Berkeley Science Review - Fall 2003

B E R K E L E Ysciencereview

Fall 2003 Issue 5

BERKELEYsciencereview

EDITOR IN CHIEF

Colin McCormick

MANAGING EDITOR

Jessica Palmer

COPY EDITOR

Kira O’Day

EDITORS

Carol HunterHeidi LedfordKira O’Day

Christopher Weber

ART DIRECTOR

Una Ren

WEBMASTER

Tony Le

SPECIAL THANKS

Keay Davidson

PRINTER

Sundance Press

©2003 Berkeley Science Review. No part of this publication may be reproduced, stored, or transmitted in any form without express permission of the publishers. Publishedwith financial assistance from the Office of the Vice Chancellor of Research, Department of Nutritional Sciences and Toxicology, Physics Department, the UC Berkeley GraduateAssembly, the Associated Students of the University of California, and the UC Berkeley College of Natural Resources. Berkeley Science Review is not an official publication of theUniversity of California, Berkeley, or the ASUC. The content in this publication does not necessarily reflect the views of the University or ASUC. Letters to the editor andstory proposals are encouraged and should be emailed to [email protected] or posted to Berkeley Science Review, 10 Eshleman Hall, Berkeley, CA 94720.Advertisers, contact [email protected] or visit http://sciencereview.berkeley.edu.

FROM THE EDITOR

Dear Readers,

Welcome to the fifth issue of the Berkeley Science Review. Like wine and cheese, we just keep gettingbetter with age. We’ve expanded our print run from 5,000 to 6,000 copies. We’ve begun a highschool outreach program, and science students in local high schools will soon be reading the BSR inclass. We’re distributing copies to several area science museums and, as always, across the Berkeleycampus and at the Lawrence Berkeley lab. We have some great stories for this issue, from LettyBrown’s walk through the UC Botanical Garden, to Nathan Bramall’s letter from his physicsresearch in Greenland, to Rupa Datta’s article on new techniques in mathematical genomics.

But all good things must come to an end, and my time at the BSR is no exception. I’m writing thisletter from Washington DC, where I just began my tenure as an AAAS Congressional Science Fellow.Although best known for publishing Science magazine, AAAS (the American Association for theAdvancement of Science) plays an extremely important role in American science policy. TheirScience Fellows program each year places scientists in congressional offices and federal agencies toprovide technical expertise to legislators and administrators. This is a fascinating opportunity for meto watch law and policy being made, and perhaps to influence its direction just a little. Among otherthings, we’re learning how the federal government spends its $2.3 trillion budget, and where allthat money comes from.…

While nobody’s accused me of lacking confidence, I know I wouldn’t have gotten this job withoutthe BSR. My interviewers asked how I would feel about giving science advice in fields outside ofphysics. In response, I showed them copies of the BSR and explained that I’d been writing andediting for a multidisciplinary popular science journal. They were impressed and I got the job,although I’m sure Una Ren’s great cover designs also helped. I’m not the first person to parlayexperience with the BSR into a job: Eran Karmon won a prestigious AAAS Mass Media fellowship,and Sherry Seethaler is now assistant director of science communications at UC San Diego.

If you like what you read here, or even if you don’t, drop us a line at [email protected] tell us what you think. You can read all our issues online at sciencereview.berkeley.edu, which also hasinformation about how to get involved. We are always interested in new writers, editors, andartists/designers. Not only is the BSR a great way to learn about the exciting science going on atBerkeley, it just might land you somewhere that you never thought you’d be.

Cheers,

Colin McCormick

Labscope

BERKELEYs c i e n c e 4r e v i e w

A paltry 5% of mammalsexhibit male parental

care. But one species of ladytuco-tucos is in luck, becausetheir mates share the respon-sibility of raising a happy andwell-adjusted brood. Colo-nial tuco-tucos (Ctenomyssociabilis) are social subterra-nean rodents native to SouthAmerica. After observingthat up to six females and onemale may share a tunnel sys-tem and single nest, gradu-

ate student Maria Soares and Professor Eileen Lacey of the Department of Integrative Biology wondered whether the malewas actually making himself useful. To find out, they observed a captive tuco-tuco colony at Cal, and also tracked thecomings and goings of a free-living colony in Argentine Patagonia by capturing wild tucos and fitting them with radio collars.The researchers discovered that the males do everything for the pups that the females do, except of course for nursing. Theyhuddle with the pups, retrieve them when they try to leave the nest, and bring food into the tunnels. Soares believes that thebenefits of a housebound tuco male may include bigger and healthier pups and a shelter for males to hide from maraudingpredatory birds between breeding seasons. And don’t underestimate the value of a little domestic harmony. Learn moreabout the social behavior of tuco-tucos and other vertebrates at http://ib.berkeley.edu/labs/lacey/.

Kira O’Day

And he changes diapers

Robert Full’s laboratory is not for the squeamish. Full, the director of thePoly-PEDAL (Performance, Energetics, and Dynamics of Animal Locomo-

tion) laboratory in the Department of Integrative Biology, uses cockroaches tomodel the mechanics of movement. In a recent study, Full equipped roaches withtiny jetpacks that shot them sideways while they ran forward. The roaches werefilmed to determine how they stabilized their bodies and regained the correctdirection. The researchers found that the recovery time following lateral propul-sion was a miniscule 25 milliseconds. Moreover, the cockroaches did not evenslow down, as we would if knocked off balance while running. Instead, they usedtheir springy legs to bounce back on track. Full theorizes that in the invertebratesystem the body can be more important than brains for balance. The Poly-PEDALlab is currently constructing a robot based on the filmed movements of cock-roaches. Learn more at http://polypedal.berkeley.edu/.

Careening cockroaches

Adam SchindlerPhoto: Robert Full

Photo: Andrea Caiozzi-Cofre


Polar bears blend into their snowyenvironment, and their camou-

flage extends beyond the realm of vis-ible light. Polar bears are also nearly in-visible in the far infrared, the frequencyrange in which bodies radiate heat—aproperty that has long vexed scientists

trying to use infrared to locate bears from the air. Researchers from the De-partment of Mechanical Engineering, led by professors Boris Rubinsky and RalphGreif, have now solved the long-standing mystery of the vanishing polar bears.By measuring infrared properties one hair at a time, they determined the hair’semissivity, a measure of how efficiently it radiates heat. They found that theconventional explanation, that the bears are so well-insulated that their surfacesare the same temperature as the snow,is correct but incomplete: the hair’semissivity in the infrared is also nearlyequal to that of snow, and lower thanthat of other arctic animals, such as cari-bou. They also determined that this lowemissivity could help to insulate thebears by lowering the amount of infra-red heat that the bears radiate away.Photo: Dr.Ralph Nelson, Carle Foundation

Giants in the mist

The fog drifts eerily through the towering redwood forests during thedry, hot California summer. A group of Berkeley researchers led byIntegrative Biology professor Todd Dawson has set out to “demistify”

this breathtaking sight. Like so many hikers and nature-lovers, biologistshave long wondered how these giants attain their incredible size in the faceof California’s long dry summers. While studying the impact of fog and cli-matic variation on the giant redwood Sequoia sempivirens, the Dawson groupuncovered the redwood’s unique solution to the lack of summer rain, andpotentially their secret to attaining great heights. Following the distinctivestable isotope fingerprints of rainwater and fogwater, the Dawson groupshowed that the trees acquire water from rain in the winter and from fog inthe summer. The fog is “stripped” from the air by the redwood foliage. Fur-thermore, the trees are so good at pulling in fogwater that the excess sum-mer redwood “fogdrip” accounts for a third of the total annual water inputinto the coastal forests—a massive natural sprinkler system! Learn moreabout redwoods and plant ecophysiology at http://ib.berkeley.edu/labs/dawson.

Delphine Farmer

Vanishing polar bears

Chris Weber

Photo: ©Vladimir Dinets [email protected]


Current Briefs

A team of Lawrence BerkeleyLaboratory and UC Berkeleyscientists, originally formed to

research heart disease, has created a newtool to probe the human genome bycomparing it to the genomes of its siblingsand cousins—apes, Old World monkeys,and New World monkeys. This newtechnique, called phylogenetic shadowing,will help scientists find genes in humansthat are primate-specific and thereforeoverlooked by previous methods. Thescientists—Eddie Rubin, director of LBL’sGenomics Division, Dario Boffelli, a staffscientist at LBL with a traditional back-ground in biochemistry, and Lior Pachter,a UC Berkeley professor of mathematics—typify the increasingly close collaborationbetween lab-bench biochemistry andmathematical analysis. The research team ishoping that phylogenetic shadowing willextend this kind of collaboration from genehunting to evolutionary biology.

Scientists have been comparing smallsections of genetic sequences fromrelated species to each other almostsince Watson and Crick first postulatedDNA’s double-helix structure. Butmany dream of comparing entiregenomes, searching through all threebillion letters quickly and efficiently forfunctional elements. Gene hunting onsuch a large and automated scalerequires sophisticated mathematics andcomplex computational tricks.

The DNA of most complex organisms isfull of “junk”—millions of base pairs (theA’s, C’s, G’s, and T’s that are DNA’s

“alphabet”) that don’t really seem to doanything useful. One way to shake theuseful genetic elements out of the junk isto compare a genome to the sequence of arelated species. Bits of the sequence thatmatch up between the two species aremore likely to be something functional.These could be sequences called exonsthat code for specific proteins, sequencesthat interact with cellular machinery toregulate the expression of those exons, orsome other functional piece of code thatwe don’t yet understand. This is because,as a species evolves, natural selection willtend to preserve genes and other func-tional bits, but won’t exert strongpreservative pressure on the junk,allowing it to mutate more rapidly.

But comparing species that are too closelyrelated, like humans and monkeys, willshow too much meaningless similarity. Alot of the junk DNA will be the same

simply because it hasn’t hadtime to mutate, so similaritywon’t necessarily meanfunctionality. “You’ll neverfigure out what’s important—it’s an impractical way to findgenes,” says Boffelli. “There’stoo much background noise.”However, when you comparesequences between extremelydistant relatives—like humansand fugu fish—Boffelli says,“anything that is conserved isfunctional, but few such thingsare found, a lot of interestingstuff is not.” It turns out that amouse is a close enoughrelative to humans that most ofthe functional genes are stillthere, but it’s far enough awayon the evolutionary tree thatjunk DNA has had time tomutate. According to Boffelli,

that is the reason the mouse genome is sopopular for genetic comparisons. “It’s agood compromise point.”

But there’s still a great deal of differencebetween mouse and man. Comparisonswith the mouse genome will miss anyrecently evolved gene that is unique toprimates. Phylogenetic shadowing is a wayto take advantage of all the variation in theprimate family tree to find these primate-specific genes. Instead of comparing thehuman genome and one other species ofprimate at a time, it compares the humangenome and several closely related speciesof primate to each other at the same time.Sequence conserved between any twospecies is likely to be junk, but sequenceconserved within the whole group isprobably something functional. “If yousampled enough species, the total accumu-lative variation is enough to see what’sfunctional and what’s not,” Boffelli says.

GENE HUNTERSSifting throughevolution’s shadows

You can imagine the set of related genetic sequences as stringslined up one above the other, with beads marking the spotswhere the genetic code differs from the sequence in human. Alight shining down from above through the beads would cast ashadow on the ground below them, indicating the “junk” se-quences. Where there is no shadow, there is very likely a geneor significant genetic information. The Berkeley team took thisone step further, comparing the sequences not only to human,but to each other closely related primate. “Mathematically wemade this robust,” says Pachter. “We came up with a good wayof defining the shadows.” (Image: Jeff Hunter)


The LBL/Berkeley team chose fourspecific sections of DNA, each about1,500 base pairs long and containing anexon they knew existed, to test this idea.The team needed to see if phylogeneticshadowing could highlight the known exonblindly in each case. They picked 17species distributed among the threebranches of primates closely related tohumans for the comparisons. Unlikehumans, none of these primates had beenfully sequenced, so Boffelli and hiscolleagues had to sequence the unknownsections themselves using genetic materialfrom the Coriell Cell Repositories and theSan Diego Zoo.

Using other primate sequence data, theteam estimated that the noncoding regionsmutate seven times faster than codingregions. Pachter and his colleagues thencreated a tree—a mathematical estimate ofhow long ago each species of primateevolved from their common ancestors.This tree was based only on the sequenceinformation, but ended up basicallymatching the traditional phylogenetic treebased on the fossil record and morphology.

Pachter and his colleagues used a com-puter program to align the sequences foreach of the four test regions. Using thetree, the team calculated the likelihoodthat each little bit of sequence from themultiple-species alignment mutated at thefast, noncoding rate versus the likelihoodthat it mutated at the slow, coding rate.Comparing this mutation rate base pair bybase pair clearly revealed small valleys—sections of DNA that had mutated veryslowly across all the species—amid steepmountains of heavily diverged sequence.The exons were found, as expected, in theslowly mutating valleys.

In all four cases, phylogenetic shadowingfound the buried exon using the sequencefrom only eight species. In fact, research-ers could have found three of these exonssimply by comparing mouse and human.But they would never have found thefourth exon that way, because it is inactivein mice.

Once they had proven the technique in thefour test cases, it was time to test phyloge-netic shadowing’s ability to find newfunctional sequences. The LBL scientistswere interested in finding the regulatoryelements for another primate-specificgene called apo(a), which codes for ablood protein that, at high levels, can be amajor risk factor for youthful heartdisease. The scientists hoped to use theirnew technique to discover these unknownpieces of code.

Using phylogenetic shadowing, Boffelliand his colleagues were able to pinpointeight conserved regions of 40–70 basepairs and show that these bits interactedwith regulatory DNA-binding proteinsmore than other segments. This discoveryprovides important new targets of studyto cardiologists trying to understand whysome people have higher levels of apo(a)in their blood—and a correspondinglyhigher chance of having a heart attack intheir thirties.

The team is now applying phylogeneticshadowing to large sections of the humangenome, trying to find as many primate-specific genes as quickly as possible. Theirstudy is an important contribution to thedebate over which primates should besequenced next, presenting scientists witha mathematical basis for picking thoseprimates that will prove most useful for

gene hunting in humans. Phylogeneticshadowing also combines the interests ofbiomedicine and evolutionary biology andcreates all kinds of opportunities forcollaboration. “My goal,” says Pachter, “isto be able to understand the evolutionaryhistory of the genome.” Understanding thegenetic threads that tie us to our primatecousins is a big first step.

Saheli S. R. Datta

Want to know more?

Phylogenetic Shadowing ofPrimate Sequences to FindFunctional Regions of the Hu-man Genome. D Boffelli et al.,Science (2003); Vol. 299,pages 1391–1394.

Current Briefs


No matter how much somepoliticians may try to deny it, theevidence for global warming is

overwhelming. Yet while we humans arebusy pumping heat-trapping carbon intothe atmosphere, our oceans are teemingwith microscopic algae that consumecarbon during photosynthesis. Scientistsand politicians alike have begun to wonderif it might be possible to harness theearth’s oceans as a carbon reservoir. JamesBishop of UC Berkeley’s Department ofEarth and Planetary Science and theLawrence Berkeley National Laboratory isdeploying remote-controlled robots tofind out if stimulating phytoplanktongrowth could reduce the amount ofcarbon in the earth’s atmosphere.

Marine phytoplankton are the primaryproducers of the ocean. As phytoplanktonphotosynthesize, they convert dissolvedinorganic carbon into organic carbon,thereby sequestering it within their cells.Some phytoplankton inevitably sink deepinto the ocean, taking their particulateorganic carbon (POC) with them. POClost from the ocean surface is replaced bycarbon from the atmosphere, and thewhole system forms a biological carbonpump that lowers the amount of CO

2 in

the atmosphere.

Scientists have long suspected that theycould increase the flux through the pumpby increasing phytoplankton activity. Thequestion was, how could phytoplanktonproductivity be enhanced on a large scale?

The answer resided within the PacificOcean, in regions that are famous forbeing high in nutrients such as nitrogenand phosphorous, but mysteriously low in

phytoplankton. For years, scientistsdebated the nutrients that might belimiting phytoplankton growth in theseareas. In the late 1990s, a ship carryingten tons of iron sulfate sailed to a highnutrient/low phytoplankton region in theSouth Pacific, south of Tasmania. There,scientists dumped their cargo of iron intothe sea, triggering a massive algal bloom afew days later. Space satellites thatmonitor chlorophyll fluorescence coulddetect the bloom for almost two monthsfollowing fertilization. The answer toocean fertilization, it seemed, was iron.

But this experiment was only the begin-ning, and much more must be learnedabout the ocean’s carbon cycle before webegin filling our oceans with iron. In thepast, data collection was limited by areliance upon manned research voyagesthat were prohibitively expensive andoften dangerous. Furthermore, eachvoyage could last only a few months at atime, and could easily miss sporadicnatural events. Bishop and his teamdecided it was time to switch tactics and

designed remote-controlled robots calledCarbon Explorers.

The neutrally buoyant Carbon Explorers canmove from the surface of the ocean to depthsof 1,000 meters, measuring POC concentra-tions along the way. Active for the greaterpart of a year, these robots can monitor theocean continuously and quickly relay theirfindings to researchers via satellite. They sendfrequent emails to Bishop, who admits, “It’slike being addicted to a computer program.”The Carbon Explorers are also incrediblycost effective: building one Carbon Explorerand operating it for many months costs about$25,000—that’s roughly equivalent tooperating an oceanographic ship for one day.

For their first deployment, two CarbonExplorers were released in a high nutri-ent/low phytoplankton region of theNorth Pacific, approximately 1,000 mileswest of Vancouver Island, British Colum-bia. On April 7, 2001, NASA satellitesdetected a large dust storm originatingnear the Gobi desert. The powerful stormchurned up debris over land and thentraveled out over the Pacific Ocean,depositing iron-rich dust in its wake.When the dust storm passed over theCarbon Explorers on April 12, high windsand seas prevented the Carbon Explorersfrom communicating with satellites.

A few days later, the storm had died downand the Carbon Explorers were againtransmitting data. Although communica-tions were temporarily interrupted duringthe storm, data collection had continuedsmoothly. Five days after the storm passedoverhead, the robots detected largeincreases in POC. Several days later, POClevels hit their peak, at nearly double thepre-storm levels.

On their first mission out, Bishop’sCarbon Explorers had made a tremen-dous discovery. They had detected acompletely natural iron fertilization

A LIVING CARBON RESERVOIRSequestering carbon in the sea

Collecting data in the stormy South Pacific is dangerouswork, so Berkeley scientists are deploying remote-controlledrobots that can continuously monitor carbon levels formonths at a time. (Photo: LBNL)


experiment, and provided the first directevidence for ocean fertilization by naturalstorms—a phenomenon that would havebeen very difficult to observe by mannedresearch voyages.

While these results make iron fertilizationseem like an easy solution to globalwarming, Bishop makes it clear that thisfield is “still in the realm of science” andnot yet at the level of practical application.In 2002, the Carbon Explorers wereinvolved in iron fertilization experimentsin the South Pacific. These experimentsshowed that adding iron can increasephytoplankton productivity, but theresponse is not always consistent. “Theresults demonstrate that there is a lot tolearn yet from the ocean,” says Bishop.

Many aspects of the ocean’s carbon cycleare unknown, and whether this methodwould be effective on a large scaleremains an open question. Furthermore,no one knows what consequences global

Jennifer Skene

climate engineering may hold. Whilethere may be good outcomes, negativerepercussions for ocean ecology are easyto imagine. Algal blooms have a terriblereputation, and sometimes triggermassive fish kills and perturbations inthe food chain. “Ocean fertilization willbe a global decision,” says Bishop, “aftera lot of people think of the conse-quences and outcomes.”

But the consequences cannot be fullyunderstood until scientists discovermore about the ocean’s carbon cycle.Bishop’s Carbon Explorers are still outthere, now exploring the NorthAtlantic, the North Pacific, and theSouthern Ocean, and investigatingother aspects of phytoplankton produc-tivity and the ocean’s carbon cycle. “Weare still trying to understand how theocean behaves naturally,” says Bishop.“Once we have a predictive basis, wewill be able to predict the outcome ofan ocean fertilization experiment.” And

even if ocean fertilization is ruled out,Bishop’s experiments provide the basisfor understanding how the naturalcarbon cycle will be affected as theoceans respond to climate change. “Eachtime the floats go out,” says Bishop,“they find something different. Andthat’s very exciting.”

TWO WAYS TO SIX LEGSCreepy crawlies will never be the same

It turns out that not every six-leggedcreepy crawly is an insect. LawrenceBerkeley Laboratory and University of

Siena researchers have made the unex-pected discovery that collembolans, a typeof primitive arthropod long thought to beclosely related to insects, are actually onlydistant relatives.

Collembolans are commonly referred toas springtails, due to an appendage ontheir abdomen that propels themthrough the air. They are small, wing-less, and harmless, although they canseem alarming when they mob moistplaces like floor drains and dampbasements. Collembolans and insects aretraditionally grouped together in the

subphylum Hexapoda (“six feet”). Likecrustaceans, spiders, and many-leggedcreatures such as centipedes andmillipedes, hexapods are members ofthe phylum Arthropoda. Hexapods arecharacterized by the presence of threemain body regions (head, thorax, andabdomen), a pair of antennae, and, ofcourse, three pairs of legs.

Scientists have found it difficult todetermine how hexapods are evolution-arily related to other types of arthropods.For many years, hexapods were thought tohave diverged most recently from centi-pedes and millipedes. But recent geneticand developmental analyses show thathexapods are actually more closely related

to crustaceans such as shrimp andlobsters. Still, it was believed that allhexapods developed from a singlecommon ancestor. However, recent workby LBL scientist Jeffrey Boore andUniversity of Siena collaborator FrancescoNardi challenges the common-ancestormodel, and provides strong evidence thatacquisition of the hexapod body planoccurred independently in the insects andthe collembolans. In fact, genomic analysisof mitochondria (cellular organelles thatcontain their own DNA) reveals thatcollembolans may have split from thefuture insect lineage even before insectssplit from crustaceans.

Collembolans are an ancient group ofarthropods, dating back 400 million years.To the untrained eye, they resemblewingless insects. But collembolans haveonly six abdominal segments whereas“true” insects have 11. Previous work by

Want to know more?

Robotic observations of duststorm enhancement of carbonbiomass in the North Pacific. JKBBishop et al., Science (2002);Vol. 298, pages 817–821.

www-esd.lbl.gov/CLIMATE/

Russell Fletcher

Francesco Nardi and colleagues placedcollembolans far from insects on theevolutionary tree, but mitochondrial DNAsequences from more species of hexapodswere needed to confirm their preliminaryresults. So, in collaboration with JeffreyBoore, who heads up the evolutionarygenetics laboratory located at LBL, theysequenced two more mitochondrialgenomes, one from an additional collem-bolan, the other from a zygentoman (aninsect order that includes silverfish andfirebrats). According to Nardi, thezygentomans are “one of the most basallineages of the ‘true’ insects.”

Mitochondrial genomic analysis offersNardi and his colleagues several advan-tages over traditional nuclear genomicanalysis when teasing apart evolutionaryrelationships. Mitochondria, often calledthe “powerhouses” of the cell, are thoughtto have descended from a bacterium thatentered into a symbiotic relationship witha primitive eukaryotic cell. Mitochondrialgenomes are relatively easy to isolate, andthey are much smaller than nucleargenomes. Mitochondrial genomes arealways inherited maternally and are highlyconserved among animals. According toBoore, “the actual sequencing of amitochondrial genome requires less thanthree minutes.” However, he adds, “thework required to prepare products forsequencing and analyze results typicallytakes a few months.”

The researchers used a series of computa-tional programs to analyze several insectand collembolan mitochondrial genomesequences. Their analysis comparedseveral specific sequences of conservedgenes that code for proteins. Changesbetween specific sequences in themitochondrial genomes of the differenthexapods were used to place them relativeto one another in an evolutionary sense.

The data Boore and his colleagues gleanedfrom mitochondrial genomic analysisindicates that although “true” insects aredescended from a common ancestor,hexapods as a whole are not. Rather, asNardi explains, “Hexapoda, as commonlydefined to include all six-legged creatures,is paraphyletic [descended from morethan one common ancestor], withCollembola originating earlier in theevolution of arthropods, possibly beforethe split of crustaceans and insects. Thisimplies an independent evolution to lifeon land, and the convergent acquisition bycollembolans and insects of many charac-ters, with six-leggedness among others.”

The independent evolution of six-leggedness on at least two occasionsdemonstrates the remarkable utility of thehexapod body plan. The convergentacquisition of useful body plans andspecific body parts is certainly notuncommon; fins and flippers wereindependently acquired in fish such as

tuna and sharks, andmammals such asdolphins and whales. Thewings of insects, thewings of birds, and eventhe wing-like structuresof mammals such as batsare another example ofconvergent evolution,demonstrating what wealready know—wingsare well-designed for

flying. So what makes having six legs sodesirable? One way to address thisquestion would be to determine whatancestral body plans might have predatedboth the collembolans and the insects.

The convergent evolution of hexapodsposes some important questions: Whatmolecular mechanisms are responsible forthe similar forms seen in these twoindependent hexapod lineages? Docollembolans and insects have develop-mental “tools” in common, or are largelyseparate sets of genes responsible for thesix-legged body plan? Perhaps as Boore,Nardi, and their colleagues collect moredata on collembolans and primitiveinsects, answers will emerge.

Want to know more?

Hexapod origins: monophyl-etic or paraphyletic? F Nardiet al., Science (2003); Vol. 299,pages 1887–1889.

Comment on “HexapodOrigins: Monophyletic orParaphyletic?” F Delsuc etal., Science (2003); Vol. 301,page 1482d.

Left, Tetrodontophora bielanensis, a collembolan. Right, Thermobia domestica, an insect commonly known as a firebrat.Although both of these arthropods have six legs and a segmented body, they are not as closely related as scientists once thought.(Tetrodontophora photo: Francesco Nardi, University of Siena; Thermobia photo: David Maddison, University of Arizona,www.tolweb.org)

Current Briefs


Nothing lives forever. Certainspecies of bacteria, however,make a pretty good attempt at

it. When available nutrients drop todangerously low levels, these bacteriarespond by forming spores that cansurvive extreme environmentalconditions and remain viable forhundreds of thousands of years. Recently,the public saw this robustness graphicallydemonstrated when processed spores ofB. anthracis were used as bioterrorismagents—sent through the mail as a drypowder fully capable of infecting asusceptible host. Anthrax was first linkedto the B. anthracis bacterium in the late1800s and has been a subject of interestto microbiologists ever since. But theattacks in 2001 drew the attention ofscientists from a wide range of otherdisciplines to the bacterium, both as athreat to national security and publichealth and as an object of scientificinterest. One of these scientists was Dr.Andrew Westphal, a physicist at UCBerkeley’s Space Sciences Laboratory,who became interested in looking forphysical properties that might distinguishthe spores of B. anthracis from those ofother Bacillus strains.

Dr. Westphal’s lab has a lot of experi-ence measuring tiny things. About 10years ago, they developed a technique tomake highly precise measurements usinga standard optical microscope attachedto a video camera. The camera takeshundreds of thousands of snapshots ofthe object, each slightly offset from theothers. By averaging these offset imagesand accounting for the spatial variationof the camera shots, Westphal is able toachieve a precision of measurementbetter than 5 nanometers—or 0.5 % of

one micron. Westphal had been using thetechnique to look at the tracks of heavyion particles from outer space in specialpieces of glass. “It seems like a strangedeparture for us, to be using [ourtechnique] to look at anthrax spores,” Dr.Westphal acknowledges.

Current testing methods for anthrax in asuspicious sample rely on biologicalcharacteristics—using antibodies that bindto proteins in the spore coat orpolymerase chain reaction (PCR)-basedtechniques to identify anthrax-specificDNA sequences. These are fairly reliable,but they take time—between 12 and 24hours—and some of the components,such as the antibodies, can be expensiveand perishable.

Noting the difficulties involved inpositively identifying the tiny anthraxspores—just two to six microns indiameter, a fraction of the width of ahuman hair—and in separating them fromother, innocuous materials, Westphal’s labdecided to see if there was anything thattheir technique could contribute. Whatthey hoped to do was to develop a systemthat could identify the spores rapidly,based strictly on physical characteristics.

“We thought it would be interesting to putsome spores [under the microscope] and

see what we see, if we candistinguish them based onsize,” he said. So they gotsome spores of harmlessrelatives to B. anthracis fromDr. Terry Leighton, a formerCal professor now atChildren’s Hospital OaklandResearch Institute, and setabout doing just that.

The lab first tried to see ifthey could detect differentBacillus strains based onspore size alone. They testedfour different types of the

bacteria—B. cereus, which can cause foodpoisoning; B. thuringiensis, which is used tokill agricultural insect pests; and twoharmless soil bacteria, B. subtilis and B.megaterium—and found that, indeed, eachtype differed significantly in size. But theirmost intriguing discovery came aboutwhen the lab tested several parameters toidentify possible sources of error in theirreadings, conditions that they thoughtmight change the size of the spores duringthe experiment.

One of the conditions they tested wasrelative humidity, chosen, Dr. Westphalsays, “rather naively,” because they didn’tknow that humidity was not expected toaffect the size of the spores. Bacterialspores have long been considered to beessentially dormant, their coats acting assolid, impenetrable shells to protect theDNA from damage. Microbiologiststhought the bacterial spores would notshow any major morphological changesuntil they were introduced to a nutrient-rich environment, where they wouldbegin to germinate.

However, to the surprise of hiscollaborators, Westphal saw that increasedhumidity caused the spores to swell in twodistinct, time-dependent stages. The datasuggest that the immediate, rapid stage of

TRACKING BIOTERRORA swell way to spot anthrax

Electron microscope cross section of a spore of Bacillus subtilis,showing the cortex and coat layers surrounding the core (darkcentral area). The spore is 1.2 microns across, a fraction of thewidth of a human hair. (Photo: S. Pankratz)


Current Briefsswelling could be due to the diffusion ofwater into the outer coat and cortex of thespore, while the second, slower stage(occurring about eight minutes after thechange in humidity) is likely due to thepenetration of water into the spore core.Altogether, the spores swelled by anaverage of approximately 4%—much toosmall to be measured by standard opticalmicroscopes.

The materials that make up the sporecoat should not take up water from theair, so the data suggest that this change insize is due to an active process within thespore. This raises some interestingbiological questions, such as how thesechanges are initiated and carried out andif they have anything to do with thespore’s eventual emergence fromdormancy. It may also have an applicationin the design of a detection system: ifdifferent spores can be shown to swell

Marjorie James

with different amplitudes or timeconstants, it might be a way to confirmthe identity of a suspicious sample.

Currently, Westphal’s lab is looking atdifferent types of spores to determine ifsize and swelling are species-dependent.Their eventual goal is to create anapparatus that will be able to identifyanthrax spores on the order of seconds—far faster than any other system, existing

or proposed. Dr. Westphal believes thatone could be made that would be nobigger than a standard cooler, at a cost thatwould be competitive with otherdetection systems. His hope is that such adevice could prove to be very useful, bothin alerting authorities to dangeroussamples and limiting the expense anddisruption of false alarms.

Want to know more?

Kinetics of size changes of individual Bacillus thuringiensis sporesin response to changes in relative humidity. AJ Westphal et al.,Proceedings of the National Academy of Sciences (2003); Vol. 100, pages3461–3466.

Resistance of Bacillus Endospores to Extreme Terrestrial and Ex-traterrestrial Environments. WL Nicholson et al., Microbiology andMolecular Biology Reviews (2000); Vol. 64, pages 548–572.


print to paying subscribers, and are rapidlyscanning in back issues (articles in Journalof the American Chemical Society are availableonline back to 1879). Berkeley recentlycanceled print subscriptions to journals of-

fered by major scientific publisher Elsevier,choosing to rely on electronic versions in-stead. But Eisen envisions more than sim-ply making research available to be readonline by paying subscribers. According tothe PLoS website, “open access” to scien-tific literature means “its free availability onthe public Internet, permitting any usersto read, download, copy, distribute, print,search, or link to the full texts of these ar-ticles, to crawl them for indexing, to passthem as data to software, to make and dis-

Scientists are often perceived to be atthe cutting edge of technology, butin one critical area they are stuck in

the past. In the midst of the InformationAge, when the Internet can rapidly deliverfree information around the globe, scien-tists are still communicating with eachother through closed, subscription-basedjournals. These expensive subscriptionsmake scientific research available only tothose who can afford it, often preventingscientists from seeing the complete bodyof published works in their field. Or so saythe founders of the Bay Area-based PublicLibrary of Science (PLoS). This fall PLoS istaking an important step in its campaignto erase obstacles to the free and easy dis-tribution of science: armed with initialfunds of $9 million, it is launching a newonline scientific journal intended to com-pete with top-tier scientific journals—andmaybe even start a new trend in open-ac-cess publishing.

Lawrence Berkeley Lab scientist and Ber-keley MCB professor Michael Eisen is oneof the cofounders of PLoS. He describes itas “a group of scientists who believe thatscience in general would be better off ifthe published results of scientific researchwere fully available.” He also believes theInternet has enormous potential for ad-vancing scientific research. Most journalsnow offer their articles online as well as in

tribute derivative works, or to use themfor any other lawful purpose.” Eisen sees a

day when scientists will be ableto “search the entire text of jour-nal articles, [electronically] linkto specific subsections, [and usethe literature] in ways wehaven’t even thought of yet.”

Eisen compares his vision ofopen-access research to publicDNA-sequence databases thatcollate DNA codes discoveredby various researchers, explain-ing how the ability to systemati-cally view whole genomes hasrevolutionized biology. If se-quences were still publishedpiecemeal in various journals,new fields such as genomics andEisen’s own field of computa-tional biology might not exist.

Computational techniques employed daily,such as BLAST and homology searches,would never have been developed, he says.These tools, which allow biologists tosearch and compare genes and proteinsacross species and even kingdoms, eluci-date everything from the function of thegene and genome to the pattern of evolu-tion. In the scientific literature Eisen sees asimilar trove of information to be minedby enterprising scientists in ways as yetunconceived, if only all the literature wereavailable in a single, easily manipulated site.He and his PLoS colleagues have set out tomake that possible.

This task has turned out to be easier saidthan done. Eisen first came upon the ideafor a universal scientific literature databaseas a post doc some years ago with his thenboss, now PloS cofounder, Dr. PatrickBrown of Stanford University. Eisen wasworking on microarrays, a biological toolused to study the activation of genes undervarious conditions. Huge amounts of priordata were require to understand the resultsgenerated by this technique. Says Eisen, “PatBrown has a photographic memory, but it’s

SCIENCE FINDS ITS PLOSIN THE SUNIs open-access publishingcoming of age?

Ben Gutman


Policy

For PLoS to succeed, it will have to be embracedby publishing scientists. (Image: www.PLoS.org)

Realizing that presenting the ideaof open access and even mak-ing a threat didn’t reshape theworld of scientific publishing,Eisen and company undertooka new approach.


just not possible to know all the things youneed to know. It just seemed logical to haveall the information to interpret [themicroarrays] in one place.” Biologists havebeen publishing research on the functionof specific genes and proteins for years, butthere was, and still is, no easy way to searchthrough all of that information for generalpatterns.

Recognizing this need and the potential ofthe Internet, Eisen, Brown, and the thirdPLoS cofounder, Harold Varmus, NobelLaureate and then director of the NationalInstitutes of Health, set to work. The firstattempt was the 1999 creation, by Varmus’sinitiative at NIH, of PubMed Central—afree online repository for life-science pub-lications. They hoped to convince publish-ers to voluntarily submit articles toPubMed Central some time after publica-tion. The delay would allow publishers tocontinue to profit by charging customersfor newly published material, but once theresearch was somewhat dated, it wouldbecome universally accessible. With a fewexceptions, notably The Proceedings of theNational Academy of Sciences (PNAS), this wasnot terribly successful.

The next approach was to formally createPLoS, and draft an open letter to scientificpublishers. The letter, which Eisen terms

“free market research,” outlined the broaddesire among the scientific community foropen access. It was widely termed a boy-cott, and was relatively unsuccessful. Signedby over 30,000 scientists from 180 coun-tries, the letter asserted that the signerswould not subscribe to, edit, or publish injournals that did not provide their contentto a centralized repository such as PubMedCentral within six months of publication.To their surprise, the journals disregardedthese threats, and the boycott fell apart be-cause the signing scientists couldn’t affordnot to publish.

To hear Eisen tell it the journals were be-ing obtuse, failing to grasp the obviousnessof the new approach. He claims that thejournals would not have lost subscribersand could have continued in much thepresent model. He points to the physicscommunity, which for years has posted pre-prints on the website arXiv.org withoutdestroying the physics journals. Dr. Nicho-las Cozzarelli, a professor in the BerkeleyDepartment of Molecular and Cell Biologyand editor in chief of PNAS, generallyagrees. PNAS follows a hybrid model, heexplains, making content “freely availableafter six months, and immediately availableto subscribers and in third-world coun-tries.” However, he adds, “We are a break-

even journal. We don’t make a profit, norincur losses, at least hopefully.” Other jour-nals concerned with making a profit maynot be willing to take a similar risk.

Realizing that presenting the idea of openaccess and even making a threat didn’t re-shape the world of scientific publishing,Eisen and company undertook a new ap-proach. They decided to demonstrate thefeasibility of open access and of a funda-mentally new business model for scientificpublishing. They would create their ownjournals operating in an open-access, au-thor-funded system, aiming to competewith top-tier journals such as Science, Na-ture, and Cell and demonstrate that thismodel is economically viable. They hope toultimately convince all of scientific publish-ing to follow their lead. This may be a moreeffective approach. “If this is a great idea,lots of people will consider it,” says DonKennedy, editor of Science. “Every timesomething clever succeeds you look at it.”

Cozzarelli agrees: “I think this is a great idea.It’s obvious that this is the way to go. Thequestion is … how to make the transi-tion.… It is difficult for existing journalsto try this model … [but] if they succeedmany journals will follow, and many willnot.” The first PLoS journal, premieringthis October, will be called PLoS Biology, andis backed by a $9 million grant from thenewly created Gordon and Betty MooreFoundation (Gordon Moore of Intel andMoore’s Law fame is a Berkeley graduate).PLoS has also secured the editorial servicesof Vivian Siegel, the well-known formereditor of Cell.

What is different about the PLoS journalsis that authors will be charged to publishan article. Eisen says this will reverse thecurrent outdated business model of scien-tific publishing, whereby the costs are borneby the consumer of scientific information.If publishing is done on the Internet, costsare fixed, and extra copies cost no more toproduce. The research can therefore be dis-

Professor Michael Eisen is one of the cofunders of PloS. (Photo: www.PLoS.org)

Policy


tributed for free, reaching the broadest pos-sible audience, and the fixed cost is borneby the producer.

But this author fee also poses potentialproblems. While journals in some fields al-ready charge authors to publish (as well ascharging for subscriptions), the proposed$1,500 fee is two to five times higher thanstandard. In biology it is new; few biologyjournals currently charge authors to pub-lish. Cozzarelli, who sits on the editorialboard of PLoS Biology, says the fee couldmake things difficult for authors if theydon’t receive additional funding. “If, asPLoS hopes, the money currentlygiven to libraries by institutions andgranting agencies, is instead givento authors, then the model willlikely succeed,” he says. “If not,then something is lost.”

Will funding agencies agree tomake publication fees a standardpart of scientific grants? In fieldsin which the author-funded sys-tem already exists, grants tendto include publication costs. A setof journals published in Britain byBioMed Central (BMC) is alreadybased on an author-funded, open-accessmodel, but the difference, apart fromBMC being for profit and PLoS not,seems to be in their reach. PLoS, accord-ing to Eisen, intends to lead from the top.A lofty goal, admits Cozzarelli: “I thinkit would be a great success if PLoS wereas reputable as The Journal of BiologicalChemistry.” (JBC is a high-quality journal,but not the most prestigious.) BMC istaking a more grassroots approach, es-tablishing a broad stable of mostly nichepublications, from BMC Ecology and Jour-nal of Biology to Filaria Journal and BMCPalliative Care. Perhaps both approacheswill be necessary to convince other jour-nals of the feasibility of open access.Eisen is confident that PLoS Biology willsucceed in attracting top-notch research.He expects to have “about a dozen out-

standing papers” in October’s premier is-sue.

Kennedy of Science agrees that PLoS Biol-ogy “might very well become a seriouscompetitor. We welcome them into thebusiness.” However, he is not rushing toadopt the open-access model, much toEisen’s dismay. Eisen feels that Science’spublisher, the American Association for theAdvancement of Science (AAAS), shouldlead the charge toward open-access pub-lishing. He points out that AAAS is a not-

for-profit publisher

with a well-established, successful journal,and the stated mission “To advance scienceand innovation through the world for thebenefit of all people … [and] foster com-munication among scientists, engineersand the public.” For his part, Kennedy says,“It’s a mystery to me why [Eisen] is so par-ticularly critical of Science.” He explainsthat Science is very different from its com-mercial competitors, already giving awaymuch free content, and denies that Scienceis a profitable magazine, since membersof AAAS receive subscriptions as part oftheir dues. “Subscriptions and ad revenuemay exceed costs, or may not,” he notes,since it “depends on how you cost ac-count every subscriber.”

That open-access publishing is still verymuch an experiment is made clear by sev-

eral qualms raised even by supporters. Rob-ert Tjian, editorial-board member of Celland professor in the MCB department,highlights an interesting concern: if pub-lishers are being paid per article there is anincentive to publish more articles. As hesays, “The biggest challenge is to make surethat there are enough filters so that noteverything gets in. The other way to dealwith that is to charge more per paper, butthat gets back to limiting access.” On thewhole, however, he is supportive of theexperiment, and while he doesn’t knowwhether Cell will eventually follow suit, he,along with Cozzarelli, puts the final judg-ment in the hands of young scientists. “Thereal clientele,” says Tjian, “is the studentsand post docs. If [PLoS] can convince themthat it’s better to publish in the new elec-tronic journals than in Science and Naturethen they’ll have succeeded. But right nowI’m not sure what would make a studentdo that.”

Will PLoS Biology succeed? With its con-siderable bankroll and all-star cast, it isoff to a strong start. But PLoS will trulybe a success only when all scientific re-search is freely available to all scientists,without the barriers of subscription feesand fragmented, unconnected informa-tion. While that goal is still far off, openaccess may one day change the way thatscience is done.

Want to know more?

visit www.plos.orgwww.sciencemag.org

www.nature.comwww.biomedcentral.com

Ben Gutman is a graduate student in theDepartment of Plant and Microbial Biology.

Image: www.PLoS.org

Profile


Place a rectangular object—yourwallet, a small book—flat on atable in any orientation. Put your

hands on either side of it with your palmsturned inward. Now close your hands likeelevator doors on the object, allowing itto rotate and align with your hands. At thispoint you are touching either the short orthe long sides of the object. Next, releaseit, rotate your hands 45 degrees and closethem on the object again. No matter whatits initial position, your hands are now onthe object’s long sides. If you were a ro-bot, you’d be ready to pick it up.

This was Ken Goldberg’s discovery as agraduate student at Carnegie Mellon,where he proved that for any polygon,there is a series of steps like those abovethat can orient it into any position in a plane.His thesis work addressed a common prob-lem in robotics. “We tend to think that ro-bots on an assembly line are working in lockstep with perfect precision. In fact, thereare slight variations,” says Goldberg, now aCal professor in Industrial Engineering andOperations Research (IEOR) and Electri-cal Engineering and Computer Science.These variations can make a big difference.Imagining his hand as a robotic arm and acoffee cup on the table as the object to belifted, Goldberg continues, “If I grab thiscup just slightly off, sometimes it can goflying. In an assembly, it can end up jam-ming and breaking everything. I was trying

to understand how I could pick up some-thing like this cup in a reliable way.”

In his evenings at Carnegie Mellon,Goldberg extended his work with robotsinto the realm of art, putting paintbrushesin a robot’s grip and programming it topaint. In an untitled work from 1987, a blueequilateral triangle composed of large,sloppy brushstrokes painted by a robot sur-rounds text that reads, “On a square latticeat least one coordinate of an equilateral tri-angle must be irrational. An irrational num-ber has no finite numerical representation.An equilateral triangle represented on acomputer is inherently imprecise.” In awhimsical way, Goldberg addressed the in-

Jessica Marshall

At home in twocultures

GOLDBERG VARIATIONSherent imprecision of robots thatmotivated his dissertation. “I madea whole series of those triangles. Iwas interested in the repeatabil-ity—no two of them were everalike. I put them all on a wall, agrid of twelve of them, and it il-lustrated a fundamental aspect ofrobots—that they’re imprecise.”

Goldberg continued to live a dualexistence as an assistant profes-sor at the University of SouthernCalifornia, proving theorems thatextended his thesis work to newgeometries and new mechanicalsituations and creating art exhib-its involving robotic painting.“These art installations wouldtake months of preparation, andthen the exhibit would be up inthe gallery for two or threeweeks, and I’d always be fixing itand making sure it worked. It waskind of exhausting.” He continues,“When the World Wide Web came

out in 1993, there was access to data andimages on the Internet, including live cam-era images. Once I saw that, I thought,‘Oh, we can have a robot.’ Then, I thought,‘I can make an art installation that will stayin my lab, and people from around theworld can come and visit it.’”

An engineer’s drive for efficiency ledGoldberg to be the first person to createan Internet-controlled robot. He and hisstudents found a robot in the corner ofsomeone else’s lab and began working onthis unfunded “hobby.” They announcedthe result—The Mercury Project—inSeptember 1994. Users could log in anddirect the robot, equipped with a stream

Professor Ken Goldberg lives at the intersection of art andscience. (Photo: Martin Sundberg)


of pressurized air, to excavate objects thatwere buried in sand. “It took off likecrazy. We were getting thousands andthousands of hits a day on the website.”Each user was given five minutes to con-trol the robot, and at times, 20 peoplewere in line.

With the success of the Mercury Project,Goldberg raised funds to build a new andimproved Internet robot. The Tele-Gar-den, launched in June 1995, evolvedInternet robotics “from hunting and gath-ering into agriculture.” Again, thousandsof users logged in to command the newrobot to plant seeds in a nine-foot-di-ameter garden. They could monitor theplants’ growth, and direct the robot towater the plants. But the garden wasn’tbig enough to sustain the seedlings ofall of the users. “So, we’d go throughthese seasons—we’d call them hurri-canes—and we’d wipe everything outand start over. When we announced ahurricane, people would be very upset.They’d send us email and say, ‘Pleasesend me my plant; I’ll pay for the post-age,’ or ‘I’ll come to USC and pick it up.’People would email each other and say,‘I’m going on vacation, can somebody wa-ter my plants?’”

While the Tele-Garden was of scientific in-terest as an early Internet robot, Goldbergand others also viewed it as an art project.“A garden was the most absurd applicationI could think of. The Tele-Garden was a cri-tique of technology, a critique of theInternet itself, and at the same time an in-teresting look at group behavior where youhad to work with others.”

Goldberg came to Cal as an assistant pro-fessor in 1995. “Berkeley was very recep-tive to making art and doing science—youcould do both.” In 1997, he started the

monthly Art, Technology and Culture col-loquium in which artists, philosophers,computer scientists, and engineers speakon issues relating to digital media, emerg-ing technologies, and art.

Ouija 2000, which appeared at the Berke-ley Art Museum and was selected to be partof the 2000 Biennial Exhibition at theWhitney Museum of American Art, ex-tended Goldberg’s critique of the Internet,and continued to explore collective behav-ior. “People believed all kinds of thingscould happen with the Internet. It was justlike a Ouija board.” Users who logged on

to participate in Ouija 2000 were told:“When you press the red button, the Ouijaboard will materialize. Concentrate on thequestion that appears. Rest your handslightly on your mouse, and move it overthe white planchette to begin playing.Warning: many people feel that Ouijaboards summon powerful forces … ” TheOuija program averaged all of the users’mouse motions to determine where tomove the robotic planchette (the block thatslides over the Ouija board) to answer suchquestions as, “Will the human genome bedecoded this year?” or “Should [user] go ona spontaneous trip to Paris?”

Goldberg’s most recent work has focusedon the idea of “collaborative telerobotics,”which originated in the Ouija project. “I

started thinking that it would be muchmore fun to move around in a physical en-vironment,” says Goldberg. Enter the Tele-actor, a person outfitted with a wirelessvideo camera and the ability to receive in-puts by cellular phone. Internet voters casttheir ballot for what the Tele-actor shoulddo next, and the Tele-actor responds ac-cordingly. The Tele-actor debuted at the2001 Webby awards, where she interactedwith Sam Donaldson on stage under thedirection of web voters. High school stu-dents have steered the Tele-actor throughthe Berkeley Microelectronics Laboratory,

a chemistry lab on campus, and Profes-sor Michael Eisen’s biotechnology lab atLawrence Berkeley National Laboratory.Students catch on very quickly to theweb interface for driving the Tele-actor.Says Goldberg, “The first time, I bud-geted an hour to teach the kids how touse the interface, which was about 59minutes too long.” But, to keep students’interest, Goldberg and his group haveadded a “leadership score.” Students gainpoints toward their leadership tally bybeing first to vote for the move that is

the eventual favorite.

In May 2003, Goldberg and IEOR gradu-ate student Dezhen Song installed the “Co-opticon” camera on Evans Hall. The Co-opticon points toward the Stanley Hall con-struction site and sends its image to awebsite. A panoramic view of the entirefield that the camera can reach is displayedbeneath the current camera shot. Usersdrag a frame onto the panoramic shot toindicate where they’d like the camera tomove next. What makes this camera differ-ent from other “webcams” is that rather thanhandling each request in sequence—whichcan cause long queues like those in theMercury Project—the Co-opticon soft-ware computes the view that best satisfiesall of the voters who are online at a given

“It’s an ongoing challengeto take something that youhave a gut interest in andfind a way to legitimize orformalize it in a way thatit can be taken seriouslyby your colleagues.”

time. This isn’t just the average. If threepeople vote to view the far left, and twopeople vote to view the far right, the aver-age would be somewhere in the middle,which wouldn’t make any viewer happy.With the Co-opticon the three voters on theleft win that camera view. The program cal-culates a satisfaction score for each voter thatindicates what fraction of their vote was inthe camera view for that round.

Projects such as the Tele-actor and the Co-opticon use technology in exciting and un-conventional ways. But some might questionwhether they belong in an academic setting.Says Goldberg, “It’s an ongoing challenge totake something that you have a gut interestin and find a way to legitimize or formalize itin a way that it can be taken seriously by yourcolleagues.” In the case of the Co-opticon thisissue was settled by Song. “Dez was able topose the Co-opticon problem in a very nice,formal way,” says Goldberg. “That completelystrikes a chord with me because it becomes ageometric algorithmic problem.” Song pointsout that “Ken was at first hesitant to start amajor research effort in this area because it’shard to do something theoretical, on paper—something with equations. Then we startedthinking about it, and there are lots of theo-

retical things to do: how to share the camera,how to make it fast enough, and they make ittheoretically valuable.” He adds, “So, I’m notjust some boy that plays with toys. That makesme happy.”

Nor is Goldberg just playing with toys. “Ithink the jury was out for a long time aboutwhether we could find a way to really makea solid contribution out of [this work], hesays, “and now I feel like we can.” Indeed,his work with Internet robotics was recog-nized in 2001 with a Major Educational In-novation Award from the Institute of Elec-trical and Electronics Engineers.

Goldberg’s unique combination of scienceand art breaks new academic ground andraises questions about the role such projectsplay in academia. Song notes, “[Ken’s]projects are double-sided. They are digitalart, but they are also very serious researchprojects. Ken himself is a hybrid. He changesbetween artist and engineer.” JaneMcGonigal, a PhD student in performancestudies who has been the Tele-actor on sev-eral occasions, has a similar view. “The factthat he’s created space in his lab where anartist like me can work as a real member ofthe lab is an amazing opportunity. Ken is re-

ally the only person I know who’s reachingout to both artists and engineers.”

In the end, Goldberg himself doesn’tdraw such a distinction. “For me, doingresearch feels very similar to making art.Both remind me of fishing, in that theyrequire observation, experience, guess-work, stubbornness, luck, and willing-ness to throw back the little ones.” For-tunately for all of us, Goldberg catchesthe big ones pretty often.

Profile


Want to know more?

To plant in the Tele-garden, askthe Ouija a question, or checkout the construction of StanleyHall,visit:www. ieor.berke ley.edu/~goldberg/

Jessica H. Marshall is a graduate student inthe Department of Chemical Engineering

Baytech Beat

In a world wherethe boundarybetween industry

and academia isblurring, everybodycould use a little extrabusiness savvy. Toprovide that opportu-nity, each year students from the HaasSchool of Business hold the BerkeleyBusiness Plan Competition. The compe-tition draws together scientists andentrepreneurs from the Berkeleycommunity to turn innovative productideas into real-world businesses. Hostedby Haas’ Lester Center for Entrepreneur-ship and Innovation, this year’s fifthannual competition saw 58 teams vie for$70,000 in cash prizes. Over the courseof three grueling months, six teams madeit to last April’s finals, at which judgesfrom leading venture capital firms chosethree winners from a field one describedas “among the best I’ve seen.”

Bay Area company Medifuel won boththird place and the People’s ChoiceAward, a $5,000 bonus awarded byaudience members at the final publicpresentation. Using technology devel-oped in Professor Liwei Lin’s lab in theUC Berkeley Department of MechanicalEngineering, Medifuel builds batteriesfor small implantable medical devices,such as pace makers, spinal cord stimula-tors, and regulated drug-delivery

BERKELEY BUSINESS PLANS RISE TO THE TOP

Theresa Ho

systems. Other batteries currently on themarket are bulky, have a limited lifespan,and need to be surgically replaced.Medifuel’s battery is roughly the size of adime and harnesses baker’s yeast to turnthe body’s own source of energy, glucose,into electricity. Since a small populationof yeast can sustain itself by replicating,the GlucoCell™ battery is essentiallyself-renewing, and should never need tobe replaced.

Second place went to Vsee Labs, acompany that uses proprietary softwareto facilitate virtual classrooms. Bydrawing on user feedback and a five-yearvisual communication study by Vseefounder Milton Chen, the company’sdesign provides the most natural class-room setting possible. Vsee has alsodeveloped algorithms to monitorstudents and to provide high-qualityvideo streams during critical times in theclassroom. While students are takingnotes or listening passively, their imagesare updated at a low frame-rate, butwhen resolution becomes important,such as when students raise their hands,

the image becomes crystal clear. Thisallows the instructor to notice subtlenuances in a student’s question, anddetect confusion or boredom, withoutsacrificing bandwidth. The frame-ratefrugality allows Vsee Labs to use low-costPCs and still provide five times thenumber of high-quality video streams astheir competitors.

Gastric Retention Technologies (GRT)took the first-place prize of $50,000, inspite of much maligning of their nameduring the competition. Regardless ofwhat the judges may have thoughtinitially, GRT has nothing to do with gas,constipation, or vomiting. Now renamedBaroNova Therapeutics, Inc., the com-pany is developing a polymer pill thatexpands in the stomach to suppressappetite. Based on polymer technologypatented by Kinam Park at PurdueUniversity, the pill hydrates quickly onceswallowed, causing it to swell and take upspace in the stomach for about a weekbefore rapidly degrading as it enters thesmall intestine. Because the polymernever enters the bloodstream, it is


An expanding T.rex illustrates the principle of the gastric retention device (kids don’t try this at home). (Photo: Kira O’Day)

classified as a medical device rather than adrug, and is therefore able to bypass thecostly clinical trials required by the FDA.Unlike other more radical weight-lossoptions like gastric balloons or gastricbypass surgery, BaroNova aims to providean easy-to-use, non-invasive alternativefor losing weight.

Each of these winners paired a goodproduct with a shrewd business plan.Teams are judged on market opportuni-ties, their competition, and the qualifica-tions of team members, at least one ofwhom must be a Berkeley student oralum. As Ilya Entin, chair of the studentorganizing committee put it, judges are“not looking for a cool gadget, they arelooking for a product they can sell.”

To help teams sell their product, thecompetition organizes and managesseveral supplementary programs. Aseries of workshops gives students adviceon running a successful business, fromthe basics of writing a business plan to

managing intellectual property orestimating profitability. TheEntrepreneur’s Exchange acts as anonline dating service for entrepreneursseeking the right product, or a businessidea looking for the right combination oftechnical, marketing, financial, and legalexpertise. The competition is organizedto provide constructive feedback at manydifferent stages. Semifinalists areassigned mentors to guide them throughthe process. Senior venture capitalistsjudge the business presentations andprovide feedback after each round ofcompetition, allowing competitors torefine and improve their pitch as thecompetition goes on.

Several teams from previous competi-tions have founded successful businesses.Timbre Technologies, the winner of thefirst annual competition, sold three yearslater for $138 million. SkyFlow handleshigh-volume calls at contact centers forcompanies such as Apple Computer andBravanta. ZipRealty sold over $1 billion

Baytech beat


in real estate in the last year via theironline realty services. Win or lose,“There’s no such thing as a bad entrepre-neurial experience,” says Nick Sturiale,founder of Timbre Technologies. Hestarted two companies that failed beforestriking gold with Timbre. According toEntin, a main goal of the competition isto help competitors make connectionsand learn skills that will “maybe startsomething big ten years down the road.”

Preparations for the sixth annual BerkeleyBusiness Plan Competition begin this fall.Keep your eyes open—you could be partof the Next Big Thing.

Teresa Ho was a graduate student in theDepartment of Molecular and Cell Biology.

Berkeley Science Review

sciencereview.berkeley.edu

ReadWrite

Advertise

M ost people thinkdiscovery is thesole motive behind

a scientist’s work. The exhila-ration of “eureka!” aside, thereal thrill of science lies in thechase; asking the right questions and find-ing the most clever and convincing meansto answer them. “The right question” is themain focus of Sydney Brenner’s memoir,My Life in Science.

Sydney Brenner has had a remarkable life inscience. During the groundbreaking days ofmolecular biology, Brenner made seminalcontributions that we take for granted today.He demonstrated the role of messenger RNAand helped to elucidate the nature of the ge-netic code. Interested in developmental biol-ogy since childhood, he then switched fieldsand established the nematode C. elegans as animportant model organism. This “lowlyworm” has been vital to studies ranging fromneurobiology to cancer. For this effort, SydneyBrenner was awarded the Nobel Prize inMedicine in 2002. Yet, in spite of being sorespected and accomplished, Brenner remainsthe same excited scientist who arrived in Ox-ford fifty years ago. He has always been moreconcerned with solving life’s puzzles than withcreating a reputation.

Like Brenner, My Life in Science is unpre-tentious. It is the transcript of a 15-hourvideotaped conversation betweenBrenner and fellow scientist LewisWolpert, with short commentaries byeditor Errol Friedberg inserted to addstructure to Brenner’s sometimes wan-dering recollections. From his humble

beginnings in South Africa to his collabo-rations with the likes of Francis Crick and

Seymour Benzer, My Life inScience recounts the personaljourney of a scientific non-conformist.

Those who have read SydneyBrenner’s monthly commen-tary in the journal Current Bi-ology know him to be humor-ous, irreverent, and, at times,brutally honest. My Life in Sci-ence displays this same candor.Brenner is liberal with his

opinions no matter what the topic––he ad-mits to stealing a book from the library asa poor boy in South Africa, and quickly sug-gests thieving if it’s the only means to aneducation. However, what resonatesthrough the text is Brenner’s love for thescientific process. His fervor for discoveryis particularly evident in his account of theexperiment that revealed mRNA’s centralrole in protein synthesis. In order to dem-onstrate that protein synthesis required notjust DNA and ribosomes, but also an in-termediate messenger, Brenner and Jacobneeded to show that new radioactively la-beled mRNA was required for proteintranslation to occur: “… we got deliriousbecause the radioactivity curve began torise and I said in French, ‘Ascendez,ascendez. It’s rising, it’s rising!’ Then itwent on rising. And then we realized it wastime for the radioactivity to drop if the ex-periment was correct. So we were bothshouting at this machine ‘Go down, godown, down, down,’ and the next tubewent up a bit but the increase was less andI said, ‘It’s less, it’s less!’ And we were ac-tually striving to bend the numbers. Thenthe numbers came down and it was abso-lutely convincing.”

It’s equally enjoyable to read how Brennerwent about choosing an uncharted researchdirection. After participating in the first ma-jor thrust of molecular biology—its “heroic

period,” according to Günter Stent—thesubsequent years seemed to Brenner just“sorting out the details.” He wanted to usethe knowledge he had gained from genesto tackle more complex questions of de-velopment and behavior. To do so he neededto find an organism with a simplified bodyplan that was amenable to genetic research.This hunt led Brenner to the“pervertebrates,” nature’s oddities, whichto him represented exaggerations of gen-eral biological paradigms. Although manyof the organisms he tested turned out notto be representative of general developmen-tal principles, the trek through zoology’souter reaches finally led Brenner to C.elegans. Due to its rapid growth, small num-ber of cells, and straightforward genetics,the nematode quickly became an importanttool for the discovery of genes affectingdevelopment and neuronal function. Froma historical perspective it is fascinating toread about the origins of C. elegans research.But it is Brenner’s philosophical reflectionson biology and on the means needed toapproach the complex workings of life thatreally drive his narration.

Scientific wisdom aside, My Life in Science’snarrative is occasionally jumpy, and the re-counting of experiments, hypotheses, andconclusions would benefit at times frommore detailed explanations. In spite of theseflaws, and perhaps because of them,Brenner’s story is engaging. The book readsmore like an intimate conversation than ashowy memoir or a textbook lecture. Fansof Sydney Brenner and those eager to read apersonal account of the exciting days afterWatson and Crick’s discovery will enjoy thisbook. However, what you’ll read is morethan just the autobiography of a remarkableindividual. What becomes evident is the uni-versal lure of science, the thrill of asking theright question.

MY LIFE IN SCIENCEBY SYDNEYBRENNERReviewed By:Giovanna Guerrero

Book Review


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Giovanna Guerrero is a graduate student in theDepartment of Molecular and Cell Biology.

LBL's Building 88, which houses the 88" Cyclotron. (Photo: LBNL)

If you walk from the Berkeleycampus uphill along Cyclo-tron Road to the Lawrence

Berkeley Laboratory (LBL), pastthe security gates and into a eu-calyptus grove, you will findyourself at the 88" Cyclotron.The “FAQ” sheet in the lobby an-ticipates the visitor’s question, “Have [scientists] ever discov-ered anything really cool at this cyclotron?” and answers, “Well,no discoveries honored by a Nobel Prize originated here. Notyet.” Now time is running out for the cyclotron’s Nobel aspira-tions. The nuclear science facility, scheduled to close in Novem-ber of this year, has already reduced its operating schedule fromseven days a week to four and a half.

The 88" Cyclotron’s very name places it in a gradually disappear-ing scientific niche. The goal of a cyclotron is to accelerate ions—atoms missing one or more electrons—to high energies and thento collide them with stationary atoms. This cyclotron’s 88 inchesmeasure the diameter of its magnet, a number that determinesthe maximum energy to which it can accelerate ions. The name isanachronistic in an era when science is largely driven by the pushto higher energies and bigger facilities, since the 88" was not thelargest cyclotron—by more than two times—even in 1961, whenit was built. To be sure, the 88" cyclotron has at various timesbeen the nation’s or the world’s best, by one measure or another.But as Stuart Freedman, professor of physics at UC Berkeley andsenior scientist at the cyclotron, points out, with an annual oper-ating budget of five to six million dollars, “this isn’t big science;this is a small operation.”

Nuclear science in the United States has set its sights on con-struction of the next big operation, the Rare Isotope Accelerator(RIA). With the field’s federal funding stagnant, nuclear sciencecan barely afford research and development for RIA, much lessRIA’s projected cost of $1 billion. In November of 2001, the USDepartment of Energy (DOE), which provides 85% of the fundsfor nuclear science in the United States, recommended closure ofthe 88" Cyclotron if budgets were to become tight.

The committee that prepared the DOE report did not want the88" Cyclotron closed and called the possible closure “a significantloss to the nuclear physics community.” Freedman points out that“these reports are meant to be used. One way to use it is for gettingmoney: to say, ‘look at all the good research that will be lost if thenuclear science budget is cut.’” The nuclear science budget did, in-deed, increase in 2002, but the strategy failed in 2003: In Februarythe DOE announced that push had indeed come to shove, and thatthe 88" cyclotron would have to close by November.

Putting new ions in an old accelerator

Nuclear scientists like those at the 88", their title notwithstanding,do not design nuclear bombs or nuclear reactors. They leave those

GOODBYE, CYCLOTRON ROAD?Feds maydeep-six Cal’snuclear pride

Chris Weber

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tasks to engineers and a few “applied” nuclear scientists, while theyexplore the fundamental properties of atomic nuclei. Their waresare the protons and neutrons (collectively “nucleons”) that make upthe nucleus, the quarks that compose nucleons themselves, and theparticles that carry forces between them. From these particlesnuclear scientists learn about the laws that govern nature, on scalesfrom subatomic to stellar.

Freedman’s own research at the 88", in collaboration with staffscientist Paul Vetter, uses low-energy ions accelerated by the cy-clotron to study the so-called weak interaction. One of the four“fundamental” forces of nature and a linchpin of modern particlephysics, the weak interaction helps to regulate nuclear reactionsin stars, and creates the nearly-undetectable neutrinos that makeup between 10––20% of the universe’s mass. Freedman collides

the accelerated ions with atoms to create radioactive nuclei, whichthen stream directly into his “atom trap.” By monitoring the ra-dioactive decay of the nuclei held in this laser-beam trap, Freed-man and Vetter hope to discover new information about the weakinteraction.

Research at the 88" represents a branch of nuclear physics, in whichrelatively low energies are desirable—though the energies are stillhigh enough to require a cyclotron. At these energies, nuclear in-teractions lead to forms of “collective” order, in which groups ofnucleons take on strange new properties. The nucleons can formpairs that become insensitive to the interactions around them, stay-ing put while the unpaired portion of the nucleus rotates, or thewhole nucleus can assume a “super-deformed” state, elongated likea football. Low-energy ions may also be collided with target mate-rials in hopes of creating new elements—an enterprise at whichearlier Berkeley accelerators excelled, beginning with the 1940 dis-covery of plutonium by Edwin McMillan, Philip Abelson, GlennSeaborg, and Emilio Segrè using a 37" cyclotron on the Cal cam-pus. The 88" Cyclotron is now the only US facility that searches forsuch heavy elements.

None of the research in this branch of nuclear science requires thatthe cyclotron accelerate ions to especially high energies. Instead,nuclear scientists seek to accelerate ions of ever-heavier elements toabout the same modest energy per nucleon. Because a cyclotron uses

electric fields to accelerate ions, the force it can exert depends on theion’s charge––that is, on the number of electrons removed. Heavierions, being more sluggish, must have more electrons removed thanlighter ones in order to reach the same energies.

When the 88" Cyclotron first opened, available ion sources onlyallowed it to accelerate ions containing a few nucleons, like bareprotons or the nuclei of helium atoms. In the late 1960s, scien-tists at Berkeley and elsewhere invented what were then consid-ered “heavy-ion” sources: devices that could remove up to six elec-trons from elements as heavy as neon, with 20 nucleons. Posi-tioned on a platform above the cyclotron, these sources delivered

Construction of the cyclotron's 88" magnet, 1960. (Photo: LBNL)


...the small size of the 88" offers“grad-student-sized projects” thata single student can complete

The Advanced ECR ion source de-livers ions through a beamline intothe cyclotron's center, where theyare accelerated to high energies.Inset: A cartoon from the series 'Thecyclotron as seen by ... (Photo andimage: LBNL)

ions through an evacuated tube—a “beamline”—down into thecyclotron’s center. The cyclotron itself, which Vetter says lookslike a “big tuna fish can,” accelerates the ions inever-larger circles until, at sufficiently high en-ergies, they escape from the edge and stream intoone of the facility’s experiments. Operation ofthe 88" Cyclotron consists, in essence, of thisprogress of ions along beamlines from source tocyclotron to experiment.

Because new ion sources can be added to theoutside of an existing cyclotron, and can even sharea beamline with an older source, cyclotronsthemselves tend not to change, instead simply adding ever betterion sources. Each new source, allowing the acceleration of yet heavierelements to energies useful to nuclear scientists, opens potentiallynew scientific territory. In 1982 Claude Lyneis, now the head ofthe 88" Cyclotron, was sent to France to learn how to build a newtype of source that used “electron cyclotron resonance” (ECR), andthat could remove thirteen electrons from argon, an atom with 40nucleons. He recalls that in late 1984, when the ECR source he wasbuilding at the 88" passed its first test-run, the scientific demandfor the new ions was immediate and ceaseless.

Terra incognita

One of the most common uses for the accelerated ions leaving thecyclotron is to collide them with a stationary target of a knownmaterial. The energy of the collision can allow the ions’ nuclei to

fuse with those of the target or can set the target nuclei spinning. Asthe nucleus or the fused nuclear complex recovers from the colli-sion, it emits particles—gamma rays, electrons, or nucleons—thatreveal its properties. For instance, scientists at the 88" have usedthe Gammasphere, the world’s preeminent gamma-ray detector,to learn about nuclear sizes and shapes. The device proved invalu-able for investigating the collective low-energy behavior of nucle-ons in super-deformed nuclei. In fact, it “nailed” the problem, ac-cording to I-Yang Lee, the cyclotron’s scientific head, who explainsthat though nuclear scientists had already seen evidence for the ex-istence of super-deformed states, the Gammasphere allowed themto determine for what combinations of nucleons the states couldform and how long they lasted.

Nuclear scientists’ ability to probe the unknown depends largelyon the creation of new, fused nuclear complexes, but they are lim-ited by the range of isotopes available as parent nuclei. Elementsare defined by their number of protons, while isotopes of a givenelement have different numbers of neutrons. Most isotopes areunstable, shedding or transforming nucleons via radioactive decay,with half-lives ranging from milliseconds to millennia. When nuclearscientists chart the number of neutrons against the number of pro-

tons in the various nuclear isotopes, they find thatthe stable nuclei lie on a nearly straight line. Ra-dioactive isotopes typically live just off of this lineof stability, having slightly more or fewer neu-trons than their stable counterparts.

Radioactive nuclei are typically created bycolliding and combining two smaller nuclei atlow energy. Most of the smaller parent nucleiare stable, and fusion yields nuclei that are eitherstable or slightly deficient in neutrons.

Substituting radioactive parent nuclei for stable ones can allowfusion-reactions to produce neutron-rich nuclear complexes, butradioactive parents are difficult to inject into a cyclotron’s ionsource. A few laboratories, like Oak Ridge National Laboratoryin Tennessee, can accelerate radioactive ions, but nuclearcompositions with significantly more neutrons than stable atomsremain, according to Argonne National Laboratory near Chicago,“terra incognita.”

Exploring this range will require the expensive Rare IsotopeAccelerator, proposed to be built either at Michigan State Universityor at Argonne. Instead of creating radioactive ions by fusion of lightnuclei, RIA, if built, will break uranium—a heavy nucleus unusuallyrich in neutrons—into nuclear fragments. It will be morecomplicated than a cyclotron; one component will produce a beam;of ions to break up nuclei in a uranium target, while a second will

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The nuclear line of stability. Black squares show the number of protons andneutrons in stable isotopes; the yellow region shows known radioactivenuclei. RIA is intended to explore the neutron-rich region marked "terraincognita". (Image: Witold Nazarewicz, University and Tennessee and OakRidge National Laboratory)

Getting biggermay just meanleaving goodscience behind.

accelerate nuclear fragments escaping the target to energiescomparable to those used at the 88" Cyclotron. The fragments willbe radioactive, neutron-rich nuclei as heavy as silver, gold, or lead—isotopes that so far have remained out of reach.

Construction of RIA still awaits federal funding, however. Nuclearscience’s money-saving measures, such as the closure of the 88"Cyclotron, are intended only to help the field to prepare for RIA.In addition to modest increases in RIA’s research and development,the DOE report suggested increased funding for the accelerators atArgonne and Oak Ridge. The experiments at these facilities bearclosely on the nuclear science to be done at RIA, so they can help toestablish a base of scientific users for RIA. Argonne is also a potentialsite for RIA. Berkeley, on the other hand, could not host the project;the city’s politics would not accommodate an accelerator ofradioactive ions. Michael Beaudrow, a former operator of the 88",sees a further connection between RIA and the cyclotron’s closure:“When you’re asking for as much money as RIA will take, you haveto give something up to show that you’re serious about it. The 88"was the sacrificial lamb.”

Bigger and better?

Many scientists at the 88" suspect, with varying degrees oftrepidation, that nuclear science might become as centralized asparticle physics, the original big science. According to Freedman,the push toward ever larger accelerators has left that field with onlytwo facilities in the United States: Fermilab, in Chicago, and theStanford Linear Accelerator Center. He points out that until 1972nearly every university with a program in nuclear science had acyclotron or a small “tandem” accelerator. Now two accelerators—at Brookhaven National Laboratory in New York and at the JeffersonLaboratory in Virginia—consume half the budget of nuclear science.

RIA will signal the consolidation of the majority of the field’s fundinginto just three facilities.

As nuclear science prepares to consolidate its budget and personnelinto the new facility, however, some scientists believe the move willdetract from the field. To justify its funding, a big facility such asRIA must direct itself toward some specific mission and consequentlytends to cut off research in avenues that don’t bear directly on thatmission. Moreover, big projects, like little ones, can fail—but athigher stakes.

Not everybody is convinced that centralization has damaged par-ticle physics. But progress in particle physics always means workingat higher energy; and high energy, Vetter notes, is a moving target:“It just means the highest energies that you can currently reach. It’slike trying to define ‘modern.’” Higher energy means larger accel-erators, which in turn means fewer accelerators. For nuclear sci-ence, on the other hand, progress is not necessarily linked to growth.Getting bigger may just mean leaving good science behind. In fact,nuclear science already comprises problems that particle physicsleft behind unsolved.

Gathering dust

Row upon row of lights, switches, and dials cover the walls of the88" Cyclotron’s control-room, from which the cyclotron’s opera-tors run the apparatus and monitor the ion beam. The room musthave looked futuristic in 1961; now it looks gaudy by comparisonwith the banks of high-resolution screens controlling modern ac-celerators. The report that recommended “termination of DOEsupport for operations” at the 88" did not, in fact, give a reason fortargeting the facility, but speculations abound. Possibly, Vetter says,the 88" was targeted because of its age and accompanying “decrepi-

tude.” It takes several full-timetechnicians—no small frac-tion of the machine’s operat-ing costs—to maintain thevacuum and electrical systemsof the old and fussy beamlines.Vetter gestures to the top ofthe cyclotron and says, “that’s40-year-old dust on there.”

Did the 88" Cyclotron sim-ply miss its date with destinyby not working with radioac-tive ions? Actually, radioac-tive ions have been intro-duced into the 88" in a lim-


Operators Mike Johnson and Diane Riley-Cole in the the 88" Cyclotron's controlroom. On the right cartoon from the se-ries 'The cyclotron as seen by ... (Photo:Chris Weber; image: LBNL).

ited way. The ions enter the 88" after traveling for twelve secondsas a gas along a capillary tube from a medical cyclotron elsewhereon the LBL site. Medical cyclotrons cost about a million dollarseach and require only a single person to operate them. Hundredsof hospitals around the nation use them toproduce radioactive isotopes for medicalimaging. Medical cyclotrons have a limiteduse for nuclear research, however, sinceonly certain ions can be piped along thecapillary tube before they decay. More-over, Lee says, the cyclotron’s radioactive beams simply have notcome on line fast enough to contribute to preparations for RIA.Beaudrow explains that the quantity of radioactive ions that theproject could deliver, though constantly increasing, was still toosmall.

Bernard Harvey, the 88" Cyclotron’s first director, wonders whatrole element 118 might have played in the DOE’s decision. In1999, amid great fanfare, scientists from the cyclotron’s “gas-filledseparator” announced the creation of an element with 118 pro-tons, the largest ever made. But in 2001, to their great embar-rassment, they retracted the claim, having traced the result tofabricated data that one scientist had inserted among the experi-mental results. Most scientists at the 88" seem to doubt that thescandal of element 118 influenced the DOE report. On the otherhand, Vetter speculates that perhaps without element 118, LBLand UC Berkeley would have opposed the closure more vocally—though possibly still unsuccessfully.

Have experiment, will travel

The money that the DOE provides to LBL’s Nuclear Science Divi-sion supports both the operation of the 88" Cyclotron and the re-search of the division’s many scientists. Many of these scientist workat the cyclotron, but since the early 1990s some have done theirexperiments at Brookhaven, where they can accelerate ions to higherenergies. They travel for a few months each year and analyze data atLBL in the remaining months. After the cyclotron’s closure the DOEwill continue to support LBL’s nuclear scientists. But those now atthe 88", like their colleagues, will have to pack their valises andvacuum-pumps and move their experiments to a different cyclo-tron—as will the 40 to 50 scientists from other institutions whonow travel to the 88" Cyclotron each year.

Freedman’s investigations of the weak interaction will certainly suf-fer from the move to another cyclotron. Vieregg explains that theiratom-trapping apparatus, which covers several tables with mirrorsand lenses, will take several years to move and reassemble. It is ashame, Vetter says, to stop the project now, since the atom-trap hasjust begun to yield high-quality data. Most graduate students inFreedman’s group will be able to finish their experiments by thetime the cyclotron closes, but future students won’t have the op-tion of doing research at the 88". Graduate students Wes Winter

and Nick Scielzo say that the cyclotron’sready availability figured prominently intheir decisions to study nuclear science;neither student arrived at Berkeley withthe field in mind. Freedman explains thatthe small size of the 88" offers “grad-stu-

dent-sized projects” that a single student can complete. He notesthat particle physics, more centralized than nuclear science and withlarger projects, finds graduate students scarce.

Because Freedman and Vetter’s experiments ask some of the samequestions as particle physics, Vetter calls them “particle physics onthe cheap.” Certainly these little experiments strike a stark contrastwith that field’s giant accelerators and transcontinental collabora-tions. Even on the scale of the 88" Vetter’s experiment is small; farfrom needing the unusual ions that RIA will provide, this projectdoesn’t even use the full capabilities of the 88" Cyclotron’s ionbeams. Both Freedman and Vetter mention the possibility of pur-chasing a medical cyclotron in order to carry on some portion oftheir research at the 88". The scheme may work for this experi-ment, but in either case Vetter detects an absurdity in the situationof the Nuclear Science Division once the 88" closes. “If we’re anuclear science lab without a cyclotron, then what the heck are wedoing?” he says.

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Paul Vetter and postdoc Reina Maruyama with Freedman's atom-trap. Theresearchers use the atom-trap to investigate the weak interaction.(Photo: Chris Weber)

“The 88" was thesacrificial lamb.”

The fates of some researchers at the 88" are currently up in the air.Winter and Scielzo are graduating. Vieregg may forsake nuclear sci-ence for atomic physics. Vetter could also switch to atomic physics,but has other options. He could remain at LBL and travel to othercyclotrons to do his experiments, or he could move to Argonne orthe cyclotron at the University of Washington.

Unlike the cyclotron’s sci-entists, its electricians,vacuum technicians, andoperators will have nochoice but to leave the 88".Beaudrow is lucky; he’s al-ready switched from oper-ating the 88" to operatingLBL’s Advanced LightSource, an accelerator thatuses high-energy electronsto produce X-rays for a va-riety of experiments inchemistry, biology, and ma-terials science. Many of the88" Cyclotron’s technicalstaff will have to changetheir field more radically;one former operator haschosen to switch to LBL’sradiation safety program.Others could lose their jobs, says Peggy McMahan, the cyclotron’sresearch coordinator, if LBL’s demand for technical staff drops. Ac-cording to Freedman, the presence of a technical staff helps drawscientists to big facilities and even to middle-sized facilities like the88". Few universities can offer individual researchers such directaccess to trained technical people.

Science’s wealthy Uncle

Despite the DOE’s report, the 88” may not be absolutely doomed.For some twenty years, the cyclotron has sold beam time to indus-trial users interested in testing how microchips intended for use insatellites stand up to ionized nuclei streaming from the sun. Theseusers make chips for aerospace companies such as Lockheed-Mar-tin that are themselves contracted to NASA or to the military. Manu-facturers pay about $800 per hour to use the cyclotron’s beams ofaccelerated ions to simulate the solar bombardment.

Since the 88" Cyclotron began testing chips, transistors have be-come smaller, and chips have incorporated more of them. The needfor testing has steadily increased and so has industrial users’ de-

mand for beam time. Because most industrial users at the 88" areultimately contracted to DOD, the Air Force sent letters to DOE inJuly expressing concern that the cyclotron’s closure could impedenational security. Later in the month, a concrete proposal emerged:DOD would put $2 million yearly toward continuous operation ofthe cyclotron, and DOE would put in the remaining $3 million.The beam time allotted to chip-testing would rise from 25% to

50%. The DOD has good rea-son to fund the cyclotron: ifthe 88" shuts down, only thecyclotron at Texas A&M Uni-versity will remain suitable forthese tests. Many scientists atthe 88" estimate that themoney DOD saves by testinga satellite’s chips pre-launch isfar more than the cost of op-erating the cyclotron round-the-clock, seven days a week.

The success or failure of theDOD proposal could meanlife or death to the cyclotron.Moreover, Freedman pointsout, “the program of testingchips for satellites has realbenefits for everybody.”Vieregg is concerned, though,

that if the 88" Cyclotron depends on the military for funding, “itslong-term future may not be secure. It will always be competingfor money with military bases in senators’ home states.” As theBSR goes to press, nobody knows the eventual outcome of thesenegotiations. But with the closure scheduled for November, there’slittle time left for discussions. McMahan says that if the deadlinegets much closer without a decision, “even more staff will leavethe cyclotron.”

Most DOE programs are directed toward specific missions, such asdeveloping renewable energy technologies. The funds for nuclearscience, however, come from a mission-exempt category. The policy,Freedman says, has historically been to treat nuclear science “like apark—something worth preserving even though it has no practicalvalue.” The 88" Cyclotron is poised to break that pattern; its prac-tical value to aerospace is all that can preserve it now. Even if thecyclotron is saved, the clouds of consolidation are gathering overnuclear science. It’s anybody’s guess how much room there will befor small facilities under that particular umbrella.


Chris Weber is a graduate student in the Department of Physics

“The cyclotron as seen by the government funding agency.” Part of the 1967 car-toon series “The cyclotron as seen by . . . “, by Dave Judd and Ronn MacKenzie.See the rest of the series at http://imglib.lbl.gov/ImgLib/photo-archive.htmlimage: LBNL.)

Pacific chorus frog, Pseudoacris regilla, on the bird's nestfern, Asplenium nidus, which is native to tropical Asia.

© 2003 Katie Standke Photography.

AN EVENING IN THE GARDEN

Touring Berkeley’s botanical treasure

Letty Brown

Photographs by Katie Standke

I arrive at the UC Botanical Garden on a midsummer eveningjust in time for the twilight tour. Already, the group of 25botanists, gardeners, orchid lovers, and people just out for a stroll

crowds excitedly around the guide. He is Jerry Parsons, horticultur-ist for the Australasian section, a tan man in his forties whose eyeslight up as he speaks. “At kilometer 73 from Xingshan Xian, hang aleft on a gravel road, continue for 1.3 kilometers …” He is readingthe acquisition record for Rosa helenae, a plant in the Asian sectionthat was collected as seed on a 1980 expedition to China. “Fagus-Quercus-Betula forest on steep slopes. Southeast exposure. Rocky soil.Shaded forest margins.” For every plant brought to the garden, expe-dition members take detailed notes on its original location and envi-ronment. These notes are one reason that the UC Botanical Gardenis often cited as the premiere university botanical garden in the na-tion. “This is far more than just a collection of pretty flowers,” ex-plains Parsons. “Each plant has valuable scientific data associated withit.” The crowd gathers closer and starts to ask questions. Parsons leadson and the tour begins.

One of the first things I notice is that the garden is divided intogeographic regions. The plantings are organized according to theirplace of origin, in settings resembling their native habitat. As PaulLicht, the garden’s new director and former dean of the College ofLetters and Science, puts it: “Where else can you visit South Africa,Australia, or Chile in December, and some of the Mediterranean,California, or Central America, all on the same day? It’s a ratherunique setting in that sense.”

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Giant horsetail, Equisetum telmateia var. braunii, native to California.


Worlds apart

At our first stop, we come to a small pond outside the fernand carnivorous plants house. This display is maintained byParsons, and he lists some of its aquatic plants: “Cannas, cat-tails, sedges, watercress, Cruciferae, waterlilies, this one’s inthe Onagraceae, water fern, papyrus.” The garden grows pa-pyrus for Professor DonaldMastronarde of the Depart-ment of Classics and GreekLiterature. He teaches a fresh-man seminar in which studentsuse it to make paper accord-ing to ancient methods fromEgypt and Mesopotamia.

The garden is a teaching tool formany departments on campus,and the class that brings the moststudents up the hill by far is Inte-grative Biology’s Biology 1B. Eachsemester, 1,000 students pourinto the garden for two differentBio 1B labs. As we walk to the nextsection and stand between theSouthern African Section and theNew World Desert, Parsons illustrates how the garden is used toteach an important evolutionary concept. He points to the aloe plantsthat dot South Africa Hill, and then to the agaves of the New WorldDesert, plants with spiky bluish-colored whorls of leaves. “Conver-gent evolution means that different types of plants in similar envi-ronments can evolve the same types of structures. These look reallysimilar, but are in completely different families. The aloes are in theLiliaceae, the agaves in the Agavaceae.” The plants have completelydivergent flower morphologies and aloe leaves have a gelatinous in-terior, whereas agave leaves are fibrous. However, they evolved thesame leaf morphology to survive climates with long periods ofdrought. Many other plants evolved this rosette leaf shape indepen-dently, including plants in the Asteraceae, Crassulaceae, andBromeliaceae families. “Another example of convergent evolution isthe cactus family and the euphorbia family,” says Parsons. He pointsto a South African plant that looks distinctly cactus-like, but, he tellsus, is a Euphorbia. “When we go to see movies we can tell if they’vereally gone to Africa or not, because if you see anything that has acactus in it and [is] supposedly in Africa, that’s not right,” explainsParsons. “The Cactaceae, with the exception of one genus of epi-phytic cactus on the African continent, is only New World.”

Moving on past the desert section, we stop to gape at the massive

Echinopsis terscheckii, a saguaro-like cactus from the Andes of Argen-tina that stands 30 feet tall. Suddenly, within a matter of feet, weleave the desert and enter a lush forest that centers around Straw-berry Creek. The climate literally shifts around us. Before this area,known as the Asian section, was established, visiting researcher andfamous adventurer and botanist Joseph Rock recognized that itsmicroclimate matched the river gorges of western China. At the

time Rock was enroute to this region,and he later broughtback many of thesection’s earliestplants.

We wander on pastthe Japanese Pool, animportant breedinghabitat for the Califor-nia newt (Tarichatorosa), and then filealong a shaded stonepath to stop at a largeRhododendron tree.Parsons recounts see-


© 2003 Katie Standke Photography.A tropical pitcher plant, Nepenthes ventricosa, an endangeredspecies from the Philippines.

Beautyberry, Callicarpa sp., from Asia.

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.

ing archival photographs from Rock’s 1932 expedition to China, black-and-white images of carts and mule trains transporting tree rhododen-drons such as this one. Indeed, many of the garden’s 13,000 taxa wereacquired during expeditions of this sort in the mid 1930s through 1960s.Now, however, that era has passed. “Those types of expeditions are un-likely to happen in the same way they did in the thirties and fortiesbecause of bioprospecting,” explains Chris Carmichael, manager of col-lections and horticulture for the garden, “The regulatory climate haschanged and [they] would no longer be allowed.” Today, most of thegarden’s plants come from wild seed, either from seed-collecting tripsor from international seed exchanges.

Two things make the garden’s collection of particular value to science. First,each plant comes from the wild; most come from seed, and some comefrom cuttings or a seedling. Second, as Parsons demonstrated, each plant isaccompanied by very specific data on location and environment. This is ofuse to scientists who study the evolutionary relationships of plants. Parsonsexplains: “If someone is doing a treatment of the genus Rosa, they don’t haveto go to China to collect it. If they are doing, say, genetic research on it, wecan send them a sample of that material with exactly where it was col-lected.” This is no small achievement. According to curator Holly Forbes,the garden has supplied hundreds of researchers with living plant materialcollected from all over the world, and demand is expanding as botanicalresearch increasingly requires fresh material for molecular techniques. Some-times this work makes life harder for the garden. Recently the lily family,Liliaceae, was broken up into many different families. This change will entaila great deal of relabeling in the garden.

The garden is also premier among botanical gardens because of the varietyof ecosystems it encompasses, which is a result of the Bay Area climate. Di-rector Paul Licht explains: “If you’re a gardener, this is paradise. We live in agardening zone that is the envy of most of the country. It doesn’t get too hotor too cold, there are rarely prolonged frosts. What this allows us to do is togrow more different kinds of plants than other places. Missouri BotanicalGarden can be under snow six months out of the year, and it gets above 100degrees in the summer. I would guess you couldn’t grow 80 percent of whatwe grow here outside.”

Golden State treasures

Continuing along, we enter the California section, where much of the garden’sconservation efforts are focused. We pass a pygmy forest (native to theMendocino coast), a vernal pool, and an alpine fell-field, host to plants foundat elevations of 8,000 to 13,000 feet in the Sierra Nevada. We come to one ofthe garden’s rarest acquisitions, the Presidio manzanita (Arctostaphylus hookerissp. ravenii), a low-growing evergreen shrub with reddish bark. It is sometimescalled Raven’s manzanita after Peter Raven, the famous botanist, Berkeley alum-nus, and director of the Missouri Botanical garden. The plant historically ranged

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Borage, Borago officinalis, in the Crops of the World Garden.



Dudleya sp., a succulent in the stonecrop family.


Agave sp.


in scattered serpentine soils along six miles of the San Franciscopeninsula. Primarily because of development, only a single plantremains in the wild, though a few individuals survive from cuttingsof the parent plant in botanical gardens such as this one. The gardenis researching options for propagation and in the future may assistin adding new individuals to the wild. Nathan Smith, the Californiasection horticulturist, tells me, “We serve as a repository. This plantis here should the original plant be lost in the wild.” This reposi-tory function is also critical to the garden’s scientific efforts. AsCarmichael points out, “This is a scientific collection—if you loseone plant, you can’t just go down to the local nursery and replaceit. Some of them are truly irreplaceable.”

In total, the garden houses near 600 threatened or endangeredspecies (one-third of which are from California), each identi-fied by a red dot on its tag. The garden works with a number ofconservation programs for these species, including the nationalCenter for Plant Conservation, of which the garden is a partici-pating institution, and various state and federal agencies. Someof these species are especially prized in the horticultural trade.Bill Barany, the horticulturist for Southern African plants, has

been using the garden's spiral aloe, Aloe polyphylla, to obtain seedsthat will be grown for future garden plant sales. The plant is anobligate outcrosser (meaning it cannot self-fertilize), so pollenhas to be obtained from a different individual. The closest indi-viduals of Aloe polyphylla that were in flower at the same timewere in the backyard of a Santa Cruz resident, who collectedseed in Lesotho as a Peace Corps volunteer many years ago. Thisyear when the spiral aloe bloomed, Barany brought valuablepollen from plants in Santa Cruz back to the garden, painted iton the flowers with a small brush, then watched closely as theyproduced seed.

We cross Centennial Drive to visit the garden’s tallest plants,the coast redwoods (Sequoia sempervirens) in the five-acre MatherRedwood Grove. As we walk into the grove, Nathan Smith tellsme a little California trivia. “Did you know that California housesthe world’s oldest plant [a creosote bush in the Mojave], mostmassive plant [a giant sequoia], and the tallest plant [a coastredwood]?”he asks. We gaze up gaze up an example of the world'stallest species. The Mather Redwood Grove is used by ProfessorTodd Dawson of Integrative Biology who studies questions re-lated to coastal redwood distribution, which is now vastly smallerthan its historic range [see the Labscopes section to learn moreabout Dawson’s research]. He uses the garden to test sensorsthat measure variables like light, temperature, wind speed, and rela-

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Fern fiddleneck


Knobby clubrush, Isolepis nodosa from Australia and New Zealand.


tive humidity. He and his stu-dents climb some of thegrove’s 70-meter trees to in-stall the small wireless sen-sors. “[The proximity of thegarden] allows me to test newtechnology, to explore ques-tions here close to campus asopposed to in remote sites—it saves us an enormousamount of resources,”Dawson tells me one after-noon while we watch hisstudents rig ropes high inthe trees.

The garden’s research focusstems from its origins as a re-search garden for botanistson campus. Founded in 1890, it was originally located whereHaviland Hall and the Memorial Glade are today. Development oncampus and a desire to be above the atmospheric inversion layerinspired its move up the hill in the 1920s to its current location on34 acres of Strawberry Canyon. Back then, its principal functionwas to support botany instructors and researchers on campus. Itwas only in the 1960s that the garden launched a program of out-reach to the wider community. Now it is the only one of the fiveBerkeley natural history museums to be open to the public, exceptfor a small arm of the Hearst Anthropology Museum. The publichas been responsive; more than 67,000 people visit the garden an-nually. The outreach program is nationally recognized, funded byNSF and other major granting agencies, and teaches about 4,000elementary and middle school students annually. Additionally, thegarden has a team of 200 volunteers who give about 20,000 hoursannually, including a corps of volunteer plant propagators who earnmore than $40,000 a year for the garden with their plant sales. Thegarden has also earned some romantic distinctions: it was votedbest place for a first date and best place for an outdoor wedding inNorthern California, according to the East Bay Express.

A garden on guard

As Parsons’s tour continues, we walk through Australasia, an areaencompassing Australia, New Zealand, Indonesia, and the SouthPacific islands. Here we pass a plant called Gahnia aspera, a tall sedgethat bears an incredible likeness to pampas grass, the Argentinianplant considered one of the worst invaders in the state. AnthonyGarza, supervisor of the garden’s horticulturists explains that al-though Gahnia looks like pampas, the garden has found that it is not

invasive. Garza and othergarden staff work with theCalifornia Exotic Pest PlantCouncil to come up with alist of alternatives to invasivespecies that people are stillplanting in their gardens.They also keep close tabs ongarden plants that are poten-tially problematic, “weedy,”or as Garza calls them, “spa-tially inquisitive.”

The garden is well aware ofthe threat posed by invasivespecies, and the role botani-cal gardens have played in

past introductions. Now bo-tanical gardens follow many

rules when importing material. The vast majority of acquisitionsbrought in by the garden are in the form of seed, which are muchless likely to contain pathogens than plants or cuttings. In the rarecase that cuttings or seedlings are transported, all soil is removedand each plant is inspected carefully by the USDA. Parsons, whohas collected for the garden in Borneo, Costa Rica, and Ecuador,explains that the USDA has lists of prohibited plant materials thatare potential hosts for disease pathogens or are known to be“weedy.” For instance, Parsons explains, “plants in the Persea (oravocado) genus are prohibited because of a weevil found in wildavocado seed. If introduced, it could wipe out California’s entireavocado crop.”

The twilight tour is wrapping up. The sun has long since set and thetour members, fatigued from their walk across five continents, haveceased to bombard Parsons with quite so many questions. Parsonscloses the gate behind us, no doubt eager to get home, as he has tobe back early tomorrow to help chase wayward deer out of thegarden’s boundaries. We walk to our cars, leaving behind us thespectacle of desert, chaparral, cloud forest, and redwood grove, allinterwoven into one 34-acre plot of land.


Want to know more?

Visit http://botanicalgarden.berkeley.edu/

Letty Brown is a graduate student in the Departmentof Environmental Science, Policy & Management.


Echeveria sp., a succulent in the stonecrop family.

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Organic Answers to Toxic Questions

J ust after midnight on March 24, 1989, the giant oil tanker Exxon Valdez ran aground on Bligh Reefoff the coast of Alaska, spilling almost 21 million gallons of crude oil into the sea. The disastercaused an oil slick that covered 3,000 square miles and contaminated 1,090 miles of coastline along

the pristine Prince William Sound, killing thousands of marine creatures and costing Exxon $1.28 bil-lion in clean-up costs.

While it was an environmental nightmare, the Exxon Valdez clean-up was also a large—and very public—field test of a technology known as bioremediation. When skimmers and other clean-up machinerycould not handle the job, scientists at the Environmental Protection Agency added fertilizer to the beachesto stimulate the growth of indigenous microorganisms and speed the natural breakdown of the toxins,cutting the time to degrade the oil on Alaska’s shoreline from five to 10 years to an estimated three tofive years.

The high-profile clean-up efforts captured headlines in the New York Times, Washington Post, Newsweek, andother major media outlets. But bioremediation technology had been used long before Exxon Valdez ranaground for more insidious environmental disasters—gasoline leaking into groundwater from under-ground storage tanks or toxic chemicals from contaminated military sites seeping into lakes and streams.

Carol Hunter

NATURAL SOLUTIONS

The cost of clean-ing up existing en-vironmental con-tamination in theUnited Statescould be as muchas $1 tril l ion.(Photo: the Envi-ronmental MiningCouncil of BritishColumbia)


Scientists from many UC Berkeley departments and the LawrenceBerkeley National Laboratory have made significant contributionsto the field of bioremediation. Three of these scientists, ProfessorJohn Coates, Dr. Hoi-Ying Holman, and Professor Norman Terry,demonstrate the wide range of research that can be put to task inthe field, from new strains of bacteria and innovative monitoringtechniques to genetically modified plants.

Putting Nature to work

Put simply, bioremediation is the use of biological organisms toreturn the environment to its natural state. Bioremediation in theform of decomposition has been around as long as life has existed,and human civilizations have been engineering systems such as com-post piles and kitchen middens to take advantage of this naturalprocess since at least 6,000 BCE.

These days, the term bioremediation usually describes more com-plex, scientifically engineered systems that use organisms such asbacteria, fungi, and plants to process toxic chemicals into less-toxicor non-toxic forms. Bioremediation has been used to clean up pe-troleum waste since the 1950s. Because petroleum is a naturallyoccurring, organic substance, the environment is full of microor-ganisms that can degrade it and often only require additional nutri-ents or an oxygen source to accelerate the process. More recentresearch has focused on other toxins: chemical solvents, heavy met-als, and radioactive elements.

In 1980, the EPA started the Superfund Program to deal with thesetoxins by identifying and cleaning up sites that were so pollutedthey posed significant risk to the environment and public health.These sites are filled with contaminants such as vinyl chloride, chlo-roform, benzene, polychlorinated biphenyl (PCBs), mercury, lead,and others, many known to cause cancer, birth defects, and liverdamage. The program has investigated almost 45,000 sites acrossthe country and placed 1,500 sites on its National Priority List. TheBay Area is one of the toxic hotspots in the country, with 27 sites onthe Superfund priority list, including the Hunter’s Point Naval ship-yard in San Francisco, the Alameda Naval Air Station, LawrenceLivermore Lab, and over a dozen semiconductor manufacturers inSanta Clara County.

The cost of removing these contaminants chemically or mechani-cally is prohibitive. The Superfund program alone has spent around$40 billion to clean up just over half of the sites on the NationalPriority List, and, according to the US Geological Survey, cleaningup existing environmental contamination in the United States couldcost as much as $1 trillion. Many of toxins have leached away fromtheir original source, contaminating rivers and lakes as well as aqui-

fers deep underground. A 1986 survey of groundwater found that36% of more than 5,000 community water sources in the UnitedStates had organic contaminant concentrations above the maximumcontaminant levels allowed for drinking water. Once a contami-nant has infiltrated a large body of water, it is almost impossible totreat chemically. For these cases, bioremediation is the only afford-able alternative.

Bacteria to the rescue

Dr. John Coates, a new professor in UC Berkeley’s Department ofPlant and Microbial Biology, has been researching the bioremediationof one of these groundwater contaminants, a chemical known asperchlorate. Used for solid rocket fuel as well as in explosives,bleaching agents, and defoliants, perchlorate interferes with iodineuptake into the thyroid gland and can cause fatal bone marrow dis-ease and thyroid gland tumors. Because the thyroid plays an impor-tant role in development, perchlorate is especially dangerous forexpectant mothers, since the fetus could suffer delayed develop-ment and learning disabilities.

Unlike petroleum contaminants, perchlorate is not naturally foundin most environments. According to Coates, it’s only known tooccur naturally in the remote Atacama Desert in Chile. Scientistsdidn’t expect many microorganisms to have evolved a way to breakit down. “As of six years ago, there were only two known bacteriaspecies that could process perchlorate,” says Coates. “It was verypoorly studied.”

Dechloromonas strain RCB bacteria can break down two toxins, both per-chlorate and benzene, in anaerobic environments. (Image: John Bozzolaand Steven Schmitt, SIUC IMAGE Facility)

But once it was found in California drinking water in the late 1990sand recognized as a threat to public health, interest in thebioremediation of perchlorate increased dramatically. In 1997,Coates, then at Southern Illinois University, along with colleagueDr. Laurie Achenbach, began searching for more microbes that couldbreak down the contaminant. Coates first developed a selectivemedium that would screen out everything but perchlorate-lovingmicrobes. He then conducted a worldwide search for these bacte-ria in almost every type of environment, including contaminatedand pristine soils, wetlands, aquifers, lake sediments, river sedi-ments—even swine waste. “You name it, we probably looked there,”says Coates.

To their surprise, they found that these microbes were not rare, butwere ubiquitous in the environment. “We found these bacteria inevery site, even in Antarctica,” Coates says. He eventually isolatedabout 40 different species of the microorganism, all belonging tothe phylum Proteobacteria. “The Proteobacteria is very broad, withfive subdivisions,” says Coates. “This metabolic pathway was foundin four of the five subdivisions. It is very phylogenetically diverse.”From an academic standpoint, these bacteria are intriguing due totheir diversity and distribution in the environment. Some speciescan flourish in very harsh conditions, from acidic to basic, as wellhigh salinity. But their ability to break down perchlorate makes theseorganisms interesting from a practical standpoint as well.

Unlike many bacteria previously used for bioremediation, theseproteobacteria eat away at the perchlorate in an anaerobic envi-

ronment. In fact, they require an anaerobic environment beforethey will start processing the chemical. Just as animals need tobreathe air that contains oxygen to survive, many bacteria mustabsorb oxygen from their environment in order to complete theirmetabolic process and get energy from their food. But theseproteobacteria will use perchlorate as an oxygen substitute whenoxygen is not present.

In the field, engineers add a nutrient source like lactic acid to thecontaminated area, stimulating the growth of all kinds of bacteriathat quickly “breathe” all the available oxygen. Once the oxygenhas been depleted, then the naturally occurring proteobacteria willstart “breathing” perchlorate. But creating the right conditions toget things working can be tricky. If too little lactic acid is added,the bacterial growth will be limited by available food, oxygen willstill be available, and the perchlorate-utilizing bacteria won’t pro-cess the perchlorate. But if too much is added, bacteria growth willbe over-stimulated, meaning the microbial populations might munchthrough all the perchlorate and turn to other oxygen substitutes,altering the natural geochemistry of the environment. Accordingto Coates, they would first use ferric iron, which can cause a badtaste in the water as well as the accumulation of rust in pipes, thenthey would turn sulfate to sulfide, creating a nasty “rotten egg” smell,and finally they would produce methane, a greenhouse gas.

Once this delicate balance is achieved, however, the results areextremely positive. “For the field trials that have been done, per-chlorate has been completely removed to all intents and pur-poses,” Coates says. “It was immeasurable or undetectable afterstimulation in the field.” Coates is currently involved in two fieldtrials, where his lab is following the remediative process moreclosely and carefully studying the microorganisms involved.Coates also discovered that these bacteria can remediate morethan perchlorate. His lab has identified a particular strain ofproteobacteria, Dechloromonas strain RCB, that can use the pe-troleum contaminant benzene as its food source at the same timeit is using perchlorate as an oxygen substitute. Benzene is a dan-gerous, carcinogenic chemical often found deep in aquifers orsoils where oxygen is not present. Not only do these particularDechloromonas bacteria take care of two contaminants at the sametime, they are also the first organisms discovered that can breakdown benzene in an anaerobic environment.

Spying on cells

One difficulty with bioremediation is that scientists don’t alwaysunderstand what is going on in the field. As Coates puts it, there isa lot of “wait and pray” in the bioremediation business—you addbacteria or nutrients to an environment and then hope that the con-

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John Coates with graduate student Romy Chakraborty at Southern IllinoisUniversity. Chakraborty was the first person to isolate a bacterium that couldbreak down benzene in oxygen-depleted environments. (Photo: J. Coates)

centration of toxins goes down. Because of the complex systemsinvolved, it can be difficult to determine what exactly is causing achange. A team at Lawrence Berkeley National Laboratory has dis-covered a method that will take some of the guesswork out ofbioremediation. Using a technique known as InfraredSpectromicroscopy, Hoi-Ying Holman and her colleagues MichaelMartin and Wayne McKinney are able to watch the inner workingsof cellular metabolism in real time.

On most days at LBL, you can find Holman hurrying up the249 steps from her office to the experimental station insidethe Advanced Light Source (ALS)—her daily workout routine,she jokes. She rushes past other stations with long thin metaltubes wrapped in tin foil transporting X-rays from the syn-chrotron in ultra-high vacuum, and finally arrives at her ownsmall space. Specially designed optics capture the infraredbeam—extremely bright but low photon energy—from theALS, where it is bounced through a series of 20 mirrors andbeamed through a combination optical/infrared microscopeat the microscope stage incubator containing her experimen-tal microbes. The bacteria inside, magnified about 300 times,appear on a computer monitor on the table nearby, along withmasses of data showing the infrared measurements. Holmansays she’s eager every day to see what her microbes are up to.“We really get attached to our bacteria,” she admits. “I alwaysfeel bad when we have to kill them.”

But the amazing thing about Holman’s technique is that she doesn’thave to kill them at all. Most other methods of monitoring cellularmechanisms involve extracting the contents of cells, destroying themin the process, or using dyes or other agents that can affect the cellchemistry. Holman’s infrared beam allows her and her colleaguesto observe molecular reactions occurring inside cells in real-time,like a live movie. By analyzing the detailed characteristics of theinfrared absorption bands produced by different compounds,


Hoi-Ying Holman (center) with colleagues Wayne McKinney (left) and MichaelMartin (right) at their experimental station inside LBL’s Advanced Light Source.(Photo: LBNL)

Unique spectral signatures show the spatial distribution of the biological protein amide II, indicative of the indigenous microorganisms (left), at the samelocation as reduced chromium, Cr(III) (right) after a four month period. (Image: LBNL)

Holman can tell exactly what chemicals are present and what reac-tions are taking place. Initial tests with human kidney cells demon-strated that the low energy of the infrared light does not affect cel-lular functions. The brightness of the ALS beam provides a spatialresolution of 2 to 12 microns, allowing the team to focus on a smallcolony of bacteria.

Holman started working on infrared spectromicroscopy in 1997.By early 1999, she had used her new method to follow the re-duction of toxic metals among natural communities of bacteriataken from the Department of Energy’s Idaho National Engi-neering and Environmental Laboratory’s Radioactive Waste Man-agement Complex. The team monitored and studied the bio-geochemical transformation of hexavalent chromium, Cr(VI),into trivalent chromium, Cr(III), as it was occurring inside theliving system. “We were the first on the planet to watch thebacteria in action as they detoxified chromium, like a play onstage,” says Holman. “It was very exciting.”

The bioremediation of a toxic metal like chromium is very differ-ent from the bioremediation of organic pollutants such as petro-leum products or organic solvents. While these are complex or-ganic molecules that can be broken down into harmless pieces, heavy

metals are atomic structures that can not be broken down further.Instead, bioremediation uses organisms to stabilize and immobilizeheavy metals by changing their species–––by adding or removingelectrons to change the metal’s valence state. Different species ofheavy metals have different chemical, physical, and biological prop-erties that have different impacts on public health.

Hexavalent chromium, a common industrial chemical used forchrome plating, dyes, leather tanning, and wood preserving, isfound at two-thirds of the EPA’s National Priority List sites. It iscarcinogenic, mutagenic, highly soluble, and biologically active,easily crossing cell membranes and disrupting DNA replicationinside cells. Trivalent chromium, on the other hand, is consideredless dangerous because it is much less soluble and can not crosscell membranes.

At the Idaho waste site, high-level radioactive waste has beenstored for more than 40 years, creating a toxic soup of inor-ganic metallic ions like hexavalent chromium, other inorganicions, and radionuclides, as well as petroleum hydrocarbons andother volatile organic compounds. Over time, these toxins haveseeped deep into the porous volcanic rock beneath the site. Atthe time of Holman’s research, it was well known that theamounts of hexavalent chromium and other toxic metals werebeing reduced by natural processes at contaminated sites, butno one knew for certain whether this was due to a microbio-logical process or a geochemical reaction with the rocks.

To find out, Holman and her colleagues compared a sterilized samplerock under controlled conditions with another sample harboring aliving community of Arthrobacter oxydans—bacteria that effectivelyreduce hexavalent chromium. Using the ALS beam, Holman foundthat, after five days, no reduction was taking place on the sterilerock sample and only small changes were measured in the samplewith A. oxydans. But when the researchers added a weak solution oftoluene, a petroleum chemical also found at the waste site, to thecolonized sample, the infrared spectromicroscopy showed evidenceof the reduction of hexavalent chromium, as well as degradation ofthe toluene where the bacteria were located.

To make sure the results accurately reflected what would occur inthe field, Holman brought thin slices of basalt rock taken from 75meters beneath the waste site, complete with their native micro-bial communities, into the lab. She exposed them to a hexavalentchromium solution and toluene vapor and watched them carefullyunder the ALS beam. After four months, spectromicroscopic graphicimages showed colonies of bacteria at the same location as new triva-lent chromium, where hexavalent chromium had vanished. The re-searchers also saw two new peaks that they believe were caused by

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Professor Norman Terry in the greenhouse. Terry is genetically modifyingplants to remove selenium from the environment more efficiently. (Photo:Martin Sundberg)

pentavalent chromium, Cr(V), an unstable, intermediate species ofthe metal. “Some of the intermediate compounds we saw can bemore toxic,” Holman explains. “But in the past there was no way tosee them because they are only stable in live systems.”

Holman has also used her new technique to examine the role mi-croorganisms play in the detoxification of other carcinogens, thedegradation of polyaromatic hydrocarbons, and the reduction ofuranium. Her work has generated a great deal of interest in infra-red spectromicroscopy, both nationally and internationally. Holmanhas even debunked some overstated bioremediation claims madeon behalf of certain microorganisms. On one occasion she was givena sample of microbes that were supposed to be remediating con-taminated soil, but didn’t seem to be having any effect. Holman putthem under the infrared beam and confirmed that, indeed, theywere not doing anything. “They were just sitting there,” she says.“They weren’t even dividing.” She later determined that the organ-isms were meant to work in aquatic environments and were inap-propriate for their intended project, a discovery that saved a greatdeal of time and money.

Solutions from the greenhouse

Bacteria aren’t the only ones doing the dirty work.Phytoremediation—the use of plants to reduce or remove toxicchemicals from the environment—also holds great promise.Norman Terry, professor of environmental plant physiology at UCBerkeley’s Department of Plant and Microbial Biology, hasfocused his research on the phytoremediation of seleniumfor almost 15 years. He has discovered that using wetlandplants such as cord grass, salt marsh bulrush, and rabbitfootbrush can be an effective, low-cost way to remove seleniumfrom oil-refinery wastewater and agricultural drainage wa-ter. The key to his research is a mechanism in some plantsand microorganisms that can turn selenium salts into the gasdimethyl selenide—a process known as volatilization.

Selenium is a naturally occurring metalloid that is abundantin the soils of California’s central valley. The detrimental ef-fects of selenium made headlines in 1983, when scientistsdiscovered that high concentrations of selenium at theKesterson Reservoir in the San Joaquin Valley were causingdead and deformed waterfowl. But in low concentrations,selenium is harmless and in trace amounts it is actually avital nutrient.

Terry started studying how volatilization occurs in plants in1989 and found that, although the plants do not use sele-nium, the structure of selenium salt is very similar to that of

sulfate, which plants need to form vital sulfur-containing proteins.“The problem is that selenium compounds are chemically analo-gous to sulfur compounds,” said Terry, “and they tend to go throughthe same sulfate assimilation pathway in kind of a competitive way.”Because it mimics sulfur, selenium is also incorporated into sulfur-containing proteins, resulting in toxicity to plants and to the ani-mals that ingest them. But not all of these elements are stored inthe plant. Fortuitously, the same metabolic pathway that changessulfur into dimethyl sulfide gas also enables plants to change sele-nium into dimethyl selenide gas.

This chance volatilization of selenium is of tremendous benefit whenit comes to phytoremediation. Volatilization takes selenium out ofthe contaminated environment—the sediments, the water, and thebiomatter—and puts it into the atmosphere. Eventually the sele-nium will come back down to earth, but since it is only harmful athigh concentrations, this is generally not a problem. “Volatilizationof selenium is an excellent way of cleaning it out of the systembecause it takes it completely out of a local area and puts it in an-other area where probably it’s going to be helpful rather than hurt-ful,” says Terry. “Toxicity spots are very, very localized. In the caseof California, if it comes down somewhere else, chances are it willcome down in an area that is suffering from selenium deficiency.”

Terry got his first field test of selenium volatilization in 1995 on anexperimental wetland in Richmond run by the Chevron Corpora-tion. The oil company had determined that their 35-hectacre marsh

This experimental wetland in front of Chevron’s Richmond oil refinery can reduce theamount of selenium in the refinery wastewater by about three quarters. (Photo: PaulKagawa/Chevron)


was successfully reducing the amount of selenium in its refinerywastewater by about three quarters, but the accumulation of con-centrations in the sediments and plant biomatter could only ac-count for about 70% of the missingselenium. They called in Terry to seeif volatilization could account for themissing metalloid. Using smallPlexiglas chambers on meter-squaretest plots in the wetland, Terry andhis colleagues were able to capturedimethyl selenide being releasedfrom the plants and show that theplants and microbes were indeedvolatilizing at a healthy rate. The re-search found that as much as 10–30% of the selenium could be vola-tilized from the marsh.Terry thought that if wetlands couldhelp remediate oil refinery water,they could probably help out with ag-ricultural water in California’s Cen-tral Valley as well, where heavy irri-gation causes selenium to leach outof the soil and into the drainage wa-ter. After the Kesterson disaster,farmers were no longer allowed toflush water into drains and insteadwere forced to use huge evaporationponds, which can be as large as 300hectares. As the water evaporates, itleaves behind highly concentratedtoxic salts.

In 1996, Terry’s team joined the UCSalinity/Drainage Program—a jointresearch project involving scientistsfrom UC Berkeley, Davis, and Riv-erside as well as the Tulare Lake Drainage District in Corcoran,CA. The researchers set up 10 quarter-acre wetland cells in theCentral Valley and planted them with species such as cord grass,salt marsh bulrush, and rabbitfoot grass. Terry’s research showedthat the miniature wetlands removed an average of 69% of the sele-nium from the inflow, with most of that being stored in the sedi-ments. But volatilization was also occurring, especially among cer-tain plant species. The team found that in one summer month, thetest wetland cell filled with rabbitfoot grass volatilized nearly halfthe selenium entering it.

Terry sees enormous potential in using engineered wetlands to re-duce the selenium concentration in agricultural drainage water. Buthow would these experimental marshes avoid turning into another

environmental disaster likeKesterson? One major difference isthat the filtering marsh would be aflow-through system instead of aclosed system like the Kesterson res-ervoir. “In Kesterson, you were justpouring selenium in and giving it no-where to go,” Terry explains, “whereaswith the flow-through systems you’retrying to filter it out, but you’ve got aconstant flow of water through there.That stops the selenium from build-ing up to super-high levels.” As partof a bioremediation project, the marshwould also be carefully monitored.Once the sediments and the plantsbecame saturated with selenium, themarsh would have to be dried out, theselenium-filled plants mowed down,and the sediments either dug up andhauled away as toxic waste orremediated further with more sele-nium-tolerant plants.

Terry is trying to develop new su-per-selenium-loving plants using ge-netic engineering. “The problem isthat plants at present work kind ofslowly. It would take quite a fewyears for them to really significantlydraw down the selenium pollutionin the soil,” he says. “What you wantis to genetically engineer plants thatwill rapidly speed up this process, so

instead of taking 10 years or 50 years or 100 years to do it, youwant them to do it in 2 or 3 years.”

Terry has spent the last eight years genetically engineering plantssuch as Indian mustard (Brassica juncea) to tolerate, accumulate, andvolatilize high levels of selenium, using genes from E. coli bacteriaor other plants such as Arabidopsis. He is currently conducting thefirst field trials in the United States of plants genetically modifiedfor phytoremediation, using genetically enhanced Indian mustardto remediate highly contaminated agricultural drainage sedimentsin a joint project with the US Department of Agriculture in Parlier.

Marsh plants like this rabbit foot grass (Polypogon monspeliensis)are very successful at removing selenium from the surrounding water.In one summer month during their research project in Corcoran,CA, Terry’s team found that the test wetland cell filled with rabbitfoot grass volatilized nearly half the selenium entering it. (Photo:Elkhorn Slough Foundation)

Feature


Terry has also been working with a plant called Astragalus bisulcatusor the two-grooved poison vetch—a small, slow-growing plant fromthe North American prairies that tolerates and accumulates ex-tremely high levels of selenium. His team has identified one of thegenes that give Astragalus bisulcatus its high tolerance for seleniumand has transplanted this gene into Arabidopsis and the fast-grow-ing, high biomass Indian mustard.

“What we will eventually do,” says Terry, “is to use the genes thatwe got from Astragalus bisulcatus and combine them with the genesthat we’ve gotten from these other places and pop them into thesame plant, trying to create kind of a super plant forphytoremediation. That’s the goal.” He hopes that, using geneticengineering, he will be able to create plants that can take up 10 to100 times as much selenium as natural plants, greatly enhancingthe chance for making plant-based remediation systems functionquickly and economically.

The future of bioremediation

Over the last 10 years, significant scientific advances have been madein the field of bioremediation thanks in part to scientists like Coates,Holman, Terry, and others at UC Berkeley and Lawrence BerkeleyLabs. Chemicals that were previously believed to be persistent inthe environment can now be broken down or contained throughproven bioremediation techniques. Bioremediation has moved far


Want to know more?

Environmental Factors That Control Microbial Perchlorate Reduction, K Swades et al., Applied Environmen-tal Microbiology (2002); Vol. 68, pages 4425–4430.

Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains ofDechloromonas, JD Coates et al., Nature (2001); Vol. 411, pages 1039–1043.

Microbial Reduction of Hexavalent Chromium:http://www-als.lbl.gov/als/science/sci_archive/bioremed.html.

Selenium Removal by Constructed Wetlands: Quantitative Importance of Biological Volatilization in theTreatment of Selenium-Laden Agricultural Drainage Water, Z-Q Lin and N Terry, Environmental Science &Technology (2003); Vol. 37, pages 606–615.

Carol Hunter is a second-year graduate student atthe UC Berkeley School of Journalism.

beyond its initial application to petroleum contaminants to theremediation of organic and inorganic solvents, heavy metals, andradionuclides. Scientists hope that bioremediation will soon be suc-cessfully applied to the complex mix of toxics commonly found atwaste disposal sites and Superfund National Priority List sitesthroughout the United States.

There are still many questions to be answered in the field ofbioremediation—whether to use genetically modified organisms,when to add organisms to an area at all, and when regulators cansimply sit back and monitor, letting nature take its course. Buteach year of research brings new discoveries and a better under-standing of the hydrology and biogeochemistry of contaminatedareas, of new species of microorganisms with unique metabolicpathways to break down toxins, and of the various environmentalconditions such as oxygen level, pH, and available nutrients re-quired to make these microorganisms function. Bioremediationis no silver bullet, but it is an important tool, offering a rapid,cost-effective, and environmentally friendly way to clean up con-taminated environments.

Before I left civil engineering professor Jack Moehle’s office,he had broken a piece of chalk, bent a paper clip back andforth repeatedly, slowly torn a piece of paper, squished an

eraser between his fingers, and jiggled a disconnected computerpower cord. While it might sound like he has a fidgeting problem,each of these acts illustrated a seismic design principle.

UC Berkeley’s proximity to the Hayward fault—which runs throughsection KK of Memorial Stadium—gives campus buildings a po-tential “fidgeting problem.” Since 1997, when the university allo-cated $1 billion over 20 years for seismic safety projects, the cam-pus community has been acutely aware of efforts to protect campusbuildings from earthquake damage; the jack hammering and chainlink fences are hard to ignore.

So, what’s the matter with these buildings? Many of the campus’soriginal buildings are made of stone or brick. These notoriouslybrittle materials perform so poorly in earthquakes that Californiabanned un-reinforced masonry construction in 1933. Campus build-ings built in the 1950s and 60s are also seismic offenders. “Theengineering aesthetic in the 1960s was beautiful minimalism,”says architecture professor Stephen Tobriner, a historian of seismicconstruction. “However, in earthquakes, what you really want isnot the slightest, lightest, most minimal structure, but somethingthat has redundancies.”

Jessica H. Marshall

FAULTY TOWERSShoring up the foundations of excellence

According to Moehle, who also directs the Pacific Earthquake En-gineering Research Center, engineers in the 1960s “didn’t reallyappreciate how big the forces during an earthquake could be. Theythought the design load was maybe one-tenth of what we now knowit to be.” Most of the 1960s-era buildings are made of reinforcedconcrete. They bear the load of gravity well, but the reinforced-concrete designs of the time were not sufficiently reinforced to re-sist earthquakes. Moehle demonstrates with a piece of chalk: whilethe chalk can withstand significant vertical pressure, it snaps easilyunder a horizontal force.

University


A shear wall partiallycovers the end ofLatimer Hall. Thebuilding’s face carriesa new frame: a fewfeet of reinforced con-crete that follows thebuilding’s originalrectangular-grid struc-ture. (Photo: KarenLevy)

Professor Moehle points out a damper in the bracing onHildebrand Hall. The damper allows the brace to change lengthduring an earthquake without buckling. (Photo: Karen Levy)

Not surprisingly, many of these minimalist, reinforced-concretestructures were rated as “very poor” when the university evaluatedthe seismic safety of its buildings in 1997. The evaluation showedthat 27% of the square footage on campus needed retrofitting. Atthe time of the report, buildings including South Hall, Wheeler,Dwinelle, Doe Library, and the Unit 1 and 2 Residence Halls hadalready been retrofitted. Since then, 2.4 million square feet havebeen retrofitted including Barker, Barrows, Hildebrand, Latimer,and Wurster Halls. These retrofits cost $700 million and representonly half of the area identified in the 1997 evaluation.

An additional 950,000 square feet and $301 million are slated forretrofitting in the next five years, including this past spring’s demo-lition of Stanley Hall and the scheduled demolition of the northside of Davis Hall. Both buildings will be rebuilt. The final 1.4 mil-lion square feet of retrofitting may take a while, since it is distrib-uted over 70 buildings on central campus and at outlying sites.

The cost of retrofitting is high, but so is the potential cost of seis-mic damage. According to architecture professor Mary Comerio’s2000 report, “The Economic Benefits of a Disaster-Resistant Uni-versity,” the campus could sustain losses from $600 million to $3.5billion depending upon the size of an earthquake. The higher costwould result from an earthquake of the size expected to occur nearBerkeley once every 1000 years.

In the face of such low probability but such high stakes, the univer-sity must decide what retrofitting standard is good enough. Retro-fitting designs are tested against two hypothetical earthquakes. Thebuilding is designed not to collapse in the case of the larger earth-quake, of a size expected to occur every 2000 years. For an earth-quake recurring with a 500-year period—equivalent to 7.0 on theRichter scale centered on the Hayward fault—the retrofit is alsodesigned to protect “life safety.” For instance, secured objects shouldremain secured, and not fall on people.

The retrofitting projects completed since 1997 have undoubtedlymitigated the potential damage, but the cost of direct physicaldamage may be the least of the university’s concerns in the eventof a large seismic event. Comerio’s report also noted that 75% ofUC Berkeley’s research funds from corporations and the federalgovernment are spent in just seventeen buildings, and that half to

three-quarters of the space in those buildings is “likely to be sig-nificantly damaged or closed after a major seismic event.” Thereport continues that such damage would “seriously disrupt ex-isting research and limit the capacity to take on new research fora long period.” Would faculty leave under such circumstances?

Moving and shaking

While much retrofitting design is done using computermodels, “real-life tests” are done here on campus. Struc-tures are tested on the second floor of Davis Hall, situatedon a “strong floor”—the top of a very rigid box, onestory tall, built down into the floor below. Structures(beams, columns, etc.) can be bolted to this floor. Gianthydraulic actuators attached to the strong floor can pusha structure with forces of the same magnitude found in anearthquake. The floor’s stiffness minimizes its absorptionof energy, so the element being tested receives the fullinput energy of the earthquake. Through these tests, re-searchers can find out how the structure breaks and whatmakes it tougher.

At the Richmond field station, a 20 by 20 foot shakingtable is used to simulate earthquakes in “real time,” andto test the performance of structures in the simulated earth-quakes. A computer tells actuators underneath the tableto push the table in a particular pattern to mimic a pre-scribed earthquake’s motion. The table can move up toeight inches (though a real earthquake can move farther)and is surrounded by a rubber bladder. The size of thetable means that test structures are not built to full scale.Since a building’s response depends on the axial load oncolumns, and since length and volume scale differently,weight must be added to the tops of structures so the ratioof size to mass matches that of a real building. The shaketable has been used to compare the performance of athree-story wood-framed apartment building with andwithout seismic retrofitting braces. It has also been usedto test reinforced-concrete columns that support a six-storyoffice building. To determine how the contents of a build-ing will behave during an earthquake, a wet lab wasbuilt on the shake table, complete with shelves, benches,refrigerators, and equipment, including the typical an-choring devices used in labs.

While it might sound fun to stand on the table and expe-rience an earthquake in a controlled setting, it’s not al-lowed. The shake table is capable of generating a shockthat could break a person’s legs!

http://peer.berkeley.edu/~elwood/research/shake_table.htm


“The last picture wewant on the news is theCampanile collapsed.”

Would students? The potential impact on Cal’s academic standingis difficult to quantify.

Retrofitting 1A

A number of retrofitting tools have been used to ensure that cam-pus buildings can stand up to earthquakes. Steel braces strengthenCal’s residence halls, and reinforced concrete shear walls stiffenthe ends of Barrows, Latimer, and Wurster Halls. An entirely newframe of reinforced concrete, like a strong exoskeleton, supportsthe north and south faces of Latimer Hall. Much of the interior ofSouth Hall was removed and con-crete walls and steel anchors werebuilt on the interior. Comerio sum-marizes campus-retrofitting strate-gies this way: “You can put a build-ing in a cage, as in the case of University Hall. You can put a cageinside the building, as in the case of South Hall. In the case ofWurster and Barrows, they grabbed the building on either endand stiffened the ends a lot.”

All of these retrofitting approaches are designed to stiffen the build-ing, reducing the amount that it sways in an earthquake. While stiff-ening a building makes it able to resist larger forces, it makes for arougher ride in an earthquake: the contents of the building, oftenincluding expensive equipment or hazardous materials, will shakeharder. Stiffening also reduces the building’s natural period of vi-bration, typically bringing it close to half of a second. Coinciden-tally, the largest forces of an earthquake tend to occur at this pe-riod. So, while a stiffer building is stronger, it experiences largerforces than a “softer” building. The goal, then, is to stiffen a build-ing, but not too much.

Brittle building elements, like the insufficiently designed reinforcedconcrete columns of the 1960s, can be protected by jacketing themwith “shotcrete” (a sprayable concrete), steel, or fiberglass. Jacketsprovide tough skins; even if a crack develops internally, the struc-ture will be held together by the jacket. Jacketing does not changethe stiffness of the building; it just makes it better able to withstandthe damage that an earthquake doles out. Fiberglass sheets—simi-lar to casting material—were tightly wrapped around columns inthe interior of Wurster Hall.

The choice of a retrofitting design balances cost, ease of installa-tion, aesthetics, and historical importance. Steel braces leave win-dows relatively unobstructed, but are very noticeable. Reinforcedconcrete walls and new frames can be designed to fit into a struc-ture well, but they often block light. Jacketing doesn’t change thefloor plan of a building since there are no new walls or beams to

contend with. On the other hand, it can be cumbersome to imple-ment, and because it covers the building’s surface, it is often inap-propriate for historical buildings.

Another way to improve a building’s performance is to reduce itsmass by removing stories. Naturally, story removal is not popularsince square footage is typically scarce, especially at Berkeley. Eventemporary loss of square footage disrupts campus operations—afact that plays a major role in the choice of a retrofit design. Inte-rior retrofitting plans often require that occupants relocate duringconstruction, which can be costly—state retrofitting funds do not

cover these costs—and logisti-cally difficult. Barrows andLatimer Halls have very high oc-cupancy, and for both buildingsan exterior retrofit plan was

chosen, allowing the building to remain fully, if not happily, occu-pied throughout the retrofit project.

The high density of campus buildings also constrains retrofittingoperations. Lay-down space for construction materials is scarce,and it can be difficult to bring in large equipment. When diggingholes for pilings to support Wurster Hall, engineers hit rock. Therock-boring equipment would not fit on site, so one of the holeshad to be dug by hand. “There was one guy with a bucket and shovel,”says Comerio, “He literally dug and sent the dirt up in a bucket,while shoring the sides as he went. It took about two months.”

Hearst Mining Building: A masterpiece of architecture—and of seismic retrofitting

In the 1970s, Berkeley civil engineering professor James Kelly pio-neered base isolation, a major innovation in retrofitting design. Thisapproach to protecting a building makes it less stiff: it is set atop“base isolators,” which are essentially giant pencil erasers that allowthe entire building to slide back and forth. The base isolators in-crease the period of the building’s oscillation to much longer thanthe half-second typical of an earthquake’s largest motions. The HearstMining Building, the only base-isolated structure on campus, has aperiod of around 2.75 seconds. Hal Davis, an engineer at Ruther-ford and Chekene, the engineering company responsible for retro-fitting the Hearst Mining Building, says that in an earthquake thebuilding “moves very slowly and deliberately back and forth.” But itmust go a long way to move so slowly: Hearst Mining Building isdesigned to move up to 30 inches.

The Hearst Mining Building was designed by John Galen Howard,the architect responsible for many early campus buildings, and islisted as a national landmark by the American Institute of Archi-

University


Hearst Mining Building is designedto move up to 30 inches.


Top Left: The ceiling of the main hall of the HearstMining Building, an American Institute of Architects'national landmark.(Photo: William Porter)

Top Right: Installation of steel braces and dampersto stiffen Hildebrand Hall. (Photo: Jack Moehle)

Bottom Left: One of 134 rubber base isolators onwhich the Hearst Mining Building rests. (Photo: JackMoehle)

Bottom Right: The "moat" surrounding the HearstMining Building allows space for the building tomove up to 30 inches.(Photo: Karen Levy)

tects. Its masonry construction made it particularly susceptible toseismic damage, and according to Davis, there was no way to stiffenthe building, inside or out, without affecting its architecture. TheHearst Mining Building’s historical importance led the Universityto spend $90.6 million to retrofit it.

To install the base isolators, workers first “dug out a big bathtubunderneath the building, and shored up the building using pipecolumns,” says Moehle. Then they built a new,heavily reinforced foundation on the bottom ofthe “bathtub.” They installed 134 rubber isola-tors on the foundation, and removed the pipecolumns, transferring the building’s weight ontothe isolators.

Moehle turns a white rubber eraser on end todemonstrate how the flexibility of the rubber al-lows the bottom of the base isolator to move in-dependently of the top. “You can see how thiseraser can wiggle back and forth in the horizon-tal direction. However,” he adds, “if you squeezeon it in the vertical direction, it tends to bulge.”Because these isolators support the entire weightof the building, whether it’s shaking or not, theisolators were built in layers, alternating steelplates with rubber slabs to prevent bulging, andencapsulated in rubber. The resulting isolators areeach 40 inches across, 18 inches high, and weigh4,500 pounds.

Because the Hearst Mining Building is so closeto the fault, engineers at Rutherford andChekene feared that the building might displacemore than the allowable 30 inches in a largeearthquake. Workers installed big, horizontal hy-draulic pistons, like the shock absorbers on acar, connected at one end to the “bathtub foun-dation” and at the other to the building. In anearthquake, part of the foundation’s lateral en-ergy will be dissipated into the fluid in the pis-ton, reducing the displacement of the building.The dampers dissipate this energy as heat, andcould reach 120–150oC. According to Davis, theuse of dampers in a variety of situations is a realimprovement in seismic engineering over thelast several years. For instance, in HildebrandHall dampers were installed in steel braces, al-

lowing the brace to change its length during an earthquake, ab-sorbing earthquake energy without buckling.

Founded safe

If retrofitting the Hearst Mining Building is worth $90.6 million,what about Cal’s signature structure, the Campanile? The 1997 seis-mic evaluation rated it “poor” and estimated that it would cost $4

University


Oh, where does all the money go?

Seismic damage could pose a greater danger to Cal’s research than to itsstudents. Comerio’s report, “The Economic Benefits of a Disaster-ResistantUniversity,” found that the funds with which corporations and the federalgovernment sponsor UC Berkeley’s research are concentrated in just a fewbuildings. Fully three quarters of these funds go to the seventeen buildingsbelow. The top seven buildings house half of sponsored research.

Building

Cory 31.12 FairLSB Addition 21.53 GoodKoshland 17.06 GoodSoda 12.73 GoodHildebrand 7.78 Very Poor

3

Warren 7.74 PoorBarker 7.42 Retrofit in progressEtcheverry 7.26 GoodLatimer 6.87 Poor

3

University 6.02 Already RetrofittedDavis (old, new) 5.36 Fair, PoorStanley 4.16 PoorDonner Lab (old, new) 4.14 Good, PoorVLSB 3.86 GoodMclaughlin 3.30 PoorMorgan 3.01 GoodTolman 2.88 Poor

* For 1994–99, in 1999 dollars.

1 Mary C. Comerio, “The Economic Benefits of a Disaster Resistant Univer-sity: Earthquake Loss Estimation for UC Berkeley” (April 1, 2000). Instituteof Urban & Regional Development. IURD Working Paper Series. PaperWP-2000–02. http://repositories.cdlib.org/iurd/wps/WP-2000-02.

2 Seismic Action Plan for Facilities Enhancement and Renewal. Universityof California, Berkeley (1997).http://www.berkeley.edu/SAFER/ .

3 Retrofitted since 1997.

Sponsored Research*1

(Million $)1997 Seismic Rating*2

million to retrofit. Its low occupancy, though, puts it low on the listof retrofitting priorities. Looking out his Davis Hall window at theCampanile, Moehle says, “I think it’s pretty safe. It has a masonrystructure, but it’s got a steel frame.” Even so, “it’s such a symbol,”says Comerio. “The last picture we want on the news is the Campa-nile collapsed.”

The flurry of “seismic activity” on campus might lead one to thinkthat until recently, the University ignored its shaky location just afew hundred feet from the Hayward fault. Actually, earthquakes werea concern during the construction of Cal’s first building, South Hall,a fact that came to light as the seismic retrofitting of South Hallproceeded in the 1980s. Engineers discovered that the brick struc-ture was heavily reinforced with iron. According to Tobriner, “Thiskind of reinforcement was exceptional and very peculiar. It revealedbeyond a doubt that the original architect, David Farquharson, hadattempted to build a seismically resistant brick structure in 1870.”The first regents insisted on such a building after seeing the damagecaused by the 1868 earthquake. “One of our first cares,” they wrote,“should be to make our buildings as safe as possible for the youthswho may be confided in our charge.” Armed with modern under-standing and new technology, the University may now be makinggood on the regents’ directive.


.Jessica H. Marshall is a graduate student in the

Department of Chemical Engineering


Quanta (heard on campus)

"If you never want to be criticized and never want to makea mistake, never do anything in science."

Norman Borlaug, 1970 Nobel Laureate, Peace PrizeJuly 10, 2003"The Story of Norman Borlaug: 60 Years Fighting Hunger"Lecture sponsored by College of Natural Resources

"We cannot repeat the early universe due to severefunding limitations."

Boris Kayser, Fermi National Accelerator LaboratoryApril 14, 2003"The Neutrino World: Present and Future"Department of Physics Colloquium

"Most of your experiences are miserable. You wouldn't want to put theminto long-term memory. Like the boring lectures you hear—who wants toremember this tomorrow?"[Commenting on why organisms evolved mechanisms inhibiting thetranscription of experiences into long-term memory.]

Eric R. Kandel, 2000 Nobel Laureate, Physiology or MedicineApril 23, 2003"The Long and Short of Long-Term Memory: Memory and Its Disorders"

Lecture sponsored by Helen Wills Neuroscience Institute

"My God, you're disrespectful! That's good."

Ignacio Chapela, Department of Environmental Science, Policy & ManagementAugust 20, 2003Graduate student orientation keynote address

Love,

Nathan

Dear Mum,

“The New York Air National Guard bringing us in.”

“Ryan deployingthe dust logger.”

“Me with the Tucker SnoCat.”

The Backpage

(Photo: Nathan Bramall)

Nathan Bramall is a graduate student in physics at Cal,

working with Buford Price. They do their research in

Greenland and on the Antarctic ice sheet. It keeps him

pretty busy, but he still has time to write home to mom.Guess what? Ryan Bay and I are at Summit Camp on top of Greenland’s ice sheet (72° 34’N 38° 29’W)!

We’re here to deploy our “dust logger” to detect dust and volcanic ash within the ice. We lower it three kilometersdown a six-inch-wide borehole and it emits light into the ice. A phototube detects how much of that light isscattered back by the dust and ash, telling us about the earth’s past climate. The ice is layered like sediment, withthe oldest climate record near the bottom of the hole.

It’s a bit warmer here than you might think, but it can get cold! Taking data the other night was the worst,as the temperature was -35°C with a sustained 20–25 knot wind and ice fog. Brrr. We had to stand outside onscaffolding all night and the next morning. Afterwards, I was glad to collapse in my Arctic Oven, sort of a sturdy 4-season backpacking tent. It may sound uncomfortable, but I’ve been sleeping like a baby on top of these threekilometers of snow and ice. It’s so peaceful and quiet! Well … except for the other night when a little storm cameup and buried my tent—excavating snow in the midst of a blow during the wee morning hours isn’t much fun.

Summit Camp houses seven staff and about a dozen scientists, who are all very cool and a bit quirky. Thecamp cook was trained as a pastry chef so she makes sure that we always have at least one dessert for every meal!Despite the cold and hard work, I’m actually packing on a few pounds. To help out with chores, I’ve become the“water boy,” which means I’m responsible for the camp’s water supply. Waste heat from the camp’s diesel generatormelts snow into potable water. I shovel mounds of snow into a hopper, let it melt, and transport the resulting waterto the main holding tank using a snow machine attached to a sled-mounted, 200-gallon container.

Of course it hasn’t all been hard work! The other day we had a fourth of JulyBBQ, complete with volleyball and booze! I can’t remember who won the game, but Ivaguely recollect a few Bloody Marys …

Berkeley Science Review - Fall 2003

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