berkeley science review - fall 2006

8/6/2019 Berkeley Science Review - Fall 2006

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BERKELEY

Fall 2006 Issue 11

The Aftermath of KatrinaStrung Out at Berkeley

Sciences Baby Gap

Plus: Quick Facts About QuicksandStanley Hall Sneak PreviewA Metamaterial World


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{READWRITECONTRIBUTE}sciencereview.berkeley.edu


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Editor in Chief

Michelangelo DAgostino

Managing Editor

Wes Marner

Art Director

Andrew DeMond

Copy Editor

Graham R. Chequer

Editors

Meredith Carpenter

Jacqueline Chretien

Wendy Hansen

Jessica Porter

Tracy Powell

Merek Siu

Layout EditorsJacqueline Chretien

Wendy Hansen

Matthew de la Pea Mattozzi

Jessica Porter

Kathryn Quanstrom

Contributing Artist

Jennier Bensadoun

Printer

Sundance Press

2006 Berkeley Science Review. No part o this publication may be reproduced, stored, or transmitted in any orm without express permission o the

ublishers. Financial assistance or the 2006-2007 academic year was provided by Lawrence Berkeley National Lab; the UC Berkeley Oce o the Vice

Chancellor o Research; the College o Natural Resources; the UC Berkeley Graduate Assembly; the Space Sciences Laboratory; the UC Berkeley Oce o

esearch and Development; the Associated Students o the University o Caliornia (ASUC); and the Department o Mathematics. Berkeley Science Review

s not an ocial publication o the University o Caliornia, Berkeley, or the ASUC. The content in this publication does not necessarily refect the views o

he University or the ASUC. All events sponsored by the BSR are handicapped accessible. For more inormation e-mail [email protected]. Letters

o the editor and story proposals are encouraged and should be e-mailed to [email protected] or posted to the Berkeley Science

eview, 5A Eshelman Hall, Berkeley, CA 94720. Advertisers: contact [email protected] or visit http://sciencereview.berkeley.edu

D e a r r e a D e r s ,

Whn th wi ld o th Berkeley Science Review gthd und th cov o night in thi hoodd

blck ob to noint m th nxt edito-in-Chi, my t intinct w to tun til nd un. Fotuntly,

thy hd lockd th doo.

at t glnc, mbling om 50 pg o t cl cinc contnt md lik quit dunting tk.

Luckily, th BSR cck tm o dito nd lyout t hv cicd countl hou cnking out

noth iu o Bkly bt gnl intt cinc mgzin (xtnding thi gdut c in th

poc)

With ll thi hd wok, Id vntu to y tht Iu 11 i on o ou bt yt. eic spotwood tll

u bout Bkly ol in invtigting th ilu o th Nw Oln food potction ytm duing

huicn Ktin (p. 33). Mdith Cpnt tk dp look into th wold o thoticl phyic

nd th ol Bkly i plying in unvling th bll o ting tht my jut b ou univ (p. 28).

a you ding thi iu o th BSR in you cmpd bmnt lb, quzd btwn th lbmt

nd th tog clot? rli i on th wy, Tcy Powll xplin in h nk pviw o th oon-

to-b-opnd stnly Hll nd LBL nw Molcul Foundy (p. 21). Ltty Bown tll u bout Bkly

ch who buy in th ld ogin o pci (p. 25). and nlly, Loui-Bnoit Doch

v up th ltt in hi Who Knw? i (bck cov). Myb you houldnt b o woid bout

tht quicknd t ll.

a lwy, w looking o contibution om wit, tit, dign, nd dito. so i you lik

wht you , think bout joining u. You cn lwy nd u onlin t sciencereview.berkeley.edu o

mil u t [email protected].

enjoy th iu,

Michlnglo Dagotino

BERKELEY

Cover: HurriCane KatrinapassesovertHegulfCoast. readaboutberKeleysinvolvementininvestigatingtHeaftermatHonpage 33. pHotoCourtesyof noaa.


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[Entered at the Post Ofce o Berkeley, C.A. as Second Class Matter.]

Features page

F Ex ........................................A real estate boom is changing Berkeleys scientic landscape. by racy Powell

W W T A ......................................5UC Berkeley researchers unearth new species. by Letty Brown

S O B .............................................8Physicists ask What are we made o? by Meredith Carpenter

F C ....................................................33Berkeley engineers investigate what went wrong during Hurricane Katrinaand how tokeep it rom happening again. by Erica Spotswood

E G ...............................................................4What it takes to fy without wings by Adrienne Davich

PolicyP S .................................................................... 38

Berkeley scientists step up to the policy plate by Kayte Fischer

UniversityM G ...................................................................... 44

Studies nd continued disparity in tenure rates between men and women with amilies.by Jennifer Skene

Berkeley, November 2006 No. 11

21

25

28

41

44

A B-ANNAL JONAL OF PACCAL NFOMAON, A, SCENCE, MECANCS, CEMS, AND MANFACES


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CurrentBriefs pageB C .......................................................... 8

Interactive learning may be a cure or ailing test scores. by achel Bernstein

W S A? .................................................. Tracking air pollution in one o the worlds largest megacities by Wendy Chou

A ..................................................................... DNA ngerprinting identies amily membersor better and or worse.

by arish Agarwal

A ..................................................................... 4Berkeley researchers study how the brain combines inormation rom multiple senses. by Peiyi Ko

(M) W ........................................................... A new class o materials promises to give scientists even greater control over Nature.

by David Strubbe

L L ......................................................................... 7Berkeley students compete to build a better bacterium. by Jacqueline Chretien

A O S D ............................................... 8Searching or specks o cosmic dust rom the comort o home by Charlie Emrich

DepartmentsL ...............................................................................

A Hitchhikers Guide by uth MurrayClayFlys Eye View by Charlie EmrichHeart, Two Heart by Jesse DillRed Spot, Jr. by Prayrana Khadye

B ........................................................................ 49T SL D by Seth Roberts by Alisa Gray

W K? ......................................................................... 5Quick Facts About Quicksand by LouisBenoit Desroches

8 10 12

16

14

17

18

6


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LABSCOPES

atonom hv long known tht th Milky Wy glxy idic-hpd with piling m. But jut it i i to th whol UC Bkly cmpu om th top o th Cmpnil

thn om th gound, it i dicult to uvy th nti Milky

Wy om ou loction inid o it. Inttll dut obcu vi-

ibl light om th ch o th glxy, blocking ou viw. To

ovcom thi poblm, UC Bkly tonomy gdut tudnt

evn Lvin nd tonomy poo Lo Blitz nd Cl Hil

hv contuctd nw mp o th glxy pil tuctu u-

ing dio wv, which tvl unhindd by dut. rch

in Lidn, agntin, nd Bonn, Gmny cntly compltd

uvy o dio miion om nutl hydogn co th nti

glxy. Uing thi dt, Lvin nd hi collgu pickd out low

contt pil m by ubtcting blud copy o th img

om th oiginl ( tchniqu mili to Photohop u un-

hp mking). Publihd in th Jun 23 iu o Science, th

mp how tht th Milky Wy i n ymmtic, multi-md

pil glxy, with clm g xtnding much th thn w p-

viouly known. Futhmo, th pil m pinchd thinn

thn th t o th glctic dic, chllnging thoit to impov

ou undtnding o how glxi bcom pil.

RuthMuRRay-Clay

fys eye view

Cm kp gtting mll thy tud by th hndul intophon nd gdgt, but mking tiny ln o thm i tough, ndmking tiny wid-ngl ln i nly impoibl. Fotuntly, ntu

h ldy ound olution: th compound y, n epcot-Cnt-lik

collction o minitu ln nd light-ning cll ud by mot inct.

Inpid, Bkly biongin in Luk L goup hv md thi own

vion. Thi wok, publihd in th apil 28 iu oScience, dmon-

tt th ction o n ticil compound y with bout 8,000 in-

dividul hxgonl ln. Ki-Hun Jong, ld utho o th tudy, ytht thi y i vy uul o minitu imging ytm lik th n-

docop ud by docto o dlict intnl xmintion. Inct y,

by vitu o thi bulging hp, collct light om ll diction nd

pcilly good t clo-up viion. Th ticil y w md om

light-nitiv polym tht bl to om light guid, which pcily

mimic th wy light i tnmittd in inct y. Thi w th gol o th

th-y ch pojct, y Jong, who ud clv, fxibl mold

to om th bulk o th ticil y. a quick do o UV light to th mold-

d y thn ctivt th l ight guid. J Goldblum would b poud.

ChaRlie eMRiCh

Labscopesa hitchhikers guide

ImagecourtesyLukeLee

Imag

eco

urte

syofS

cience


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Wht imny month bo you w bonth tm cll in-tndd to bcom you lt lg hd gottn conud nd tundinto p m intd? Byond th unwntd commnt it would bing

on th plygound, thi would clly mk o om poblm lt in

li. Th complx molcul cu ponibl o guiding mbyonic tmcll into pcic tiu nd ogn till not ully undtood; how-

v, pp publihd in th Novmb 2005 iu o Development by

Bd Dvidon nd Wiyng shi (both potdoctol ch in Michl

Lvin lb t UC Bkly) h uncovd th ntu o on uch citicl

ignl. studying quit clld Ciona intestinalis, thy clid th ol

o Mp, potin tht initit th dvlopmnt o ht mucl tiu in

vtbt. In noml quit mbyo, two cll divid twic to om

ight gndchildn. Fou o th migt to om th ognim ht;

th oth ou ty put nd om th til. Dvidon nd shi md mutnt

oC. intestinalis in which ll ight cll poduc highly ctiv om o

Mp. Thi ld om cll to om ht in th wong loction, cting

n ognim with two ht. extnding th ult in n upcoming

ticl in Genes and Development, Dvidon nd shi timultd th gowth

o ingl ht with two ctionpoibly ticulting th volutiony

oigin o multi-chmbd ht lik ou own.

Jesse Dill

Jupit Gt rd spot, c tom twic th izo plnt eth, h bn mili phnomnon totgz o nly 400 y. But, on eth, Jupi-

t climt i chnging, nd o th t tim, dtild

img o nw d pot hv bn cptud by UC

Bkly Poo o atonomy Imk d Pt nd h

collgu. Th nw tom, dubbd rd spot, J., m-

tilizd t th whit pot mgd in 2000, but

ppd d only cntly t o ny pot in -

codd Jovin hitoy. Cuiouly, th ouc o th d

colo i till mtt o dbt. On thoy uggt

tht th tom huicn-lik wind, on th od o

400 mil p hou, wil up ubtnc om th pln-

t tmoph tht pp d whn xpod to ult-

violt light. Th chmity tht mk th d colo

i likly to b vy tmptu nitiv, o nw d

pot i vy intting, xplin UC Bkly Pooo Fluid Dynmic Philip Mcu. Climt i iouly

ctd by th tnpot o ht, which i vy nitiv

to th pttn o vticl tom on plnt, whth

it b Jupit o eth. Though littl i known bout

tom bhvio on th gint plnt, om tonom

bliv tht th Gt rd spot nd rd spot, J. my

vntully convg to om ingl titnic tmpt.

PRayRana KhaDye

heart, two heart

red spot, jr.

Imagecourtes

yofBradDavidson

ImagecourtesyofNASA


8/52

BRIEF

sttwid tting ult om th ptcdmic y vl tht 30 pcnt oClioni tudnt gdut om high choolwith blow bic o blow bicundtnding o co cinc uch biol-ogy, chmity, nd phyic. studnt pomvn mo pooly whn th tt mpl vity o topic intd o ocuing on ingl diciplin; in thi c, th numb o

undpoming tudnt jump to n to-nomicl 50 pcnt. Byond lling tt co, cinticlly illitt voting public couldt cinc policy in dngou diction iu lik globl wming nd tm cllch tk politicl cnt tg. To vitl-iz cinc duction, UC Bkly duction

ch dvloping tool tht nggtudnt with tchnology-bd lning ndctiviti outid th tditionl cloom.

UC Bkly poo o ductionMci Linn oundd nd dict pogmclld Tchnology enhncd Lning in sci-nc, o TeLs, tht u comput to ctn intctiv lning nvionmnt in whichtudnt dict complx cintic topic.Linn nd collgu hv dvlopd twlvintctiv, onlin lon pnning topicom globl climt chng to gntic tht vilbl t no chg to tch coth county. Fo xmpl, in th aibg:Too t, too uiou? lon, tudntxplo th phyic o motion by contolling

th pd o dummy hdd o n ibg,whil chmity ion illutt th cto chnging tmptu on molcul mo-tion. animtd imultion coupld withqution tht invit tudnt to mk ndtt hypoth until thy com to logiclolution, which hlp tudnt tin thlon long-tm. Futhmo, lon top-ic uch cnc mdiction nd ngy-cint c how tudnt tht cinc ilvnt to thi vydy liv, liztiontht otn pu nthuim nd ult inbtt lning. TeLs bnt tch wllbcu it llow thm to tc tudntpog though th lon nd idntiygp in undtnding. although th lon

Beyond the ChalkboardInteractive learning may be a cure or ailing test scores.

Current BriefsBeyondtheChalkboard

Briefy Noted

Beyond the ChalkboardPage 8

Whose Smog Is It Anyway?

Page 10

Its All RelativePage 12

Taking It All InPage 14

(Meta)material WorldPage 16

Legos o LiePage 17

Another One Sights the DustPage 18


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ldy ud in t lt 30 chool coth county, th TeLs Cnt i continullywoking to dvlop nw id nd impovth pogm.

Whil comput cn b xcllntlning tool inid th cloom, tkingduction outdoo i noth gt wy tomk cinc xciting. Mo thn jut idyllictt, gdn ip with mth nd ci-nc, n id tht Kthin Btt, ocit

dicto o duction t th UC BklyBotnicl Gdn, hop to h thoughMath in the Garden. Thi book o 36 unnd ductionl outdoo ctiviti o 5- to

14-y-old, publihd in Jnuy 2005, ith culmintion o mo thn v y och nd dvlopmnt by Btt ndh cowok. a pnt o tch lngthough th book will nd ctiviti ngingom quntittiv tudy o th viou plntnd inct tht mk up gdn cologyto nutition ctiviti tht cn vn b donin gocy to. anoth ctivity intoductudnt to mthmticl coodint gid by

nding thm on tu hunt. Lik TeLs,Math in the Garden ct oppotuniti ochildn to gu thing out o thmlv.Dicovy lning h bn mlignd upcil, Btt y, but it much mopowul, mo mmobl, nd mo po-tnt. Th nd to b noy connction.

Nobody cn mk ombody ln.Dpit xtniv vidnc om th

TeLs Cnt wll mny oth ductionch goup tht uppot th implmn-ttion o intctiv lning ctiviti uch TeLs nd Math in the Garden, it i otndicult o tch to t thm into thihighly contolld cuicul. It ll boutchiving th tndd, Btt y, ndbcu cinc i typiclly not mphizdon tnddizd tt until high chool, it ilgtd to midgn o tnoon tim hnd th. On th oth hnd, mth i nimpotnt ocu o th tt, o Math in theGarden combin mth with dint ct oth cinc cuiculum, uch biology nd

gology, imultnouly tching tudntquntly-ttd mtil nd ngging thmwith hnd-on cinc. Thi intdiciplinycuiculum povid tudnt with xpouto bic cintic concpt in un nvion-mnt wh thy cn litlly gt thi hnddity.

TeLs c imil obtcl gdingcl tim nd tch fxibility. High choolcuiculum quimnt only llow bouttwo dy to cov ch o th ppoximtly60 quid topic vy y, whil chTeLs modul i dignd to tk v clpiod. Th cuiculum bknck pddo not llow tudnt th tim to pocwht thy ln nd intgt it into lg

contxt o knowldg, but whn tchnd th tim to implmnt TeLs lon, thdinc i cl. In augut, Linn publihd tudy in th jounl Science dmonttingtht tudnt civing TeLs intuctionhow impovd knowldg intgtion ovp tught by tditionl mthod. Intt-ingly, th tudnt ll cod qully wll on

th multipl choic potion o th -mnt th tudy i bd on, but th TeLstudnt pomd lmot 20 pcnt bttthn thi countpt on xplntion itm.Thi ult highlight th bility o th TeLscuiculum to mphiz dp undtnd-ing o cinc intd o th impl cll ocintic inomtion. Linn bliv tht thipoitiv xpinc will cy ov into oth bcu TeLs lon giv tudntth tool to b poductiv ln in nydiciplin.

Php mot impotntly, tch tllLinn toi o tudnt gly king whnthy tting th TeLs lon o bggingo noth on t thy hv bn into-

ducd to th pogm. Thi ot o nthui-m, not otn n in typicl high choolcinc cloom, highlight th potntilo cinc duction. With th implmnt-tion o pogm lik Math in the Garden ndTeLs, cinc cloom cn b tnomdom boing lctu hll to it o xcitingponl dicovi o tht th nxt gn-

tion o tudnt will hv tu undtnd-ing nd ppcition o cinc.

Rachel BeRnstein is a graduate student inchemistry.

Want to know more? Check out:Tching nd aing Knowldg Intg-

tion in scinc: Linn, M. t l, Science313, 1049-1050 (2006).

TeLs wb it:http://www.telscenter.org/

Math in the Garden:http://botanicalgarden.berkeley.edu/

education/eduMIG.shtml

A child investigates lea structure and geometry during a Math in the Garden lesson at UC Botanical Garden.


10/52

BRIEF

0

smog in cowdd ubn tting i nothingnw. Mot Clionin hv pobbly nth bownih hz blnkting Lo angl,Bkld, o Fno on hot umm dy.

Until cntly, howv, mog w conidd city poblm. But now th wold ldingtmophic cintit king whthciti cn gnt gionl pollution wll.and how xctly do uch pollution pd?In Mch 2006, goup o cintit omronld Cohn lbotoy in UC BklyCollg o Chmity tvld to Mxico City,on o th lgt, mot pollutd citi in thwold, to xplo th qution nd toxmin om o th bod nvionmntlconqunc o ubniztion.

Th Cohn goup w pt o lgcintic cmpign, th Mgcity Inititiv:Locl nd Globl rch Obvtion(MILaGrO, o micl in spnih).Th cm-

pign, ponod by both th Unitd sttnd Mxicn govnmnt, bought hunddo cintit to Mxico City to monito uito tmophic contminnt. Uing mplingtchniqu nging om lg ict togound-bd mumnt, th chxmind ulu oxid, cbon monoxid,tmophic ool pticl uch oot,nd impotnt mog-oming chmicl, in-cluding voltil ognic compound (VOC)nd nitogn oxid. a th t chto invtigt i qulity on uch lg cl,MILaGrO pticipnt hopd to impovundtnding o th pollution mging omth wold mgciti, tchniclly dnd tho with ov 10 million inhbitnt.

ai pollution in you typicl mgcitycom om numou ouc, omtimgntd by intn indutil ctiviti, ndomtim iing om dtuctiv nvion-

mntl pctic common in poo, dvlop-ing communiti. In Mxico City, locl oilni blch out hydocbon (on typo VOC) nd chmicl plnt l bnznnd oth toxin. Mnwhil, mny idnttill bun wood o hting nd cooking, po-ducing oot nd cbon monoxid, nd m- tiliz cop with mmoni, voltilom o nitogn which cn cp into thtmoph. On top o th nthopognicouc o pollution, ntul condition ply ol wll: Popoctptl, nby ctivvolcno, pw out ulu compound, ndth city 7,300-oot lvtion nu plntyo ultviolt dition to omnt chmiclction. Finlly, ing o mountin u-

ound th city, tpping pollution in thvlly o long piod o tim.

Th Cohn lb h xpti in moni-toing vl typ o nitogn-continingpollutnt, nd o thi contibution toMILaGrO, tm mmb w ctiv on thgound nd in th i. Two gdut tudnt,Dlphin Fm nd Chik Minjim, ndt cintit Pul Wooldidg md lnd-bd obvtion o i qulity in Tcmc, Mxico City ubub bout 25 mil noth-t nd downwind o Mxico City plum oi pollution. Fom thi loction, thy couldcomp thi locl mumnt to imildt collctd lwh ound th city todtmin th chmicl chng pollutnt

undgo thy dit wy om thi ouc.In ddition, two Cohn goup tudntw onbod Nasa DC-8 it fw omHouton to Mxico City nlyzing nitogn

oxid.It i known tht ctin nitogn com-

pound, lik nitic cid (which ld to cidin) o th mog-oming nitogn oxid, untbl, bk down, nd cu loclpollution. By contt, poxylkyl nitt,condy by-poduct o mog omtion, tbl nough to tvl o vl houbo bking down into nitogn oxid,which cn thn ct to -om mog. In thihion, poxylkyl nitt cn tnpotmog o long ditnc. Th poxylkylnitt o dditionl intt bcuthy clid iitnt nd coniddpollutnt in thi own ight. Th mot com-mon pci in thi ctgoy i poxyctyl

nitt, o PaN.To mu poxylkyl nitt in i

mpl, gdut tudnt Dlphin Fmiggd up tll mtl tow on th oo o til in Tcmc. attchd to thi toww n i mpling inlt nd mtl box.Inid w h nlyticl intumnt, whichud ht to bk pt th poxylkylnitt into nitogn dioxid nd thndtctd it uing tchniqu clld l-inducd fuocnc. Howv ctivt mpling i, h tup w omtimpciou. On on occion, cd with nncoching thundtom, Fm ikdbcoming humn lightning od huhd to wtpoo h quipmnt. In ct,

Humans have infuenced the Mexico City valley or millenia. About 25 miles northeast o Mexico

City, the Pyramid o the Sun marks the center o the ancient civilization o Teotihuacn.

Whose Smog Is It Anyway?Tracking air pollution in one o the worlds largest megacities


11/52

pcil on-it mtoologit hd bn hidto wn MILaGrO cintit o incomingchng in wth tht might ct thichmicl mumnt; unotuntly, thpdiction typiclly ild. Wht did thyu n ltntiv? Yhoo wth wlwy ight on, Fm xplin.

Dpit pow outg nd n-lc-tocution, th Cohn lb month o oth yildd novl dt on lvl o PaN in

th i. Pviouly, no on hd v tidto pdict PaN concnttion o wyom ubn ouc. evntully, th dtcollctd by Fm nd h collgu will

b ntd into comput modl tht tckmog omtion nd dipl thoughoutth gion. Th modl hould b modciptiv nd ccut thn ny in th ptbcu dt om th xtniv cmpigncn now ll in gp tht ud to b lt togu nd hnd-wving. W w bl toviw th it gint xpimnt whid odinily ttd umptioncould ctully b ttd, y Fm. On

pttn tht tund out to b mo complxthn pviouly umd w th bhvio oMxico City plum. at th Tcmc it, thnotht xpot o th Mxico City plumw obvd bout 30 pcnt o th tim.On th mining dy, th plum ollowdon o two gnl pttn: in on, it ild

to mov bcu i w tppd in tgnntly. Th cond cnio, known lot-ing, occud on dy whn th plum obov th o-clld boundy ly, th lyup to which i odinily mix. Duing thloting vnt, th plum otn wtd towdth Gul o Mxico th thn ollowing thnotht tjctoy ov Tcmc.

Th MILaGrO cmpign lo howdcintit th h mgnitud o th pollu-tion poducd by mgciti. Mxico Cityhigh pollution lvl chllng th txtbookxplntion o mog omtion, whichuully involv ction btwn nitognoxid nd hydocbon. accoding toFm, Wh typiclly w might kwhich on i limiting, th nitogn oxido th hydocbon? tht typ o qutionint y to nw whn both o high.In oth wod, whn ingl pollutnt typ

i limiting, policy mu cn b dictdt minimizing th onding contminnt.In Mxico City, th no y wy out, ndboth typ o pollutnt mut b dcd toduc mog lvl.

Ultimtly, by linking pollution oucto pollution outfow, MILaGrO ch willhlp dd th qution o how mgciticn chiv conomic dvlopmnt whilpotcting public hlth. Tk th iu o

tnpottion: on poibl olution i tocut down on th city ou million motovhicl, which ccount o bout thid oMxico City nitogn oxid nd hydoc-

bon. Mxico did not intoduc miiontndd o nw vhicl until th ly1990, nd citic clim th tndd wkly nocd. To it cdit, Mxico Cityo om o th mot odbl publictnit in th wold, including tt-o-th-t ubwy ytm nd th Mtobu, pid tnit ytm lunchd in Jun o2005. Would btt modl o mog om-tion povid th vidnc ndd to xpnd

m tnit option vn uth? althoughit till ly to pcult on utu policy out-com om MILaGrO, mny viw Mxiconthuitic uppot o th cmpign, omboth cintic nd politicl tndpoint, dditionl poo tht th city i wll on thpth to om.

Wendy chou is a graduate student in environ-mental science, policy, and management.

Want to know more? Check out:

http://www.windows.ucar.edu/

tour/link=/milagro/milagro_intro.html

http://www.eol.ucar.edu/

projects/milagro/media/

MILAGRO-Factsheet-Final.pdf

Helium-lled balloons carry instruments to measure

ozone and other pollutants.

As Dr. Ron Cohen looks on, Delphine Farmer shuts o

her peroxyalkyl nitrate-detecting instrument beore

bad weather sets in.

PhotobyPaulwoolDRiDGe

Pollutants and dust over Tecmac scatter light,

emphasizing orange and red wavelengths at sunset.


12/52

BRIEF

ItsAllRelative

In 1988, Lyntt Whit w mudd inCdi, Wl. Th DNa vidnc ldpolic to th ciminl cod o 14-y-old

boy who hd gntic typ with thmud, but did not xctly mtch thgntic ngpint. Polic upctd mlltiv o th boy w th l pptto,but wb o hi th DNa lo yildd

mimtch. Futh invtigtion unthd Jy Goo, th boy uncl, who w nxct mtch to th cim cn vidnc ndvntully convictd o th cim.

Tking thi cu om thi nd imilc, Fdick Bib, pthologit t H-vd Mdicl school, Dvid Lz, Hvdociologit, nd Chl Bnn, viitingchol in th Fonic scinc Goup t

UC Bkly school o Public Hlth, pub-lihd n ticl ntitld Finding CiminlThough DNa o Thi rltiv in th Jun2006 dition o Science. Mnwhil, cocmpu t stphn Hll, eic stov, thhd o th Bkly Humn right Cnt,wok on th DNa runiction Pojct.

Lunchd in 1996, th pojct i n ot tou gntic ngpinting to unit miliptd duing el slvdo civil w,which ltd om 1980 to 1992. Duing thw, mny childn w ptd om thipntom tkn ocibly, oth implyput up o doption by dpt pnt.Th idntiction o mily mmb ndltiv though DNa i nw nd xcitingppliction o xiting tchnology; howv,

mny o th thicl qution tht ccompnyit u hv yt to b nwd.

Php th mot publicizd u o

gntic ngpinting i in th n ociminl jutic. sinc it w intoducd intoth coutoom in 1985, DNa ngpintingh bcom incingly pominnt in th

pocution, nd xontion, o ciminl.Cim cn outinly xmind oDNa vidnc. Th mpl cn thn bcompd gint DNa dtb. Th DNacod o convictd x ond, wll tht o cim cn DNa, mintindin dtb by vy tt in th Unitdstt. Th FBI implmntd th CombindDNa Indx sytm (CODIs) in 1998, whichogniz ll o th locl tt cod into

ntionl dtb.Th cod do not contin th nti

th billion nuclotid qunc o pongnom; indd, it took y to qunc ingl humn gnom, nd it i unliklytht nyon would b willing to wit thtlong o th ult o gntic ngpinting

tt. Luckily, cintit hv dicovd wtick to xpdit th poc. rth thnxmining th nti qunc o nuclotid(th mili a, G, C nd T tht thbuilding block o DNa) in DNa mpl,thitn dint pot, o loci, on th gnom lctd. Th loci known to b thit o hot tndm pt, o sTr, onmd bcu thy contin pt o mllqunc (th to v nuclotid long) o

DNa. a it tun out, thi lg vibility in thnumb o pt, clldth lll, n individulmy hv t locu.

a powul gntic

ngpint i obtind byxmining mny dintsTr loci to idntiy thipcic lll. Whil ind my b wing thm colo hit you, iti unlikly tht h o hwould b wing th mcolo hit you bothtody nd tomoow. In thm wy, lthough thi light chnc tht twoindividul h th mlll t on sTr locu, on xmin mo loci,it bcom incingly

unlikly tht thy h th m lll tll loci. CODIs cod th lll t thitnsTr loci; th odd timtd t 1 in 1029

(tht 1 with 29 zo!) tht unltdindividul will hv n idnticl CODIscod. Cim cn DNa cn b compdgint th cod o o-clld cold hit,o xct mtch, with n ond DNa.

Bib nd hi collgu uggt tht otho c in which CODIs do not yild cold-hit, th comput hould gnt l ito popl who my b cloly ltd to thindividul who DNa i bing xmind.Thi lit could thn ld invtigto to upct, jut in th Lyntt Whit c.

How do th comput pick out po-tntil ltion om th million o cod

in CODIs? It i wll-known tht ltdindividul hv mo imil gntic ng-pint thn unltd individul. accod-ingly, individul mo likly to b ltdi thy hv in common lll which vy in th gnl popultion, o i thy hvvy imil pttn o lll. Uing miv

comput imultion nd pviouly pub-lihd dt on lll qunci, Bib ndhi collgu w bl to dmontt thtin dtb o 50,000 individul, th i 99 pcnt chnc tht th biologicl th o child will pp in th top 100 mtch toth child DNa mpl. Th utho uggt numb o oth milil ching mthodtht cn b ud to impov th odd vnuth. Howv, th ch dcibd bovcn b implmntd without ny modic-tion to th xiting dtb.

although th milil ching tch-niqu i pomiing, ciminl jutic i notimply plygound o onic cintit,no mtt wht CsI my hv u bliv. a

gntic idntiction cod i much moponl thn impl ocil cuity numb,bcu it ci with it inomtion bouton gntic hitg. a conqunc, thdtb o gntic ngpint i hoto pivcy iu. som tt hv ldyxtndd th lw quiing DNa collction,oiginlly tictd to x ond, to ll -t, vn pon who hv not yt bnconvictd o cim. Futhmo, lthoughth thitn sTr loci thought to b ingion o th humn gnom which notmdiclly lvnt, th phyicl DNa mpl,which contin ll o th gntic inomtiondcibing n individul, i otn tod on indnit piod o tim by cim lb.

Its All RelativeDNA ngerprinting identies amily membersor better and or worse.

Comparing the number o shor t tandem repeats, or STRs, at dierent

locations in the human genome to records in the CODIS database can

lead investigators to relatives o the suspect. The suspect was not in the

database, so the relatives DNA was the top hit because it matches the

crime scene DNA at three o our loci ( in reality, more loci are included).

This leads investigators to the suspect, whose DNA matches the crime

scene DNA exactly.

How DNA FingerprintingWorks

GRaPhiCbyMeReDithCaRPenteR


13/52

Th lgl mwok uounding llo th iu i inucint, ccoding to

ein Muphy, ocit poo o lw t UCBkly. som cintit clling o thu o mo sTr loci to dnitivly ul outn impop mtch to gntic ngpint.In ddition, th utility o th tchnology itlh not bn dqutly tudidwhil thhv bn bout 30,000 cold hit to dt u-ing CODIs, th h not bn ytmtictudy o th ubqunt conviction obtinduing th hit. Finlly, th ociologicl im-pliction o gnticngpinting dunting. WhilDNa dtbhould contin uniom mpling

o ciminl o-nd co thnti popultion, itmy, in pctic, bmo likly tht nt nd hi oh ccompnyinggntic ngpintcom om poon i g h b o h o o d .Thu, mililching h thpotntil to uthxcbt th pob-lm o uni polic-ing, y Poo

Muphy.Whil th u o DNa tchnology in th

jutic ytm i thony qution, mililching tchniqu cn lo b plyd out onl thiclly mbiguou tg. although thel slvdon govnmnt h yt to ddth tmth o it civil w, th aocicinPo-Bqud d Ni y Nio Dpcido(aocition in sch o Miing Childn), volunt ogniztion, h md conidblpog in locting miing childn uingconvntionl invtigtiv tchniqu.

accoding to rchlshigkn o th UCBkly Humn rightCnt, sinc 1994, Po-Bqud h gitd768 c o miingchildn, nd 316 o thc hv bn olvd.ech o th mtchh bn conmd by

gntic ngpint withth hlp o eic stov tth UC Bkly Humnright Cnt nd hi DNaruniction Pojct. In

cnt y, voluntom Po-Bqud ndth Humn right Cnthv tvld thoughoutel slvdo to collct DNampl om pnt ndoth mily mmb.Th mpl w thnbought to Clioni,

wh th ClioniDptmnt o Juticdontd it onic lb -

ouc duing o-hou nd vl oniccintit voluntd to poc th mpl.With th dtb complt, Po-Bqud ipoid to u milil ching tchniqu

to mtch childn with thi mili. Lotlovd on cn now void wding thoughcomplictd ocil nd buuctic iu inlocting doption documnt, which om-tim do not vn xit, to loct ch oth.

Th contt btwn th Po-Bqudch nd th u o DNa vidnc in thcoutoom dlint th ky to movingowd with DNa tchnology: undtnd-ing tht whil th tchnology itl i notinhntly unthicl, th ppliction othi tchnology mut b cully xmind.Tht cutting-dg tchnology cn hv ocilimpliction i nothing nw; om m toth intnt, humn ocity h lwy hdto gult it dvnc. a w continu to

innovt, it i woth kping in mind tht ouinvntion do not xit in vcuum.

haRish agaRWal is a graduate student inphysics.

Want to know more? Check out:UC Bkly Humn right Cnt :

www.hrcberkeley.org

Liz Barnert (let), a UC Berkeley/UCSF medical and public health student who has

assisted with the DNA reunication project, and Angela Fillingim (right), who was

adopted rom El Salvador by a Berkeley couple when she was six months old and

later reunited with her mother.

Eric Stover, director o the UC Berkeley Human Rights Center, takes a blood sample rom a relative o a missing

child in a village in central El Salvador.

PhotoCouRtesyofR

obeRtKiRsChneR


14/52

BRIEF

In plit cond on th bktbll cout,you mk dozn o dciion bd oninomtion om ll o you n. Youtmmt cll you nm, you h it, youtun towd him, clcult hi loction ndth tjctoy o th bll fying towd you.

In n intnt you hv judgd th ltivloction nd pd o you tmmt, thbll, nd you opponnt uing you no hing, ight, touch, nd blnc. It lotto hndl, but ou bin pom compli-ctd noy intgtion lik thi vy dy.somhow, thy bl to poply mtch thcoponding tu potd by ou di-nt n nd not mijudg th dictionnd dg w hould tun. and thy kp

u om ching o ou opponnt hdintd o th bll.

animl ntully good t combin-ing multipl noy input to dl with thdynmic fow o inomtion, nd humn no xcption. But how i noy inomtionintgtd to ct unid pictu o th

nvionmnt? sinc w cnnot poibly p-civ nd ct pctly und ll condition,how do th bin dcid which input mot impotnt in od to optimiz itpomnc? UC Bkly Mtin Bnk,poo in th Viion scinc Pogm ndHln Will Nuocinc Pogm, tcklth qution in th multinoy tudiin hi lb.

snoy intgtion h bn tudidinc th ly 19th cntuy, but cnt tch-nologicl dvnc hv givn chmo tool o mnipulting noy input toundtnd how th bin i bl to combinthm. Fiv y go, Bnk nd potdoctolch Mc ent, now ch cin-

tit t th Mx Plnck Intitut o BiologiclCybntic, cquid on uch nw tool, oc-dbck dvic clld th Phntom,dvlopd nd mktd by th snablTchnology. Th Phntom i ud with vi-tul lity viul diply tool nd llow thch to tudy th intgtion o touch(hptic inomtion) nd viion in pcivingth hight o vitul idg. Duing typiclPhntom xpimnt, th ubjct look t viul diply whil plcing thi thumb ndindx ng into mtl thimbl connctd to obotic m which tck nd cod thng 3D loction. a th ng tvl todigntd poition, th thimbl/m xtth pop oc on th ng to imult th

ntion o touching idg. In contolcondition, thi oc-dbck would mtchth viul diply; tht i, th ubjct would thi vitul ng in th om o moupoint, touching th dg o idg whncoponding itnt oc givn. Butby indpndntly mnipulting th dbckoc nd th viul diply, th ch bl to intoduc unctinty o confictbtwn wht th ubjct touch nd whth o h . Undtnding how th binolv th vitul lity-inducd unc-tinti nd confict cn vl undlyingcomputtionl pincipl o noy intg-tion nd i o gt intt to ch in

Bnk lb.so, how do th bin do it? In tudy

on viul-hptic intgtion publihd in thjounl Nature in 2002, ent xplin thtth bin u[] inomtion in ttiticllyoptiml hion. In oth wod, th bindo wht mk th mot nit int-gt th inomtion om dint n,but wight ch noy input ccoding tohow libl it i. Fo xmpl, i you bini tying to dcid wh th hndl o thcup i in th dk, it will wight th judgmntmd by touch mo highly thn you viultimt o it loction. In low light, youbin will liz tht you touch i pobblymo ccut thn you viion. Clly thi

dont mk much dinc whn ll oyou n poting th m thing,

but in confict itution, lik tho thtcn b ctd in th Phntom xpimnt,thi wightd intgtion bcom citicl indtmining pon pcivd vlu o

th timuli.Thi wightd combintion modl o

noy intgtion i dptd om mth-mticl nlyi pocdu, th MximumLiklihood etimt (MLe) modl. accod-ing to th MLe modl, you bin ttiticllydtmin th mot likly outcom bdon i o wightd input, with thwight djutd ccoding to th ttiticllibiliti o th input. Th phyiologicl

nd nul mchnim ponibl oclculting th mximum liklihood timt till not ully undtood, but entnd Bnk hv md th t tp towdmodling th poc in th hop o on dycomphnding it mo ully.

Hving dmonttd tht ou bin

could b uing th MLe modl to intgtviul nd hptic noy inomtion, thBnk lb i now woking to idntiy whththi pincipl hold co viou modliti,including viul, uditoy, touch nd vtibu-l (blnc) ytm. In n idl itution,wht pon , h, o l bout nobjct would indict conitntly wh iti. Gdut tudnt Cml Lvitn u thPhntom in conjunction with vitul-lityviul diply nd hdt to mnipultth touch, viul, nd uditoy inomtionching humn ubjct, uch tht thy p-p to oigint om dint loction. shthn tudi how th pon dl with thdicpnci to com up with dciion

bout th objct loction.Th ult indict tht whn th

dicpnci btwn th n mll,w tk into ccount th ccucy o chnoy input nd wight thm ccodingly, th MLe modl would pdict. Howv,whn th dicpnci bcom too lg, wntily igno th inomtion tht i motonou nd intd ly on th two tht mot conitnt.

a clic xmpl o noy intgtioni judging th diction o gvity, o whichth bin mut intgt inomtion omth viul nd vtibul ytm. In thBnk lb, gdut tudnt Pul McNilgmnipult viul nd vtibul noy in-

Taking It All InBerkeley researchers study how the brain combinesinormation rom multiple senses

Taking

ItAllIn

In a split second on the basketball court a players

brain must accurately combine inormation rom

the senses o vision, hearing, balance and touch to

complete a play.

GRaPhiCbyhansonlee


15/52

put indpndntly nd tt popl bilityto judg th diction o gvity. McNilgxpimntl ubjct td in chitht tilt lowly om id to id with thubjct hd t th cnt o wid c.Th ubjct look though cicl t viulcn, which my b otting t th m odint t th chi. Th xpimntindict tht wht w cn infunc th judgmnt md by ou vtibul ytm.

Whn th viul input i litic cn uch living oom ( oppod to ndom dotlik ty ky), ou pcption i bidtowd th upight diction dpictd in th

img, vn whn ou vtibul ytm itlling u omthing dint.

Multinoy intgtion ch hmny potntil ppliction in lik

mchin ptil nvigtion nd th dign ogonomic vitul lity nvionmnt. Onuch xmpl i th l-nvigting c, stn-ly, th winn o DarPa Gnd Chllng2005. Dignd by tm om stnod,th c w bl to div 132 mil coth Mojv Dt by intgting noyinomtion om d, l nging, tocm, GPs, intil guidnc ytm,nd n odomt. Th ch dignd

guidnc ytm tht intgt ll o thiinomtion in wy tht imult humnbhvio.

Vido gm dign lo im to includ

noy inomtion byond jut viion. Ytth till mny chllng in vitulnvionmnt dign, uch mking vitulxpinc litic nough, o pvnting

diointtion conficting noy mgbombd th ply. By hlping to undtndhow w dl with dynmic fow o inom-tioncquiing, lning, nd ogtting thntion tht w hv xpincdentch my on dy hlp to pct uchimmiv nvionmnt.

Pei-yi Kois a graduate student in vision science.

Want to know more? Check out:ent M.O. & Bultho H.H. Mging th

n into obut pcpt. Trends Cogn Sci.8:162-169 (2004).

Bnk Lb Wbit:http://bankslab.berkeley.edu/

Graduate student Paul MacNeilage

uses a tilt chair and vir tual reality

display to study how the brain com-

bines visual and vestibular inputs to

tell up rom down.


16/52

BRIEF

(Meta)material WorldA new class o materials promises to give scientists even greater control over Nature.

Tody mtil md om th pl-tt o 116 lmnt known th pi-odic tbl. slct om cbon, littl ulu,myb bit o dypoium, nd voil nw

ubtnc. scintit hv only ctchd thuc o th myid chmicl combintiontht cn b md om th lmnt, butwht i you could mix up om xt colo

o th pltt?Th nw ld o mtmtil pom-

i to do jut tht: ct ticil tomtht cn b combind into ubtnc withnovl popti. Fd om th continto ntu building block, ngin cnhion mtmtil tht ct light bck-wd, tht ocu img o unpcdntdolution, o tht my vn on dy om thbi o cloking dvic. On o th

ld in thi mging ld o mt-mtil i Poo Xing Zhng oUC Bkly Nnocl scinc ndengining Cnt nd Dptmnto Mchnicl engining. Wvbn vy inttd in dvlopingticil mtil with xtodiny

popti tht do not xit in ntu,Zhng told th Bkly Nw Oc.In cnt ch pp publihdin Nature Materials, Poo Zhng nd hicollgu dcibd th biction o thwold t coutic mtmtil.

so wht xctly i mtmtil? Con-id chunk o conct th iz o Mnht-tn: tht n odiny mtil md o moo l uniom ubtnc. Now conid thl Mnhttn, in which th conct ictully ngd into building yd on gid o city block: tht mtmtil. evnthough thy hv imil compoition, thcity with it kycp h mo compli-ctd ubtuctu thn th conct lb. a

ult, th city h dint chctiticthn conct lb. Th cn b chngdby tuning th ubtuctuo xmpl,lting th hight o th building o th izo th city block.

rplc th conct with copp ndth building with coil nd wi, nd thnhink th whol thing down by bout cto o billion (think micon th thnkilomt), nd you hv th bic o mtmtil. It i th ubtuctu o thmtmtilth ngmnt nd iz oth coil nd witht i cucil. Whn light wv o ound wv p thoughn ngmnt o tuctu tht muchmll thn it wvlngth (th ditnc om

on wv to th nxt), th wv xpincth mtil though it w uniom, butwith dint popti thn th contituntmtil. In ct, th wv dont know

bout th pt ubtuctu nd n ntily nw mtil.

Fo mot odiny mtil, th tuc-tu ngd on th cl o tom.

Mtmtil ngin, howv, wok withlg-cl, mo ily mnipultd compo-nnt th thn ttling o ntul tomicngmnt. In th c o th micon-izdcopp coil, th tuctu i dignd to wokwith micowv. Th popti o thi y tund o th coil ntully ont t quncy vy clo to th quncy o thincoming wv.

Contuctd poply, mtmtil cnchiv ngtiv indx o ction. Whnn lctomgntic wv lik light tvlom low-indx mdium to high-in-dx mdium (om i to wt, o xmpl)it bnd towd lin ppndicul to thuc. Howv, i th light i nting ngtiv-indx mtil, it bnd in thoppoit diction, though it fctd oth ppndicul lin. Thi uniqu popty

cn b ud to dign upln tht hvmuch high olution thn odiny ln.Lt y, Zhng goup dmonttd ilvupln ( Th shpt Img, BSR Fll2005). Woking t wvlngth o which thin lm o ilv hd ngtiv indx, thycould olv lin tht w much thinnthn th wvlngth o th ultviolt lightthy w uing nd up th dictionlimit o tndd optic.

Now Zhng lb h tund it ttntionom lctomgntic wv to ultoundnd md th t coutic mtmtil.I you hv v blown co th top o bottl to mk ound, you mili withth bic building block thy ud. It clld

Hlmholtz onto chmb con-nctd to th outid vi now nck. Thquncy o vibtion i t by th volum oth chmb nd th iz o th nck.

Potdoc Nichol Fng (now poot th Univity o Illinoi t Ubn-Chm-pign) nd cowok bictd lin yo 59 luminum onto ch bout on

cm in iz, tund to vibt t 33 kHz. Thchmb nd chnnl to which thy wconnctd w lld with wt, in whichthi ultound h wvlngth o 4.4 cm,ou tim th onto iz.

Fng y h w inpid by muiclintumnt. Think bout fut, h toldth mdi oc t UIUC. Whn w plymuic, w uing om intumnt tht

ci ound wv, nd yt ch o

th button [i] much mll thnth wvlngth thy poduc. soh w tk imil philoophy.W uing vy tiny lmnt, tinyonto cviti, nd in n nloguto th fut, w ty to ct thotuctu in od to mnipult o

contol th onting qunci oultound.

Fo lctomgntic wv, thgol hd bn to chiv ngtiv indx oction. Fo coutic wv, Zhng goupchivd wht known ngtiv modu-lu in th mtmtil, imilly tngpopty. Th ltic modulu o mtilntilly nw th qution, How muchdo mtil comp whn you puh onit? I th modulu i ngtiv, it dont com-pit xpnd. To b u, thi i only tui you puh on it t quncy o 33 kHz.But ngtiv modulu i uniqu popty,not obvd in ny ntul mtil.

Zhng goup pln to tun th lin

y into two- o th-dimnionl mt-mtil which could hv mny inttingppliction. Cunt coutic dvic mutb lg thn th wvlngth o th wvwith which thy intct, but on withmtmtil ln could b much mllnd mo compct. Two poibl ppliction mdicl ultound imging nd onytm (th goup i ptilly undd omth Oc o Nvl rch). Thy lo hopto tk dvntg o th ngtiv modulu toct n coutic upln to bt th di-ction limit, lik th ilv upln.

Th humbl pincipl o th fut mightom dy ld to th mot cinc-ctiono cnio: cloking dvic. rch-

(Meta)materialWorld

By giving them complex substructures like those

shown in the electron micrograph above, scientists can

ashion materials with new and interesting properties.

GRaPhiCbyMeReDithCaRPenteR


17/52

dm o wpping n objct in opticlmtmtil pcilly dignd to bndlight ound th outid nd thn continuin it oiginl diction, though th wnothing th t ll. Tht omthing you jutcnt do with odiny tom.

david stRuBBeis a graduate student in physics.

Want to know more?Fng, N. t l, Nature Materials5, 452-456(2006).Xing Zhng goup wbit t

http://xlab.me.berkeley.edu.

Legos of LifeBerkeley students compete to build a better bacterium

Bcti wondully div nd cn doom ptty mzing thing, uch lightup t night nd nutliz chmicl wt.But th om thing thy typiclly cnt

do: photogph thmlv, ply z tg,dd nd ubtct, initit bttl o thipti dih, o mll lik pum intd o,wll, E. coli. Th Intntionl Gnticllyengind Mchin (iGeM) comptition,

indly contt in th ld o ynthtic biol-ogy, im to chng ll tht.

In th iGeM comptition, tm o un-dgdut nd high chool tudnt ttmptto ynthiz uul biologicl dvicoxmpl, colony o bcti tht, thoughcoodintd ignling btwn cll, cn lightup fuocntly in gul pttn, o, inth c o thi y MIT pojct, convt

unplnt mlling molcul to nutl oplnt mlling on. In th poc, thtudnt gnt BioBick, dict pico DNa tht cod o o gult cllulmchiny nd cn b ud ov nd ov.

Th nlogy o-tn md i tht th

pt lik wi,cpcito, ito,tnito, nd diodud to mk lc-tonic cicuit, yChi andon, potdoctol llow inBiongining po-o adm akin lbnd dvio to thBkly iGeM tm.But intd o lcti-cl componnt, thtudnt u (ndmnipult) BioBickto build thi biologi-

cl mchin.Th cunt t o

BioBick includ gn tht ncod cll ig-nling molcul, mting cto (molculo mll potin tht lt bcti whn potntil ptn i nby), fuocntpotin, light-ning potin, nd potintht povid ntibiotic itnc. But thBioBick hdly limitd to potin-cod-ing DNa. Th toolbox lo contin pico gultoy DNa tht ct witch todtmin whth nby gn i tundon o o, o whth gn cn b tnltdinto potin.

Goup o BioBick cn b ud to cyout complx unction, lik cting dbck

loop o ignl mpliction. Th hop itht mo nd mo pt ddd, thmchin tht cn b md with vioucombintion will bcom incingly

complx. an nlogu to obotic comptition

tht gt tudnt pychd bout ngining,th iGeM comptition w bon in Jnuy

2003 out o n indpndnt tudnt pojctt MIT. sinc thn, iGeM h volvd into nintntionl comptition to which goupcn dign th coolt cllul mchin. UCBkly h pticiptd in th comptitiono th pt two y.

In 2006, 38 tm o undgdut ndhigh chool tudnt om univiti on v-y continnt xcpt antctic pnt th tov month ov th umm woking on thi

pojct. Th tudnt, bout hl o whomldy hv xpinc in biology, nd hlo whom hv bckgound in nginingnd comput cinc, gt ch cou inmolcul biology nd lb tchniqu. Thn

thy bintom withdvio bout th di-

ction o th pojct.at tht, thy pndth mjoity o thitim t th lb bnchxpimnting. at UCBkly, akin ndChmicl enginingpoo Jy Kling th pojct pon-o, with potdoctolllow Chi and-on nd John Dubpoviding dditionlguidnc.

Th cuntUC Bkly tm

i iming to dvlopn ddbl two-

wy communiction ytm in bcti.Thy hop to chiv lctiv dlivy o DNa mg by mnipulting conjugtion(th xchng o gntic mtil btwnbcti) in th common ch ognimE. coli. evntully, th tm will b bl tomnipult thi bctil communictionto pom logic clcultion o implmthmticl unctionin ct, cting bctil bin.

Thi y Bkly tm w plit intoth mll goup, ch ocuing on onpct o th lg pojct. On goup tckldth conjugtion poc, moving two gn

Gearing up bacteria: The 2006 international Geneti-

cally Engineered Machine competition in the eld o

synthetic biology gathers high school and undergradu-

ate students to gear up bacteria with a whole host o

new unctions.


18/52

BRIEF

(which ignl copy m nd p m long!to th bcti) om on pic o DNa ndputting thm into noth. Thi ctivlydtmin which gn will b tndduing conjugtion. a cond goup wokdon mking th conjugtion poc dd-bl. a gultoy DNa lock i ddd toth DNa mg to pvnt poduction o

it ncodd potin. som cll, howv,po noth pic o DNancoding

molcul kytht nbl thm to dth lockd DNa mg civd duingconjugtion. Finlly, thid goup dvlopdntwok lyout nd logic cicuit tht uthi ytm to pom impl clcultion.

Th tm will pnt thi pojct tn nd o th y iGeM Jmbo, cinci-mt-connc to howc thiwok. at ll th tm hv pntd,wd both iou nd light-htd

givn. Lt y Bkly tm won th MotInnovtiv Bick awd (o pcil ttit o DNa pliction tht i ctivtd onlywhn cll i conjugting with noth cll), wll Bt Concptul advnc nd Mot

XXXtm Pnttion. Th 2006 Jmbowill b hld in ly Novmb t MIT.

Ultimtly, th pojct nd vn thdvlopmnt o nw BioBick condyim o th iGeM comptition. Th mingol, y andon, i t nd omotduction, nd to pk th intt o bighttudnt who will ld th wy in thi youngld.

still, th i tong n mongtth pticipnt tht pojct lik iGeM going to chng th wy biology i don. Iw tuck by th h potntil o ynthticbiology nd th bod pplicbility o wokin th , om phmcuticl, indu-til poc, conum poduct, nd bic

thoticl dvnc, id Dnil Kluing, nio t UC Bkly who wokd on th2006 iGeM tm. It i only mtt o timbo th BioBick put to wok po-ducing hydogn o ul cll, chuning outnti-mlil dug, nd doing you tx.

Jacqueline chRetien is a graduate student inmolecular and cell biology.

Want to know more? Check out:2006 Bkly iGeM wiki:

http://openwetware.org/wiki/IGEM:

UC Berkeley/2006

iGeM : http://parts.mit.edu/igem

LegosofLife

Samantha Liang at the bench. iGEM students get a

crash course in molecular biology beore spending the

summer researching.

Some members o the 2006 iGEM team outside their Potter Street base: (let to right) Matt Fleming, Kaitlin Davis,

Bryan Hernandez, Jennier Lu, Samantha Liang, and advisor J. Chris Anderson.

AnotherOne Sightsthe Dust

Searching or speckso cosmic dust rom thecomort o home

I youv v pid to b pc cintitbut wntd to kip th y o choolingnd Nasa tining, now i you chnc,thnk to n innovtiv pojct clldstdut@hom. Bgun in ly augut, thiwb-bd pogm om th Bkly spcscinc Lb put odiny popl in contolo vitul micocop to ch o tinygin o tdut collctd by Nasa pc

pob.Th Nasa stdut pob, lunchd

in 1999, tvld hlwy to Jupit botuning to th Uth dt lt Jnuy.Duing it tip, th stdut pob dployd tnni-ckt izd collcto gid to cptutdut o nlyi bck on th.

Thi i th tu tht w md o, y andw Wtphl, ld o th stdut@hom pojct. Ou ol ytm i thought tohv bn omd om g nd dut, nd itpoibl tht om o th tdut tundby th pob i ctully old thn th olytm itl.

But bo th tdut cn b nlyzd,ch o th hundd o o mot h to bound. Tht why w nd th hlp o vol-unt, y Wtphl, bcu w couldntdo thi oulv. ech pic o tdut i otiny, ccoding to Wtphl, tht nding thmi nly impoibl, but inc th tdut izipping though pc t bout 45,000 milp hou, it blt hol in th collcto gid

tht wll-tind y cn pot. Wtphl oiginlly plnnd to u

comput to nd th tdut impct, lo

NASA stardust probe.

PhotosCouRtesyofMelissali


19/52

clld tck, but hd limitd ucc. It myb poibl, h y, but w imply not

clv nough to pogm comput tond th tdut tck.

so with th stdut pob till inpc, Wtphl dcidd to nlit th hlpo volunt to ch th collcto gid otdut om th comot o thi ponlcomput.

To pticipt in th stdut@hom pojct, ll volunt imply viitstardustathome.berkeley.edu, go though 15 minut tining ion to hlp thmidntiy tdut tck, nd thn p 10qution tt to how tht thy cn potgnuin tck. (Dont t: i, lik th utho,you dont p th tt th t tim, you cnkp tking it until you do p.)

at ping th tt, volunt ctn ccount nd tt hunting o l tdut

tck by looking t cn om th ctulstdut collcto gid nd djuting th ocuo thi vitul micocop to nd th tlltlign o tdut tck. a tck look lik littl tnpnt cot gowing into thcollcto, y Wtphl.

I you tck, you click on it, nd i

you dont tck, you click on button,y Wtphl, dding tht th poc ikind o lik vido gm.

To kp volunt hp nd lnd comptitiv pct, th stdut@homtm h ddd k cn, in much thm wy th Tsa Tht Img Pojctionytm dd k gun nd contbnd toluggg X-y to tt th ltn o bg-

gg cn. Volunt whococtly idntiy tck willgt co-uthohip on public-tion om th stdut@homtm, wll th dmitiono mo thn 15,000 stdut@hom volunt who hil om

counti ll ov th wold.On o th mot tounding

pt o th pojct i th collc-to gid itl, which, jut lik gint mhmllow ctchingbullt, h otly cptud thpciou gin o tdut.

Th gid i md o 132til o ogl, pcil om oilic tht i on thound timl dn thn gl, giving chtil th ppnc o olidpic o mok.

Th tk o cnning thgid blong to ron Btin,pojct ngin t Nasa

Johnon spc Cnt in Tx, who ntici-pt tht cutting th micocopic pck o

tdut out o th ogl will b th nxtchllng in th pojct, bcu it downyntu mk th ogl lik pic o dutwith pic o dut in it.

Wtphl tm got hlp with th wbintc om llow ssL cintit Dvandon, th l dcibd comput gk

ound th lb who lo dict th mouseTI@hom nd BOINC ditibutd comput-ing pojct ( BSR sping 2005). Dpitimiliti in th wy th two pojct mout wok to volunt, thy two dintthing, y andon, nd both cn vn bun t th m tim. seTI@hom u youpoco. stdut@hom u you binnd ybll.

andon hop tht stdut@homwill hlp to dmoctiz cinc, llowingpopl o ll g nd bckgound to ptici-pt in th dicovy poc, nd ccodingto Wtphl, thi t-o-it-kind ndvo imony wll pnt.

Th stdut miion h cot $200 mil-

lion ov it tn-y litim, which Wtphlput into ppctiv bout th ly o wll-pid bbll ply. Fo cinc bu,stdut@hom i gnd lm.

chaRlie emRich is a graduate student inbiophysics.

Want to know more? Check out:stardustathome.berkeley.edu

Parts o this story originally appeared in the August 9, 2006 edition oThe SacramentoBee, where the author interned under the

AAAS Mass Media Fellowship Program.The ethereal aerogel is one thousand times less dense than glass, giving

it the appearance o solid smoke.

The collector grid, made o 132 tiles o aerogel, scoops up dust in its path. Tracks o cosmic dust.


20/52

FoundationsforExcellence

FEAT

URE

0

A view of the East Bay fromthe Molecular Foundry.


21/52

For those whove spent years scurry-

ing to avoid careening backhoes, hard-hat-

ted laborers, and the sweet siren song of the

jackhammer, it will come as no surprise: new

buildings are popping up all over campus.

Fortunately for the Berkeley scientic com-

munity, this construction boom includes two

major research facilitiesLawrence Berke-

ley National Laboratory (LBL)s recently

completed Molecular Foundry and the new

Stanley Hall, scheduled to open in March.

Each promises to provide new collaborative

opportunities to scientists in and around Cal,

as the Berkeley Science Review recently saw

rsthand while touring both facilities.

Lost and foundry

A six-story, cantilevered edice jutting

over the edge of the Berkeley hills, the new

Molecular Foundry is an imposing struc-

tureand as a agship facility of the National

Nanotechnology Initiative, it should be. The

federal government spent $85 million to con-

struct and equip the Foundry, which is one

of ve Nanoscale Science Research Centers

funded by the Department of Energy (DOE);

beginning in 2007 this will be augmented by

an operating budget of $1819 million per

year. The result, says Associate Director JimBustillo, is a real centerpiece of the basic en-

ergy sciences division within the DOE.

Providing core facilities and research

space to a burgeoning community of perma-

nent and visiting researchers, the building is

intended to foster innovation and interdis-

ciplinary collaboration in nanotechnology, a

growing eld that explores the properties

and uses of materials mere billionths of a

meter large. Says Bustillo, The key is to bring

in organic chemists and inorganic chemists

and biologists and theoreticians who are all

doing their own thing, shake it all up, and see

what happens. To ensure a fertile mixing of

knowledge and expertise amongst Foundry

researchers, interaction was a big theme

with the facility from the design on up,

states building manager Joe Harkins. Weve

tried to make areas where paths will cross,

that are nice places to aggregatewhere

people will stay and exchange ideas.

True to this vision, coffee lounges are no

longer traditionally dismal, uorescent-lit base-

ment affairs. Instead, the architects capitalized

on the buildings commanding hilltop views

of the East Bay, installing kitchenettes, reading

lounges, ofces, and meeting rooms along the

scenic western face of the building.

But appeasing scientists who want some-

place scenic to imbibe caffeine is relatively

simple. Far more challenging is meeting the

technical and environmental requirements

of a facility that houses agonizingly precise

nanotechnological research. The minute ef-

fects of particulates in the air, imperceptible

vibrations, or even ambient electromagnetic

(EM) elds can disrupt research conduct-

ed on the scale of individual molecules. As

Bustillo points out, One dust particle ordandruff ake is a huge boulder compared

to the features that were [working with],

and the tunneling electron microscope in a

neighboring building is reportedly sensitive

enough to record the impact of waves on the

shore miles away.

To insulate delicate instruments from

stray vibrations caused by ocean waves,

street trafc, or other environmental

sources, the Foundrys rst two oors are

A real estate boom is changing Berkeleys scientic landscape.

Foundations

of Excellenceby Tracy Powell


22/52


FEAT

URE

underground, surrounded by thick retaining

walls tied directly into the foundation slab.

Commenting on the eerie silence of the

lower levels, Bustillo elaborates, All of the

pumps, all the compressorsall those things

that hum in the basement of every building

on campuswe dont have them here. In-

stead, basic mechanical support equipment is

housed in a separate two-story, underground

facility connected to the Foundry via a ex-ible foamboard accordion joint that pre-

vents transmission of any vibration. Layers of

acoustic insulation paneling along the walls of

underground labs add another protective el-

ement; conversations held in the dead silence

of these basement cells sound at and muf-

ed, robbed of the slightest reverberation.

Despite these precautions against vibra-

tion, tiny uctuations in EM elds can also

cause trouble. For instance, says Harkins,

even the mass of the elevators counter-

weight moving through the earths magnetic

eld creates an electromagnetic disturbance

that can be problematic. In one case, it was

a simple matter to locate the lab housing a

sensitive scanning tunneling electron micro-

scope in the center of the building, as far

away from the two elevator shafts as pos-

sible. (Researchers later decided the micro-

scope would t better in a larger room, ten

feet closer to one of the elevator shafts. Its

not yet clear whether additional shielding

against the elevators counterweight will have

to be installed.)

Other architectural tricks to minimize

unwanted EM elds are more subtle. For

instance, even when sheathed in concrete,

a buildings reinforcing steel can channel

enough ground current to disrupt sensitive

instruments. For the Foundrys rst three

oors, which house such instruments, the ar-

chitects therefore used special epoxy-coated

steel to prevent EM conduction. Directly un-

der the most sensitive equipment, the rebar

was replaced entirely with berglass rein-

forcing bars. Additionally, instead of standard

AC electrical wiring, which carries electrical

current in a single phase with a strong back-

ground signature that may show up in sensi-

tive nanoscale measurements, the architects

installed multiphase wires. These split the same

electrical current into three staggered phases,

minimizing EM noise. Pairs of multiphase

electrical wires were then twisted around oneanother during installation, further minimizing

electromagnetic interference.

While these elaborate measures provide

the Foundrys electron microscopes with op-

timal working conditions, a series of special

rooms on the second oor protects against

another hazard: particulate matter. Paint

akes, bacteria, worn particles from tools or

instrumentsall can disrupt nanoscale ma-

terials. As Harkins points out, however, The

biggest contaminant in a clean room is the

people you put in there. According to indus-

try sources, a single person sitting motionless

sheds enough skin, hair, and liquid droplets

to produce 100,000 microscopic particles

each minute; by moving around, the number

jumps to 5,000,000 particles per minute. (Its

best not to contemplate what happens if this

hypothetical person sneezes.) Encasing re-

searchers in puffy white bunny suits helps

to minimize the blizzard of tiny particulates,

but its only part of the solution.

To scrub minute debris from the en-

vironment, the Foundry boasts a Class-100

clean room, which ensures that each cubic

foot of air has fewer than 100 particles larger

than 0.5 microns. Encased in glass and vis-

ible from the hallway through large bay win-

dows, this ultra-clean nanofabrication room

uses approximately 150 lter units to clean

and circulate air. But cleanliness comes at a

price: All those hard-working fans and lters

vibrate, disrupting sensitive equipment. Each

lter unit was therefore designed so its activ-

ity can be individually, temporarily dampened

while sensitive fabrication functions are un-

derway, then reactivated when these delicate

processes are complete.For the truly meticulous scientist, a sec-

ond, even more stringent clean room is nest-

ed inside the rst, permitting only ten 0.5-

micron particles per cubic foot of air. Built

specically to house the Foundrys electron

beam lithography system, which can print

features 10,000 times smaller than a human

hair, this Class-10 clean room also permits

exquisite control over humidity and tem-

perature, which can be maintained to within

0.1 F of a given target.

Above this suite of ultra-clean nanofab-

rication rooms, spacious laboratory, comput-

ing, and ofce areas ll the four upper levels

of the Foundry, which project out over the sur-

rounding hillside. (In this, the building embod-

ies faith in science beyond a multimillion dollar

investment: You have to really trust modern

seismic technology to sit atop the Hayward

Fault, calmly thumbing through Nature, while

cantilevered out over the edge of a cliff.)

When asked how the cantilevered lay-

out gured into the buildings design, Bustillo

laughingly recalls that one of the premiere

characterization instruments for a nano-

technologist is an atomic force microscope

(AFM), the [essence] of which is a little sili-

con cantilever tip. The architects claimed that

the grand scheme design for this building was

symbolic of a gigantic AFM tip. According to

Harkins, they also described the Foundry as

a bridge to the campus and beyond.

When a building inspires that many

overheated architectural metaphors, the

We didnt want to build an-

other Evans monstrosity.


23/52

designers have probably been successful on

some level. But architecture isnt the only

standard of success; ultimately, Bustillo as-

serts, well be measured by the quality of the

science that we do, the number of satised us-

ers that we have, and how nanotechnology is im-

pacting the economy. Only time can prove the

Molecular Foundry a success on these terms.

Meanwhile, members of the LBL community can

settle into their new research spacea luxurytheir on-campus colleagues, impatiently awaiting

completion of the cutting-edge Stanley Hall, are

anxious to enjoy.

Stanley 2.0

A combination of seismic instability and

outdated facilities led to the demolition of

the old Stanley Hall in 2003. Now, its copper-

tiled successor has nally been erected on

the same site as the original, near UC Berke-

leys East Gate. At 11 stories and 285,000

gross square feetmore than four times

larger than its predecessorthe new facility

represents a signicant increase in modern

research space on campus. (So modern, in

fact, that with 6,000 control pointsinclud-

ing temperature sensors, alarms, and other

electronic and mechanical controlsStanley

Hall alone accounts for a 20 percent increase

in control points on campus.)

Though the building is massive, much

of its bulk is distributed in three basement

levels; as a result, its silhouette hugs the hill-

side rather than towering over eastern cam-

pus. We didnt want to build another Evans

monstrosity, says Susan Marqusee, professor

of molecular and cell biology and lead faculty

advisor throughout the buildings design and

construction. It had to be beautiful, and we

didnt want to give a sense of it being too

huge, too monolithic.

Though effectively disguised from pass-

ersby, the buildings large size is necessary to

fulll several functions. These include harbor-

ing six scientic core facilities that will serve

the campus community: mass spectrometry,

protein purication, functional genomics,

proteomics, nuclear magnetic resonance(NMR) imaging, and a new biomolecular

nanotechnology fabrication center: Stanley

will also contain teaching laboratories, class-

rooms, and lecture halls that together will

accommodate up to 450 students. The build-

ings principal role, however, will be to house

the laboratories of 36 faculty members who

participate in the California Institute for

Quantitative Biomedical Research (QB3), a

cross-disciplinary organization intended to

spur collaboration between quantitative and

biomedical researchers.

As host to QB3, the buildings central

purpose is, like the Foundry, to foster inter-

actions between disparate scientic disci-

plinesin Stanleys case bridging computa-

tional biology, tissue engineering, chemistry,

physics, and molecular and cellular biology.

Marqusee explains, We were looking for

much more than just cohabitationwewanted to foster active collaboration. To

enable these interactions, the architects in-

stalled social areas (workrooms) on every

oor, each complete with kitchen, computer

stations, cubicles, and whiteboard walls for

spur-of-the-moment, cross-disciplinary brain-

storming sessions. An on-site caf just outside

the buildings main entryway will offer anoth-

er venue for impromptu discussions.

But beyond these social areas, Stanleys

architects had a subtler strategy to promote

interaction: The laboratories were designed

with an emphasis on common space, placing

freezers, centrifuges, tissue culture rooms,

and other equipment in central areas away

from individual labs. Harry Stark, QB3s facili-

ties and engineering director, explains, You

give people a home, but you dont make the

home complete, so that they need to go out

into the neighborhood in order to get their

job done. By being in the neighborhood they

bump into each other, work with each other,

communicate, and develop ideas that they

might otherwise not have.

This mischievous sense that scientists

need rm architectural prompting before

theyll venture forth to socialize pervades

the designs of both Stanley and the Molecu-

lar Foundry. But do Berkeley researchers re-

ally need this sort of prodding? Judging from

the enthusiasm of Stanleys future residents,

they do not. Dan Fletcher, a bioengineering

professor who will work in the new building,

asserts that the collaborative atmosphere

is going to be very exciting. Im a strong

believer in proximity being a real motivator

for research, and I look forward to interact-

ing with colleagues on a much more regularbasis. Marqusee concurs, stating, Stanley

should create a new intellectual environ-

ment, and everyone is excited to strike up

collaborations that wouldnt have happened

without the building.

This enthusiasm will serve Stanleys new

residents well, given that they will have an

extra motive to talk science with their col-

leagues: The University plans to make the

building available for outside conferences

Facing page: Because certain wave-lengths of light can damage photosensi-tive materials inside, only yellow light isused inside clean rooms at the MolecularFoundry (left). Brand-new glove boxes,which allow researchers to manipulateexperiments in an oxygen-controlledatmosphere, await use in the MolecularFoundry (center). Snorkel exhaust fanswill act as exible fume hoods in StanleyHall (right). Above: An artists renditionof Stanley Halls nished faade (top);Stanleys current appearance (center).A view from an interaction room atthe Molecular Foundry (bottom).


24/52


FEAT

URE

and meetings for part of each year. Normal-

ly, says Stark, general assignment classrooms

are used year-round, so if someone wants to

have a professional conference, they cant do

anything on campus because they dont know

two years in advance if a room will be avail-

able. To ease this situation, the registrar has

opted not to schedule classes in Stanley dur-

ing the summer, leaving it available for meet-

ings and symposia.

Indeed, the four-story, windowed atrium

just inside the main entrance has ample space

for poster sessions, breakout groups, or re-

ceptions after talks in the large lecture halls.

Between such special events, the entry halls

lofty skylights, tiered balconies, and modernist

glass chandeliers will provide an attractive hub

to the bustling building, which will eventually

house as many as 700 full-time workers. Merci-

fully, Stanleys designers avoided the spiral-stair-

case-as-DNA motif that has become so mo-

notonously common in science building lobbies

of the past few decades. Instead, the atrium will

be graced by a series of works by contempo-

rary artist Sarah Sze in glassed recesses.

But for many researchers on campus,

these architectural niceties are beside the

point; they just want a laboratory to call

home. In a process reminiscent of sliding

block puzzles, where mobile squares are end-

lessly toggled into a single free space, faculty

members displaced from the original Stanley

(or newly arrived since its demolition) have

been shufed around campus for years while

the new building is completed.

As Fletcher, hired four years ago in an-ticipation of the completed QB3 facility, diplo-

matically phrases it, We have had the oppor-

tunity to experience several of the campuss

facilities. Some of these proved more hospi-

table than othersat one point his lab was

housed, briey, next to the civil engineering

departments concrete testing facility, which

posed some vibration issues for the labs

high-resolution microscopy experiments. Re-

location to OBrien Hall brought respite from

quivering concrete slabs, but Fletchers atomic

force microscope and suite of sensitive optical

equipment ultimately require modern, low-

vibration facilities for optimal performance.

The new Stanleys low-vibration facilities will

therefore provide a welcome haven from the

noise of a busy campus.

As previously noted by Chancellor Birge-

neau (see BSR, Spring 2005), the lack of cut-

ting-edge facilities on campus has sometimes

hampered research efforts by scientists like

Fletcher. In part to address this problem, Stan-

ley Hall will introduce several new high-tech

features to campus. In particular, the lowest

basement level is anchored to bedrock, which,

along with antivibration shielding of mechani-

cal equipment, provides an exceptionally stable

substrate for delicate equipment. Two EM-

shielded slabs in the deepest portion of the

building are isolated from the rest of the build-

ing via exible joints, providing an even more

sheltered environment (one of these slabs will

house Fletchers sensitive optics equipment).

Also found on Stanleys lower levels is

the Central California Ultra High Field Nucle-

ar Magnetic Resonance (NMR) Imaging Facil-

itya huge, vaulted basement chamber nearly

as impressive as its name. Of the twelve NMR

machines to be installed there, several will be

shifted from other campus locations. Their

magnets range in strength from 150700 MHz,

but a brand new, 900 MHz shielded NMR (one

of only 1012 in the world) has also been

ordered. Accommodating this equipment re-

quires a large facility because the magnets are

far too massive to t the connes of a stan-dard oor. The powerful magnetic elds they

generate can also be a health hazard to any-

one with a medical implant; the vaulted ceiling

therefore provides enough vertical space to

buffer the upper oors from the magnets.

In addition to the NMR suite, another

new facility making its campus debut will be

the Biomolecular Nanotechnology Fabrica-

tion Center (BNC). The BNC, a series of clean

rooms equipped with equipment for generat-

ing minute devices and materials, will allow

manufacture of nanoscale tools for studying

the behavior of cells and molecules. The facili-

ty will share many capabilities with Cory Halls

Microfabrication Laboratory, but with one vi-

tal difference: the BNC will permit biological

materials, generally considered a contaminant

in traditional microfabrication facilities. This

will allow Stanleys researchers to apply na-

noscale sensors and other fabricated materi-

als to biological systems.

Fortunately, Fletcher, Marqusee, and their

fellow researchers wont have long to wait

for all of these new facilities. In an elaborately

choreographed migration, the rst of Stanleys

new occupants will arrive at their new home

in March 2007. Rather than contend with

hundreds of scientists stampeding into the

building (Just cut the ribbon and everybody

runs! quips Fletcher), different labs will arrive

in staggered shifts over subsequent months.

Final landscaping, including restoration of the

reecting pool currently buried under por-

table construction trailers, should then be

completed by October 2007.

And for many, its about time. After being

blighted by years of construction (neighbor-

ing Hearst Mining Hall underwent a three-

year seismic retrot shortly before Stanley

was demolished), Hearst Mining Circle could

do with a return to pastoral calm. Hopefully, Stan-

leys researchers will conclude that their new

home was worth the tumult, and the wait.

Construction on StanleyHall nears completion (left).A view of Stanleys faade,including the pavilion thatwill house a coffee stand(right).

a

llPhotosbytracyPowell

Tracy Powell is a graduate student in plant and

microbial biology.

wanttoknow more?http://foundry.lbl.gov/index.html

http://qb3.org/stanleyfactsheet.htm


25/52

Rare and ound only in remote alpine terrain, this in-

sect, ound by ESPM graduate student Sean Schoville,may be a new species o ice crawler.

Where the WildThings Are

High bov th tlin in th Tho

Bin Doltion Wildn, sn

schovill co th nowld,

bcd gint th cold. amd with high-

powd hdlmp nd inct-collcting vil,

h wp th nowy uc hd ching

o btl, hd don countl tim b-

o. But on thi pticul night, und th

moonl ky, h omthing dint: n

inct, lg thn ny o hi btl, cingco th now hd o him with tound-

ing pd. Goldn nd ft-bodid, with long

ntnn, thi i omthing unuul.

A rare new species?schovill, gdut tudnt in th

dptmnt o nvionmntl cinc, policy,

nd mngmnt (esPM), knw immditly

tht th inct blongd to goup clld th

ic cwl, mmb o mll od clld

th Gylloblttod. r nd ndmic to

high lpin tin, thy hunt th nowld

t night, ching o inct blown in om

low lvtion nd ozn in th now. H

tnpotd th ic cwl bck to th lb,

ttmpting to dtmin how long it h bn

ioltd om oth known popultion. Thu

, th dt uggt tht thi individul, nd

oth schovill h inc ound in th Whit

Mountin on th Clioni-Nvd bod, mmb o vy ditinct popultion o

Gylloblttid, php vn nw pci.

spci dicovy ing o bygon

, whn th lik o Chl Dwin t

cou o ditnt lnd nd hippd hom

poo o tng nw ctu in th om

o plt, ktch, nd bon. Biologit by

td, th mn w lo intpid xplo-

nd globtott, nd th ctu thy

ound w nmd o xotic loction o

oigin. Tody, th qut o nw ognim

continu, nd modn-dy incntion o

Dwin xit ight und ou no. Wllmn

Hll nd th Vlly Li scinc Building

hom b o uch ho: UC Bkly

biologit who tvl nd wid to ngg

in cintic tudy, dicoving nw pci in

th poc.

In th ld o ntomology, pci di-

covy i otn condy to bod cinticqui into volution, cology, bhvio, nd

bioytmtic. Fo xmpl, schovill tudy

o th ic cwl will ocu on whth

thi divity nd ditibution i linkd to

glcil hitoy. Likwi, Mtt Mdio,

gdut tudnt in intgtiv biology, h

dicovd vl nw pci in th poc

o invtigting th volution o fightln

in cv-dwlling moth. som inct lb,

howv, uvy mot pciclly


26/52

FEATURE

BerkeleyCritters

o th pupo o uncoving nw pci.

rcntly, th rodick nd Gillpi lb in

esPM hv won gnt to uvy th socity

Ilnd n Thiti, whil elizbth ai, potdoctol ch in th Gillpi lb,

h civd gnt to ch o nw ogn-

im in Chil.

Uncharted biodiversityscintit timt th totl numb o

pci on eth to b ound 9 to 20 million,

lthough th ot-citd bod ng o 3 to

112 million btt illutt th unctinty.

Pnt knowldg o th pci i mg.

Humn hv nmd 1.5-1.8 million pci

to dt, but only 1 pcnt o tho hv bn

tudid in ny dtil byond bic chct-

iztion o hbitt nd ntomicl tu.

Dicovi o lg ognim lik mmml

o bid till occu tody, but thy .

Mot nw pci dicovd o mll

ilk: ungi, bcti, nd inct. Mnwhil,

pci going xtinct in cod numb,

nd ch dpt to idntiy nd

tudy novl pci bo thy dipp o

good.

Though mny nw pci ound in

mot plc, om toi un count to

th img o th lonly cintit ld in

mudboot. Pt Oboyki tll on uch toy.

an esPM PhD tudnt, h tudi Hwi-

in moth gnu clld Cydia, bownih-gy

moth who lv might b th wom you

whn you bit into n ppl. To dt,

Oboyki h dicovd ou nw pci o

Cydia. Whil woking in th low lvtion

o Kuui, otn dimid by cologit too

dgdd by humn o pci dicovy,

Oboyki toppd on night long th id

o highwy. a c dov by, h t up hi

moth collcting pptu, ht with n

ultviolt light ttchd, tinging on nd to

tlphon pol nd th oth to pd limit

ign. I thought Id hv no chnc, Oboyki

id. Imgin my upi whn within v

minut, nw pci howd up.

What qualies as dierentenough?

Dtmining whth nwly-dicov-

d pcimn i tuly novl pci i

not lwy y. In th opning cn o th

movi Arachnophobia, goup o cintit

tvl to mot con o inot in

Pu: a pid ll out o t, nd thy

xclim, W ound nw pci! stv

Lw, PhD tudnt in th Will lb o esPM,

mil t thi potyl. In lity, you og

t in th amzon nd lg numb o

pid ll out, mny o which pobbly

nw to cinc. But you not going to know

o long tim. Th poc o cliying

th individul cn b tim-intnivdy

t th micocop, nd wk poing though

book nd conulting xpt. Th

thound o pid tht nw to cinc

itting in j in ntomology collction

ound th wold, nd mot o thm go-

ing to ty undcibd o whil, y Lw.

at thi point, I dont vn know how mny

nw pci Iv ound in Clioni.

Futh complicting mtt, ou no-

tion o wht xctly contitut nw p-

ci continu to volv. Tditionlly, pci

w dnd ognim tht would not o

could not mt with on noth to poduc

til oping. But thi dnition i not

pticully uul o pci tht poduc

xully (lik ungi), o tht cpbl o

coing pci boundi to bd nd

om hybid (lik ok t). Dogm lo

onc hld tht nw pci would look

phyiclly dint om ny oth, vn ith dinc w vy ubtl.

Now, dvnc in molcul biology hv

chllngd th convntionl viw. rcnt

ch h hown tht vn whn th

no ppnt mophologicl dinc

btwn two goup o ognim, th cn

till b molcul o bhviol dinc

tht hv gt impotnc. Th inviibl

dinc cn pvnt th individul om

BerkeleyCritters

Integrative Biology graduate student

Matt Madeiros is happy to explore this

cave in his studies on the evolution o

fightless moths.

ESPM graduate student Pete Oboyski has identied sev-

eral new moth species within the Hawaiian Cydia genus.

NomenclatureWhen you discover a new species, you dont get to name itrst you must describe it. To assist

you, theres a big book o rules. The International Code o Zoological Nomenclature is a set o rules

in zoology that has one undamental aim: to provide the maximum universality and continuity in

the naming o all animals according to taxonomic judgment. The code is meant to guide only the

nomenclature o animals, while still leaving zoologists some degree o reedom in classiying new

species and higher-level taxa. In other words, whether a species itsel is or is not a real entity is a

subjective decision, but what name should be applied to it is not. Regarding naming ater yoursel: Its

not a hard and ast rule, but some consider it poor orm to bestow a new species with your name.

Better to name it so it tells something about where it lives, what it eeds on, and how it looks.

PhotoCouResyofseansChoville

PhotoCouResyofPeteoboysKi


27/52

cognizing ch oth mt ky

tp in th pcition poc. It i uncl,

howv, whth uch popultion quliy

pt pci. Whil th vilbility

o inxpniv DNa quncing h md

it i to comp potntilly nw pci

with xiting on t th lvl o th gnom,

th i now qunt contovy ov how

much o dinc i quid to dw th

pci lin. Oboyki cution, Though itlookd lik th molcul volution w go-

ing to olv ou poblm, wv now lizd

tht w till cd with qution. Wht

quli dint nough? W till hv to

intpt th ult.

Get em beore theyre goneWhil cintit nvigt th txonomic

jungl o pci idntiction, th ugnt

nd o dicovy bcom ll th mo

cl. spci continu to go xtinct in cod

numb: ccoding to th Wold rouc

Intitut, 100 pci go xtinct ch dy

(ou vy hou) du to topicl dot-

tion lon. Moov, pci lo xtnd

byond th topic. Th By a ntiv

Xc Blu buttfy (Glaucophyche xerces),

o intnc, w lt n in 1943, nd i

th t buttfy in Noth amic known to

hv gon xtinct du to humn ditubnc.

a om inhbitnt o th vt nd dun o

sn Fncico, it hbitt w lmot ntily

dtoyd by ubn dvlopmnt. schovill

ic cwl my pnt pci who

utu i unctin; und ctin climtchng cnio, much o Clioni glci

nd nowpck i thtnd. Hopully,

Bkly cintit will continu to unth

nw pci in thi qut o nw

bout volution, niml bhvio, nd col-

ogybo th ubjct thy nd dipp

o good.

letty BRoWn is a graduate student in environ-

mental science, policy and management.

Want to know more? Check out:

The International Code of Zoological No-

menclature: www.iczn.com

I its not a new species, its a new trait. Dan

Rubino, a proessor at the University o

Hawaii (who holds his undergraduate, masters,

and doctoral degrees rom UC Berkeley) and

members o his lab have discovered several species

o carnivorous caterpillars. Another Hawaiian

caterpillar, Hyposmocoma molluscivora has evolved

a novel trait: It hunts snails. In the July 2005 issue

oScience, Rubino describes how the caterpillar

captures its prey. Once it nds a resting snail, thecaterpillar spins a web o silk rom the snail shell

to the lea to capture and immobilize the snail.

Then it sidles up next to the trapped snail and

pursues it down the shell, Rubino says, literally

eating it out o house and home. There have

been other examples o specialized predatory

behavior in Hawaiian Lepidoptera larvae, but these

new species represent the rst time a carnivorous

caterpillar has eaten anything outside its own

phylum. It is also the rst case o a caterpillar using

its silk to capture prey.

Snail-eater


28/52

StrungOutatBerkeley

FEATURE

Wht xctly w md o? Dpnding on whom you k t UC Bkly, nw to thi qution could ngom cll ( biologit) to tom ( chmit) to I m lg, I contin multitud (n englih poo). Butk phyicit, nd you my jut gt th tngt nw yt: on-dimnionl vibting ting. Indd, mnyphyicit tody bliv tht th ting ctully th mot undmntl contitunt o th univ. Thy mk upth ubtomic pticl tht mk up th tom tht mk up ou bodind vything l in th wold. Much oth ch in thoticl phyic tody volv ound ting thoy bcu o th pomi it hold o xpliningvything om th oundtion o mtt itl to th oigin o th univ. Phyicit nd mthmticin h t UCBkly on th cutting dg o thi xplotion into wht h bn clld th thoy o vything, tudying topicnging om xotic typ o blck hol to why th univ hppn to hv jut th ight popti to utin li.

From a drop o watera logician could iner thepossibility o an Atlantic or a Niagara without having

seen or heard o one or the other. So all lie is a greatchain, the nature o which is known whenever we areshown a single link o it.Sir Arthur Conan Doyle

Strung Out at Berkeleyby Meredith Carpenter


29/52

Its all relativeTo undtnd wh ting thoy i

going, w mut t tk whilwind touo th lt hundd y o phyic to un-dtnd wh it cm om. In 1905, albteintin popod hi goundbking thoyo pcil ltivity. Thi thoy contdictdIc Nwton notion o bolut pc ndtimwhich w th pdigm in phyico hundd o yby popoing tht

tim nd pc v-chnging contucttht pcivd dintly dpnding onth obv. Th ct not noticd invydy xpinc (which i why Nwton

qution cn till ccutly dcib howt bll will oll down mp), but thycom into ply mo nd mo objct p-poch th pd o light. although it mconty to th wy w xpinc th wold,

n tonut tvling in pc would gmo lowly thn hi twin both on ethbcu hi high vlocity infunc th p-g o tim.

spcil ltivity w monumntlchivmnt, but it hd on poblm: It didnot ccount o gvity. It took eintin 10mo y to omult hi thoy o gnl

ltivity, which xtndd pcil ltivityto includ gvity with noth thhkinginight: Gvittion i not du to oc butth to th cuving o pc nd tim. Fomthmticl pupo, phyicit combinth th dimnion o pc nd th outhdimnion o tim into tuctu clldpctim, which i otn nvigd ttchd-out bic. I plnt i itting onthi bic, it cuv pctim much lik bowling bll ting on tmpolin. Moonnd plnt ty in obit bcu thy tppd in th cuvd gion o pctimtht ult om th mo miv plnto un. a th mou amicn phyicit John Whl xplind, spctim gip

m, tlling it how to mov, nd m gippctim, tlling it how to cuv.

Quantum leapeintin union o pcil ltivity nd

gvity in th thoy o gnl ltivitywok xtmly wll on th lg iz clo cltil bodi nd th univ, but thingttd to gt vy hy whn chuch Mx Plnck, Wn Hinbg,

nd ewin schding tudid intctionon mll cl. Th dicovy tht wvcould b mud in mll pckt o ngyclld qunt ld to th bnch o phy-

ic known quntum mchnic, whichdcib th bhvio o mtt on th x-tmly mll tomic nd ub-tomic cl.Thi i tng wold, wh photon, thcontitunt o light, hv both pticl-lik

nd wv-lik popti; wh Hinbgunctinty pincipl tt tht on cnnv imultnouly mu both th poi-tion nd th momntum o ubtomic p-ticl with pct ccucy bcu th ct omumnt itl mk th mumntunctin; nd wh two ptilly ptdpticl cn b ntngld uch tht thi

phyicl popti lwy coltd

berkeley science review - fall 2006

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