, if one were so inclined, but we are quite happy to accept the premise at face value for the purposes of this post. Besides, his communication instincts were spot on: it's a perfect opening for non-scientists, since we can look at a rock, and look at a bird, and determine that, indeed, the animate object is clearly in motion.

Nolte brought it up for a reason: his new imaging technique essentially measures the motion of organelles inside cancer cells to determine whether they're living or dead. Organelles play a key role in fostering the out-of-control cancer cell division that so often proves fatal to the patient, and therefore it's a primary target of many anti-cancer drugs, like colchicine, a derivative of the autumn crocus (a.k.a., "meadow saffron") traditionally used to treat gout. Colchicine does this by blocking the formation of the microtubules that make it possible for organelles to navigate around the cell. Microtubules are "the highways of the internal cellular structure," says Nolte.

His digital holographic imaging system creates a hologram of a tumor ( in this case, an osteogenic sarcoma -- bone cancer -- tumor in a rat), whose center is usually filled with dead (necrotic) tissue surrounded by an outer shell where the cells madly multiplying with wild abandon. Laser light shines on both the object and the CCD camera, and the reflected light is fed into the system, which records very detailed information about depth and motion (among other properties) of the components at work in the tumor tissue.

All that outer shell activity shows up as a bright shimmer in the resulting image, while the dead tissue at the center doesn't move at all (What little shimmer there is at the center can be attributed to the incidental motion of the CCD cameras recording the experiment, according to Nolte.) Using this technique, it's possible to create handily color-coded "motility maps" of cellular activity at three different tissue depths (120, 190, and 330 microns). Red indicates high activity, and is found at 120 microns. By 330 microns, that activity has slowed sufficiently that the contrast color is predominantly yellow. Completely dead tissue shows up as blue.

So cellular motion becomes a built-in contrast agent used to enhance the image, making digital holographic imaging a vital emerging tool in measuring the effectiveness of anti-cancer drugs like colchicine. If the drug is working, there will be a reduction in the motion of the organelles, which will show up with less shimmer in the image displayed on the computer display, and can then be quantitatively analyzed. "We have moved beyond achieving a 3D image to using that image for a direct physiological measure of what the drug is doing inside cancer cells," said Nolte. "This provides valuable information about the effects of various doses of of the drug and the time it takes each does to become significantly affected."

It's exciting stuff, plus the shimmery pictures are quite pretty. But Nolte's isn't the only research group finding innovative new ways to image biological molecules, thereby gleaning useful new knowledge about how they function.  Andre Brown of the University of Pennsylvania (who also blogs at Biocurious) has employed the force sensing mode (as opposed to the imaging mode) of standard atomic force microscopy to image molecules of fibrin, a protein that acts as a molecular spring to keep blood clots structurally stable, but still flexible enough to allow blood to flow through them. Fibrin develops in the blood from another protein called fibrinogen, when blood cells release the enzyme thrombin in response to encountering damaged tissue. Fibrin forms around the damaged area in a mesh-like pattern, which dries and hardens to stop the bleeding -- a good thing for wound healing, when you want the blood to clot, and not so good if said blood clot results in a heart attack or stroke.

Last year, researchers at Wake Forest University, Harvard, and the University of North Carolina used AFM to test the stretchiness of fibrin, and found these fibers can stretch much further than other biological fibers before breaking -- including collagen, spider silk (known to be pretty darned rugged) and keratin. That property is crucial to fibrin's ability to stop the flow of blood, which exerts a great deal of mechanical stress on the fibers. There have also been studies demonstrating that fibrinogen taken from patients with heart problems forms stiffer clots than that taken from healthy control patients.

So Brown saw an intriguing correlation between, say, heart disease and the mechanics of fibrin in blood clotting, and thought that protein unfolding might play a role in the unusual elasticity ("stretchiness") of fibrin fibers. He used AFM  (in combination with total internal reflection fluorescence microscopy) to measure the force with which this unfolding occurs -- marking the first time the mechanics of fibrinogen has been measured at the single molecular level. And he found that protein unfolding does indeed seem to play a role in the mechanics behind blood clotting. Next on the agenda is to explore whether this unfolding plays any kind of role in clot mechanics at more modest extensions. (Brown wrote a very nice blog post on his recent work a few weeks ago, for those interested in a more technical description of the research. And for some nifty video footage of a fiber  in the process of stretching, go here.)

Today's post would not be complete without taking a moment to wish a very happy 50th birthday to the incomparable PZ Myers -- mild-mannered Midwestern biology professor by day, fire-breathing atheist who battles Creationist wingnuts by night. But what to get for the heathen biologist who has everything? Jen-Luc Piquant scoured the Internets for this nifty recipe for stir-fried squid in shrimp sauce -- complete with tantalizing how-to photos -- but it turns out that PZ craves poetry. We're much too lazy to emulate Richard Dawkins, who wrote PZ a birthday poem. (Harumphs Jen-Luc: "Show-off.")  Instead, we humbly offer this 17th century haiku by Matsuo Basho, who died in 1694 at the age of... 50. So it's especially a propos, especially if read over a steaming plate of stir-fried squid. Enjoy!

The Squid Seller's Call

The squid seller's call

mingles with the voice

of the cuckoo.

 

 

much depends on dinner

Physicists are pondering all manner of difficult problems and daunting challenges here at the 2007 APS April Meeting in Denver, but  among the most pressing questions at the end of each day is, where do we go for dinner? There's always the hotel bevy of eateries to assuage hunger pains in a pinch, but savvy meeting attendees invariably whip out their pocket Zagat's Guide for the area to locate recommended restaurants in the nearby vicinity. (I'm more inclined to rely on the concierge, or Jen-Luc Piquant, who's a whiz at ferreting out online restaurant guides for the city du jour.)

But what do you do if you're not a hungry physicist or science writer, and are, instead, a single-celled organism? Where's the handy Zagat's Guide for amoebae? Apparently, they don't need one, because they've got a built-in mechanism for an optimal food-foraging strategy. Amoeba are smarter than we think (there goes that classic schoolyard taunt). For instance, scientists have always assumed that microbes move in random patterns unless they are specifically hot on the scent of tasty nibbles, but recent research has shown otherwise. A species of amoeba called Dictyostelium seems to remember its previous "steps" and uses that remembered information to explore new ground, thereby increasing its chances of finding food.

What remains unclear is how, exactly, this simple organism manages to have any kind of memory at all, even the recollection of something as short term as where it was located just a minute ago. It's not like it has a fully functioning, complex brain. Liang Li of Princeton University thinks there may be a clue in the mechanism by which the creature moves. The amoeba moves by rearranging its squishy body into a protruding shape known as a pseudopod.

It's simple four-step sequence involving an initial protrusion, followed by adhesion to the surface on which the creature is moving, then a contraction/tension of the pseudopod, followed by "deadhesion" so the creature can move instead of sticking in one place.  Using phase contrast microscopy, she tracked a bunch of Dictyostelium over 100 hours, charting the "runs" and "turns" they made, which formed a zigzag pattern of motion. She specifically looked at how often the creatures made a left turn followed by a right turn, and found they showed a clear bias for that kind of variation.

How could this possibly have anything to do with an amoeba's hunting strategy? Li speculates that the formation of these pseudopods leaves temporary "scars" in the cell's cytoskeleton -- a bit like short-term memory, since the scars fade over time -- and this makes it far more likely that the next pseudopod the creature forms will point in a new direction. Because it changes direction and doesn't retrace its steps, it covers more ground and therefore increases its chances of successfully finding food.

What about more complex, higher organisms, like zooplankton? Ricardo Garcia has something to say on the subject. He's with the Center for Neurodynamics at the University of Missouri in St. Louis, and was on hand yesterday to talk about his research on the role of specific swimming characteristics in achieving optimal food foraging strategies for zooplankton. The work was billed in the press release as "the first observation in a living animal of an inherent swimming characteristic -- the turning angle -- that optimizes the food obtained in a patch of fixed size for an organism foraging for a fixed time."

Garcia and his University of Missouri colleague, Frank Moss, studied the zooplankton Daphnia, more commonly known as water fleas. They looked at the swimming movements of five different Daphnia species of varying sizes, both adults and juveniles, all of which exhibit a distinct hop-pause-turn-hop again sequence while swimming. Specifically Garcia and Moss analyzed the turning angles the creatures made after each hop in th sequence, plotting the number of times a given angle was observed in a type of chart known as a histogram. These turning angles were almost, but not quite, completely random -- they found evidence of a preferred turning angle value.

What kind of evidence? Well, it all sounded very complicated as Garcia described their work, but the gist, as far as I can tell is this: they did a mathematical analysis of the underlying random processes, or "noise intensities" in the water fleas. "Noise" in this context refers to neural (brain-related) noise, or the "random electrical 'static' in the neural systems of the zooplankton." Most of us find any kind of outside noise distracting or irritating if we're trying to focus on a particular task -- even more so if dinner is involved -- never mind if it's our own brain activity wreaking havoc with our concentration. But in the case of the humble water flea, it's helpful while foraging for food. The neural noise influences the turning angle in such a way as to  enable the water flea to explore the most amount of space and gather the most food within a given time frame.

While Garcia and Moss were watching water fleas, their theoretical collaborators at the Laboratory for Applied Stochastic Processes at Humboldt University in Berlin, Germany, were developing a theory of the foraging process, complete with computer simulations. Scientists have known for many years that biological systems frequently rely on stochastic resonance (or noise) as a stimulus to the sensory systems, which in turn can affect the behavior of creatures both great and small -- usually in positive, optimizing ways that improve said creatures' chances or survival.

It's a pretty counter-intuitive notion at first glance: stochastic resonance involves adding random noise to a weak signal bearing "information" -- say, the signal from a country-western radio station in the Denver area that is just beginning to be out of range. Imagine trying to get that radio station to come in clearly on your car radio while driving through downtown Denver, but instead of fine-tuning to decrease the static, you decide to increase the level of static instead. What would prove disastrous to your enjoyment of the latest Tim McGraw opus, turns out to be beneficial for living organisms. In this case, adding noise actually enhances the detectability and/or effective transmission of the information-bearing signal.

Researchers like Garcia suspect that natural stochastic resonance may have a played a significant role in the evolution of sensory systems, although he is careful to emphasize that his results don't outright prove this hypothesis; they merely offer strong supporting evidence in favor of that notion. In the case of Daphnia, Garcia suspects that the water flea's distinctive swimming patterns evolved over tens to hundreds of millions of years via Darwinian natural selection.

It all comes down to the intensity of the neural noise signals. Those noise intensities correlate with the width of distribution of the turning angles favored by the water fleas, and it turns out that the creatures gather the most amount of food in a single foraging session at a very specific noise intensity. Per Garcia: "A small noise intensity means that the animal obtains less than the maximum possible amount of food within its patch during its fixed feeding time. Likewise, less fod is ingested if the distribution is too broad." (Jen-Luc thinks it sounds an awful lot like Goldilocks and the Three Bears: "This noise intensity is too small." "Well, this noise intensity is too large." "But THIS noise intensity is juuuust riiiight....") The findings were consistent across all five species of Daphnia studied, regardless of size or age of the organisms. So Garcia and Moss' experimental data fits the Berlin collaborators' theory just fine, and a technical paper on their work is pending publication in Mathematical Bioscience even as I type.

Which brings us to dessert. It's something I generally skip, but when I do choose to indulge, I'm partial to cookies or more elaborate concoctions like bread pudding and tiramisu. My pals MondoBob and El Finster have simpler tastes: they swear by their nightly dish of ice cream. They're not alone: according to this 2004 article from Discover on the physics of ice cream, US sales of ice cream top $20 billion, with Americans consuming as much as 20 quarts per capita. Only New Zealanders eat more ice cream. The article also contains a brief sidebar noting that some ice cream manufacturers combat the formation of unwanted ice crystals in their products by adding antifreeze or ice structuring proteins (ISPs) found in certain fish, insects, plants, fungi and bacteria. (It's all about achieving an optimally appealing mouthfeel. Nobody likes a crunchy dish of ice cream, unless it's from the addition of nuts or candies.)

Yes, ISPs can prevent recrystallization. The high fat content of most ice creams serves the same purpose, but if you're watching your cholesterol, like El Finster and Mondo Bob, you're probably buying sherbets or lower-fat varieties, which do contain antifreeze proteins to step in for the missing fat. From a medical standpoint, recrystallization is undesirable because it can also cause damage to the structure of biological tissue, limiting the "shelf life" or vital organs awaiting transplant, for example. In fact, that's one of the greatest challenges in cryogenics. Cells contain a lot of water, you see, and water expands when it freezes, bursting the cell walls in the process. That's why the Pittsburgh scientists who revived the infamous "zombie dogs" a few years ago had to replace the canine's blood with a kind of "antifreeze" to prevent tissue and brain damage during the thawing out process.

The ISPs accomplish this by attaching to the surface of ice crystals in such a way as to inhibit their growth. But some creatures have more effective ("hyperactive") ISPs, such as the spruce budworm. According to Ohio University's Ido Braslavsky, who reported on his latest research in this area yesterday, the hyperactive ISPs of the spruce budworm stop ice crystals from growing in particular directions. He and his collaborators fluorescently tagged the ISPs from fish and the budworms and studied them under a fluorescent microscope to see how the proteins interacted with the surfaces of ice crystals, on order to reach that conclusion. Future applications could include prevention of frostbite in crops; reducing highway damage from de-icing procedures in the winter; and the aforementioned food preservation and improved organ preservation.

So clearly, when it comes to science, much depends on dinner... or dessert. We shall try to bear that in mind when we undertake yet another food-foraging mission this evening in beautiful downtown Denver.

the legend of finn mccool

Irish legend is rife with memorable characters, among them a giant named Fionn mac Cumhaill -- or, more colloquially, Finn McCool. As with all myths, the details vary but the essence of the tale is this. Finn McCool lived on the north coast of Ireland with his wife Oonagh. One day his rival, the Scottish giant Benandonner began taunting him from across the channel  -- the usual "I'm bigger and tougher than you, little wuss-boy" macho drivel, no doubt accompanied by much beating of chests and flexing of biceps. (Clearly Benandonner was a wee bit insecure, perhaps because he didn't have a catchy moniker like Finn McCool.) Put bluntly, Benandonner said he could kick Finn's ass if only that pesky channel wasn't in the way to stop him. No self-respecting giant would stand for that insult to his masculinity. So Finn called his rival's bluff, and built a causeway (bridge) out of huge stones across the water, since no boat at the time was large enough to hold a giant. And he invited Benandonner to come right on over and prove his point.

The variations diverge at this point, with some versions saying Finn merely wanted a chance to rest before the confrontation, after exerting so much energy to build the causeway, and others claiming he was frightened when Benandonner loomed into view and he realized his rival was indeed the bigger, stronger giant. (I'm inclined to favor the latter.) Finn's wife Oonagh was smarter than either male giant; she knew that battles aren't always won on the basis of size and strength. She suggested stealth. She disguised her husband as a baby in a large nightgown and bonnet -- possibly even a supersized rattle -- and placed him in a gigantic cradle. When Benandonner arrived, she invited him in for tea and asked him to be quiet so as not to wake the "baby." Benandonner took one look and decided that if this enormous creature was Finn McCool's infant, he had no desire to meet the father, and fled home to Scotland, ripping up the causeway behind him to ensure Finn McCool couldn't follow him. (Jen-Luc Piquant thinks this proves they were both pathetic girly-men, for all their tough talk and macho posturing.)

The remnant of Finn McCool's legendary bridge is still there, in what is now County Antrim in Northern Ireland. It's called the Giant's Causeway, and is considered one of the seven wonders of the United Kingdom. Justly so -- it consists of nearly 40,000 interlocking basalt columns, some as tall as 36 feet. The tops of the columns form "stepping stones" leading form the foot of the cliffs before disappearing under the sea.  I've had the privilege of standing on those columnar formations in person, during a visit to Northern Ireland many years ago, and they're pretty damned impressive. (The locals at the time were far from welcoming. We stopped off for a quick bite at a local pub in Bushmills, and all conversation ceased the moment we walked in. The bartender slipped into the back, never to be seen again, and after waiting 20 minutes in total silence -- a highly unnatural state for a pub -- we got the message and took our leave. To this day, I still don't know what was going on. But the causeway? It's bloody breathtaking.)

Finn McCool is just a legend, on a par with the American giant, Paul Bunyan, dreamed up to explain how such a bizarre formation like the causeway ever came into being in the first place. It looks far too regular in terms of its patterned structure to have been caused by natural processes. And yet it did. First "discovered" in 1692 by the then-Bishop of Derry, Sir Richard Bulkeley II officially announced the causeway's existence in a presentation before the Royal Society of London, of which he was a member.

(Historical sidenote: There's little record of Sir Richard II -- a Google search yielded plenty of information about his father, but little about the son, who left no heirs and was therefore the last scion of that particular baronetcy. He was apparently deformed, but well-educated, a fellow of Trinity College and at Oxford, and in addition to his paper on the Giant's Causeway, he also presented papers on a self-propelling chariot of his own invention, and a scheme for improving Ireland by cultivating the planting of maize. Alas, he succumbed to religious fervor in his dotage, falling in with a cult of self-proclaimed French prophets whom he believed would cure him of his deformity. They didn't.)

Theories abounded as to how the causeway had formed: some said men had made it with picks and chisels, and of course, there was the legend of Finn McCool. The scientists were inclined to favor nature but were mystified as to the mechanism until 1771 when a Frenchman identified only as Demarest announced that it was the result of volcanic activity. (There's even less Google-info on Demarest than there is on poor Sir Richard II.) That's still the accepted explanation, although it's continually being refined as science progresses. The columnar joints that make up the causeway were formed roughly 60 million years ago by the cooling and shrinking of molten lava from a massive volcanic eruption.

According to physicist Lucas Goehring of the University of Toronto, who presented a paper today at the APS March Meeting on his recent work in this area with fellow Toronto colleague Stephen Morris, this is what probably happened. When the lava flowed into the sea, it quickly cooled, contracted, and crystallized into the near-perfect hexagonal columns we see today. (In fact, geologists believe there were three major lava flows, giving rise to lower, middle and upper basaltic layers, with the causeway columns occurring in the middle layer.) That kind of shrinkage inevitably causes stresses that fracture the rock. Per Goehring: "The columns are formed as a sharp front of cooling moves into the lava flow, assisted by the boiling of groundwater. As the front advances, it leaves behind a crack network which evolves into an almost hexagonal arrangement. This network carves out the columns."

Columnar joints are more common than one might think: they are also found at Devil's Tower National Monument in Wyoming, at the "Organ Pipes" formation on Mount Cargill in New Zealand, and at the Devil's Postpile National Monument in California. Similar structures can be created with a simple kitchen experiment: mix equal parts corn starch and water and place into a coffee cup. Dry the mixture by shining a bright light above it. Within a week or so, the mixture will be completely dry and you can break it apart to reveal an interior that is broken up into "starch columns."

In addition to studying the genuine article in situ in both Ireland and Scotland, Goehring and his cohorts have figured out how to control this tabletop kitchen experiment so precisely that they can study the formation process in much greater detail than scientists could in the past, augmented by X-ray tomography to give the first genuinely 3D imaging of the internal structure of the columns. Among the more surprising findings: (1) the columns are not quite as perfectly hexagonal as previously believed, and (2) the continuous dynamics of the formations can be found even deep inside the structure, similar to, say, dry foams. Also, the size of the columns depends on the speed at which the cracks advance, and the rate at which the water can move through the starch. That's why lava-formed columns are 1000 times larger than the tabletop experiment: the analogous properties of lava are much slower.

I'm always appreciative of how much of scientific knowledge seems to get its start simply because someone took the time to notice unusual patterns or structures in nature, and set about asking questions, forming hypothesis, and devising ways to test those ideas. For instance, sharing the session with Goehring was  Meredith Betterton of the University of Colorado, Boulder, who became enthralled by the large icy spikes -- called penitentes because they resemble a procession of white-hooded monks -- she observed while viewing glaciers in the Andes.  "I thought, 'Wow, what's going on here?'" she admits, and being a scientist, she set about figuring it out. (She's not the first to be thus fascinated. Charles Darwin described penitentes in 1839, while relating a March 1835 excursion in which he squeezed his way through snowfields covered in penitentes on the way from Santiago, Chile, to the Argentine city of Mendoza.)

Along with colleagues at the Ecole Normale Superieure in France, Betterton created the first artificial versions of these spiky ice formations, which can be found quite frequently on high-altitude glaciers where the air is particularly dry. She also devised a mathematical model to predict the process. The hope is that this research will yield useful insights into how glaciers evaporate; it may also lead to a practical strategy for preserving glaciers in light of global warming.

There's probably a fascinating legend somewhere on a par with Finn McCool to explain how these spikes of ice form, but science is more than capable of stepping with its own explanation. Penitentes arise when the sun's rays evaporate snow in such a way that the ice turns directly into water vapor, without melting into water first. The process is called sublimation. The snowy surface might start out smooth, but it gradually develops depressions as some areas sublimate faster than others, and the resulting curved surfaces concentrate more sunlight and speed up the sublimation even more, leaving behind a forest of towering spikes of ice. Penitentes are nature's ice sculptures.

Rising temperatures slow the formation of penitentes quite a bit, an especially alarming factor in light of global warming, because fewer ice spikes could accelerate the melting of glaciers. The spikes cast shadows, you see, and serve as a natural cooling mechanism. There's a working hypothesis that spreading a small layer of dirt over glaciers could help preserve them by fostering faster formation of penitentes. This turned out to be true with the small-scale versions Betterton created in her lab. She spread printer toner on her artificial snow layer to simulate pollutants common to glaciers around the world, and found that the ice spikes grew more rapidly as a result. It's a bit counter-intuitive, since carbon-based pollutants actually increase melting rates on glaciers because the ice absorbs more sunlight and therefore heats up more quickly. The formation of more penitentes could offset that damage.

Not that Betterton thinks she has all the answers now about the mechanisms behind penitentes -- not by a long shot. "There's lots of things not yet explained, and that's what makes this field so fascinating," she said.

(Postscript: In my last post I mentioned that the folks at Physics Buzz are also blogging the March Meeting. This is true, but they're doing it at a separate site, so for their ongoing coverage, check it out here.)

strange attractor

If it's Sunday night, it must be Denver. Jen-Luc Piquant and I flew into the Mile-High City today for the 2007 APS March Meeting. While waiting for the plane to take off, I distracted myself from the cries of the inevitable Wailing Infant by playing a little game I like to call "Spot the Physicists." It's easy enough to do so, especially since this time of year, they tend to be clutching a copy of the Bulletin of the American Physical Society containing abstracts for the meeting -- although this year, the APS only published the session titles and speakers to save the trees. The 2007 conference features some 7000 abstracts, which would pretty darned unwieldy in printed form. (In the recent past, the March meeting Bulletin was published in two parts, it had gotten so big.) One of the flight attendants must have noticed the high percentage of science types on the flight. After an impressively smooth landing, she got on the intercom to praise the pilots and remarked, "Once again, skill and technology trump fear and superstition."

It was a nicely appropriate kickoff to a conference that celebrates  the latest research in materials and condensed matter physics, biophysics, and related subfields, all of which play key enabling roles in the development of new technology. Even the tiniest, seemingly insignificant effect can turn out to be important, especially as one gets down to micro- and nano-scales. Take, for example, the case of something dubbed "the Casimir effect." Basically, it refers to the attraction between two objects should they come within, say, 1/5000 of an inch of each other. It's related to the energy inherent in the quantum vacuum. Empty space isn't as empty as one might thing, since it roils and boils with matter/antimatter pairs of virtual particles that pop into existence and just as quickly annihilate into radiation, i.e., electromagnetic waves. (There's even an ongoing debate as to whether the Casimir effect could account for the attraction between ships moored too closely together in a harbor.)

The effect gets its name from a Dutch physicist named Hendrik Casimir, who first proposed the existence of such a force (along with Dirk Polder) and proposed an experiment in 1948 to detect it. It involves two uncharged parallel metal plates. Normally there would be no electromagnetic charge to exert a force sufficient to pull the plates together or push them apart. Casimir proved that if the plates were close enough, however, there is still a tiny attractive force between them.

His explanation was that, because the parallel plates are so close together, the virtual particle pairs can't easily come between them, so there are more pairs popping into existence around the outside of the plates than between them. That imbalance creates a force that pushes the plates inward ever so slightly. The smaller the separation between the plates, the greater the inward attraction.  Really, it's quite a nifty confirmation of  Casimir's theory, and provided  critical evidence of the existence of virtual particles, which don't hang around long enough to "observe" directly via the usual means (i.e., the electromagnetic force).

In fine scientific tradition, physicists weren't content to just accept those 1948 results outright. They kept testing it, devising new, improved experiments to measure the Casimir effect more accurately. For instance, scientists at Los Alamos National Laboratory and the University of California, Riverside made some excellent measurements in 1997, followed in 2001 by the measurement of the Casimir force between parallel plates using micro-resonators, by scientists at the University of Padua.

About a month ago, the Casimir Effect was back in the news (among physics sorts) thanks to new results published in Physical Review Letters from a research group at the National Institute of Standards and Technology and the University of Colorado in Boulder, led by Nobel Laureate Eric Cornell. They were testing another prediction, this one made in 1955 by Evgeny Lifschitz, that temperature affects the Casimir force.

Cornell et al. specifically studied the Casimir-Polder force between a neutral ultracold rubidium atom and a glass surface a mere few microns away. Then they doubled the temperature of the glass to 600 degrees Kelvin. The surrounding environment was still at room temperature. The result: the sharp rise in temperature caused a threefold increase in the attractive force exerted by the glass on the rubidium atoms. I'm still a bit fuzzy as to why this happens, but the good people at Physics News Update (via the American Institute of Physics) explain it thusly:

According to quantum mechanics, the vacuum contains fleeting electromagnetic waves, in turn consisting of electric and magnetic fields. The electric fields can slightly rearrange the charge in atoms. Such 'polarized' atoms can then feel a force from an electric field. The vacuum's electric fields are altered by the presence of the glass, creating a region of maximum electric field that attracts the atoms. In addition, heat inside the glass also drives the fleeting electromagnetic waves, some of which leak onto the surface as 'evanescent waves.' These evanescent waves have a maximum electric field on the surface and further attract the atoms. Electromagnetic waves from heat in the rest of the environment would usually cancel out the thermal attraction from the glass surface. However, dialing up the temperature on the glass tilts the playing field in favor of the glass's thermal force and heightens the attraction between the wall and the atoms.

Well, I trust that clears everything up for everyone. The non-scientists reading this are probably wondering, "Why should we care?" That's a very good question. Back in the late 19th century, Nikola Tesla put forth the notion that the vacuum held enormous reservoirs of energy, which he believed to be sufficient to revolutionize human society if we could only figure out how to harness it. His instincts were right about there being energy in the vacuum, but not about how much there might be: the estimates I've heard peg the Casimir to be equivalent to the weight of 1/30,000th of an ant. Scaled up to macroscale units of measurement, even if we could release (and harness) the energy stored in a single cubic meter of the quantum vacuum, it would yield maybe one ten-billionth of a joule. That's not even sufficient to light a tiny 10-watt bulb.

Okay, so if the Casimir force is so darned small it can't really have a significant effect, why bother studying it? Well, it does have a significant effect at very small scales. In fact, the Casimir effect sometimes causes the moving parts in nano- and microelectromechanical systems (NEMS and MEMS) to stick together, so gaining a more detailed understanding this bizarre force could have practical benefits. On a more esoteric level, many tabletop experiments designed to test for exotic new forces can also be stymied if the Casimir effect isn't taken into full account. Virtual particle pairs popping up near the event horizon of a black hole are believed to result in the "Hawking radiation" that causes these objects to evaporate -- the smaller the black hole, the shorter the time it takes for it to wink out of existence. And vacuum energy is one of the leading contenders for the mysterious dark energy physicists believe is causing the expansion of our universe to accelerate. Wouldn't you like to know how the universe will end? We'll be long dead before that happens, but still... the point is, this strangely attractive force matters.

There might not be any papers this week in Denver about the Casimir effect, but there will be papers providing research updates on graphene and "metamaterials" (those with negative indices of refraction); medical physics; pattern formation in granular media; and bubble logic, to name a few. Jen-Luc Piquant and I will be reporting on some of the science stories in play this week; so will the folks at Physics Buzz.  While you're waiting -- because writing blog posts takes time -- check out the latest Philosophia Naturalis carnival at GeekCounterpoint, and the new carnival on women in science and technology.  Stay tuned!