A Face for Politics

7/29/2019 A Face for Politics

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face for politics: New study shows we can tell Democrats from Republicans in head shots

ou can tell a lot about a person by their faceeven theirpolitical affiliation, new research claims.

a study published in the January 18 issue ofPLoS One, subjects were able to accurately identify candidates from the 2004 and 2006 U.S. Senate election

ther Democrats or Republicans based on black-and-white photos of theirfaces. And subjects were even able to correctly identify college students as belon

Democratic or Republican clubs based on their yearbook photos.

o investigate the basis of these judgments, subjects were asked to rate photos of faces on a seven-point scale assessingpersonalitytraits such as assertiven

aturity, likeability and trustworthiness. Subjects consistently associated Democrats with warmth (likeable and trustworthy) and Republicans with power

ominant and mature). These findings were independent of the gender of the person in the photo.

he authors concluded that people possess "a general and imperfect" ability to infer political affiliation based on facial appearance, which is related to stere

out Democrat and Republican personalities. The ability to surmise other perceptually ambiguous traits, such as sexual orientation and religious group

embership, has been reported in similar studies.

he consequences of this general and imperfect ability are worrisome, with career opportunities, court rulings and financial success potentially falling subje

prejudicialjudgments, according to the authors.

ut surely these judgments dont interfere with election results, do they?

a study published in Science in February 2009, subjects were able to predict from a pair of photos of faces alone which political figure would win an elec

ven children could pick the winner when asked who they would prefer to be captain of their boat. And in a study published in the Proceedings of the Nati

cademy of Sciencesin November 2007, researchers linked competence perceived from a candidates face to his or herelectoral success.

he latest study adds to the growing body of evidence suggesting that certain traits once thought to be indistinguishable based on looks alone are in fact wri

l over our faces.

unning barefoot is better, researchers find

other Nature has outpaced science once again: the bare human foot is better for running than one cushioned by sneakers. What about those $125high-tec

nning shoeswith 648 custom combinations? Toss em, according toa newstudy published online January 27 in the journalNature(Scientific American is

Nature Publishing Group).

Most people today think barefoot running is dangerous and hurts," Daniel Lieberman, a professor of human evolutionary biology at Harvard University, saprepared statement. "But actually you can run barefoot on the worlds hardest surfaces without the slightest discomfort and painIt might be

ssinjuriousthan the way some people run in shoes."

eberman and his group used 3-D infrared tracking to record and study the running and strike style of three groups of runners: people who had always run

refoot, people who had always run with shoes, and people who had switched from shoe to shoeless.

hey found that when runners lace up their shmancy sneakers and take off, about 75 to 80 percent land heel-first. Barefoot runnersasHomo

piens hadevolved to beusually land toward the middle or front of the food. "People who dont wear shoes when they run have an astonishingly differen

rike," Lieberman said.

ithout shoes, landing on the heel is painful and can translate into a collision force some 1.5 to 3 times body weight. "Barefoot runners pointtheir toesmo

nding," which helps to lessen the impact by "decreasing the effective mass of the foot that comes to a sudden stop when you land," Madhusudhan Venkad

applied mathematics and human evolutionary biology postdoctoral researcher at Harvard who also worked on the study, said in a prepared statement. Bu

shioned kicks have hit the streets andtreadmills, that initial pain has disappeared, and runners have changed their stride, leading to a way of high-impact

nning that human physiology wasnt evolved forone that the researchers posit can lead to a host of foot and leg injuries.

rhaps it should come as no surprise that our bodies are still better engineered than new-fangled trainers. When taking into account our ancient ancestors,

umans have engaged in endurance running for millions of years," the researchers wrote in their study. "But the modern running shoe was not invented un

70s."

nother recent study, by the American Academy of Physical Medicine and Rehabilitation and published last December in the academys journal,PM&R, f

at wearing running shoes "increased joint torquesat the hip, knee and ankle," when compared to barefoot running. Even a jog in high heels was better for

an specialized tennis shoes.

espite the growing movement of barefoot (or more lightly shod) runners, many researchers are calling for more evaluation before all those sweaty sneake

andoned. "There is no hard proof that running in shoes causes injuries," William Jungers, a professor of anatomical sciences at Stony Brook University

ong Island, NY, wrote in a commentary that accompanies the new study. But, he asserted, "In my view there is no compelling evidence that it prevents the

ther." And as a boost to the barefoot argument, he added: "There are data that implicate shoes more generally as a plausible source of some types of chron

ot problems."

o perhaps you can skip those sneaks, say the study authors. "All you need is a few calluses," Lieberman said.

mage comparing the footfall of two Kenyan runners from the study courtesy of Benton et al. The runner on the left has worn shoes most of his life and lands heal, whereas the runner on the right has primarily run barefoot and lands on the ball of her foot.

acteria Transformed into Biofuel Refineries

ynthetic biology has allowed scientists to tweakE. coli to produce fuels from sugar and, more sustainably, cellulose. The bacteria responsible for most cas

od poisoning in the U.S. has been turned into an efficient biological factory to makechemicals, medicines and, now, fuels. Chemical engineer Jay Keaslin

e University of California, Berkeley, and his colleagues have manipulated the genetic code ofEscherichia coli, a common gut bacteria, so that it can chew

ant-derived sugar to produce diesel and other hydrocarbons, according toresults published in the January 28 issue ofNature. (Scientific American is part

ature Publishing Group.)

We incorporated genes that enabled production of biodieselesters [organic compounds] of fatty acids and ethanoldirectly," Keasling explains. "The fu

produced by ourE. coli can beused directly as biodiesel. In contrast, fats or oils fromplantsmust be chemically esterified before they can be used."

rhaps more importantly, the researchers have also imported genes that allowE. coli to secrete enzymes that break down the tough material that makes up

lk of plantscellulose, specifically hemicelluloseand produce the sugar needed to fuel this process. "The organism can produce the fuel from a veryexpensive sugar supply, namelycellulosic biomass," Keasling adds.
http://blogs.scientificamerican.com/observations/2010/01/27/a-face-for-politics-new-study-shows-we-can-tell-democrats-from-republicans-in-head-shots/http://blogs.scientificamerican.com/observations/2010/01/27/a-face-for-politics-new-study-shows-we-can-tell-democrats-from-republicans-in-head-shots/http://www.scientificamerican.com/article.cfm?id=political-science-skeptichttp://www.scientificamerican.com/article.cfm?id=political-science-skeptichttp://www.scientificamerican.com/article.cfm?id=political-science-skeptichttp://www.scientificamerican.com/podcast/episode.cfm?id=we-like-a-winning-face-09-03-03http://www.scientificamerican.com/podcast/episode.cfm?id=we-like-a-winning-face-09-03-03http://www.scientificamerican.com/podcast/episode.cfm?id=we-like-a-winning-face-09-03-03http://www.scientificamerican.com/article.cfm?id=ruled-by-birth-orderhttp://www.scientificamerican.com/article.cfm?id=ruled-by-birth-orderhttp://www.scientificamerican.com/article.cfm?id=ruled-by-birth-orderhttp://www.scientificamerican.com/blog/post.cfm?id=selective-vision-the-brains-spin-mahttp://www.scientificamerican.com/blog/post.cfm?id=selective-vision-the-brains-spin-mahttp://www.scientificamerican.com/article.cfm?id=the-look-of-a-winnerhttp://www.scientificamerican.com/article.cfm?id=the-look-of-a-winnerhttp://www.scientificamerican.com/article.cfm?id=the-look-of-a-winnerhttp://blogs.scientificamerican.com/observations/2010/01/27/running-barefoot-is-better-researchers-find/http://blogs.scientificamerican.com/observations/2010/01/27/running-barefoot-is-better-researchers-find/http://blogs.scientificamerican.com/blog/post.cfm?id=will-a-highly-customized-shoe-help-2009-06-02http://blogs.scientificamerican.com/blog/post.cfm?id=will-a-highly-customized-shoe-help-2009-06-02http://blogs.scientificamerican.com/blog/post.cfm?id=will-a-highly-customized-shoe-help-2009-06-02http://dx.doi.org/10.1038/nature08723http://dx.doi.org/10.1038/nature08723http://dx.doi.org/10.1038/nature08723http://www.nature.com/http://www.nature.com/http://www.nature.com/http://blogs.scientificamerican.com/blog/60-second-science/post.cfm?id=new-york-city-marathon-common-injur-2008-10-31http://blogs.scientificamerican.com/blog/60-second-science/post.cfm?id=new-york-city-marathon-common-injur-2008-10-31http://blogs.scientificamerican.com/blog/60-second-science/post.cfm?id=new-york-city-marathon-common-injur-2008-10-31http://blogs.scientificamerican.com/blog/post.cfm?id=the-evolutionary-origins-of-the-newhttp://blogs.scientificamerican.com/blog/post.cfm?id=the-evolutionary-origins-of-the-newhttp://blogs.scientificamerican.com/podcast/episode.cfm?id=good-sprinters-have-long-toes-09-11-05http://blogs.scientificamerican.com/podcast/episode.cfm?id=good-sprinters-have-long-toes-09-11-05http://blogs.scientificamerican.com/podcast/episode.cfm?id=good-sprinters-have-long-toes-09-11-05http://blogs.scientificamerican.com/podcast/episode.cfm?id=dieting-and-the-tv-to-treadmill-rat-09-10-27http://blogs.scientificamerican.com/podcast/episode.cfm?id=dieting-and-the-tv-to-treadmill-rat-09-10-27http://blogs.scientificamerican.com/podcast/episode.cfm?id=dieting-and-the-tv-to-treadmill-rat-09-10-27http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JHF-4XX36D1-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bea7b09825dec6d17d30e7ec502b545http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JHF-4XX36D1-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=0bea7b09825dec6d17d30e7ec502b545http://blogs.scientificamerican.com/podcast/episode.cfm?id=running-shoes-jog-joints-10-01-18http://blogs.scientificamerican.com/podcast/episode.cfm?id=running-shoes-jog-joints-10-01-18http://blogs.scientificamerican.com/podcast/episode.cfm?id=running-shoes-jog-joints-10-01-18http://www.scientificamerican.com/article.cfm?id=turning-bacteria-into-plastic-factories-replacing-fossil-fuelshttp://www.scientificamerican.com/article.cfm?id=turning-bacteria-into-plastic-factories-replacing-fossil-fuelshttp://www.nature.com/nature/journal/v463/n7280/abs/nature08721.htmlhttp://www.nature.com/nature/journal/v463/n7280/abs/nature08721.htmlhttp://www.nature.com/nature/journal/v463/n7280/abs/nature08721.htmlhttp://www.nature.com/nature/journal/v463/n7280/abs/nature08721.htmlhttp://www.scientificamerican.com/blog/post.cfm?id=solid-catalyst-simplifies-turning-a-2009-03-26http://www.scientificamerican.com/blog/post.cfm?id=solid-catalyst-simplifies-turning-a-2009-03-26http://www.scientificamerican.com/blog/post.cfm?id=solid-catalyst-simplifies-turning-a-2009-03-26http://www.scientificamerican.com/topic.cfm?id=plantshttp://www.scientificamerican.com/topic.cfm?id=plantshttp://www.scientificamerican.com/article.cfm?id=grassoline-biofuels-beyond-cornhttp://www.scientificamerican.com/article.cfm?id=grassoline-biofuels-beyond-cornhttp://www.scientificamerican.com/article.cfm?i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heE. coli directly secretes the resulting biodiesel, which then floats to the top of a fermentation vat, so there is neither the necessity for distillation or othe

rification processes nor the need, as inbiodiesel from algae, to break the cell to get the oil out.

his new process for transformingE. coli into a cellulosic biodiesel refinery involves the tools ofsynthetic biology. For example, Keasling and his team clo

nes fromClostridium stercorarium andBacteroides ovatusbacteria that thrive in soil and the guts of plant-eatinganimals, respectivelywhich produce

zymes that break down cellulose. The team then added an extra bit of genetic code in the form of short amino acid sequences that instruct the alteredE.

li cells to secrete the bacterial enzyme, which breaks down the plant cellulose, turning it into sugar; theE. coli in turn transforms that sugar into biodiesel

he process is perfect for making hydrocarbons with at least 12 carbon atoms in them, ranging from diesel to chemical precursorsand evenjet fuel, or

rosene. But it cannot, yet, make shorter chain hydrocarbons like gasoline. "Gasoline tends to contain short-chain hydrocarbons, say C8, with more branch

hereas diesel and jet fuel contain long-chain hydrocarbons with few branches," Keasling notes. "There are other ways to make gasoline. We are working o

ese technologies, as well."

fter all, the U.S. alone burns some 530 billion liters of gasoline a year, compared with just 7.5 billion liters of biodiesel. But Keasling has estimated in the

at a mere 40.5 million hectares ofMiscanthus giganteusa more than three-meter tall Asian grasschewed up by specially engineered microbes, like th

li here, could produce enough fuel to meet all U.S.transportationneeds.* That's roughly one quarter of the current amount of land devoted to raising crop

e U.S.

coli is the most likely candidate for such work, because it is anextremely well-studied organismas well as a hardy one. "E. coli tolerated the genetic cha

ite well," Keasling says. "It was somewhat surprising. Because all organisms require fatty acids for their cell membrane to survive, if you rob them of som

tty acids, they turn up the fatty acid biosynthesis to make up for the depletion."

coli "grows fast, three times faster than yeast, 50 times faster thanMycoplasma, 100 times faster than most agricultural microbes," explains geneticist an

chnology developer George Church at Harvard Medical School, who was not involved in this research. "It can survive in detergents or gasoline that will k

sser creatures, like us. It's fairly easily manipulated." Plus,E. coli can be turned into a microbial factory for almost anything that is presently manufacture

ganicfrom electrical conductors to fuel. "If it's organic, then, immediately, it becomes plausible that you can make it with biolo gical systems."

he idea in this case is to produce a batch of biofuel from a single colony throughE. coli's natural ability to proliferate and, after producing the fuel, dispos

eE. coliand start anew with a fresh colony, according to Keasling. "This minimizes the mutations that might arise if one continually subcultured the micr

says. The idea is also to engineer the new organism, deleting key metabolic pathways, such that it would never survive in the wild in order to prevent esc

thunintended environmental impacts, among other dangers.

ut ranging outside of its natural processes,E. coli is not the mostefficient producer of biofuel. "We are at about 10 percent of the theoretical maximum yie

om sugar," Keasling notes. "We would like to be at 80 to 90 percent to make this commercially viable. Furthermore, we would need a large-scale product

ocess," such as 100,000 liter tanks to allow mass production of microbial fuel.

evertheless, several companies, including LS9, which helped with the research, as well as Gevo and Keasling-founded Amyris Biotechnologies, are work

akingfuel from microbesa reality at the pumpnot just at the beer tap.

enetic testing may become a new weapon in the fight against chimpanzee smugglers

NA testing could be used as a tool to help fight smuggling of endangered chimpanzees, according to a study published this week in the journalBMC Ecol

though they are still the most common apes in Africa,chimpanzees(Pan troglodytes and their related subspecies) have experienced population drops of a

percent in the past 30 years, and are listed as "endangered" on theIUCN Red List of Threatened Species. Much of this decline is because of poachers an

muggling. A live chimpanzee can fetch $20,000 on the international black market. The animals are also often victims of thebushmeat trade.

hereas wild chimpanzee populations plummet, more and more chimps end up in rescue and rehabilitation centers, such asLimbe Wildlife Center(LWC)

ameroon. But the path taken before a chimpanzee ends up at a rescue center is long and convoluted, leaving few, if any, clues as to where in Africa the an

as first captured.

he new study may help provide answers as to where these rescued chimpanzees came from, and therefore identify poacher hunting patterns and smuggling

utes so they can be targeted and shut down by authorities.

he study, a collaboration between the LWC and the University at Albany, State University of New York, examined the mitochondrial DNA (mtDNA) and

icrosatellite (STRP, or short tandem repeat polymorphic marker) genotypes of 46 chimpanzees from LWC, then compared it with geo-referenced chimpa

mples from 10 locations throughout Cameroon and Nigeria. The team found that the chimpanzees came from throughout Cameroon, suggesting that smug

rife throughout the country and not all done internationally as previously believed.

he tests also found that most of the chimps at LWC were NigeriaCameroon chimpanzees (Pan troglodytes vellerosus), the most endangered of the four

mmon chimpanzee subspecies.

he results indicate that "international smuggling is less of a problemthan local trade," lead scientistMary Katherine Gonderof the University at Albany saprepared statement. "The problem seems to occur throughout Cameroon, with some rescued chimps even coming from protected areas." Within Cameroo

ve chimpanzee sells for $100, far below the international black market price, but still a tempting amount for residents of the economically challenged coun

onder and her co-authors say this study is just the first step, and are now calling for "a broader sample of rescued chimpanzees compared against a more

mprehensive grid of geo-referenced samples" in the hopes of revealing what they call "hot spots" of chimpanzee hunting and smuggling routes in Camero

ou'll Go Blind: Does Watching Television Close-Up Really Harm Eyesight?

seems the worst effects are not on one's eyes, and may come from watching too much television, no matter what the distance to the screen. Dear EarthT

ears ago I read that children should be kept at least two feet from the television because of harmful electronic emissions. Is this still relevant? Is t

difference regarding this between older and new flat-screen models?

Horst E. Mehring, Oconomowoc, Wisc.

uckily for many of us and our kids, sitting too close to the TV isnt known to cause any human health issues. This myth prevails because back in the 196

eneral Electric sold some new-fangled color TV sets that emitted excessive amounts of radiationas much as 100,000 times more than federal health offi

nsidered safe. GE quickly recalled and repaired the faulty TVs, but the stigma lingers to this day.
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le.cfm?id=navy-investigates-biofuels-to-power-ships-airplaneshttp://www.scientificamerican.com/article.cfm?id=how-to-kill-synthetic-biohttp://www.scientificamerican.com/blog/post.cfm?id=synthetic-biology-advance-genome-tr-2009-08-20http://www.scientificamerican.com/blog/post.cfm?id=evolution-details-revealed-through-2009-10-18http://www.scientificamerican.com/topic.cfm?id=transportationhttp://en.wikipedia.org/wiki/Miscanthus_giganteushttp://www.scientificamerican.com/article.cfm?id=are-jet-biofuels-ready-for-takeoffhttp://www.scientificamerican.com/article.cfm?id=are-jet-biofuels-ready-for-takeoffhttp://www.scientificamerican.com/topic.cfm?id=animalshttp://www.scientificamerican.com/article.cfm?id=video-instant-egghead-synthetic-biologyhttp://www.scientificamerican.com/blog/post.cfm?id=solid-catalyst-simplifies-turning-a-2009-03-26


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ut even though electronic emissions arent an issue with TVs made any time after 1968 (including todays LCD and plasma flat screens), what about caus

rm to ones vision? Dr. Lee Duffner of the American Academy of Ophthalmology isnt concerned, maintaining that watching television screensclose-u

herwisewont cause any physical damage to your eyes. He adds, however, that a lot of TV watching can surely cause eye strain and fatigue, particula

ose sitting very close and/or watching from odd angles. But there is an easy cure for eye strain and fatigue: turning off the TV and getting some rest. With

od nightssleep, tired eyes should quickly return to normal.

ebra Ronca, a contributor to the How Stuff Works website, argues that some parents might be putting the cart before the horse in blaming close-up TV

atching for their childs vision issues. Sitting close to the television ma y not make a child nearsighted, but a child may sit close to the television because

e is nearsighted and undiagnosed, she reports. If your child habitually sits too close to the television for comfort, get his or her eyes tested.

f course, excessive TV viewing by kids can cause health problems indirectly. According to the Nemours Foundations KidsHealth website, chi ldren who

nsistently watch TV more than four hours a day are more likely to be overweight, which in and of itself can bring about health problems later. Also, kids

atch a lot of TV are more likely to copy bad behavior they see on-screen and tend to fear that the world is scary and that something bad will happen to th

emours also finds that TV characters often depict risky behaviors (likesmokingand drinking) and also tend to reinforce gender-role and racial stereotype

here has also been much debate in recent years on the effects of TV viewing on infants. A 2007 Seattle Childrens Research Institute study found that for e

ur per day infants spent watching baby DVDs and videos they learned six to eight fewer new vocabulary words than babies who never watched the video

2009 study by the Center on Media & Child Health at Children's Hospital Boston found no negative cognitive or other impacts whatsoever on those infan

posed to more television than less.

hile it may be inevitable that your kids will watch TV, the key, experts say, is moderation. Limit kids exposure to screens of any kind, and monitor what

e allowed to watch. As KidsHealth points out, parents should teach their kids that the TV is for occasional entertainment, not for constant escapism.

arly Cometary Bombardment May Explain the Divergent Paths of Jupiter's Biggest Moons

anymede and Callisto, the two largest Jovian satellites, appear to have similar origins but have led very different lives. Ganymede and Callisto are the largpiter's so-called Galilean satellites, the four moons of the giant planet that were discovered 400 years ago,in January 1610, by Italian astronomer Galileo

alilei. Ganymede, the largest moon in the solar system, even bigger than the planet Mercury, boasts its own magnetic field andbears the marks of past tect

tivity. But Callisto, of roughly equal size and with a similar makeup of rock and ice, has neither a magnetic field nor an apparent history of tectonicsth

oons' geologic histories have proceeded very differently.

anymede seems more evolved, so to speakits constituents appear to have differentiated further than those of Callisto. Specifically, most of its rock and

ve migrated to the core, whereas those components are more widely distributed throughout Callisto, which appears to host a smaller core as a result.

he circumstances that could have led Ganymede to differentiation without fully affecting its sibling moon have been debated for years. One suggestion is

anymede's orbital history included a phase in which the moon experienced strong gravitational tides that heated the icy body and allowed the rock and me

alesce at its center.

a paper published online Sunday inNature Geoscience, planetary scientistsAmy BarrandRobin Canupof the Southwest Research Institute in Boulder,

opose an alternative scenario: heating by cometary impacts, which should have been plentiful several hundred million years after the moons formed, coul

ve liberated the materials that now constitute Ganymede's core. (Scientific American is part of Nature Publishing Group.) Callisto orbits much farther from

piter and so would have endured less bombardment from comets drawn in close to Jupiter by the massive planet's gravitational pull.

ach time a comet strikes an icy satellite, Barr explains, a portion of the moon's surface melts from the heat of the impact; the heavier metallic and rocky

nstituents mixed in sink to the bottom of the melt pool. With enough impacts providing sufficient melting, the sinking rocks' gravitational potential energ

leased as heat, producing more melting, and the separation of rock and ice becomes self-sustaining, a process known as "runaway differentiation."

uring the solar system's period of intense impacts about 3.8 billion years ago known as the late heavy bombardment, tremendous amounts of cometary ma

ould have been flying around Jupiter and the outer gas-giant planets. Barr and Canup estimate that Ganymede's proximity to Jupiter, the latter of which ac

mething of a gravitational sink, led to Ganymede's experiencing double the impacts of Callisto, and at higher velocities, to boot. "Ganymede gets 3.5 tim

uch energy in the late heavy bombardment as Callisto," Barr says. That energy differential, Barr and Canup realized, could account for Ganymede's much

mplete state of differentiationthe so-called GanymedeCallisto dichotomy.

y their calculations, a broad range of starting conditions for the source population of comets could produce Ganymede's full differentiation but stop short

naway differentiation at Callisto. Importantly, the debris disk described bythe so-called Nice model, a popular dynamical simulation for the solar system

olution, would do the job. "There is a huge range of masses of planetesimal disks that lead to the formation of the dichotomy," Barr says, noting that prio

potheses for the divergent histories of Ganymede and Callisto required fine-tuning of parameters or worked for only a very narrow set of circumstances.

s in with what is already known about dynamical sculpting in the outer solar system, and it works for a broad range of parameters," she says.anetary scientistWilliam McKinnonof Washington University in Saint Louis notes that work in recent years has complicated a competing explanation fo

chotomy, in which tidal heating during the orbital evolution of the Jovian moons melted Ganymede enough to differentiate it. Some research has in fact s

strong dynamical preference for Ganymede to have settled quickly into its present orbital resonance with the moons Io and Europa. "And if that's true the

no later special time for Ganymede to be tidally heated," McKinnon says. The fact that Barr and Canup's model dovetails with a primordial development

oons' orbits makes it attractive, he adds.

he new hypothesis is "a completely plausible explanation," McKinnon says. "What they've shown is that the effect of a strong late heavy bombardment m

the answer."

ebt crisis threatens UK science

abriel Aeppli has spent decades probing the nanostructure of materials, but today it is financial woes that are on his mind.s director of the London Centre for Nanotechnology, Aeppli is responsible for making sure the laboratory continues to bring in funding at the current leveout 10 million (US$16 million) each year. "I am worried, obviously," he says in his soft American accent. "I worry all the time."ke many scientists in Britain, Aeppli has grown more anxious in recent months. Faced with a rapidly growing debt that stood at 800 billion in March 20cording to government figures, the United Kingdom is poised to make deep cuts in public spending. It is probably not alone: governments across the glob

ve run up high deficits in recent years (see 'Debt threat'), and economists expect that many will soon be faced with the stark choice of raising taxes or lowdgets.
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Britain, policy experts say that funding for science will probably decline no matter who takes power in this year's general election, which must be held bne. The cuts will mark the first time in more than a decade that research spending has not grown.s a familiar worry for an older generation of British scientists who can still remember when a conservative government led by Margaret Thatcher slashedsearch spending in the 1980s. Denis Noble, a cardiologist at the University of Oxford, recalls serving on grant committees that had to choose just one out zens of applications. "The meetings became pointless really," he says. "At that level of cut you really can't cope."

ut British science has flourished under a science-friendly Labour government. Since the late 1990s, UK research has enjoyed strong growth in funding (seritish science boom'). The money has supported endeavours such as the Centre for Nanotechnology, a joint venture between Imperial College London andniversity College London (UCL). The centre was kicked off in 2002 with 14 million from a government grant and the Wellcome Trust, Britain's largestarity, which funds biomedical research.

he commitment helped to lure Aeppli, then a senior scientist at the research campus of Japanese electronics manufacturer NEC in Princeton, New Jersey, ad the centre. At the time, other countries were making larger sums of money available for nanotechnology, but Aeppli says he was promised a great dealdependence in setting up his new lab. "That was quite unique," he recalls. "I was just handed [the money] and told to go figure it out." When the centre op2006, it had drawn in additional funding and constructed an eight-storey laboratory in central London. Today the lab houses state-of-the-art scanning

nnelling microscopes and fabrication facilities, which are used to study a wide variety of basic and applied problems in materials science.he government could afford to finance such projects because the British economy was booming. Throughout the late 1990s and e arly 2000s, a strong proparket and financial sector swelled the treasury's coffers. But the collapse of those areas in 2007 and 2008 has left the UK government short of revenue at ahen it needs it the most. The government has run up a heavy deficit bailing out banks and stimulating consumer spending, and public-spending cuts are thay to balance its books.global problem

ritain's predicament is hardly unique. The United States, Japan and several European nations, including Ireland and Greece, have seen deficits rise sharplyey attempt to jump-start their economies. In December 2009, the newly elected Japanese government proposed cutting back or closing down several largeience projects as part of a 3-trillion (US$33.7-billion) budget-trimming process (seeNature462, 835; 2009), sparking outrage in the scientific communite government subsequently revoked most of the proposed cuts.the United States, a US$787-billion stimulus package has boosted research in the short term, but few expect to see further increases in this year's budget,ending will drop after the stimulus runs out. Moreover, falling state budgets and university endowments are taking a heavy toll, says Matt Owens, an assoce-president for federal relations at the Association of American Universities, a university advocacy group in Washington DC. "At US research universitiey're looking at significant budget shortfalls in the near future," he warns.he 'near future' may yet be a year or two away for American scientists. But in Britain, cuts will bite within months. The current Labour government has deawing up its next three-year budget until after this summer's election, but a pre-budget report released on 9 December 2009 called for "efficiency savingsveral sectors, including research. In late December, Peter Mandelson, the UK minister for business, innovation and skills, warned that universities would 50 million in government support between 2010 and 2013but he emphasized that the reduction was less than 5% of the total expected over that perioddon't think Watson and Crick could have existed under the current regime.

any universities, including leading research institutions such as Imperial and UCL, are already tightening their belts in p reparation. Between July andptember 2009, Imperial cut 48 jobs from its faculty of medicine; roughly half were academic posts. And on 14 January, UCL a nnounced that it hopes to t million6% of staff costsfrom its faculty of life sciences. Because much of Britain's research funding is distributed according to a formula based oiversity's size and quality, smaller and less-research-intensive universities are expected to be hit harder.

esearch councilsthe government funding bodies that provide some 3 billion annually in grantsare also likely to feel the pinch. For the past decadesearch-council funding has increased steadily. But at a recent debate on science in central London, none of the research ministers of the nation's three majlitical parties could promise that funding would continue at present levels.

ne council in particular is already acutely aware of the recession. Since its creation in 2007, the Science and Technology Facilities Council (STFC), whichstributes most of Britain's physics and astronomy grants, has been chronically short of cash. Battered by a falling pound, which raises the cost of overseasojects, and a flat budget that has never met its needs, the STFC is facing a 40-million spending deficit, which has forced it to make cuts to research gran

ts have also caused the council to rethink its international commitments: it is now planning to withdraw from the Gemini project, which operates twinlescopes in Chile and Hawaii (seeNature 462, 396; 2009).hn Womersley, the STFC's director for scientific programmes, sees little relief in sight. The only sure thing, Womersley says, is that after the election minll be fighting over spending on big government items such as defence, health and education. "There's likely to be a tough scramble over how the budget w

located," he says. "The question is: is science special?" If research funding is to be protected, Womersley believes, scientists will have to present a unifiedall political parties. Some politicians are already talking about cutting back on fundamental research that lacks an obvious application, he says. It will be ientists to show the relevance of their work, either by providing a potential link to an area of economic activity or by showing its educational benefits.his emphasis on the broader impact of research is also expected to be a key part of the Research Excellence Framework, a system that will be used to asseiversity research quality to determine funding levels (seeNature 463, 291; 2010).

ut some researchers are uneasy about making such justifications. Too much emphasis is already being placed on publication rates and economic benefit, sobert May, a zoologist at the University of Oxford and a former government chief scientific adviser. "I don't think Watson and Crick could have existed ue current regime," he adds.ack in London, Aeppli is preparing the nanotechnology centre as best he can for the difficult times ahead. He is encouraging his staff to bring in grants fron-governmental sources, including charities and the European Union. He is also steering the centre's research agenda towards issues such as climate and eas he believes the government will fund to help improve the economy in the long term.

alancing those projects against fundamental science will be tricky, he admits, but he believes the centre will survive and could even prosper in the difficulars ahead. "We've been planning for this downturn for a while," he says. "I think that if we're working in the right areas, there will be growth."

ranslational research: Talking up translation

short, laminated article has fallen off the wall of press cuttings outside Alan Ashworth's London office. It is an editorial published in 2000 by Britain's wad and notoriously opinionated tabloid newspaper, The Sunand it is praising geneticists who study cancer. "They are, without doubt, the most importaople alive," it crows. "People like Professor Alan Ashworth and his team at the Institute of Cancer Research are dedicated to the cause."

ast year, Ashworth's work was lauded, somewhat more quietly, in an editorial in theNew England Journal of Medicine (NEJM)1. "Readers may be surprise editors' decision to publish a small early-stage trial," the journal wrote of a study largely based on Ashworth's discoveries, "but this trial not only reports

mportant resultsit also points to a new direction in the development of anticancer drugs".hat Ashworth has won praise from these diverse camps is a testament to his record in 'translational' medicinemoving developments in basic science intctor's surgery. In just under 15 years, he has gone from early work on the major cancer-risk geneBRCA2, to involvement in the development of a promisncer drug based on knowledge about the gene's biology. His work "is really the shining example of successful translation of a basic biology idea into succinical application", says Julian Downward, from Cancer Research UK's London Research Institute. Ashworthwho prefers the term 'integration' to tran

plans to make his approach a central tenet of the Centre for Molecular Pathology, the London facility he will lead, which is scheduled to break ground ea

is year and should be completed in 2012 at a cost of 20 million (US$33 million). He has even become something of an integration evangelist, chastisingho do basic cancer research without considering the work's future application. "This integrated approach is something I demand of everybody," he says.
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et what Ashworth makes look easy, others find extraordinarily hard. He says that the key to his success has been a thorough understanding of basic biologcommitment to seeing it through to application, plus a sprinkle of serendipity. But others say that Ashworth is also set apart by his drive, his charm and hiility to win over others to build the networks of expertise needed for integration. "One of his big achievements," Downward says, "has been to actually hogether this grouping of people who aren't usually very good at talking to each other."

This integrated approach is something I demand of everybody.

the 1980s, when Ashworth started a PhD in biochemistry at University College London, molecular biology was in the "really early phase of gene cloningys. It was his flair in this field that led him in the 1990s to Mike Stratton, then at the Institute for Cancer Research in Sutton, UK, who had recentlyown2thatBRCA2which, along withBRCA1, was known to be important for determining breast cancer riskwas localized to a small region ofromosome 13.shworth says that he was brought in "as kind of a hired gun" to help clone the gene. And he was confident that he would. Over a bawdy meal in April 199shworth predicted that the gene would be in hand within a year and scrawled his prediction on a napkin, witnessed by several colleagues. The group didn'e whole year. In December 1995,Nature reported3the cloning ofBRCA2.shworth recalls when the first woman was tested forBRCA2mutations; she had been scheduled for prophylactic mastectomy because of her family's cance

story. The tests were negative, and the surgery was called off. "It was only then that I realized I could apply what I was good at to patient benefits," he sayy the end of the 1990s, Ashworth was directing a team at the Institute of Cancer Research in London and had developed a mouse with a mutatedBrca2 geat was highly susceptible to cancer4. Work by several groups showed that the gene is involved in repairing DNA damage by a process called homologouscombination (see graphic). When it is mutated, DNA breaks start to accumulate, increasing the risk that a cell will turn ca ncerous. "We had to retool essend start to understand DNA repair," says Ashworth. In 1999, he was chosen to lead the Breakthrough Breast Cancer Research Centre at the Institute of Can

esearch, where he came into close contact with patients and physicians.

ouble jeopardy

shworth became interested in the idea that a mutatedBRCA gene could not only render cells susceptible to cancerit could also be exploited to target thhe team turned to a concept in genetics called 'synthetic lethality', in which mutations are harmless on their own but together will kill a cell. They theorizencer cells bearing a mutatedBRCA2 were now reliant on another leg of their DNA repair machinery. Taking out a second repair pathway should bring thee floor.he opportunity to test the theory presented itself when, as Ashworth puts it: "I met a bloke in a pub and he offered me some drugs." That bloke was Steve

ckson, a DNA-repair researcher from the University of Cambridge, UK. The company he had started, KuDOS Pharmaceuticals, had developed the drug

aparib, which inhibits an enzyme vital for the repair of DNA breaks: poly(ADP-ribose) polymerase, or PARP. Over a drink, Jackson and Ashworth hit on

ea of testing whether Jackson's 'PARP inhibitor' would take out the second leg inBRCA2 mutant cells (see graphic).t wasn't months; it was days or weeks after the compounds went down to his lab that they told us about these absolutely stonking results," says Jackson. Tam showed in 2005 thatBRCA2 mutant cells died when they were hit by Jackson's drug5, and a back-to-back report from Thomas Helleday, then at theniversity of Sheffield, UK, echoed the finding6.He holds together people who aren't usually very good at talking to each other.

hen it came to testing the drug in people, Ashworth had a head start: olaparib had already passed many of the early safety and regulatory hurdles requiredw drug. But human trials bring other challenges: intellectual property, financing and mountains of regulatory bureaucracy can be enough to smother anyo

anslational ambitions.shworth, who had access to clinical expertise via the cancer centre and nearby hospital, is sanguine, and says that the key has been to listen to those fromfferent disciplines "so I can understand what they do". Part of Ashworth's success may lie in his air of being a regular, amiable scientist who can seem sligcomfortable in a suit. "It may be because he was slightly outside the normal operation of all those things," says Downward. "He's not a clinician, he's notarma person."iller instinct

f the 60 participants recruited into the eventual phase I clinical trial, 23 had mutations in one of theBRCA genes; and after treatment, 12 of these people sh

clinical benefit'7

, such as no progression of their disease for 4 months or longer. The synthetic lethality approachthe new direction in anticancer drugsferred to in theNEJMeditoriallooked highly promising, and the cancer community was abuzz. AstraZeneca, which acquired KuDOS in 2006, is nowveloping the drug and the results of a phase II trial, presented at the American Society of Clinical Oncology meeting in 2009, showed that more than a thitients taking the maximum dose showed some improvement in their tumours8. "I've no doubt this approach will work," says Ashworth. The drug might alork against cancers with other DNA-repair defects. Last year, his team showed that PARP inhibitors were also lethal in cancer cells with mutations inPTEe of the genes most commonly disrupted in cancers9.

shworth cites another example of the integration he seeks between basic and applied research. His team knew thatBRCA- mutant tumours develop resistane platinum-based drugs such as cisplatin that are a mainstay of treatment; the group went back to the lab to work out whether the PARP inhibitors would rainst the same problem. The resulting paper inNature10, along with one from another group11, showed that drug resistance arises when theutantBRCA2 undergoes a deletion, restoring DNA repair. This means that PARP inhibitors might sometimes need to be used with other therapies. .shworth's evangelism is persuasive. "It is a fantastic feeling to think that the work you've done in the lab can actually have an output in patients," he says,ink many other people want to feel like that." He imagines a future in which all tumours are targeted according to their precise genetic characteristics, a vat many researchers are now working towards. At the new Centre for Molecular Pathology, he plans to collect genetic and molecular profiles of patients ater trials to work out which people are most likely to benefit from the therapies being tested.e is also heavily involved in running Breakthrough Generations, a study into the genetic and environmental causes of breast cancer that has recruited 100,

ritish women and has received 12-million in start-up funding from the Institute of Cancer Research and the Breakthrough Breast Cancer charity. The plallect detailed health information over the next 40 years to improve understanding of the causes and prevention of cancer.

oday, he finds some escape in the basic biology. "It's a relief to look at data rather than at higher-level political things," he says. "What really drives me isoking at experiments. I still get very, very excitedsome would say too excitedwhen there's a hint of a good result."

anetary science: A whiff of mystery on Mars

or the past decade, NASA's mantra for exploring Mars has been to 'follow the water'. The agency based its aqueous obsession on the idea that finding evidpast or present water would yield clues to whether life once graced the planetor still exists there. Now, some scientists are chanting a new slogan: 'fol

e methane'.his small hydrocarbon is tantalizing because much of the methane in Earth's atmosphere is produced by microbes, within soils and inside the guts of cowsher mammals, including humans. So the fact that methane has been discovered on Mars could signal the presence of life somewhere on the red planet. Orethane can also form through geological processes.either case, the methane findings signal that unknown processes are happening. "Methane is one molecule that really tells us that Mars is a coupled syste

e interior, the surface and the atmosphere," says Sushil Atreya, director of the Planetary Science Laboratory at the University of Michigan in Ann Arbor.November, fans of Martian methane gathered in Frascati, Italy, to puzzle over the new data. They hope to pinpoint where the methane is coming from an

gets scrubbed from the atmosphere so quickly. Solutions to these conundrums will require better data, so researchers are working out how to sniff out theture missions to Mars.
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he excitement over methane started to build in 2003 and 2004, when three groups1,2,3spotted methane in the atmosphere of Mars using spectroscopiceasurements from telescopes on Earth and data from the European Space Agency's Mars Express spacecraft. The amounts of methane detected by the teaffered, but the planetary average was estimated to be about 10 parts per billion by volume3, an extremely low level. And the amount changed over timeggesting that the gas is still being released, even though it might have been produced at some point in the past.January 2009, the leader of one of the teams, Michael Mumma from NASA's Goddard Space Flight Center in Greenbelt, Maryland, published a paper4th

analysed his 2003 and 2006 observations from the Keck telescope and the Infrared Telescope Facility in Hawaii. Mumma's team showed that threeighbouring areas on Mars, Nili Fossae, Terra Sabae and Syrtis Major, were 'hot spots' o f methane production during 2003. But by 2006, methane levels hopped at those sites, signalling that some active process was venting the gas.he quick drop also suggests that something is rapidly destroying the methane. "For us atmospheric chemists, it is still very difficult to understand how metn vary so rapidly in time and space," says Franck Lefvre at the Laboratory of Atmospheres, Environments and Space Observations in Paris.

efvre calculated that the atmospheric lifetime of methane is less than 200 days5hundreds of times shorter than prevailing models of Mars's atmospheredict. "If the measurements are correct, this means that we are missing something really important," says Lefvre.aina Gough, a PhD student at the University of Colorado at Boulder, tried to fill that gap by testing how methane reacts with samples made up to resemble

artian soil. But none of the soil samples removed methane that quickly, she reported at the meeting.ough's results were among the most important presented there because they "tend to rule out what was thought to be the most likely explanation for theserved methane variations on Mars", Lefvre says. "The mystery deepens."here the gas is going is not the only problem. "The big question really is what is producing the methane," says Atreya. Is it biological or geological, past oesent?though conditions on the surface of Mars are extremely harsh, there may be spots below the surface where microbes could survive. In research in the high

rctic, microbiologist Lyle Whyte from McGill University in Montreal, Canada, has found methane-making microbes within extremely salty pools in thermafrost, the permanently frozen ground. Martian microbes, if they exist, could be making methane in conditions somewhat like this on Mars, he suggestternatively, the methane could be forming geologically as a by-product of a process called serpentinization, which happens on Earth when water reacts wivine, a mineral that is present on Mars6.nother debate that dominated the meeting revolved around the location of the methane sources. Vittorio Formisano and Anna Geminale from the Institutehysics of Interplanetary Space in Rome have tried to pinpoint the seasonal bursts using the Planetary Fourier Spectrometer on the Mars Express spacecraftheir findings suggest that trace amounts of methane are released from the northern polar cap when its surface melts during summer.he Keck data argue otherwise, say Mumma and Geronimo Villanueva, also at Goddard. The water released from the north pole in summer does not contaiethane, they say. And although the pair found their first three methane hot spots in the northern hemisphere, they have also identified methane releases in uthern part of the planet during that hemisphere's spring. The team is now using the Keck telescope to pinpoint the sources to regions as small as 80 kilomom the original best resolution of 500 kilometres.he reason for the different conclusions could stem from the methods the two teams used. The Mars Express data are averaged over many thousands of sped over time, whereas the Keck maps are snapshots. The disagreement and the failure of atmospheric models to explain the methane measurements has mat some researchers remain sceptical about the interpretation of the data. Todd Clancy at the Space Science Institute in Boulder is particularly troubled byuctuations in time and space that Mumma reports. "These variations are unphysical for any plausible photochemical processes active in the Mars atmosphys Clancy. Yet, he says, if the observations are right, "the existence of such methane in the current Mars atmosphere would be profound on so many levelnstitute the highest priority for planetary mission studies".ith so many questions swirling around the issue of methane, researchers agree that only new missions to Mars will provide the answers (see graphic).

hasing a gas

rst up is NASA's Mars Science Laboratory, which is due to launch next year. This car-sized rover will carry a tunable laser spectrometer, which should beanswer one of the burning questions about Martian methane: what is the isotopic make-up of the carbon? If the carbon is mostly the lightest stable isotoprbon-12, this could hint at a biological origin.2016, NASA and the European Space Agency are scheduled to send an orbiter to monitor trace gases. At the Frascati meeting, Richard Zurek, chief scien

r the Mars programme at NASA's Jet Propulsion Laboratory in Pasadena, California, described this newly selected mission, which would be the first to lopressly for methane and other trace gases in the Martian atmosphere. The mission has methane enthusiasts salivating, and the call for instrument proposast gone out. For researchers with questions about the methane data, the 2016 mission should provide some firm answers. "It will measure the level of met Mars unambiguously and determine whether it really is seasonally and latitudinally variable," says David Catling from the University of Washington inattle.

ut some researchers are looking beyond the planned missions and are drawing up proposals for other ways to study the gas. Mumma would like to find acnts and watch them closely to see how methane releases change over time. He has proposed the Mars Organics Observer, which would sit at Mars's first

agrange point, a special orbit around the Sun that is locked to the movement of Mars by the gravity of both bodies. The telescope could monitor the red plery day and locate methane bursts with a resolution of 10 kilometres.thers have placed drilling operations at the top of their wish lists. "Most astrobiologists believe that the best hope for detecting microbial life will be in thebsurface," says Whyte.esearchers are also dreaming up other schemes for tracing methane sources. Atreya, and Paul Mahaffy from Goddard, propose using a balloon to measurethe Martian atmosphere. Joel Levine, at Nasa Langley Research Center in Hampton, Virginia, is developing a Mars plane that could soar over the planet onitor methane releases from the surface.ut those not directly involved in methane research caution about leaping on to the gas bandwagon. "We know that methane can be made by processes that

thing to do with biology," says David Stevenson from the California Institute of Technology in Pasadena. Water should remain the research priority, he sefvre, however, says he is happy that mission planners are hearing the wishes of methane enthusiasts. "Atmospheric chemistry has rarely been the trendiepic in Mars science, but this has completely changed since the discovery of methane," he says. "We are now designing space missions entirely devoted totection of trace species, which was impossible to imagine a few years ago."

terature mining: Speed reading

cientists are struggling to make sense of the expanding scientific literature. Corie Lok asks whether computational tools can do the hard work for

em. In 2002, when he began to make the transition from basic cell biology to research into Alzheimer's disease, Virgil Muresan found himself all buterwhelmed by the sheer volume of literature on the disease. He and his wife, Zoia, both now at the University of Medicine and Dentistry of New Jersey in

ewark, were hoping to test an idea that they had developed about the formation of the protein plaques in the brains of people with Alzheimer's disease. Buwcomers to the field, they were finding it almost impossible to figure out whether their hypothesis was consistent with existing publications.t's really difficult to be up to date with so much being published," says Virgil Muresan. And it's a challenge that is increasingly facing researchers in everyhe 19 million citations and abstracts covered by the US National Library of Medicine's PubMed search engine include nearly 830,000 articles published in09, up from some 814,000 in 2008 and around 772,000 in 2007. That growth rate shows no signs of abating, especially as emerging countries such as Chd Brazil continue to ratchet up their research.
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he Muresans, however, were able to make use of Semantic Web Applications in Neuromedicine (SWAN), one of a new generation of online tools designelp researchers zero in on the papers most relevant to their interests, uncover connections and gaps that might not otherwise be obvious, and test and generw hypotheses.f you think about how much effort and money we put into just Alzheimer's disease research, it is surprising that people don't put more effort into harvestinblished knowledge," says Elizabeth Wu, SWAN's project manager.

WAN attempts to help researchers harvest that knowledge by providing a curated, browseable online repository of hypotheses in Alzheimer's disease resehe hypothesis that the Muresans put into SWAN, for example, was that plaque formation begins when amyloid-, the major component ofbrain plaques, feds in the terminal regions of cells in the brainstem that then nucleate the plaques in the other parts of the brain into which the terminals reach. SWAN prvisual, colour-coded display of the relationships between the hypotheses, as derived from the published literature, and shows where they may agree or conhe connections revealed by SWAN led the Muresans to new mouse-model experiments designed to strengthen their hypothesis. "SWAN has advanced ousearch, and focused it in a certain direction but also broadened it to other directions," says Virgil Muresan.he use of computers to help researchers drink from the literature firehose dates back to the early 1960s and the first exper iments with techniques such asyword searching. More recent efforts include the striking 'maps of science' that cluster papers together on the basis of how often they cite one another, or

milarities in the frequencies of certain keywords.s fascinating as these maps can be, however, they don't get at the semantics of the papersthe fact that they are talking about specific entities such as ged proteins, and making assertions about those entities (such as gene X regulates gene Y). The extraction of this kind of in formation is much harder to autcause computers are notoriously poor at understanding what they are reading. Even so, informaticians and biologists are working together more and makinsiderable progress, says Maryann Martone, the chairwoman of the Society for Neuroscience's neuroinformatics committee. Recently, a number of compd academic researchers have begun to create tools that are useful for scientists, using various mixtures of automated analysis and manual curation (seeTaower tools').eeper meaning

he goal of these tools is to help researchers analyse and integrate the literature more efficiently than they can do through their own reading, to hone in on tost fruitful experiments to do and to make new predictions of gene functions, say, or drug side effects.he first step towards that goal is for the text- or semantic-mining tool to recognize key terms, or entities, such as genes and proteins. For example, academblisher Elsevier, headquartered in Amsterdam, has piloted Reflect in two recent online issues of its journal Cell. The technology was developed at the

uropean Molecular Biology Laboratory in Heidelberg, Germany, and won Elsevier's Grand Challenge 2009 competition for new tools that improve themmunication and use of scientific information.

eflect automatically recognizes and highlights the names of genes, proteins and small molecules in the Cell articles. Users clicking on a highlighted term we a pop-up box containing information related to that term, such as sequence data and molecular structures, along with links to the sources of the data. Retains this information from its dictionary of millions of proteins and small molecules.

uch 'entity recognition' can be done fairly accurately by many mining tools today. But other tools take on the tougher challenge of recognizing relationshiptween the entities. Researchers from Leiden University and Erasmus University in Rotterdam, both in the Netherlands, have developed software calledregrine, and used it to predict an undocumented interaction between two proteins: calpain 3, which when mutated causes a type of muscular dystrophy, arvalbumin B, which is found mainly in skeletal muscle. Their analysis found that these proteins frequently co-occurred in the literature with other key ter

xperiments then validated that the two proteins do indeed physically interact (H. H. van Haagen et al. PLoS One 4, e7894; 2009).evelopment role

t the University of Colorado in Denver, bioinformatician Lawrence Hunter and his research group have developed a tool called the Hanalyzer (short for 'hroughput analyser'), and have used it to predict the role of four genes in mouse craniofacial development. They gathered gene-expression data from three sues in developing mice and generated a 'data network' showing which genes were active together at what stage of development, and in which tissues. Tham also mined relevant abstracts and molecular databases for information about those genes and used this to create a 'knowledge network'.sing both networks, the researchers homed in on a group of 20 genes that were upregulated at the same time, first in the mandible (lower jaw area) and theout 36 hours later, in the maxilla (upper jaw). A closer look at the knowledge network suggested that these genes were involved in tongue development,

cause the tongue is the largest muscle group in the head and is in the mandible. Further analysis led them to four other genes that had not been previouslynked to craniofacial muscle development but that were active in the same area at the same time. Subsequent experiments confirmed that these genes were volved in tongue development (S. M. Leachet al. PLoS Comput. Biol. 5, e1000215; 2009).

Somebody staring at the data or using existing tools would never come up with this hypothesis.

don't see that there is any way that somebody staring at the data or using existing tools would have ever come up with thi s hypothesis," says Hunter.though extracting entities and the relationships between them is a common approach for literature-mining tools, it is not enough to pull out the full meanisearch papers, says Anita de Waard, a researcher of disruptive technologies at Elsevier Labs in Amsterdam. Scientific articles typically lay out a set of coaims, together with the empirical evidence that supports them, and then use those claims to argue for a conclusion or hypot hesis. "Generally that's where tal, interesting science is," de Waard says.apturing the higher-level argument is an even more difficult task for a computer, but a small number of groups, such as the SWAN group, are trying to dohe SWAN website, which opened to the public in May 2009, was developed by two Boston-based groups, the Massachusetts General Hospital and the

zheimer Research Forum, a community and news website for Alzheimer's researchers. For each hypothesis in the system, SWAN shows the factual claim

pport it, plus links to the papers supporting each claim. Because claims from the various hypotheses are linked together in a network, a user can browse fr

e to the next and see the connections between them. The visualization tool uses a red icon to show when two claims conflict and a green icon to show wh

ey're consistent, allowing the user to see at a glance which hypotheses are controversial and which are well supported by the literature (see graphics, abovt the moment, this information is unlikely to surprise experts in Alzheimer's disease. In its current stage of development, SWAN may be more useful forwcomers trying to get up to speed on the subject. Beneficiaries could include more established scientists such as the Muresans who want to move into afferent field, or researchers with a pharmaceutical or biotech company who have just been put on an Alzheimer's disease project.uilding up

WAN also has scalability issues. The vast majority of the hypotheses, claims and literature links in SWAN have been annotated and entered by the site'srator, Gwen Wong, with the help of authors. This curation is a painstaking process that has so far produced only 1,933 claims and 47 fully annotatedpotheses. But the intent is for these early hand-curation efforts to set a 'gold standard' for how the SWAN knowledge base should be built by the commun

whole. The SWAN developers plan to improve the user interface to encourage scientists to submit their own hypotheses, post comments and even do some curation themselves.he need for some level of manual curation is common to the various literature tools, and limits their scalability. The SWAN team is working to automate pthe curation process, such as extracting gene names. Elsewhere, de Waard and other researchers are investigating ways of automatically recognizingpothesesfor example, by looking for specific word patterns.

or most of these tools, however, curation is unlikely to become fully automated. "Literature mining is hard to do in a way that is both high scale and highcuracy," says John Wilbanks, director of Science Commons, a data-sharing initiative in Cambridge, Massachusetts. Developers say a more likely solution
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ast in the short term, is that papers will have to be curated and annotated through some combination of automated tools, professional curators and the papthors, who might, for example, be prevailed on to write their abstracts in a more structured machine-readable form.

he right people

re authors willing to add to the already arduous task of writing an article? And are authors even the best people to do this job? The journal FEBStters experimented in 2009 with structured digital abstracts to see how authors would respond and perform in shaping their own mach ine-readable abstra

he results were not encouraging. Authors presented their abstracts about proteinprotein interactions as structured paragraphs describing entities, thelationships between the entities and their methods using specific, simple vocabularies (for example, 'protein A interacts with protein B'). But the curators otein database didn't accept them, says de Waard. "Authors are not the right people to validate their own claims," she says. The communityreferees, erators, readers at largeis still needed.

his could be a business opportunity for the publishers, says Wilbanks: they could curate and mark up their publications for text and semantic mining andovide that as a value-added service.

There's a lot of business out there for the publishers, but it's not the same business," says Allen Renear, associate dean for research at the Graduate School brary and Information Science at the University of Illinois at Urbana-Champaign. "If they keep making PDFs, that's not going to work for them. They hav

t into more of the semantic side of this."rhaps the largest challenge is getting scientists to use these tools. It will be up to the developers to demonstrate the benefits and make their wares easy to

hat's going to be difficult, says Hunter. Academic informaticians are rewarded more for coming up with new algorithms, and less for making their programable and widely adoptable by biomedical scientists, he says. Only a few tools are being developed by companies for more widespread use.ajor issues that all technology developers will need to tackle are transparency, provenance and trust. Scientists won't trust what a computer is suggesting irms of new connections or hypotheses if they don't know how the results were generated and what the primary sources were. "We as informaticians are gohave to take on these more user-driven and less technology-driven problems," says Hunter.

ven if researchers do start to trust the new tools, it's not clear how much of their reading they will delegate. "As reading becomes more effective," says Reome people have speculated that we won't do as much because we'll get done what we need to do sooner." Or, he says, "it may be that we'll do more readicause it's more valuable. Which one is true is actually an empirical question."nalysing articles in new ways leads to the larger question of whether the articles themselves should change in structure. If an article is to be boiled down iachine-readable bits, why bother writing whole articles in the first place? Why don't researchers just deal with statements and facts and distribute and masem up to generate hypotheses and knowledge?

Human commentary and insight are still extraordinarily valuable," says Martone. "Those insights don't immediately fall out of data without human ingenuu need to be able to communicate that and that generally means building an argument and a set of supporting claims. These things are not going to go awy time soon."

olorizing Dinosaurs: Feather Pigments Reveal Appearance of Extinct Animals

ong the range of the imagination, the coloration--and origin--of feathered dinosaurs and ancient birds has begun to be revealed through fossilized organell

or nearly two centuries, people have struggled to imagine what the great extinctdinosaurslooked like. Thanks to modern paleontology and physiology, the

apes, masses and even how they might have moved andinteractedhave been deduced. But one of the most basic questions about their appearance, their

loring, seemed unanswerable.

new study, however, proposes some of the first cellular hints. Extrapolating from primitive pigment-giving organelles known as melanosomes (which co

e coloring compound melanin and are still prevalent in modernanimals) that have been found in fossilizeddinosaur feathersfrom the Cretaceous period,

search team paints a picture of dark wings and brightly striped reddish tails.The findingswill be detailed in the January 28 issue ofNature. (Scientific

merican is part of Nature Publishing Group.)

sing high-powered scanning electron microscopy, the researchers examined 125-million-year-old feathers found in the Jehol group, a geologic formation

rtheastern China. One of the animals analyzed, the Sinosauropteryx, a small, meat-eating dinosaur, appears to have had alternating bands of dark and ligh

ong its tail. "In this case at least, the dark band was [a] russet, gingery color," Michael Benton, a professor of vertebrate paleontology at the University of

ristol in England and co-author of the study, said in a press conference Tuesday in London. "It's the first time anybody has had evidence of original color.

prevalent pigment

he discovery of this pigment in ancient dinosaur andbird feathersdid not begin at a dinosaur dig, but rather in a lab studying fossilized squid.Jakob Vinth

w a PhD student in paleontology at Yale University who was not involved with the new study, was examining preserved ink sacs from Jurassic

riodsquidwhen he found that the fossilized melanosomes appeared identical to those in modern-day squid ink.

he similarity led him to propose that "there must be melanosomes preserved in other kinds of structures" in other animals. "So I said, 'It would be interesti

ok at bird feathers,'" he said in a phone conversation. In these fossilized feathers he saw the very same structures.

fter bringing his findings to the attention of his graduate supervisor, Vinther was told that he had only found a common bacteria that had long been known

ist in these feather fossils. But he was not convinced. After studying feathers with a known color pattern, he found that t he dark-pigment particles appear

ly where the black bands didand in the fossils they aligned perfectly with the individual feather filaments, an unlikely arrangement for bacteria. In 200

nther and colleagues publisheda paperinBiology Letters describing the find, in which they proposed, "The discovery of preserved melanosomes opens u

ssibility of interpreting the color of extinct birds and other dinosaurs."

was no great stroke of luck that thesepigment particleswere still left in the fossilized feathers. In fact, they are what had been fossilized from the feather,

nther: "The reason that you have a fossil feather is because there are pigments. So if you have a white feather, it would not leave a fossil."hat does seem like good fortune, at least to the researchers studying these ancient particles, are their shapes. "We're extraordinarily lucky that each of the

gments of the melanosomes are contained in a different-shaped organelle," Benton said at the press briefing.

he melanosomes that have been found no longer exhibit their original colors because their chemical properties have changed in the intervening millions of

ars. But researchers can still ascertain the extinguished hues by looki

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