Berkeley Science Review - Spring 2006

BERKELEY SCIENCE REVIEW SPRING 2006 1

B E R K E L E Ysciencereview

Spring 2006 Issue 10

Berkeley vs. Intelligent DesignThe Dawn of MulticellularityEthical Technology Licensing

BSR turns 10 Origins of Chocolate A Star is Born Congress 101 Pennies from HellPlus:

Editor in Chief

Jessica Porter

Managing Editor

Wes Marner

Art Director

Jack Lin

Copy Editor

Tai Po Ping

Editors

Meredith Carpenter

Michelangelo D’Agostino

Charlie Emrich

Wendy Hansen

Jacqueline Chretien

Charlie Koven

Chief Layout Editor

Andrew DeMond

Layout Editors

Charlie Emrich

Wendy Hansen

Jessica Porter

Kathryn Quanstrom

Printer

Sundance Press

© 2006 Berkeley Science Review. No part of this publication may be reproduced, stored, or transmitted in any form without express permission of the publishers. Financial assistance for the 2005-2006 academic year was provided by Lawrence Berkeley National Lab; the UC Berkeley Office of the Vice Chancellor of Research; the College of Natural Resources; the UC Berkeley Graduate Assembly; the Space Sciences Laboratory; the UC Berkeley Office of Research and Development; and the Associated Students of the University of California (ASUC). Berkeley Science Review is not an official publication of the University of California, Berkeley, or the ASUC. The content in this publication does not necessarily reflect the views of the University or the ASUC. Letters to the editor and story proposals are encouraged and should be e-mailed to [email protected] or posted to the Berkeley Science Review, 10 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 ,

It is my pleasure to introduce you to this, the 10th issue of the Berkeley Science Review. Beginning with our first issue published five years ago this spring, the BSR has time and again brought you the best of Berkeley’s research in areas as diverse as astronomy, ethnobotany and immunology. For me, this is the 4th issue I have taken part in–and it really does keep getting better and better!

In this issue we take a look back at some of the BSR’s memorable stories and give you updates on the latest progress (p. 6).

New this spring, Michelangelo D’Agostino takes a hard look at UC Berkeley’s role in the controversy surrounding teaching evolution in public schools (p.31). Former BSR editors Temina Madon and Heidi Ledford tell us about how scientists can talk to policy makers (p.43), and what to expect from the world of intellectual property licensing (p.36) respectively. Jesse Dill and Harish Agarwal report on a possible resolution to a long-standing debate over star formation (p.12). Returning “Who Knew” columnist Louis Desroches debunks another science myth–the legend of the lethal penny (back cover).

Also new to the BSR, starting this fall we will be offering paid subscriptions to the magazine. So if you want to guarantee delivery of each BSR right to your door, or if you want to read our submission guidelines, peruse past issues, or check our upcoming events page, visit our website at sciencereview.berkeley.edu.

In the spirit of reflection brought on by this anniversary issue, I want to thank all of the editors, writers, layout staff, illustrators, donors and, of course, readers who have contributed to the success of the Berkeley Science Review these past five years. Many of our ranks have gone on to exciting careers in science journalism, public policy, and academia–and we continue to rely on incoming Berkeley students of all types to keep the magazine running.

In looking back on our first Editor in Chief ’s opening letter, I realized that his comments were just as true, and possibly more chilling today than ever. To quote Eran: “If my advisor knew how much time I’ve spent on this…he’d boot me out the door. I’d be working at Andersen Consulting as fast as you can say ‘creative business solutions’.”

Enjoy the issue,

Jessica Porter



COVER: SINGLE-CELLED ORGANISMS SUCH AS THOSE IN THE DRAWINGS ON THE FRONT AND BACK COVERS BY W. SAVILLE KENT MAY REVEAL HOW ANIMALS EVOLVED TO BE MULTICELLULAR. STORY ON PAGE 16.

Categories

06 We Just Turned 10

08 Labscopes

12 Current Briefs

26 Main Features

48 Outreach

50 Book Review

51 Who Knew

Current Briefs

10 Like Beer for Chocolate

12 A Star is Born

14 Mammoth Rocks

16 United We Stand

18 H2YDROPOWER

20 Earthquake Prediction

22 Seeing Chemistry

24 Faster, Better, Smaller

review

Main Features

26 Getting Back To Nature

31 In The Matter of Berkeley v. Berkeley

36 IP: Ideas for Purchase

40 Science And Sustainable Development

Others

43 Congress 101

48 Field Trip

50 Slow Food

51 Who Knew

One of NASA’s many recent science successes, the RHESSI satellite is still taking pictures of

solar flares, four years after its 2002 launch. Designed and built at the Berkeley Space Science Lab, RHESSI was profiled in our first issue. It has been instrumental in studying solar flares—huge bursts of energy

released from the sun that can wreak havoc on electronics here on earth. Despite having an original mission life of only 2–3 years, RHESSI is still going, and has even trained its sights on Earth, imaging the gamma rays let off by lightning strikes. Pictures are downloaded to a dish in the Berkeley hills during its six daily passes. Who knows, it might be above you right now. —CE

Our second issue found Jessica Palmer exploring the lighthearted world of fruit fly gene names like cheapdate

(flies carrying the mutation get drunk easily) and the Monty Python-inspired I’m not dead yet (for longevity). But one gene, Pokemon, has really been in the news recently. An acronym for POK Erythroid Myeloid ONtogenic, the Pokemon gene was found to be associated with some human cancers. This

discovery prompted headlines like “Pokemon Causes Cancer,” leading Pokémon USA to exert its legal right to the trademark over the cartoon character. The gene is now called Zbtb7, but geneticists are undaunted—2006 has already witnessed the christening of enigma, serpentine, and big bang. —MC

Nanomachines! The word doesn’t roll off the tongue like “micromachines”, but they are coming nonetheless. They’ll be

replacing microelectromechanical systems, or MEMS, which now operate air bags and high-def TVs. Temina Madon explained

how the Maboudian lab was advancing the “MEMS revolution” by studying the material properties of these devices and

improving their fabrication. Now MEMS have shrunk into NEMS, and a nano-electromechanical revolution has begun. Today, the Maboudian lab is trying to make synthetic nanohairs that mimic the surface of the ultra-sticky gecko foot to generate

adhesives that stick to any surface, finally affording Lionel Richie his dream of dancing on the ceiling. —WM

In our Spring 2003 issue, Julie Waters reported on the successes that Geoff

Marcy and colleagues have had in spotting planets orbiting distant stars. At the time, they had discovered over 100 extrasolar planets orbiting 10 stars. Marcy and his band of planet hunters were optimistic about the upcoming mission of NASA’s Terrestrial Planet Finder, a satellite designed specifically to identify new planets. Since then, the news on planet finding has been mixed: While Marcy and colleagues have brought the list of known extrasolar planets to 172, the orbiting Planet Finder mission has been, in NASA-speak, “deferred indefinitely” due to budget cuts. —CK

BERKELEY SCIENCE REVIEW SPRING 20066

SP

EC

IAL

Our

10

th Iss

ue

AUTHORSSTAFF

We’ve just turned 10! (issues, that is) The BSR has covered a lot of ground since we

began, but since we’re always looking forward, we never get a chance to look back. Here, we follow up on a story from each of our issues...

Our first 9 issues were a lot of work and a lot of fun. Just yesterday, it seems, the BSR was merely an idea. Since then, grad students from all over the Berkeley campus have been slaving away to bring you what’s now the top

pop-sci student journal in the country. (our opinion)Huge thanks go to everyone who helped along the way: the authors, editors, and layout people; the artists and photographers; all the faculty members we’ve badgered for stories; all of our advisors for “not minding” that we weren’t in the lab; and most of all, YOU, for reading.The totals: 428 pages, 183,971 words, 53 staffers, 96 authors. (not quite Conde Nast, but we’re getting there)

Aaron PierceAdam SchindlerAinsley SeagoAlan Moses

Allison DrewAlysia Marino

Aman Singh GillAngie MoreyAngie Morey

Annaliese BeeryApril Mo

Ariana ReguizzoniAubrey Lau

Audrey HuangBen GutmanBill Monahan

Brendan BorrellCarol HunterChad Heeter

Charlie EmrichCharlie Koven

Cheryl HackworthChris Weber

Colin McCormickDaisy JamesDan Roche

Delphine FarmerEliane TrepagnierElizabeth ReadEmily SingerEran Karmon

Giovanna Guerrero

Heidi AndersonHeidi Ledford

Jane McGonigalJanes Endres Howell

Janet FangJeffrey Natchtigal

Jennie RoseJennifer SkeeneJennifer Skene

Jess PorterJessica MarshallJessica PalmerJimmer EndresJosephine LeeJoshua GarretJulie WaltersKaren Levy

Karen MarcusKaspar Mossman

Kira O’DayKristen DeAngelis

Letty BrownLisa R. Girard

Loraine LundquistLoren BentleyLorraine Sadler

Louis-Benoit DesrochesMarjorie James

Mark AbelMelissa Fabros

Merek SiuMichael Downes

Michelangelo D’agostinoMike Daub

Nathan BramallNathanael Johnson

Noah RolffNoam Sagiv

Padraig MurphyPrayana KhadyeRachel Shreter

Rachel TeukolskyRebecca Sutton

Robert C. FroemkeRoger O’BrientRussell Fletcher

Ruth Murray-ClaySahelt S. R. DattaSarita ShaevitzShefa GordonShena Gifford

Sherry SeethalerSheyna GiffordShirley DangSneha Desai

Stephanie EwingSteve BodzinSteven BodzinTeddy Varno

Temina MadonTheresa HoTracy Powell

Una RenWill Grover

Aaron GolubAinsley SeagoAmber Wise

Andy DeMondAngie MoreyAnna Ross

Antoinette ChevalierBryan Jackson C. Ric Mose

Carol HunterCarol Hunter

Charlie EmrichChris Weber

Christopher WeberColin McCormickDan HandwerkerDelphine Farmer

Donna SyDula ParkinsonElissa PrestonEran KarmonHeidi Ledford

Jane McGonigalJess PorterJesse Dill

Jessica Marshall

Jessica PalmerJinjer Larson

Joel KamnitzerJosephine Lee

Kaspar MossmanKira O’Day

Kristen DeAngelisLetty BrownLisa Green Merek Siu

Michaelangelo D’agostinoPadraig Murphy

Paul ChangSarita Shaevitz

Sherry SeethalerTania HaddadTeddy Varno

Temina MadonThomas Thomaidis

Tony LeTony WilsonTracy Powell

Una RenWendy HansenWes Marner

how the “mate

Photo courtesy of Kellar Autumn

Image Courtesy of NASArteoegadb

ISSUE

F

AL L 2 0

01

d“Prcnaws

ISSUE

SP

RI N G 2 0

02

ISSUE

F

AL L 2 0

0

2

ISSUE

SP

RI N G 2 0

03

It’s been a busy year for BOINC—the Berkley Open Infrastructure for Network Computing (boinc.

berkeley.edu). BOINC, which is based at the Space Sciences Laboratory, has been trying to make it easier for scientists to harness the massive computing resources that often lie dormant in people’s homes and offices. Harness it has: over 800,000 computers are now crunching away on fifteen BOINC-based projects. Its success has propelled it onto the cover of Science and into the pages of Nature. Now BOINC and climateprediction.net have teamed up with the BBC on a new climate change simulation that will be followed and televised on Britain’s BBC-4. —MD

The missile defense program won’t work. This was the gist of a review by the American

Physical Society reported last issue, pitting scientists against policy makers. Responding to the conflict, over 60 researchers last year signed a statement by the Union of Concerned Scientists (UCS) criticizing the Bush administration’s “distortion of scientific knowledge for partisan political ends.” They charge the administration with suppressing and manipulating the results of studies on global climate change and environmental hazards, as well as systematically removing voices of dissent from scientific advisory boards. The administration released a point-by-point rebuttal of the statement, but the UCS statement has continued to gather signatures—over 8,000 at last count.—JHC

It’s hard to start a new journal, especially if you want to make it freely accessible to the world. Ben Gutman reported the 2003 launch of the journal Public Library of Science

(PLoS) co-founded by Berkeley’s Michael Eisen. Less than two and half years later, the ‘library’ has grown by four : PLoS Medicine, PLoS Computational Biology, PLoS Genetics and PLoS Pathogens, with a fifth, PLoS Clinical Trials, set to launch later this year. In June of 2005, PLoS was ranked #1 among general biology journals—with an impact factor of 13.9—placing it among the most highly cited journals in the life sciences. Not bad for a publication that is barely older than the Schwarzenegger administration. —JP

When banks compete, you win, or so goes the slogan—but what about contracts for nuclear labs? 2004 marked the first time that the

University of California, which has managed Lawrence Berkeley, Lawrence Livermore, and Los Alamos National Labs since their formation in the 1940s and 50s, was forced to compete for their contracts. In April of 2005, UC received a 5-year contract to continue running Lawrence Berkeley, the lab closest to home. Last December, UC teamed up with industry to win a 7-year contract for Los

Alamos, out-competing the University of Texas and Lockheed Martin. UC’s recent contract successes are helping to quiet rumors of lab mismanagement and bode well for the Livermore contract, up for competitive renewal in 2007. —WH

Mind over body. This is what meditation

is supposed to achieve, and research by David Presti and

colleagues into the physiological effects of deep meditation in Buddhist

monks seems to confirm it. When we caught up with Presti this spring, he had just returned

from another trip to the monasteries of northern India. This time, Presti was there to teach, rather than to study, as part of the 7th annual Science for Monks workshop. Each December since 2000, a group of 50 Tibetan monk scholars have gathered at the Dehra Dun monastery to learn physics, mathematics, and neuroscience from leading western experts. —JP


SP

EC

IAL

Our

10

th Iss

ue

Photo courtesy of David PrestiPhoto courtesy of LBL

ISSUE

F

AL L 2 0 0

3

asmLr

ISSUE

SP

RI N G 2 0

04

fotpwgglf

ISSUE

F

AL L 2 0 0

4

ISSUE

SP

RI N G 2 0

05

ISSUE

F

AL L 2 0 0

5


LA

BS

CO

PE

S labscopes

Hmm ... fuzzy dots ... Or so you might think to yourself upon entering the lobby of the de Young Museum in San Francisco as you gaze at the

giant mural on the west wall. But this is no piece of abstract art. Rather, it’s an image of gritty realism. You are looking at the crystal lattice of

the material strontium titanate (SrTiO3) as seen by high-resolution transmission electron microscopy. As a commission for the de Young’s October

2005 reopening, German artist Gerhard Richter (one of the most expensive living artists in the world) created Strontium by manipulating micro-

graphs from researchers at the Max Planck Institute for Metal Research and then applying his signature blurring of images. In the mural we see this

material’s “perovskite” structure as horizontal lines of bright Sr-O columns separated by lines of more closely-spaced, alternating Ti and O columns.

Perovskites aren’t just pretty to look at though. Berkeley physicist Marvin Cohen’s theoretical studies of SrTiO3 in the 1960s played a role in the

discovery of the high-temperature superconductors, and materials scientist Ramamoorthy Ramesh is working on perovskites for nonvolatile RAM

that won’t lose your data when the power goes off. Strontium may be a glimpse inside your next computer. - David Strubbe

The archery range isn’t the only place you see a bull’s-eye. Another striking example—one million times smaller—occurs at the immune

synapse, a complex junction that forms between an immune system T cell and an infected or infection-detecting cell. The structure consists

of a variety of molecules which signal to each other, activating T cells and leading to a large-scale immune response. Among these molecules are

T cell receptors, which initially cluster at the periphery of the synapse. Eventually, the receptors move towards the inside of the bull’s-eye and

stop signaling. What happens if you block inward movement of these molecules? Researchers in Jay Groves’s lab at UC Berkeley have done just

this, using patterns of 100nm thick chromium particles as roadblocks to restrict the mobility of receptor clusters. One pattern blocked inward

transport of the receptors, forcing them to stay corralled on the periphery of the synapse. The peripheral receptors continued to signal, a result

that established a direct link between the spatial position of T cell receptors in the synapse and the duration of signaling. Apparently, hitting the

bull’s-eye of the immune synapse doesn’t score you any points, at least as far as signaling is concerned. - Hari Shroff

When did humans first enter the Americas? Most textbooks would say 11,500 years ago, so history was thrown for a loop in 2005 when

a team from the UK claimed to find 40,000 year old human footprints in Puebla, Mexico. Many archaeologists were skeptical of the

results because the footprints were found in carbon-poor volcanic ash, making the group’s radiocarbon dating methods questionable. More

troublesome, “the prints in Mexico were not arranged in [a right foot-left foot pattern]. There may have been two right footprints in a row and

then another print,” said Paul Renne, adjunct Professor of Earth and Planetary Science at UC Berkeley. A team led by Renne re-dated the rock

at 1.3 million years using argon dating—more reliable for material older than 50,000 years. Later, measurements of the latent magnetism of

the rock showed that the ash had to have cooled more than 790,000 years ago. With recent genetic studies suggesting Homo sapiens is at most

200,000 years old and data indicating the ash fell while still hot, it seems likely that the “footprints” are just dents in the ground. Despite the

initial buzz, a rewrite of human history is unlikely to star our 1.3 million-year-old, firewalking American ancestors. - Angie Morey

Anyone who has ever had the flu knows just how tempting it is to briefly sneak out of the house during those first few incredibly boring,

albeit highly contagious, days. “How many people could really be at the Tuesday matinee of ‘Harry Potter and the Goblet of Fire’?” you may

have thought to yourself. This type of reasoning can lead to a superspreading event in which an infected individual, dubbed a “superspreader,”

prolifically transmits a disease. Historically, models of disease propagation have ignored these events and treated all individuals as having the

same infectiousness. However James Lloyd-Smith, a recent graduate of the Getz lab at UC Berkeley, has confirmed that individual variability is a

key factor in the spread of many diseases. Measles, for example, was introduced to Greenland by a superspreading sailor who infected an aston-

ishing 250 people at a dance party. Lloyd-Smith’s work also demonstrated that these diseases exhibit a qualitatively different mode of spreading.

They are the high risk venture capitalists of the disease world: Prone to early extinction, they do exceedingly well only if they are lucky enough

to infect a superspreader. Therefore, intensive disease control (e.g., quarantine) of randomly selected individuals is more effective than uniform

but moderate treatment of the entire population in suppressing diseases that spread in this manner. Moreover, if we can learn how to identify

superspreaders during an outbreak, treatment of these individuals would be an effective method of preventing an epidemic. Unfortunately, this

makes a pretty strong argument for waiting to see Harry Potter on DVD. - David Richmond

Bull’s-Eye!

Firewalk With Me

Outbreak

Richter Scale


LA

BS

CO

PE

S


Nothing satisfies a craving like the subtle

flavors of fine chocolate. Every year, over

three million tons of cacao, the raw material for

chocolate, are produced worldwide. For a food

loved by so many though, the origins of cacao

remain a mystery. UC Berkeley anthropologist

Rosemary Joyce now thinks she may have found

the answer: beer.

Cacao is produced from the almond-shaped

seeds of the quirky rainforest tree Theobroma cacao,

a native of the Amazon and Orinoco river basins

(cacao is the name of the tree and its seeds while

cocoa is the name of the defatted powder made

from the finely ground seeds). The seeds grow in

pods hanging from the trunk of the tree. Monkeys

and other forest animals split these pods open

to reach the sweet, juicy pulp that surrounds the

30–40 seeds inside. Raw, the seeds are bitter and

inedible. To produce the raw material for chocolate,

they must be fermented, dried, and roasted.

No one knows when humans first began

to consume cacao. We do know that in the early

1500s, Columbus, Cortez, and other Spaniards

noted the widespread use of cacao throughout

Mesoamerica—the region of Central America

and southern Mexico that nurtured the Olmec,

Mayan, and Aztec civilizations. Joyce has recently

discovered chemical residues of cacao beverages

on pottery shards dating to 1100 BCE, but the use

of cacao could have begun even earlier.

Like Beer for ChocolateA Star is Born

Page 12

Earthquake Prediction Page 20

H2ydropower

Page 18

Like Beer for Chocolate

Mammoth Rocks

Page 14

Seeing Chemistry

Page 22

United We Stand

Page 16

UC Berkeley anthropologist Rosemary Joyce has discovered evidence of chocolate residues on Meso-american pottery from as early as 1100 BCE.

The Mayas and Aztecs believed that a feathered ser-pent god discovered cacao and gave it to humans.

The Origins of Cacao

Current BriefsTh

e O

rigi

ns o

f Ca

cao

All images courtesy of Michael Barnes

BR

IEF


For both the Mayas and Aztecs, cacao had

divine origins—according to their mythology, a

feathered serpent god discovered cacao and gave it

to humans. The Aztecs reserved cacao beverages for

priests, high government officials, important military

leaders, and occasionally for sacrificial victims.

The Mayas and Aztecs ground cacao beans

using the metate, a flat stone table with a stone

rolling pin. Nuts, seeds, herbs, and roasted corn

were sometimes added for flavor, and the mixture

was whipped or poured between vessels to create

a froth that kept the solids in suspension. Com-

pared to the modern melt-in-your-mouth choco-

late bar, cacao consumption for several centuries

was a gritty, foamy experience.

Joyce has also found evidence that before

making chocolate beverages, the early peoples of

Mesoamerica used cacao to produce a cacao chi-

cha (pronounced “chee-cha”), from the pulp sur-

rounding the seeds. Cacao chicha is one of many

fruit beers still common in Central America.

“Anthropologists like me have always as-

sumed that the chocolate beverages were the

basis for cultivation of cacao,” says Joyce, “but this

conventional argument puts the cart before the

horse.” She explains that the process of ferment-

ing and roasting cacao beans to produce chocolate

is so complex and the changes in flavor are so

dramatic that no one could have known the result

beforehand.

But where did humans first begin to ex-

periment with cacao and when did they make

the transition from chicha to chocolate? A good

candidate is the Ulua River Valley on the Atlantic

coast of Honduras. During its pre-European popu-

lation peak from 1000–1500 CE, the valley floor

was home to extensive cacao plantations covering

thousands of acres. Radiocarbon dating has placed

the earliest settlements in the Ulua valley at 1650

BCE, among the earliest settlements discovered

in Mesoamerica. Joyce, currently the chair of

UC Berkeley’s Department of

Anthropology, has been traveling

to the valley since 1977 to docu-

ment these settlements.

Joyce can trace the transition

from chicha to chocolate to 900

BCE, plus or minus a century. Her

estimate is based on the changing

shape of bottles that contain resi-

dues of theobromine, a chemical

that is found only in cacao and its

South American relatives. Work-

ing with Patrick E. McGovern of

the University of Pennsylvania’s Museum Applied

Science Center for Archaeology, an expert on

chemical analysis of ancient fermented beverages,

she has identified theobromine in round bottles as

early as 1100 BCE These bottles were traditionally

used for holding liquids like chichas.

“Anthropologists had blinders on about cacao,”

says Joyce. “Ancient Mesoamericans were doing far

more with cacao than we first imagined.” She cites as

another example the existence of Aztec court docu-

ments that describe an intoxicating “green cacao”

beverage made from unripe cacao pods.

The importance of fermentation is not lost

on chocolate maker Robert Steinberg, co-founder

of Scharffen Berger Chocolate here in Berkeley.

Steinberg believes that proper fermentation of ca-

cao beans is key to developing their flavor, and he

supports Joyce’s hypothesis that making chicha may

have been the reason humans began to ferment ca-

cao. Steinberg points out that chocolate bars and

candy are relatively recent additions to the ways

humans have used cacao throughout history. “We

tend to forget that chocolate as we know it today

is a product of the industrial revolution,” he says.

“Grinding cacao beans into very fine pieces and

mixing in extra cacao butter pressed from other

beans to enhance smoothness requires an amount

of force that only machines can produce.”

If Joyce’s theory is correct, humanity’s love

affair with chocolate has spanned three overlap-

ping phases. First there was beer (chicha), followed

by a frothy suspension of ground fermented beans

sometime around 900 BCE, and finally, the ma-

chine-made chocolate bar.

Joyce returns to the Ulua valley almost every

year to continue her research. “We have found

evidence that people were consuming cacao 2600

years before the arrival of the Spanish,” says Joyce.

“Who were these people? Did they have patron

gods for cacao? Was cacao chicha consumed as

part of elaborate social rituals? These are myster-

ies and may always be, but these are mysteries I’d

like to learn more about.” �

MICHAEL BARNES is a freelance science writer.

Want to know more?

Check out cocoatree.org

Human consumption of chocolate may have had its roots in the Ulua River Valley on the Atlantic Coast of Honduras. Professor Joyce studies the remains left by these ancient settlements, including pottery that may have held chocolate or cacao beverages.

A cacao pod, broken open to reveal the fleshy pulp surrounding the hard seeds.

Cacao seeds must be fermented, dried, and roasted, like those seen here, to produce the raw material for chocolate.

The

Ori

gins

of

Caca

oB

RIE

F


The night sky is an awe-inspiring sight. From the

ancients who sat around fires telling creation

stories about the constellations to modern day

astrophysicists, the question has always been “how

did that get there?” With the advent of orbiting

space telescopes, we’ve finally been able to begin

answering this question.

The basics of star birth are now well under-

stood. Enormous regions of gas, sometimes light-

years wide, swirl around and occasionally develop

clumps. Over the course of a few million years, the

clumps grow as their gravity sucks in nearby gas.

These “protostars” eventually collapse under their

own weight, turning their now-dense interiors into

infernos. Soon the star is hot enough that hydrogen

atoms begin to collide and fuse together to create

new elements—fusion—liberating the energy that

powers the star, some of which eventually escapes

as starlight.

This straightforward story of star forma-

tion still holds secrets and big questions. Even

medium-sized stars like our Sun are heavy beasts,

needing millions of times the mass of the Earth to

sustain fusion. So how do protostars manage to

collect such a huge quantity of matter? In the No-

vember 17, 2005 issue of Nature, three Berkeley

astrophysicists—professors Chris McKee, Richard

Klein, and Mark Krumholz (once their graduate

student and now a post-doctoral researcher at

Princeton)—think they’ve answered this question

for good.

Two dueling theories have been proposed to

describe the manner by which protostars collect

all their matter. The first, known as “competitive

accretion,” likens building a star to building the

head of a snowman. A small, dense clump, only a

fraction of its final weight, gradually accumulates

nearby matter, suggesting that a star can start small

and grow huge over time. In the other corner sits

the theory of “gravitational collapse,” which Don-

ald Rumsfeld might describe as “you form a star

with the mass you have, not the mass you wish

you had.” Imagine that, in the heat of a snowball

fight, you grab a handful of snow and compress it.

The snowball’s final weight is determined as soon

as you pick up the snow to form it. Similarly, a star

formed by gravitational collapse has already col-

lected most of its mass by the time it undergoes

its initial compression.

The competitive accretion theory was

originally developed in response to some of the

shortcomings of gravitational collapse. Early mod-

els of star forming regions suggested that the rush

of escaping light from a young star would gener-

ate extreme outward pressures. This would keep

more gas from falling in and would prevent large

stars, more than five to ten times the mass of the

Sun, from forming in a single initial compression

event. A quick telescopic survey of the sky, how-

ever, reveals many stars this heavy. To reconcile

theory with such observations, astronomers

proposed that these stars formed in the gradual

manner suggested by competitive accretion theory.

While further work has since resolved these early

problems with the theory of gravitational collapse,

competitive accretion still hung around as a viable

alternative model of star formation.

Through computer simulations, Krumholz,

McKee, and Klein now think they’ve put the last

nail in the coffin for the theory of competitive

accretion. Their work suggests that, though com-

petitive accretion might work in certain types of

star-forming regions, nobody has actually observed

any. In addition to observations of seven star-form-

ing regions, a key player in the team’s success was

the incredible computing power available to them

at the San Diego Supercomputer Center and

Lawrence Berkeley National Laboratory, which al-

lowed them to simulate star-forming regions with

unparalleled precision. While the image of a small

star growing in a placid cloud of gas is attractive

for its simplicity, the reality is much more complex.

Therefore, modeling star formation requires calcu-

lating interactions between swirling clouds of gas

which change dramatically over time—calculations

which are far too complicated to solve without

such serious computational resources.

The results of the team’s simulations pinpoint

the failure of competitive accretion theory to one

crucial phenomenon: turbulence. Turbulence mani-

fests itself in everyday life—open a water faucet

too far, and a smooth flow turns into a chaotic

mess. It’s no surprise, then, that turbulence also

makes itself known in the chaos and flowing

gases present in star formation. While competi-

tive accretion theorists had included some initial

turbulence in their simulations, they let it artifi-

cially decay over time (as turbulence usually does

unless there’s energy to sustain it). In the Berkeley

researchers’ simulations, the light and gas flowing

out from the protostar itself fuels even more tur-

bulence, maintaining it long after the initial tumult

would die down. The proof, as they say, is in the

telescopic pudding; According to McKee, “no one

has ever seen a region where the turbulence has

decayed.”

Although it seems that Krumholz, McKee,

and Klein have firmly kicked competitive accretion

to the curb, the controversy may burn on as other

theorists respond to these claims. In the meantime,

stargazers rest assured: the next time you look

at the stars and wonder where they came from,

someone is assiduously working on an answer.

JESSE DILL and HARISH AGARWAL are graduate students

in biophysics and physics, respectively.

A Star is Born

A St

ar is

Bor

nB

RIE

F


Stars are born in nurseries of hot, dense, swirling gas. The one shown above was caught in the act by the Hubble Space Telescope.

A St

ar is

Bor

n

Photo courtesy of NASA

BR

IEF

MAMMOTH ROCKSlong the precipitous Sonoma coastline

just south of the Russian River lie two

behemoth seastacks and a smattering of boulders.

These fixtures of the landscape are increasingly

popular with local free-climbers, who clamber

from crack to crevice as they strive for the 60-

foot summits and their breathtaking views of

the Pacific Ocean. The lower reaches of these

stacks—known to climbers as Sunset Rocks—

have been worn smooth over untold years and

present another obstacle to overcome, another

three inches before a rough depression offers

purchase. Now, climbers are learning that as they

brush against these ancient stones, they just might

be rubbing shoulders with giants.

One blustery September afternoon five

years ago, California State Parks Senior State

Archaeologist and UC Berkeley Associate

Researcher E. Breck Parkman, together with

paleontologist Raj Naidu, took shelter from

the wind behind these seastacks. Over the

next two hours, they noticed something they

had overlooked in years past. All over the bulk

of the stacks, from ground level to as high as

fourteen feet, they observed polished swaths of

Franciscan chert and blueschist stone. The nature

of these features—specifically their strategic and

seemingly intentional location along the rock

edges and overhangs—led the two to suspect

that these were once “rubbing rocks.” Through

a process of elimination, they settled on a likely

culprit: 10- to 125-thousand-year-old Pleistocene

megaherbivore species such as the Columbian

mammoth, American mastodon, and Harlan’s

ground sloth. Parkman dubbed these stacks the

Mammoth Rocks.

More than ten

thousand years ago dur-

ing the late Pleistocene,

the present-day Sonoma

Coast lay at the eastern

end of a broad coastal

terrace some seven to

nine miles wide. This

grassland savanna (now

below sea-level) would

have attracted grazing an-

imals such as mammoths

and mastodons from in-

terior pastures during

the summer months. Mammoth Rocks lie below a

pass in the hills that might well have been a natu-

ral terminus for migrant megaherbivores moving

west along the Russian River Valley. As Parkman

envisions it, mammoths and other megaherbi-

vores would have been inclined to take advantage

of such an obvious and opportune landmark to

shelter from the wind, bathe nearby in the

mud of what Parkman suspects is a prehis-

toric wallow, and rub themselves clean on

neighboring outcrops.

Such scratching posts are a relatively

common feature of California’s landscape

today. Domestic cattle, horses, and sheep

have grazed here for some hundred-odd

years, polishing fence posts and rock out-

crops to an oily sheen. While Parkman con-

cedes that livestock might be responsible

for the more recent (and more polished)

rubbings along the lower reaches of Mammoth

Rocks, a cow can’t account for rubbings fourteen

feet high.

As part of what he calls “The Rancholabrean

Hypothesis,” Parkman is working with a

multidisciplinary network of scientists to

demonstrate that Pleistocene landscape features

like Mammoth Rocks might still persist and be

identifiable today.

“What we’ve done is disprove all the oth-

er theories,” explains Parkman, referring to the

battery of alternative scenarios he’s entertained

over the last few years. “You might not see what

it is, but you can see what it isn’t.” The most intui-

tive of theories—weathering by rain and wind—

would be expected to polish the rocks indiscrimi-

nately, not in the strategic locations the rubbing

patterns suggest.

In 2003, a team of researchers at Sonoma

State University led by Stephen Norwick ana-

lyzed samples of the rubbed rocks using high-

powered microscopes. The results of their analy-

sis confirmed that the polished surfaces didn’t

coincide with elemental weathering. Instead, the

signature scratches worn into the stone—by grit

left in fur after a mud-bath, if Parkman’s theory

holds true—bear more resemblance to those on

wooden rubbing posts used by zoo elephants.

Parkman has also unearthed blade-like tools

at the base of these and neighboring rubbing

rocks that bolster the archaeological component

of his theory, including a chert flake with traces

of an as-yet unidentified blood that might prove

to be mammoths’.

At present, Parkman is working with re-

searchers at Texas A&M University to analyze

samples of the rubbings to determine whether

carbon-containing organic material from hairs,

oils, or blood is present in the rocks. If they can

confirm the presence of carbon, the next step will

be a needle-in-a-haystack search for ancient DNA.

While some have criticized Parkman for


Ma

mm

oth

Rock

sB

RIE

F

Above: The prominent Mammoth Rocks outcrops (left), known to local climbers as Sunset Rocks, sit prominently along the Sonoma coastline where they might once have attracted prehistoric mam-moths as rubbing rocks. Below: Archaeologist Breck Parkman points to an overhanging edge that shows evidence of rubbings.

A

All Photos by Sarah Anne Bettelheim

drawing attention to the rubbings because of the

unavoidable vandalism and foot-traffic that will fol-

low, he contends Mammoth Rocks can’t be saved

if he doesn’t publicize them. In an effort to raise

awareness, Parkman regularly leads trips to the

park for school children and has recently taken

steps toward organizing a volunteer group of site

stewards with the climbing contingent of Stewards

of the Coast and Redwoods to make sure park visi-

tors leave the rocks as they find them. Still, each

time Parkman runs his hands over the glassy rocks,

he notices another callous chip—a rock-hound’s

souvenir—which serves as a reminder that if we

don’t tread lightly in the footsteps of giants, our

tenuous link to the rich history of the Sonoma

Coast may vanish forever.

MATTHEW BETTELHEIM is a freelance science writer, wildlife

biologist, and natural historian.


Ma

mm

oth

Rock

sB

RIE

F

The rubbing rocks vary from smooth-worn

ridges to large sweeps of polished stone like

the rock face pictured here.

Want to know more?Check out Mammoth Rocks atwww.parks.ca.gov/default.asp?page_id=23566

Interested in research or volunteering? Contact Parkman at [email protected]


United

We

Sta

nd

BR

IEF For most of us, our common ancestry with

chimps is not hard to grasp. The idea of our

common heritage with other mammals is also not

a stretch—rat or monkey, we all share mammalian

faces, sets of limbs, live births, and fur. But go back

further along the animal lineage and things start

to get blurry. What’s the story of the first four-

limbed beings to walk the land? Go further back.

What creature gave rise to the first bilaterally sym-

metrical organisms, ancestors of everything from

flatworms and beetles to sharks and wolves? Or

even further back in time, down near the base of

the tree of life, to that clichéd primordial ooze

that spawned the first animals.

It was at that time, some 600 million years

ago, that one of the most pivotal evolutionary

leaps in the history of life took place. In a largely

unicellular world far different from ours, a group

of single-celled organisms joined together and

became one multicellular organism, opening the

door to a novel range of evolutionary possibili-

ties. This was the birth of a new way of life, the

founding event of the storied animal kingdom. But

as important as these early events in the tran-

sition to multicellularity are to the story of life,

they are also poorly understood. UC Berkeley

Molecular and Cell Biology and Integrative Biol-

ogy professor Nicole King and her lab want to

find out more.

The search starts with the genetic tools re-

quired to be multicellular: genes that control cell

adhesion (the glue that binds cells), cell signaling

(allowing cell-to-cell communication), and cell

differentiation (establishing multiple cell types to

allow for division of labor). Understanding the

evolution of these essential functions likely holds

the key to understanding how animals appeared

and flourished.

Though paleontologists can dig through pits

full of clues to the past, researchers of animal ori-

gins lack anything like fossils to aid their search.

Instead, King focuses on choanoflagellates, a

group of single-celled organisms (protozoa) that

swim, powered by a whip-like flagellum, through

many of today’s marine and fresh waters. But

how exactly do these simple cells offer a window

more than half a billion years into the ancient

past, when the first animals appeared?

The key is knowledge of the tree of life. Re-

cent studies have established that choanoflagel-

lates are the single-celled organisms most closely

related to multicellular animals. In fact, choano-

flagellates even resemble the specialized feeding

cells found in sponges (the most basic multicel-

lular animal). Thus, it was probably descendents

of an early choanoflagellate ancestor—close

cousins of the choanoflagellate lineage—who

participated in the evolution of multicellularity,

and today’s choanoflagellates likely remain com-

parable to these pioneers in many ways. Research

from other groups indicates that every animal

species evolved from this single evolutionary

step—though multicellularity evolved multiple

times elsewhere on the tree of life (among plants,

fungi, slime molds, and others), it happened just

once for animals. So, for insight into animal ori-

gins, the choanoflagellate genetic code is required

reading. And thanks to recent advances in genome

sequencing (decoding the entire genetic contents of

organisms), King can employ the powerful tool of

comparative genomics to make sense of this code.

By stacking the choanoflagellate genome

up against animals and more distantly related

groups like plants and fungi, King can determine

which gene families are shared only by animals

and choanoflagellates. Already, King’s group has

identified choanoflagellate versions of cell signal-

ing and adhesion gene families previously consid-

ered unique to animals. These are two parts of a

UNITED WE STANDThe Origins of Multicellular Animals

choanos sponges jellyfish arthropods mollusks starfish vertebrates

emergence of multicellularity

tim

e

Choanoflagellates stained to show their flagella (green), collars (red), and DNA (blue). (Left) individual cells; (right) a colony of cells.

Images courtesy of Melissa Motts/Current Biology (left) and Susan Young (right).

According to the animal family tree (not to scale), choanoflagellates diverged from the animal lineage right before the emergence of multicellularity. This means that choanoflagellates are more closely related to multicellular animals than any other non-animal we know of so far. Study of these organisms may help us understand which characteristics of multicellularity the single-celled ancestor of animals already possessed and which had to evolve during the transition to multicellularity.


United

We

Sta

nd

BR

IEF

An 1880 drawing by W. Saville Kent of a choanoflagellate, a single-celled marine organism whose name comes from the collar surrounding a whip-like flagellum used for swimming. The red dots represent bacteria, which are engulfed by the cell in vesicles. In the center is the cell’s nucleus. The King lab studies these organisms because they are the closest single-celled relatives to multicellular animals, and therefore may help us to understand more about the transition to multicellularity.

choanoflagellate genetic toolkit for multicellular life

that King believes may hold the key to the story of

animal origins.

Discovering animal-style genes in single-celled

organisms is exciting, but it also raises a paradox—

how and why did the machinery of multicellular

organisms evolve in a lineage that continues to live

the single-celled way of life? What is the pre-his-

tory of the most basic animal gene groups?

The evolutionary role of genes has everything

to do with their functions, and it is the function

of these key gene groups in unicellular organisms

that King wants to uncover. For example, hungry

choanoflagellates attach to and engulf unsuspecting

bacteria, a process King argues could be the single-

cell antecedent to cellular adhesion. And protozoa

are known in some instances to respond both to

other organisms and their environment based on

secreted proteins, a potential precursor to the kind

of cell-to-cell signaling essential in animals. Some

species of choanoflagellates even form colonies,

though the function of the colony in the life cycle

of the organism is still unclear.

The function of the gene groups later co-

opted for animal multicellularity is only part of the

picture. King is also interested in other aspects of

that lost unicellular world, such as the external fac-

tors that shaped the development of multicellular-

ity. Here too are ideas to be tested. A multicellular

body is more than any unicellular predator could

swallow, so perhaps multicellularity evolved as a de-

fense strategy. Also, choanoflagellates use the same

cell parts to power their flagella and to divide into

new daughter cells. Because of this constraint, the

first multicellular animals (and perhaps choanofla-

gellate colonies) may have benefited from a divi-

sion of labor between swimming cells and dividing

cells—the world had not yet seen organisms that

could simultaneously grow and move.

Many details in the story of animal origins re-

main mysterious. But King’s work has established

that further study of the evolution and biology of

choanoflagellates will shed more light on this 600-

million-year-old story. As King says, “let protozoa

show the way.”

AMAN SINGH GILL is a UC Berkeley graduate in environ-

mental science and policy management.

Want to know more?

Check out:

The King lab homepage:

mcb.berkeley.edu/labs/king Tree of Life: tolweb.org


H2y

dro

pow

erB

RIE

F

Whether it’s air quality, a desire to protect

pristine Alaskan wilderness, political

instability in the Middle East, or dwindling supply

in the face of increasing global demand, there are

many reasons to move away from our current

petroleum-based economy. While a number of

alternative fuel options are under investigation,

when it comes to cars, these days hydrogen is all

the rage.

Hydrogen is appealing because it reacts very

cleanly and efficiently with oxygen to release

energy inside a fuel cell, producing water as the

only byproduct. However, a number of practical and

technical potholes lie in the road to the hydrogen

future. From issues of infrastructure to hydrogen

storage, Berkeley researchers are working to

smooth that road and to help hydrogen realize its

promise as the ultimate fuel.

The future of the hydrogen economy looks

bright at Partners for Advanced Transit and

Highways (PATH), a branch of Berkeley’s Institute

of Transportation Studies. Headquartered in

an old converted home down a dusty road off

Highway 580, the weathered building belies the

innovative work being done inside. This past

December, PATH researchers began two years

of testing the Daimler-Chrysler F-Cell, a fuel cell

vehicle that runs on compressed hydrogen gas.

Daimler-Chrysler wants to get its car out

for some real road experience to expose any

problems. Tim Lipman and Susan Shaheen, Berkeley

researchers and co-managers of the project,

plan to put the car through its paces by using it

as a company vehicle for business-related trips.

Each night, the F-Cell is parked in a special spot

where it wirelessly relays the day’s performance

data back to Daimler-Chrysler in Germany. This

approach will also allow Lipman and Shaheen to

investigate an interest of their own: the role of

hydrogen-powered cars as fleet vehicles. One

of the major obstacles facing the development

of any new fuel is the lack of refueling stations.

In a fleet setting though, companies can make

arrangements for fueling and for repair that would

likely inconvenience individual owners. The PATH

F-Cell gets its hydrogen fix from a special station

in Richmond.

Outside of a fleet setting, ease of use is a top

priority for private vehicle owners, so without

the appropriate infrastructure, even the most

promising technology is likely to fail. In the case of

hydrogen, the variety of fueling options complicates

infrastructure development. Hydrogen can be

stored and dispensed in a variety of forms—as

a liquid, as compressed gas at a number of

different pressures, and as a metal hydride. Most

cars available now, including the F-Cell, require

compressed gas at 5000 psi, and most fueling

stations are being built to accommodate this type

of vehicle. In an effort to support the hydrogen

economy, Governor Schwarzenegger plans to

increase the number of hydrogen fueling stations

in California from the 16 currently in place to at

least 50 by the year 2010.

However, current hydrogen storage techniques

have serious shortcomings. Compressed hydrogen

gas requires extremely high pressures and a heavy

storage cylinder, reducing its efficiency. For example,

just compressing hydrogen to 3000 psi costs

about 20% of its potential energy. Furthermore,

compressed gas vehicles have very limited range

due to the size and weight of the storage cylinder

required. Liquid hydrogen is another option used in

some cars, but its storage requires a heavy cooling

system to maintain temperatures of around -250o

Celsius (20 Kelvin).

In contrast, the ideal storage system is

lightweight and able to store a lot of hydrogen

H2YDROPOWERGetting a grip on hydrogen to fuel tomorrow’s cars

Photo by Charlie Emrich


H2y

dro

pow

erB

RIE

F

near ambient conditions. Furthermore, it must be

efficient enough to offset the energy consumption

and pollution that result from using water or

hydrocarbons for producing the hydrogen in

the first place. The Department of Energy has

proposed hydrogen storage system

targets for the year 2010 that

include 6% hydrogen by weight,

0.045 kilograms hydrogen per liter,

an operating temperature between

-30o and 50o Celsius, a maximum

operating pressure of 1500 psi, and limits on

refueling time and cost.

In an effort to help meet these ambitious

targets, nine UC Berkeley faculty members, in

departments ranging from chemistry to physics

to materials science, came together in 2004 to

form the Hydrogen Storage Program. None of the

groups involved in the program had been directly

involved in hydrogen storage research preceding

the program’s establishment, but they all thought

they might have new ideas to contribute to the

field. The team hopes that one of these new

approaches will result in a hydrogen storage system

that is lightweight, reusable, clean, and efficient.

Although all the researchers have very different

approaches, “it’s intended to be very synergistic,”

says Jeff Long, a chemistry professor involved in

the project.

Long hopes to use synthetically-produced

porous solids as hydrogen storage devices. He

is currently investigating the synthesis and

hydrogen-binding characteristics

of a number of metal-organic

frameworks. All of these lattice

structures have very high surface

area to volume ratios, creating

many potential hydrogen binding

sites. Long’s ideal material is lightweight, easy

to produce, and able to reversibly bind hydrogen

for the lifetime of the car. Furthermore, it will

release hydrogen from the storage lattice to the

fuel cell upon small changes in pressure. He sees

“a lot of promise” in porous materials, but he also

notes that refining the solids so they are viable for

use is going to be a challenge.

The next few years will likely determine the

future for the hydrogen economy. Whether

hydrogen’s potential can be fully realized is still an

open question. Great strides have been made in

the past 15 years to put fuel cell vehicles on the

road, something that many people never thought

possible. Perhaps in another 15 the dream of

hydrogen power will truly become a reality. �

RACHEL BERNSTEIN is a graduate student in chemistry.

Want to know more?

CA Partners for Advanced Transit and Highways:

path.berkeley.edu

Long research group:

alchemy.cchem.berkeley.edu

e, it must be

consumption

ng water or

ydrogen in

nergy has

d limits on

e ambitious

members, in

y to physics

in 2004 to

None of the

been directly

ch preceding

y all thought

says Jeff Lon

the project.

Long hop

porous solid

is current

h

sites. Long

to produce,

for the lifetim

release hydro

fuel cell upon

“a lot of prom

notes that refi

use is going to

The next

future for t

Hydrogen is much trickier than gasoline to store, prompting researchers to develop porous solids as an alternative. Jeff Long’s group develops hydrogen sponges like the one shown above which uses magnesium atoms (green) to bind hydrogen atoms (red).

This is not your father’s Oldsmobile. The Daimler-Chrysler F-Cell car (facing) gets its power from a hydrogen fuel cell, runs a Linux-powered center console, and wirelessly communicates its driving data to headquarters back in Germany. Pop the gas cap (below) and you’ll find an odd fitting for hydrogen refueling. Driving around the Richmond Field Station, CCIT scientist Tim Lipman (center) points to the console where the F-Cell displays its energy use. Electricity is produced by the fuel cell and a regenerative braking system, and can go from there either to the car’s rechargable battery or the electric motor.

All photos by Charlie Emrich

Image courtesy of the Long lab


Eart

hqua

ke P

redi

ctio

nB

RIE

F

EARTHQUAKE PREDICTION In the north entrance hall of UC Berkeley’s

Doe Library, a large memorial poster hangs on the

wall recapping “The History of a Disaster.” With a

black-and-white photo showing foot-wide cracks

in the ground, the poster charts the devastating,

260-mile, minute-long tear through San Francisco

of the Great Quake of 1906. On the quake’s 100th

anniversary, the banner commemorates the Uni-

versity’s contribution to search and rescue efforts

and to the medical care and temporary sheltering

of refugees. “On April 18, 1906 at 5:12 am,” the

memorial poster’s subtitle reads, “the San Andreas

Fault ruptured in a magnitude 7.9 earthquake...”

But rewind 100 years to the first few

seconds of that minute-long rupturing, shaking,

and jolting. While people were just beginning

to feel the earth’s movement, the quake’s full

magnitude would remain unknown until well after

its calamitous completion. What if, instead, one

could predict the magnitude of an earthquake just

as it is beginning to occur? Furthermore, what if

such knowledge could allow for precious seconds

of warning? Such a task has stymied generations

of researchers, and the feasibility—let alone the

accuracy—of such prediction still remains conten-

tious. Now, a paper, published in the November

10 issue of Nature by UC Berkeley seismologist

Richard Allen and colleague Erik Olson seems

to have revived both the expectations, and the

skepticism, surrounding earthquake warning.

When an earthquake occurs, two types of

seismic waves are created. The first, called the “P”

or primary wave, is a burst of pressure, like a really

loud sound. The second, called the “S” or secondary

wave, consists of violent back-and-forth shaking,

what seismologists call shear. Allen and Olson

hope to exploit the basic fact that the P-wave

travels faster than the S-wave (hence it’s name),

while the S-wave is responsible for most of the

quake’s damage. So, the thinking goes, if detectors

can interpret the strength of the impending S-wave

the instant they detect the first P-wave, they gain a

few seconds—up to 70 seconds depending on how

far they are from where the earth ruptures—to do

things like warn emergency personnel before their

communications networks are interrupted, shut

down power plants before their pipes rupture, or

even initiate a public alarm system.

There has always been debate in the

seismological community over whether the first

P-wave actually provides useful information about

an earthquake’s ultimate magnitude before it ends.

The dominant theory, the “cascade model” of fault

rupture, argues that rupture spreads from one

patch of the fault to another neighboring one like

falling dominos. All activity terminates when the

rupture energy falls below a certain threshold

necessary to move the next patch. This theory

predicts that small and large earthquakes both

start out identically; the ultimate size of the

earthquake is only determined as the earthquake

All Photos courtesy of the Bancroft Library

Shake, Rattle, and Roll

What if you could see 30 seconds into the future...

San Francisco in ruins, April 1906


Eart

hqua

ke P

redi

ctio

nB

RIE

F

On the other hand, after examining the

waveforms of 71 earthquakes from Japan, Taiwan,

California, and Alaska, Allen and Olson now believe

they have finally identified a way to determine an

earthquake’s strength from those first instants of

shaking. They suggest that the key to predicting the

ultimate magnitude of an earthquake is information

contained in the frequency of shaking that occurs

in the P-wave. In contrast to the cascade model,

their model predicts that there is a deterministic

relationship between the initial shaking and the

final earthquake energy. A key difference between

the two schools of thought is what signal to look

for. “They look at the amplitude of the initial

rupture, which is how much it shakes,” Allen says

of his colleagues in the cascade model camp, “while

we look at the frequency, that is how quickly

it shakes.”

In a 2003 study, Allen and Professor Hiroo

Kanamori, a Caltech colleague, found such a

relationship between the frequency content of

the quake’s first four seconds and its ultimate

magnitude. Their sample consisted of southern

California earthquakes with magnitudes 3.0 to

7.3 (only 3 of which had a magnitude greater than

6.0). In Allen’s latest study of 71 quakes—24 of

which were 6.0 or greater—they examined both

the velocity and acceleration caused by the P

wave. They found a high correlation between the

frequency content of the P wave’s first few sec-

onds and the final magnitude, further reinforcing

the deterministic theory of earthquake rupture.

Allen admits, however, that the correlations are

reduced for earthquakes with magnitude 5.7 or

greater. But, he says, overall “the correlations are

pretty strong.”

Others dispute the team’s conclusions.

“If you look at their figures, the correlation

is not that strong,” says William Ellsworth, former

chief scientist with the US Geological Survey

(USGS) in Menlo Park, California. Ellsworth also

urges caution, warning that, even if researchers

find a correlation, there is a large step from

demonstrating a correlation to developing a

reliable early warning system that operates on the

finding. Ten years ago, he and Stanford University’s

Gregory Beroza examined the relation between

initial amplitude and final earthquake magnitude.

While their results were consistent with Allen’s

they did not go on to design a warning system,

partly because of the high cost such a system

would require.

Allen is continuing his work. While he admits

that it will most likely take several years to make

certain how accurate the method is, he is seeking

funding, primarily from the USGS, to begin testing

the system, which he calls ElarmS. The test system

would use real-time data fed from monitoring

stations to predict a final quake magnitude.

Michael Blanpied, associate coordinator of the

agency’s Earthquake Hazards Program in Reston,

Virginia, said in an interview that his agency

has received three different proposed testing

techniques, including Allen’s. The algorithms show

some promise, Blanpied said. “But there is an

open question whether it is possible to distinguish

between magnitude 5 and 7 earthquakes in a very

short amount of time, although it’s quite possible

to use only a few seconds to tell magnitudes of

up to 5.”

With a two-year initial investment of

$100,000 per year, Blanpied says, the USGS

expects to get a sense of how much improvement

would be needed to make the algorithms work.

These funds are being channeled to Berkeley

and to Caltech to start the necessary computer

programming and to provide grants to researchers

and graduate students for the current feasibility

testing. “A lot of us hope that this would work

well,” Blanpied said. “Great things could be done.

This has very exciting prospects.”

MICHAEL ZHAO is a graduate student in journalism.

Timeline for an ideal earthquake warning:

0 sec. Earthquake begins. Epicenter is located near Mendocino triple-junction, around 200 km NW of the Bay Area. Fast-moving P-waves and slower but more destructive S-waves begin radiating outward from epicenter.

3 sec. P-waves reach the nearest detec-tors, which begin analyzing the frequency content of the seismic waves.

7 sec. The ElarmS analysis requires 4 seconds of P-wave data to make an initial prediction of earthquake intensity. The algorithm decides the earthquake is likely to be powerful and initiates the warning system.

10 sec. Alarms transmitted to Bay Area cities. Schoolchildren warned to get under desks, BART trains automatically brake to avoid derailing, voltage is reduced along power transmission lines, etc.

30 sec. S-waves reach the Bay Area. Shaking begins in earnest...


Seei

ng C

hem

istr

yB

RIE

F

One of the things I learned in high-school

chemistry class is that you can’t see atoms.

Wrong. Decades ago, researchers at IBM invented

a microscope powerful enough to both see atoms

and to move them around one at a time. Being able

to see individual atoms ushered in a sea change

in the understanding of materials like metals and

ceramics. Recently, researchers at Berkeley have

upped the ante, inventing a technique that allows

them to see atoms as they move in the fastest of

chemical reactions.

The work, published in the November 11

edition of the journal Science, sheds new light on

a very old question: How do our eyes “see”? The

retina lining the insides of our eyes brims with

rod and cone cells that convert light into a signal

that our brains interpret as vision. What makes

these cells sensitive to light is the protein rho-

dopsin. Rod cells are packed with thousands of

molecules of rhodopsin, each of which contains

a small molecule called retinal that absorbs light.

(Retinal, incidentally, is made from beta-carotene,

lending credence to the conventional wisdom that

beta-carotene-rich carrots are good for your eyes.)

When retinal absorbs light, it twists, forc-

ing the surrounding rhodopsin protein to change

shape and kicking off a long chain of events that

leads to vision. This much

has been known for the

better part of the last cen-

tury—it led to a Nobel

prize in 1967—but many

of the specifics of this re-

action remained elusive.

In particular, knowing the

exact details of how retinal

twists when exposed to

light is key to understand-

ing how remarkably effi-

cient the visual process is.

Retinal by itself is

nowhere near as efficient

at capturing light as when

it’s embedded in the rho-

dopsin protein. A group of

Berkeley researchers, led

by professor Richard Ma-

thies, found that the rho-

dopsin protein pre-twists

retinal a bit, priming it to

undergo the full twist when

it absorbs light. As gradu-

ate student Phil Kukura,

lead author on the study,

“cis”

“trans”

Graduate student Phil Kukura stands over part of the complicated optical system that can watch atoms move during a chemical reaction.

Seeing Chemistry

(Left) The human eye senses light on its back surface—the retina, which is made up of hundreds of millions of rod and cone cells. The cone cells are responsible for color vision and the rod cells (middle) handle low-light vision. Each rod cell is packed with the protein rhodopsin, which actually absorbs and senses light. The first step in vision occurs in the molecule retinal that’s buried within each rhodopsin protein. When exposed to light, retinal undergoes a reaction that twists the molecule (as shown above right) from the “cis” to “trans” configuration. Each of the atoms in retinal is represented as a ball and bonds between those atoms are drawn as sticks. The motion of two hydrogen atoms (shown in green) was key to understanding why our eyes are such good light detectors.


Eye diagram courtesy of the National Eye Institute/National Institutes of HealthRetinal diagram by Dan Wandschneider

light

optic nerve

iris

retina

lens

cornea

rod cells

Berkeley scientists peek into the ultra-fast world of chemical reactions and discover why the human eye works so damn well


Seei

ng C

hem

istr

yB

RIE

F

explains, absorbing light is like “pulling the trigger”

for the reaction.

The meat of the discovery is that the first step

in this twist involves the swinging of two hydrogen

atoms around the length of the

retinal. The seemingly insignifi-

cant swing of these hydrogen

atoms kicks off all the events

leading to vision, like a snow-

ball starting an avalanche. But

hydrogen—the lightest of all at-

oms—moves extremely fast in

chemical reactions, making it al-

most impossible to track using

standard measuring techniques.

How fast? A few femtoseconds.

A femtosecond is a millionth of

a billionth of a second, or as Ku-

kura puts it, “There are as many

femtoseconds in a minute as

there are minutes in the exis-

tence of the universe.”

One of the fundamen-

tal reasons that this reaction occurs so

fast is that speed is inexorably linked to

efficiency: All efficient reactions happen

quickly, and the eye is a very efficient light

detector. To detect these ultra-fast chang-

es in molecules, Kukura and colleagues

developed a technique called femtosecond

stimulated resonance Raman spectrosco-

py. In essence, they fire extremely short

pulses of laser light at the rhodopsin and

look at the changes in the color of light

that bounces off of it.

This brings me to another thing that

I learned in high-school chemistry: All molecules

and atoms are constantly vibrating, as if they’ve

been put together with springs. This much was

right, but what the teachers left out was that each

type of molecule has its own signature vibrations

that can tell scientists a wealth about what the mol-

ecule is, how it is arranged, how it bumps up against

its neighbors, and even about tiny shifts in the posi-

tions of the atoms that make it up.

As Kukura puts it, “If you wanted to stretch

a human being [to] twice his size, it takes a couple

of horses. To stretch a molecule to twice its length

also takes a certain amount of energy, and you can

actually measure those energies.”

The wiggling atoms in a molecule can absorb

small, characteristic amounts of energy from light

as it hits the molecule. By deciphering subtle chang-

es in the color of reflected light, scientists can infer

which wavelengths of light were absorbed and use

this information to draw a picture of a molecule

like retinal—hydrogens and all.

Measuring these energies requires a sophis-

ticated array of lasers capable of producing the ul-

tra-short bursts of light needed to take snapshots

of the retinal/rhodopsin reaction as it happens.

According to Kukura, this wasn’t the most difficult

(Top) Kukura points to the small piece of glass that makes ultra-fast pulses of laser light needed to study fast chemical reactions. Laser light that goes in a single color comes out as a spectrum of colors—an odd consequence of how short the pulses are.

(Bottom) These lasers got bling. A green laser shines at a large sapphire, whose red glow becomes the pulsing heart of the system producing femto-second laser pulses.

part of the work. The hard part was “convincing

ourselves that we weren’t full of [it].”

“As I started to read the literature and as I

started to understand the basic laws behind it, I

realized it’s never going to work, because there’s a

million reasons why this [shouldn’t] work… It was

completely accidental that we saw what we did and

interpreted it the way we did.” Indeed, it took over

a year for analysis and double-checking between

the time the measurements were made and when

the paper was written.

Despite the huge amount that’s already

known about vision, these results may have long

legs. Rhodopsin belongs to a class of proteins called

G-protein coupled receptors that are responsible

for many kinds of communication and signaling

within the body. In fact, more than 70% of drugs

on the market target G-protein coupled recep-

tors. Understanding how these receptors work is

fundamental to drug development. Kukura sums it

up with an unintended pun, saying, “This technique

certainly has a bright future.”

CHARLIE EMRICH is a graduate student in biophysics.

Want to know more?

Check out: “Structural Observation of the Pri-

mary Isomerization in Vision with Femtosecond-

Stimulated Raman”: Kukura, P. et al, Science 310, pp.

1006–1009 (2005).

Photos by Charlie Emrich


Ha

rd D

rive

sB

RIE

F

Imagine flying a Boeing 747 half an inch above

the ground, all the while counting blades of

grass. Most pilots would balk at this mission, but

David Bogy and his colleagues at the Computer

Mechanics Laboratory (CML), an industrial

consortium composed of five research labs at

Berkeley and twelve industrial partners, tackle a

similar problem with aplomb. They engineer the

mechanics of one of the last moving parts in a

computer—the inner workings of a hard drive.

Over the 1990s, the data storage density of

hard drives doubled every year. That feat surpasses

the oft-cited Moore’s law, which claims that the

doubling time for the number of transistors in a

computer chip is eighteen months. Now we have

HD Tivos and video iPods with huge data storage

capacity within a small space—a testament to the

new ubiquity of hard drives. How did the capacity

of these data storage workhorses increase at

such an astounding rate? One key factor has been

piloting the 747 with ever increasing precision.

The 747 in this case is the hard drive’s

“slider”, the tiny object that actually flies less than

a thousandth of a hair’s width above the spinning

disk. On the end of the slider lie a miniature

electromagnet (for writing data) and an ultra-

thin, perfect magnetic crystal (for reading data).

Aerodynamic foils are machined into the lower

surface of the slider so that when the disk spins,

the wind it creates pushes on the slider, causing it

to both take off and to fly.

To increase the storage capacity of a hard

drive, engineers cram more data into less space.

Advances in storage capacity require the solution

of tough mechanical problems. For one, the slider

has to fly ever closer to the disk—nowadays about

100 angstroms, the equivalent of 100 atoms end-

to-end, is all that separates the disk and slider.

The CML engineers face a Goldilocks

problem: If the heads are too far away from the

disk surface, data can neither be read nor written.

But if the heads get too close to the surface, Bogy

says, the head “will slap the disk,” crashing into the

disk surface. The flying height must be just right,

and the lower it has to be, the less room there

is for error. Bogy’s lab carries out simulations of

the aerodynamics of the slider to figure out how

to make it fly at the right height throughout the

working lifetime of the hard drive.

Maintaining the correct flying height is

not the end of the story; horizontal precision is

important as well. The problem is like following

“a curving road,” says mechanical engineering

professor Roberto Horowitz. Since data is stored

as circular tracks on the disk, the read/write head

must follow the track exactly or risk reading the

FASTER, BETTER, SMALLER One of the last moving parts in your computer is the hard drive

The business end of a hard disk drive is the millimeter-long slider seen above. The surface that faces the disk (above) is terraced aerodynamically to fly extremely close to the disk surface.

End-on view of the slider above. Data is written by the tiny electromagnet—look close and you can see its mirofabricated coils of wire. There’s also a heater that helps control the distance between slider and disk, zabout 10 nanometers for this drive.

An experimental slider designed by graduate student Jia-yang Juang. The central tab containing the read/write heads can be actively lowered to fly 2 nanometers above the disk.

A typical computer hard disk drive made by Seagate, sans cover. The slider is at the end of the metal arm that’s touching the disk.

All photos courtesy of Jia-Yang Juang


Ha

rd D

rive

sB

RIE

F

wrong data. To increase storage capacity, the

tracks must become narrower and closer together,

and precision of horizontal control becomes even

more important.

If the concentric tracks were perfectly circular

and centered around the axis of the spinning disk,

the task would be relatively easy. But real life is

not so simple. In practice the tracks are slightly

off center (like the grooves on many records),

and any movement of the disk—knocking your

laptop, dropping your iPod, or just vibration from

the cooling fans—can bump the slider off its flight

path. This means that the head’s position has to be

actively controlled on the sub-millisecond scale.

Horowitz and fellow mechanical engineering

professor Masayoshi Tomizuka are working on

the problem of keeping the read/write head over

the data tracks as the disk spins and is jarred by

external vibrations.

Even if Bogy and his colleagues at the CML

can meet these mechanical demands, the magnetic

hard drive industry must confront another looming

problem: the superparamagnetic limit. Data is

stored on a hard disk by writing tiny magnetic

zones, each having a North and a South pole.

But just like bar magnets that repel each other if

you put North pole to North pole, the magnetic

zones on a disk can repel their neighbors. One

consequence, says Bogy, is when these zones get

“too small and too close they won’t be stable.”

This is because the bits are constantly being kicked

by the wiggling of surrounding molecules—that is,

thermal energy. The amount of energy required to

flip the orientation of one of these magnetic zones

decreases as the size of the zone shrinks. Once the

magnetic zones are small enough, ambient thermal

energy alone will be enough to flip a bit of data.

The smallest a bit can get without spontaneously

flipping is the superparamagnetic limit.

Until recently, “magneticians” predicted

that this limit would be reached at a density of

100 billion bits/square inch. But the folks at the

CML along with the national Information Storage

Industry Consortium (InSIC) have set themselves

a goal of reaching a tenfold greater density by the

end of 2008.

To meet this challenge, engineers are

exploring new approaches to saving space by

reorienting bits so that they stand up vertically.

Another approach is to use more stable magnetic

materials that require a laser to heat small areas

of the disk while data is written. The mechanical

advances being developed at Berkeley’s CML

may well prove critical to appeasing the world’s

insatiable appetite for data storage. �

MEREK SIU is a graduate student in biophysics.

Want to know more?

Check out the

Berkeley Computer Mechanics Lab:

cml.berkeley.edu

This little dynamo has a 1-inch disk that holds 4-GB of data, enough for about 1,000 songs. Drives this small are made specifially for portable devices like iPods. To guard against bumps, the head assembly retracts automatically to a white ramp (it’s there now) when not in use.

GETTINGB A C K T ON AT U R EIn the Museum of Vertebrate Zoology (MVZ), director Craig Moritz walks to a row of cabinets and

pulls out a shelf. Inside lie rows of chipmunks, carefully stuffed and labeled, with a tiny skull sealed in a glass jar next to each.

To the untrained observer, they look like replicas of the same species. To Moritz, they tell a story that crosses the boundaries of both space

and time. These specimens are part of a unique biological survey project launched by Joseph Grinnell, the museum’s first director, in 1908. The

Grinnell survey, which lasted over 30 years, covered over 700 locations spanning the state of California. The resulting database, encompassing over

20,000 specimens, 13,000 pages of field notes, and 2,000 photographs, represents one of the most comprehensive collections of its kind in the world.

Adam Leaché


REVISITING THE 1914 SURVEY OF CALIFORNIA WILDLIFE

Photo by Adam Leaché

by Erica Spotswood

Moritz must have known he was stepping

onto the shoulders of giants when he began his

position as director in April 2001. Looking for

background information on the history of the

museum, he was given Grinnell’s Philosophy of

Nature, a compilation of writings published by his

predecessor in the late 1940s. In the book, Grin-

nell predicts that the real value of his field work

“will not be realized until the lapse of many years,

possibly a century.” Excited by the idea of using

the museum centennial to complete Grinnell’s

prophecy, Moritz began to think about returning

to the original sites to see how the ecological

communities had changed over the years.

What followed was the development of the

Grinnell resurvey project, begun in 2002 in Yo-

semite. After three summers of intensive field-

work and collaboration between the National

Park Service, the MVZ, and the U.S. Geological

Survey, the resurvey team has revisited all of the

original 42 sites. Armed with the detailed infor-

mation from the past provided by the original

survey and the newly collected data from the re-

survey, a diverse group of contemporary Berkeley

scientists is using the Grinnell collection to study

a series of interrelated issues—from the changing

distribution of vertebrates to the impacts of cli-

mate change to the developing patterns of genetic

diversity. Because the original database is so com-

plete, it is providing a rare opportunity for mod-

ern researchers to get a glimpse into the past, to

examine the present, and to predict the future.

Remembrance of Things Past

On October 28, 1907, benefactor and avid

naturalist Annie Montague Alexander wrote a

letter to the UC Berkeley president proposing

$7,000 towards the running of a museum dedi-

cated exclusively to the mammals, birds, and rep-

tiles of the west coast. All the University had to

do was come up with the means to construct a

building complete with electric light and heat. And

so the Museum of Vertebrate Zoology was born.

Joseph Grinnell, who was its first director

from 1908 until his death in 1939, was not sim-

ply concerned about collecting specimens for the

museum. His goal was to understand how spe-

cies and communities were distributed across

space and across ecological gradients within the

state. According to Jim Patton, Professor Emeri-

tus and curator of mammals, “He was looking at

geographic variation and change of characters in

space and time. He wanted to understand the

kinds of factors that might influence local ad-

aptation and … variation among individuals and

within populations.” These ideas were unique at

the time because they called into question the ac-

cepted notion that species are static and unchang-

ing. Grinnell’s ideas were more contemporary with

those of the biologists of the 1940s, who developed

the notion that differences between species are

driven by ecological and geographical barriers.

The result of this philosophy was a one-

of-a-kind collection. “There are lots of specimen

collections in the world, but what is missing from

them is the Grinnell philosophy and the meth-

ods he used,” Patton explains. “He went out and

looked at organisms in a controlled way rather

than haphazardly saying ‘we don’t have any speci-

mens from location X so let’s go out and get

some.’ There is an ecological and conceptual

framework that underlies all of the localities that

were visited.” Grinnell also developed a method for

recording information (the Grinnell field note sys-

tem) that is still used around the world to this day.

The resurvey team is attempting to adhere

as closely as possible to Grinnell’s original meth-

odology. First, they must find the exact location

where a given survey was conducted. In some

cases, this is easy. A description of the site plus

a point on a topographic map was sufficient for

Jim Patton to find the exact slope in Lyell canyon

where Grinnell set his traps. Where precise infor-

mation is missing, or where changes in land use

have rendered a resurvey at a location irrelevant,

things are more complicated. For example, the

original trapping location at one site now sits in

the parking lot of a Wal-Mart. Instead of trapping

next to the dumpster, a comparable site nearby

with similar vegetation in a similar habitat was

chosen in its place.

Once the location is determined, a camp-

The Grinnell resurvey project began in 2002 here in picturesque Yosemite. Researchers have spent the past three summers collecting specimens and re-canvassing the original Grinnell sites.

Chipmunks enjoy some of the benefits of acupunc-ture while awaiting transfer to the Museum of Ver-tebrate Zoology where they will join the rest of the Grinnell collection.

Each mouse specimen is carefully labeled with in-formation on where and when it was collected. Skulls, useful to taxonomists for identifying closely related species, are preserved in small glass jars.

Adam Leaché


Photo by Erica SpotswoodPhoto by Adam Leaché

Because the original database is so complete, it is providing a rare opportuinity for modern researchers to get a glimpse

into the past.

FE

AT

UR

EBa

ck t

o N

atu

re site is chosen close by and traps are set out for

four days. Here, too, it is impossible to mimic pre-

cisely the methods Grinnell used. For one thing,

Grinnell’s team shot animals—something that’s

impossible inside the park, and impractical, at

best, outside of it. As a result, the resurvey team

does not survey for carnivores (which are usually

larger, rarer, and more difficult to trap without

shooting them), though they have made use of

data collected by the park to inform them about

current distributions.

The traps they use are different as well. Live

traps are used in the resurvey, whereas a small

lethal trap called the “museum special” was used

for most of the small mammals in the original sur-

vey. Named for its niche market, the trap protect-

ed the skull by breaking an animal’s neck instead

of hitting it on the head. Valuable to taxonomists,

the skull is used in identifying closely related spe-

cies. Current bird survey methods have also been

modified slightly. The surveyors still walk along a

path, as Grinnell did, but now birds are surveyed

only at specific points along the way. At these

locations, called point counts, all birds heard or

seen over a seven minute period are recorded.

Survey Says…

Equipped with volumes of data from the two

surveys of Yosemite, a small army of people associ-

ated with the MVZ is now working to analyze and

catalog the differences in vertebrate communities

between the two time periods. Documenting and

verifying these changes is no small feat though. In

order to prove beyond all reasonable doubt that

a species is present where it did not exist before

(or vice versa), one must be able to show that the

absence of that species was because it was not

there and not simply because it was not found.

The presences are more straightforward. If a spe-

cies is found and you have a good taxonomist to

identify it (and a specimen to prove it), you know

it was there. But how do you prove something is

really not there if you can’t find it?

Moritz is working with population biologist

Steve Beissinger from the Department of Envi-

ronmental Science, Policy, and Management to

build models of how “trappable” each species is

by looking at the total number of sites and the

animals observed at each site. Mammal curator

Chris Conroy explains that by using this method,

“If an animal was always trapped on every trap

line, every night, you get an idea that it is an easily

trapped animal. If you then go to a place and don’t

trap it, you can be more confident that it truly

isn’t there and that you didn’t just miss it.”

Determining what was trapped and when

during the original survey has also proved more

difficult than expected. Roughly three times more

information exists in the field notes than in the

specimen collection. The field notes are scanned

and available for anyone to view online via the

MVZ webpage, but there is currently no easy way

to search this database, other than, of course, by

looking through each entry. The museum wants

to make this simpler, and they are working to

develop software to recognize key words in the

field notes or to convert them all into text. For

now though, each question asked can only be an-

swered by hiring someone to pore through all of

the field notes.

In some cases, this has been worth the ef-

fort. Juan Para, a PhD student in integrative bi-

ology, spent a year sifting through 13,000 pages

of field notes recording every mammal caught

on every trap line between 1910 and 1925. The

database shows that small mammals have been

moving around in some surprising ways. Several

species have shown a shift in their altitudinal

ranges of up to 2,000 meters. Four species not

originally found in the park have expanded their

ranges upward in elevation into the park. Four

species of small mammals which were formerly

common have contracted their ranges. One, the

shadow chipmunk (Tamias senex), has gone from

being very common to virtually non-existent.

In some cases, the reasons for these chang-

es in species distribution are related to fire. Since

the mid 20th century, the National Park Service

has aggressively suppressed fires inside the park.

Comparing current photographs with those

taken during the original Grinnell survey show

marked increases in tree density, as well as some

encroachment of trees into what were once

meadows. Corresponding decreases in the abun-

dance of small mammals that prefer forest floors

that are open with dappled sunlight, such as the

Golden Mantled Ground Squirrel, are easy to ex-

plain when one considers the increase in forest

canopy density. But there are other species in

which no such explanation can be found. Why, for

example, has the piñon mouse expanded its range

into the park? Now found 2,000 meters higher in

elevation at locations as high as 10,200 feet, the

mouse has been trapped miles from the its near-

est preferred habitat of piñon pines and junipers.

Likewise, the alpine chipmunk and the American

pika were formerly common at elevations as low

as 7,800 feet. Far less numerous today, neither has

been found below 9,500 feet.

Photo by Adam LeachéPhoto by Adam Leaché


Photo b

But how do you prove something is really not there

if you can’t find it?

FE

AT

UR

EBa

ck t

o N

atu

reMovin’ On Up

Moritz, Patton, and their crew of research-

ers fear that these changes in elevation could be

linked to global climate change. There is another

line of evidence that supports this idea. Contrary

to what the mammal researchers have been find-

ing, bird diversity appears to be increasing inside

the park. Birds such as the blue winged teal are

now found breeding in the high lakes of Yosemite.

These birds look for lakes that are free of ice to

land in. Earlier ice-out dates associated with glob-

al warming could be the explanation. Addition-

ally, several high elevation species are declining in

numbers. Thus similar evidence across the very

different bird and mammal taxa suggest that climate

change may be an important factor influencing the

declines in abundance of high elevation species.

To explore further the impacts of climate

change on the survey species, researchers have

been using climate data from the early 1900s to

develop species distribution models. Most clima-

tologists do not have access to species distribu-

tion data from multiple time periods and therefore

cannot directly test how species have moved as

the climate has warmed. To get around this, models

must look at changes across many locations during

the same period of time. The assumption is that

the locations differ in climate, and nothing else. In

practice, nature is never so simple.

The Grinnell project offers a rare oppor-

tunity to do the opposite—look at the effects of

climate change over time instead of across space.

PhD candidates Bill Monahan, Juan Parra, and

Morgan Tingley have been taking the opportunity

to use climate models created from the Grinnell-

era to predict species distribution in the present.

Then, the current survey will show if their predic-

tions match up with what the survey team actu-

ally finds. Likewise, current climate models can be

used to predict past species distribution based on

past climate, which can then be compared to the

original Grinnell survey findings.

As Monahan explains, the project provides

an opportunity to train the models and increase

their accuracy, which can then be used to more

precisely predict how species will change in the

future. What they have done so far is preliminary.

“For some species, the model did really well

while for others, the model did a horrible job,” he

adds. But when Jim Patton looked at the predic-

tions for the alpine chipmunk, what he saw was

accurate. “If you model its distribution based on

Grinnell climate and distribution and then predict

its distribution now, you actually see this altitudi-

nal shift. It is impressively clear.”

The high elevation species are of particular

interest for several reasons. First, high elevation

areas are those in California that are most likely

to have experienced the least amount of land use

change in the past 100 years. The effects of cli-

mate change can therefore be isolated and inves-

tigated alone. Second, the high elevation areas are

predicted both to experience more warming and

to contain species that are more vulnerable to

climate change. Restricted to high elevations to

begin with, as the climate warms, the habitats of

these species are predicted to shrink, eventually

leading to their extinction. These patterns should

be visible much sooner in animals than in plants

because they move around so much faster.

Other explanations for the altitudinal shifts

in mammal distributions do exist, and more work

needs to be done before the Grinnell team will

be able to say with certainty if climate change is

to blame. One hurdle in this research is the lack

of a good control—a place where the climate is

known not to change—since climate change is a

worldwide phenomenon. It’s also possible that

competition between species for similar resourc-

es like food could be the cause of the shifts in

population—a good hypothesis, but one that is

difficult to measure. The Grinnell resurvey team

has not looked closely enough at the behavior

of the study species to rule competition out as

an explanation. Only further research and the

completion of the current resurvey project can

hope to shed more light on the potential causes

of these observed trends.

What the Future Holds

With the resurvey of Yosemite largely

completed, Lassen National Park is next on the

team’s list. Work will begin this spring on this part

of the project, which extends from Red Bluff in

northern California, east to the Nevada border.

Facing page, from left to right: Jim Patton, professor emeritus and curator of mammals at the Museum of Vertebrate Zoology, makes a new friend. Field specimens from the survey. A map of Lyell Canyon

from Grinnell’s original notes. This page, left: Jim Patton sexes a shadow chipmunk. Right: Emily Ru-bige, a Ph. D. student in environmental science and policy management, sifts through pages of journal

articles. The original Grinnell database consists of over 13,000 pages of field notes and over 2,000 photographs.


by Jim Patton Photo by Adam Leaché Photo by Erica Spotswood

The assumption is that the locations differ in climate, and nothing else. In practice, nature

is never so simple.

FE

AT

UR

EBa

ck t

o N

atu

re Post-doctoral fellow John Perrine has been

working for the last five months in the planning

stages. Finding the sites where Grinnell originally

surveyed has proved much more difficult than

it was in Yosemite and has taken a great deal of

historical sleuthing.

Digging through old maps, tax records, and

historical land tenure documents, Perrine has

managed to locate many of the sites, though he

has had to contend with quite a few obstacles:

towns that have disappeared, names that have

changed, railroads that have been built and then

abandoned, ferries that used to transport people

across rivers that now have bridges, and giant cat-

tle ranches owned through land grants by Span-

ish rancheros that no longer exist and whose

precise locations were never defined. If his work

is any indication of how the rest of the project

will go, the team will learn a lot about history

in the process. More importantly, they hope to

build on what they learned in Yosemite, verifying

or disproving the patterns they have begun to see

emerging. It’s a big world out there, and with the

Grinnell data and the resurvey team’s effort, we’ll

be able to sneak a peek into how human activi-

ties are changing, and will continue to change, that

world in the future.

ERICA SPOTSWOOD is a graduate student in environmental science,

policy, and management.

Above: Both the original and the new specimens will be stored here in the Museum of Vertebrate Zoology. Above Bottom: Brokeback Survey. Grinnell and his original team shown here in the field. Below left: Researchers prepare collected specimens at one of the camp sites. Below right: Emily Rubige works with some of the originals back in the Museum.

Genes from Drawers:

In addition to shifts in distribution, the ge-netic diversity of mammal populations may be changing as well. Access to museum specimens from 100 years ago with precise information on the locality where they were collected provides a rare opportunity to study how changes in dis-tribution have influenced the genetics of mod-ern populations. Emily Rubidge, PhD student in the Department of Environmental Science, Pol-icy, and Management, is using new techniques for extracting DNA from old museum skins to compare them to the resurveyed collection. Looking at a set of genetic markers to determine variability, she will be able to determine if there has been an overall change in the total genetic diversity between the two time periods.

The way in which a species has declined is expected to be reflected in the present gene pool. If an entire population of alpine chipmunks moved up in elevation, one might expect that they would have maintained the same degree of genetic diversity within the contracted range. Alternatively, if the range contracted when the lower elevation population went extinct, one would expect the current population to be less genetically diverse than the original. Rubidge’s preliminary results suggest that the alpine chip-munk has lost genetic diversity, suggesting the latter hypothesis. As she explains, “One of the big problems conservation biologists face is that we don’t know what things were like before. Al-though the environment obviously wasn’t unal-tered in the 1900s, it is a baseline that we can use to look at changes. It is exciting to be able to ask population genetic questions about popula-tions 100 years ago.”

Want to know more?

Check out:

mvz.berkeley.edu/Grinnell/index.html


Photo by Chris Conroy Photo by Erica Spotswood

Photos by Erica Spotswood


In the matter of Berkeley v. Berkeley by Michelangelo D’Agostino


FE

AT

UR

EBer

kel

ey v

s. B

erk

eley

Stepping into the Valley Life Sciences Building can be like taking a walk back in geological time. Archaeopteryx—one of the pit stops on the evolutionary road from birds to dinosaurs—greets the visitor from a large glass case, its death throes immortalized in a limestone block. Further on, Pteranodon swoops in low over T. Rex, majestically holding sway over the entrance to the UC Museum of Paleontology.

A quick trip up three flights of stairs and a more familiar realm again emerges: long, austere hallways filled with offices and labs and research posters. But while the evolutionary trip from the Jurassic to the present day may have been just as quick and easy from the perspective of Mother Nature, it only takes a glance at the clippings on the office door of Kevin Padian, Professor of Integrative Biology and Curator of the Museum of Paleontology, for a reminder that, from the human perspective, the journey has been littered with endless controversy, politicking, and rancor. Articles on the “merits” of teaching different viewpoints in science. A Bruce Springsteen quote from the pages of Esquire: “Dover, PA—they’re not sure about evolution. Here in New Jersey, we’re countin’ on it.”

And perhaps most significant, a small sticker with a drawing of Charles Darwin that reads “Charles Darwin, 5’11”, 163 lb., has a posse.” Padian, a staunch defender of evolution and president of the National Center for Science Education (NCSE), a public interest group that supports the teaching of evolution in public schools, is surely part of that posse. It was in this capacity that he testified as one of the two scientific expert witnesses for the plaintiffs in the landmark trial over the teaching of intelligent design that took place this past autumn in Dover, Pennsylvania.

In October 2004, the Dover Area School Board voted to have ninth-grade biology teachers read their students a now infamous one-minute statement. Its intent was to make students “aware of gaps/prob-lems in Darwin’s theory and of other theories of evolution, including, but not limited to, intelligent design.” “Intelligent design,” the students would be told, “is an explanation of the origins of life that differs from Darwin’s view. The reference book Of Pandas and People is available in

the library along with other resources for students who might be inter-ested in gaining an understanding of what Intelligent Design actually involves.”

That December, eleven Dover parents filed a lawsuit in federal court against the school board, alleging that the statement amounted to an unconstitutional state sanctioning of religion. For six weeks last fall, Judge John E. Jones III patiently presided over the scientific, philo-sophical, and legal arguments in what came to be known as Kitzmiller et al. v. Dover Area School District.

But while quiet Dover is several time-zones and several states of mind away from “ultra-liberal” Berkeley, the case hit much closer to home than many would have expected. Padian wasn’t the only Berkeley figure in the trial. Arrayed on the other side were an emeritus Profes-sor of Law and a former Lawrence Berkeley Laboratory post-doctoral researcher. Though not physically present in Dover or formally involved in the trial, their words and actions cast long shadows in its tran-scripts. In the cultural landscape of intelligent design, the fault lines run through some unexpected places. Like Escher’s drawing of a hand sketching a second hand which, in turn, reaches around and sketches the first, Berkeley both shapes the culture around it and is a reflection of that same culture.

Darwin’s Golden BearPadian is tall and lanky and, from a distance, where his shock

of grayish hair is less visible, easily mistakable for a graduate student half his age. Soft-spoken and deliberate, he weighs his words carefully. Perhaps he’s learned from experience. He points to countless examples of the anti-evolutionist strategy of “quote-mining”: using the out-of-context words of scientists against them. This soft-spokenness, though, masks an intensity about science and how it’s presented in the public sphere.

Padian found himself traveling to Dover at the invitation of the plaintiffs’ lawyers. The NCSE and the legal team, consisting of repre-sentatives from Philadelphia firm Pepper Hamilton and the American


Illustration by Colin Purrington

FE

AT

UR

EBer

kel

ey v

s. B

erk

eley

Civil Liberties Union, crafted a two-pronged legal strategy. First, they set out to show that the Dover school board, specifically, and the intelligent design movement, in general, acted with a particular religious intent in mind: in speaking of a “designer,” they were really speaking of the Chris-tian God. Second, they wanted to show that the theory of intelligent design has no standing at all within the scientific community. As a pale-ontologist specializing in major adaptations in the history of vertebrates, including the origins of flight and the evolution of birds from dinosaurs, Padian was well-placed to show the successes of Darwinian evolution.

Far from being the dry and clinical expert, Padian peppered his day-long testimony with af-fectionate references to “crit-ters” and “guys” and “Paleozoic roadkill.” All kidding aside, much of Padian’s testimony was dedicated to a detailed, point-by-point criticism of Of Pandas and People, the intel-ligent design textbook that was to be made available to Dover students. He attacked its notion of “adaptational packages”—that species appear abruptly and intact in the fossil record, fish with fins and scales and birds with wings and beaks—by showing that complex features can arise in a step-by-step fashion. And he pointed to examples from the fossil record where such transitions from one form to the other can actually be observed. Overall, the effect of Pandas would be to mislead students, he told the court. “What is a kid supposed to think when you tell him you can’t get from Point A to Point B and then evidence is uncovered that shows that, well, in fact, it looks pretty conceivable that you can?”

Padian ended his testimony with an impassioned plea. Asked why, as a scientist, he has a problem with reading the one-minute statement to students, he replied:

I think it makes people stupid. I think essentially it makes them ignorant. It confuses them unnecessarily about things that are well understood in science, about which there is no contro-versy…I can do paleontology with people in Morocco, in Zim-babwe, in South Africa, in China, in India, any place around the world…We don’t all share the same religious faith. We don’t share the same philosophical outlook, but one thing is clear, and that is when we sit down at the table and do science, we put the rest of the stuff behind. [see page 34 for more of the BSR’s interview with Padian]

Of Pandas and ProfessorsIronically enough, Padian wouldn’t have been called upon to de-

liver impassioned defenses of evolution on a national stage without the work of another Berkeleyan—Philip Johnson, Professor of Law Emeritus at Boalt Hall and the widely recognized father of the intelligent design movement. Professor Johnson also serves as an advisor to the Discovery Institute, the Seattle based think-tank that has been the driving force behind intelligent design.

Johnson’s publication of the 1991 book Darwin on Trial is as close to a birthday as the intelligent design cause has. “I approach the creation-evolution dispute not as a scientist but as a professor of law,” he writes in its first chapter, “which means among other things that I know something about the ways that words are used in arguments.” Johnson’s intent was to bring his lawyerly skills to bear on the task of analyzing the logic of and the assumptions behind Darwinism. The essence of his argument was that the logical structure of the evolution debate is framed in such a way as to favor evolution from the outset; scientists “have to rely on a definition of science that does not permit an alternative to

naturalistic evolution.” Further-more, he maintained that the evidence for the creative power of

the Darwinian mechanism is scant at best. Two years later, Johnson organized a meeting at Pajaro Dunes near

Monterey to bring like-minded thinkers together. Its participants would become the major public figures in intelligent design: Scott Minnich and Michael Behe, who would testify on behalf of ID in Dover, Steven Meyer, who would direct the Discovery Institute’s Center for Science and Culture, and Jonathan Wells, who pursued a PhD in molecular and cell biology at Berkeley after becoming convinced that he “should devote [his] life to destroying Darwinism.”

Pandas, too, had its origins much closer to home. Dean Kenyon, one of its two authors and another fellow at the Discovery Institute (and a Pajaro Dunes participant), spent his career as a Professor of Biology at San Francisco State University. His pedigree includes a stint on this side of the Bay as well, though. After receiving his PhD in biophysics from Stanford, Kenyon worked as an NSF post-doctoral fellow under Melvin Calvin at the Lawrence Radiation Lab (as Lawrence Berkeley National Laboratory was known in its early days). Calvin, one of Berkeley’s most renowned chemistry professors, was awarded the 1961 Nobel in chemistry for his work elucidating the chemical processes involved in photosynthesis.

So while evolution was being taught to introductory biology classes and was guiding the research of countless professors in diverse depart-ments around campus, up the hill at Boalt and across the Bay, the intel-ligent design movement was taking shape.

Exapt or DieOne of the most powerful scientific weapons in the arsenal of evo-lutionary biologists is the concept of “exaptation.” As Padian explains in his trial brief, exaptation is the idea that “a structure that initially is developed in the service of one function may be modified to serve a completely different function.” So it is that the bones which held the upper and lower jaws together in reptiles were later used to transmit sound in the mammalian middle ear. Feathers insulated certain small theropod dinosaurs and shaded their eggs before they became vital for the flight of the birds that evolved from them. In this way, many of the features that the proponents of intelligent design claim are “irreducibly complex” can be shown to have evolved in a step-by-step fashion.

“ I think it makes people stupid.”

Exapt or DieOne of the most powerful scientific weapons in the arsenal of evo-lutionary biologists is the concept of “exaptation.” As Padian explainsin his trial brief, exaptation is the idea that “a structure that initially is developed in the service of one function may be modified to serve a completely different function.” So it is that the bones whichheld the upper and lower jaws together in reptiles were later usedto transmit sound in the mammalian middle ear. Feathers insulatedcertain small theropod dinosaurs and shaded their eggs before theybecame vital for the flight of the birds that evolved from them. In thisway, many of the features that the proponents of intelligent designclaim are “irreducibly complex” can be shown to have evolved in a step-by-step fashion.



Reprinted by permission of evolution.berkeley.edu

FE

AT

UR

E

SURVIVAL OF THE LITIGIOUSThe university finds itself embroiled in legal battles over evolution and intelligent design on its own turf as well. In August, the Association of Christian Schools International and the Calvary Chapel Christian School in Murrieta, California filed suit against the UC, alleging religious bias in its high school course certification

policies. All public and private schools in the state must apply to the UC for certification in order to have their courses counted as college-prep credits in the admissions process. While 43 courses from Calvary were approved, a handful were rejected because of their content or text book selection. The UC says it will not certify science classes that use overtly religious texts such as those from Bob Jones University Press. The introduction of one such biology text states that “the people who have prepared this book have tried consistently to put the Word of God first and science second.” The University is fighting the suit, maintaining that it has a right to set such standards and that the standards apply to everyone equally.

In October, a California couple brought another suit against the UC over “Understanding Evolution” (evolution.berkeley.edu), a web site meant to serve as a resource for high school biology teachers on the topic of evolution. Jeanne and Larry Caldwell maintained that the site violates the separation of church and state by making the statement that religion and science are very different things and that one need not make a “choice” between the two (the site features a cartoon of a labcoat-clad, fossil-hugging scientist shaking hands with a Bible-toting priest). By linking to an NCSE site that features quotes from particular religions that state that evolution is not incompatible with religion, the public UC is also using federal money to promote these particular religious views over others. The suit was dismissed in March when a federal judge ruled that the couple lacked legal standing to sue in federal court.

Ber

kel

ey v

s. B

erk

eley

Boalt From AboveNothing about Johnson’s white hair and grandfatherly demeanor

suggest that he would spark a national controversy. He sits in his third-floor Boalt Hall office surrounded by books and papers, the very picture of a welcoming, open-minded intellectual. A stuffed gorilla wearing a suit and smoking a cigar sits on his desk (a gift from some students, he laughs). He smiles and quips that he wouldn’t mind being related to gorillas; after all, a handful of dust is not necessarily a more noble beginning.

“I considered [Dover] a loser from the start,” Johnson begins. “Where you have a board writing a statement and telling the teachers to repeat it to the class, I thought that was a very bad idea.” The jaw drops further when he continues:

I also don’t think that there is really a theory of intelligent design at the present time to propose as a comparable alterna-tive to the Darwinian theory, which is, whatever errors it might contain, a fully worked out scheme. There is no intelligent design theory that’s comparable. Working out a positive theory is the job of the scientific people that we have affiliated with the movement. Some of them are quite convinced that it’s doable, but that’s for them to prove…No product is ready for competition in the edu-cational world.

Throughout the interview, Johnson maintains that his interest in Darwinism is purely intellectual rather than political: “The key question to me is not what happens in a particular federal district court, but whether or not that claim is correct.” Politics only hurts this search for the truth. When President Bush came out in favor of teaching both sides of the debate, Johnson had mixed feelings. “I’m glad to see the idea that there’s something to discuss here get further off the ground, but the fact that it was Bush who said it put the issue into the red state blue state po-litical mix…I was more dismayed than elated to see the thing surface in the context of our political divide.” [see page 34 for more of the BSR’s interview with Johnson]

It’s difficult to tell if Johnson is being completely forthright about wanting to stay out of politics and the public schools. In the past, Johnson has certainly put considerable effort towards injecting intel-ligent design into the public realm. In 2002, he told the Berkeley Science Review that “where controversial subjects like biological evolution are taught, educators should teach the controversy, preparing students to be informed participants in public debates.” As an example, he pointed to

the Santorum Amendment, a “teach the controversy” amendment to No Child Left Behind proposed by Republican Senator Rick Santorum of Pennsylvania but ultimately dropped in the final bill. Johnson told the Washington Times that he himself “helped frame the language” of that

amendment. In addition, Johnson was one of the main architects of the Discovery Institute’s Wedge Document. In that document, he outlined a strategy that would act as a wedge to split the tree of cultural and scientific materialism.

Perhaps he’s had a change of heart, and his position truly has evolved in a more apolitical direction. It’s clear that Johnson genuinely believes what he writes and espouses. And it’s hard to doubt that he has a burning intellectual interest in the fundamentals of evolution and design. But it’s also hard to doubt that he’s helped to further intelligent design in the public realm, whether through his writing, his organiza-tional skills, or his work with the Discovery Institute. His attitude has the flavor of the old Billy Joel tune: “We didn’t start the fire. It was al-ways burning since the world’s been turning.” But surely Philip Johnson helped to start the fire.

It Ain’t Over ‘Til…And so the stage was set for Dover. After six weeks of delib-

eration, Judge Jones delivered a strongly-worded decision, ruling for the plaintiffs and holding that the Board’s actions had clearly violated the separation of church and state. Padian’s testimony featured prominently in the decision, as did the words and actions of Johnson and Kenyon,

While supernatural explanations may be important, and have merit,

they are not a part of science.


FE

AT

UR

E

interviews continued on page interviews continued on page

Ber

kel

ey v

s. B

erk

eley

though they were not physically present in the courtroom. “The evidence at trial demonstrates that ID is nothing less than the progeny of creationism,” Judge Jones wrote. But he went even further. Asked by both sides to address the fundamental question of whether or not intel-ligent design is science, he wrote:

While supernatural explanations may be important and have merit, they are not part of science…While we take no posi-tion on whether such forces exist, they are simply not testable by scientific means and therefore cannot qualify as part of the scien-tific process or as a scientific theory…ID is not science and can-not be judged a valid, accepted scientific theory as it has failed to publish in peer-reviewed journals, engage in research and testing, and gain acceptance in the scientific community. ID, as noted, is grounded in theology, not science.

Science cannot be defined differently for Dover students than it is defined in the scientific community as an affirmative ac-tion program…for a view that has been unable to gain a foothold in the scientific establishment.

Both Defendants and many of the leading proponents of ID make a bedrock assumption which is utterly false. Their pre-supposition is that evolutionary theory is antithetical to a belief in the existence of a supreme being and to religion in general.

For Padian, the decision represents an incredible victory: “Not a single sentence of the judge’s decision would give comfort to the ID crowd. We don’t see how it could have been any better.” “The judge’s

decision made a lot of things easier for the American public,” he continues. “He drew the line that scholars and educators asked him to draw. He didn’t muddy the line like the fundamentalists asked him to do. For Phil Johnson and the Discovery Institute, the fat lady has sung…No one who can fog a mirror intellectually can have any more illusions that this drivel should be taken seriously as science, or even as social studies.”

For his part, Johnson agrees: “I think the fat lady has sung for any efforts to change the approach in the public schools…the courts are just not going to allow it. They never have. The efforts to change things in the public schools generate more powerful opposition than accom-plish anything…I don’t think that means the end of the issue at all.”

“In some respects,” he later goes on, “I’m almost relieved, and glad. I think the issue is properly settled. It’s clear to me now that the public schools are not going to change their line in my lifetime. That isn’t to me where the action really is and ought to be.”

Whether Dover really was the swan song of intelligent design remains to be seen. Either way, the decision has dealt a serious blow to the cause. The movement that Phil Johnson started may just have run aground on the rocks of Padian’s testimony. Or rather on the fossils in the rocks of Padian’s testimony.

Michelangelo D’Agostino is a graduate student in physics.

BERKELEY SCIENCE REVIEW:

After the Dover decision, do

you think there will still be mo-

mentum for changing curricula

to “teach the controversy”

without insisting on a particular

alternative, as the Dover school

board tried to do?

KEVIN PADIAN: Yes. That will

continue to be well-funded,

whether it’s through the Dis-

covery Institute’s “Center for Science

and Culture,” or whatever they’re calling it this week. There will always be

money around to fund people like this. There will always be a place for it in

the fundamentalist community. But their influence on mainstream culture is

done.

BSR: Do you think in the past that the mainstream media has had a role in

the success the intelligent design movement had, that they took their claims

more seriously than they should have been taken?

KP: Yes and no. In this country when someone talks about fairness, we all

put down our guns and listen. Because to the American people fairness is

one of the cardinal virtues, and we do think that people have a right to their

opinions. We do believe very strongly in religious freedom. But there are times

when certain people take advantage of this by warping what is actually going on.

THE BSR SITS DOWN WITH PHILIP JOHNSON AND KEVIN PADIAN

Professor of Integrative Biology Kevin Padian testified in defense of evolution in Dover. Philip Johnson, Professor of Law Emeritus at Boalt Hall, is the widely-recognized father of intelligent design. In the aftermath of the Dover decision, they both sat down to talk with the Berkeley Science Review.

BERKELEY SCIENCE REVIEW:

What was your reaction to the

Dover decision?

PHILIP JOHNSON: The key

question to me is not what

happens in a particular federal

district court, but whether or

not that claim is correct. So,

if it’s not correct, if random

mutations and differential sur-

vival really can take a bacterium

through all the changes that are necessary upward through the tree of life to

end in you and me, then we certainly…ought to vanish from the scene. But

what really convinced me that there’s something here was the need that the

Darwinist’s have to rely on a definition of science that does not permit an

alternative to naturalistic evolution. That seems to me a very unsatisfactory

way of resolving the issue.

My own contribution to the movement, seminal though it may have been,

in Darwin on Trial, was simply to argue that the Darwinian mechanism has no

demonstrable creative power, much less the creative power needed to do all

the innovation that has appeared in the history of life. So that’s my position.

BSR: So you think that Dover was the wrong battle to try to fight?

PJ: Oh yes it was. And my friends and I argued that they shouldn’t have done

that, and that having done that, they should have withdrawn the policy to moot

the case.

Illustrations by Rachel Eachus


Padian interview cont’d:Johnson interview cont’d:

FE

AT

UR

EBer

kel

ey v

s. B

erk

eley

And these guys are warping their

presentation of science in both the

evidence and the methods and the

philosophy of science…And this is something that it takes ordinary people a while to find out, and for good reason, because sci-ence is a world of jargon and very arcane and abstruse knowledge that scientists make very little attempt to make palatable and interesting to ordinary people. We could do it, we just don’t place a premium on it, and that’s our fault.

BSR: Why do you think it is that evolution gets such a visceral reac-tion from people? A lot of things about cosmology and astrophysics seem like they could similarly shake people’s worldviews.

KP: Because they don’t under-stand it. They don’t understand the first thing about relativity. If you tell them that the universe is 15 billion years old they go “Oh” and they don’t have to deal with it anymore. And in fact there are a lot of physicists who as you know are very much engaged in cosmological metaphysical questions, many of which have completely non-scien-tific dimensions that they take very seriously. But the problem here is that once we start talking about how life changes through time it’s getting closer to everybody’s backyard. And people don’t want to hear that they are animals, that they are mammals. They don’t want to hear what they share with a gorilla.

BSR: What does it say about us as a country that ID has made this headway?

KP: That’s a good question. I think it’s made this headway because it was carefully crafted as a socio-political movement. A cultural movement that wanted to get a materialist view of life replaced by a particular Christian theistic worldview. This is exactly what the Discovery Institute says in its wedge document, its mission statement.

BSR: But in some sense there must have been fertile ground for it…

KP: Well, you never go broke in this country asking people to think

more about God and less about materialism, as long as they don’t actually have to give anything up. You can always demonize someone who is not you, and that’s ex-actly what the Discovery Institute people have done. They’ve demon-ized scientists, they’ve demonized the practice of science, they’ve deliberately tried to create a big tent of people who disagree with each other on nearly everything, the other creationists, older cre-ationists, fundamentalists, moderate evangelicals.

BSR: What’s your personal opin-ion on the co-existence of science and religion in general? It seems like there must be another group of religious people in this country who wouldn’t call themselves fundamentalists who don’t have a problem with science…

KP Fundamentalists can’t co-exist with anyone. I mean that’s just it. They can’t coexist with anyone. Particularly not other fundamental-ists. To them, everyone is an enemy.

BSR: It seems like on both sides there’s a little bit of demonizing of the other side. Do you think scientists share some of the blame at all?

KP: Well, scientists really don’t go out in the world talking about how stupid religion is. It isn’t that they couldn’t, it’s just that they don’t. When pressed, you’ll get people like Richard Dawkins, who’ll say that it’s just superstition and all of the claims it makes for its good works and uplifting effects are just balderdash, and he can point to evidence for this. This is nothing new. And no, I don’t think it’s the scientists’ fault about that. I think the scientists are at fault for not explaining our disciplines more clearly to the public so that they can’t be misconstrued. If our level of scientific literacy were higher in this country we might not have this problem. But you see, these people have been working for 85 years so that we don’t even get to teach this.

BSR: Where do you think things will go from here?

PJ: I think that the issue will con-tinue to be debated in the public forum. In the United States, it’s no secret that the overwhelming ma-jority of people are unconvinced by the Darwinian claims. Only about 10 percent of the American pubic is convinced of the fundamental Darwinian claim that mankind and all other living things on the earth were produced by a process of ran-dom mutation and natural selection as the textbooks say in which God played no part, the creator played no part. The other 90 percent would be divided between outright creationists…and then those who say there was a process of evolu-tion…which was God-guided.

BSR: What do you think about the organizations and think tanks that are pushing this as a political issue rather than as an intellectual issue? Do you think the debate should just stay within universities and the academe?

PJ:: Well that’s always the way I had thought of it. Now, I have to confess to some guilt here myself, because I have talked about the moral conse-quences or cultural consequences of Darwinism, and I mean that as a reason for saying, well this is impor-tant, so we have to really be sure that what we’re saying is science is really backed by powerful evidence. And I would say that the claims for the creative powers of mutation and selection are not backed by powerful evidence.

BSR: Do you think Judge Jones overstepped his judicial role?

PJ:: I would say so, yes. I wouldn’t say that that necessarily means the judgement’s going to be reversed. It probably doesn’t. He plainly decided to join the cultural war, the cultural battle, and say, “I’m gonna settle this

thing.” There were specific things in the record…that convinced me that it was a loser and that made it quite easy for him to give judgment for the plaintiffs. I’m not at all com-plaining that he did that. When you have members of the school board saying things like we ought to stand up for Jesus because he died for us, that’s really asking for it. Even so, the thing is not what anybody’s mo-tive is, but how good the evidence is. The issue over Darwinism in the public and university world does not hinge on what the motives are for anybody proposing or oppos-ing the claims of the Darwinian mechanism.

BSR: Do you think that you scien-tists and philosophers are going to keep trying to work on this issue?

PJ: Yes. They do. In fact, I get email every week from graduate students.

BSR: Would you say that Berkeley has been an open and hospitable place in your experience?

PJ:: They put up with me all these years. I would say Berkeley has been open in my experience, as a whole. Some people at Berkeley are not. People whose livelihood is all mixed up in conventional evolution or biology tend to get quite angry and don’t want anything heard about it. I would say the Berkeley campus on the whole…it would surprise many people how open it is and has been. Even people who are quite conventional in their Dar-winist beliefs themselves will often think that it’s a good idea for the students to hear something that contradicts the official story. So yes, I’m quite approving of Berkeley on the whole.

When you have members of the school board saying things like we ought to stand up for Jesus because he died for us, that’s

really asking for it. - Johnson


IP: Ideas for Purchase?1965: Touchdown for the Gators

Once upon a time, a college football team sweated their way

through practice in the searing heat of central Florida. Their coach was

worried. His team, the University of Florida’s “Fighting Gators,” lost pro-

digious amounts of weight during practice. Trips to the hospital for heat

exhaustion were common. The coach consulted a couple of university

kidney specialists who performed the necessary tests, enlightened the

coach about perspiration, and concocted a beverage that could both re-

hydrate and restore electrolytic harmony. Gatorade was born.

Over forty years later, Gatorade-drinking athletes now exert them-

selves freely without fear of collapse. The University of Florida receives $9

million a year in trademark royalties from PepsiCo, Inc. According to the

university, royalty money is reinvested in a wide range of research. As

for those brave fighting gators, the Gatorade-fueled team went on to win

the Orange Bowl for the first time in school history in 1967.

“It’s okay to make money.”

On a clear day, the view from Dr. Carol Mimura’s tidy corner office

on the fifth floor of the PowerBar building in downtown Berkeley is spec-

tacular. Mimura, UC Berkeley’s technology transfer guru, is pleasant and

professional, laughing quietly at all the right moments and just occasion-

ally letting frustration nudge the pitch of her voice a touch higher. Which

is what happens when she says the following: “There’s a perception that

we’re just out there to try to maximize revenue, which is just wrong we’re

a university.”

The confusion is understandable. Mimura negotiates the shifting line

between university and industry, and she excels at maximizing revenue.

The profound bureaucracy that she tackles is implicit in her absurdly

long official title, Assistant Vice Chancellor of the Office of Intellectual

Property and Industry Research Alliances (IPIRA), which means that she

brokers the licensing of patented technologies developed at UC Berkeley.

In these deals, licensees often agree to pay royalties to the university in

exchange for access to a patented technology. Berkeley currently brings

in $8-13 million a year in licensing revenues, and during Mimura’s two

years as Director of the Office of Technology Licensing, revenues have

increased by 150%.

But Mimura says that her obligation to the university goes beyond mere

moneymaking, and she’s backed that up by leading UC Berkeley’s“

socially responsible licensing program.” The idea behind the program is to

create licenses that encourage the development of technology that will

benefit developing nations. In some cases, that encouragement takes

the form of royalty-free licenses; sometimes the licensee also agrees to

provide any resulting technology—for example, a malaria drug to

developing nations at the lowest possible cost.

The Myth of the Cash CowFor a dry piece of intellectual property legislation, the Bayh-Dole Act

has been the subject of a surprising number of barnyard metaphors. Whether a “cash cow” or a “golden goose”, the meaning is clear: royalty revenue from university patent licenses is a gift that keeps on giving.

But in reality, most technology transfer offices are hardly raking in money. Although there are the occasional blockbuster patents such as UC San Francisco’s hepatitis B vaccine (worth $20 million yearly) or even UC Davis’s Camarosa strawberry hybrid ($3 million per year), those moneymakers lie well outside of the norm, according to a survey conducted by the Association of University Technology Managers. Of the 27,322 cumulative active licenses in 2004, only 167, or 0.6%, generated more than $1 million in royalty income.

Furthermore, universities and federal research institutions reported an average licensing income of just over $7 million per institution in 2004, with half of the 196 university respondents pulling in less than $1 million. An individual million-dollar paycheck seems great, but overhead expenses and salaries for the average four licensing experts and four administrative support staffers per technology transfer office reduce net revenue considerably. “The cost of these offices is high,” says Haas Business School Professor David Mowery, who adds that many universities are actually losing money.

So why bother? Because these collaborations between academia and industry have rewards that go beyond direct royalty revenue. Mowery believes it’s important to keep this in mind during Proposition 71 discussions. Rather than demanding large royalties for their patents, the state should do what it takes to stimulate industry investment, he says. “Net licensing revenues from Prop 71 patents are likely to be very modest,” says Mowery. “By comparison, the economic effects of juicing the biotech industry far outweigh income from licensing.”

hem-

ves $9

to the

h. As

o win

office

spec-

t and

asion-

Which

n that

we’re

g line

enue.

surdly

ectual

at she

But Mimura says that her obligation to the university goes beyond mere

moneymaking, and she’s backed that up by leading UC Berkeley’s“

takes to stimulate industry investment, he says. “Net licensing revenues from Prop 71 patents are likely to be very modest,” says Mowery. “By comparison,the economic effects of juicing the biotech industry far outweigh income from licensing.”

Illustration by Jennifer Bensadoun

by Heidi Ledford


The three-year-old program is currently the only one of its kind, but

Mimura has recently been in discussions with other universities to explore

ways of expanding UC Berkeley’s socially responsible licensing efforts.

And in 2005, she was called before the state senate Subcommittee on

Stem Cell Research Oversight to explain how such licensing policies could

be extended to the transfer of technology resulting from California’s

Proposition 71 stem cell research initiative.

This outside interest indicates a general trend toward expanding the

scope of technology licensing to incorporate the social mission of univer-

sities. “It’s okay to make money,” says Mimura, “It just shouldn’t be your

main goal. We think there’s a role for the university to change the whole

public dynamic of intellectual property.”

At present, the public dynamic of university intellectual property is

somewhat messy. Until 1980, the legend of Gatorade was the exception

that proved the rule—discoveries made in academia rarely found their

way to the private sector, partly due to the bureaucratic labyrinth that

federally-funded researchers faced when trying to patent their inventions.

The Bayh-Dole Act, penned in 1980 by Senators Birch Bayh (D-Indiana)

and Robert Dole (R-Kansas), aimed to facilitate technology transfer from

academia to industry by explicitly granting universities the right to patent

inventions made with federal funding. The reasoning was clear—industry

would benefit from the infusion of technology, universities would benefit

from the royalties of their patents, and the public would benefit from the

many fruits of marketable innovation.

The Bayh-Dole act has generally been credited with achieving each

of those goals. As technology transfer offices sprouted in universities

across the country, Google, nicotine patches, the chemotherapy drug

Taxol, and others climbed down out of the ivory tower and into the

marketplace. The number of patent licenses originating from universities

increased nearly ten-fold between 1979 and 1997, significantly higher

than the two-fold increase in non-university patent applications during

the same period. Attributing all of those achievements only to Bayh-Dole

is a common oversimplification, and the Bayh-Dole Act has consequently

come to symbolize the economic power of university-industry collabora-

tions.

Unfortunately, the newfound collaboration between industry and

academia also ushered in an era of competing interest statements and

material transfer agreements. Scientists began to complain about increased

secrecy among colleagues trying to protect patent rights. Increased

alliances between industry and academia brought increased scrutiny

and skepticism from the press, and nowhere is that skepticism more

intense than in the licensing of biomedical technology. One question bobs

persistently to the surface: How is a university serving the public good

when it demands large royalties for promising pharmaceuticals? Even

though much of that royalty money is funneled back into research, it is

always hard to justify a profit when lives are on the line. Gatorade was

easy—no one is likely to accuse PepsiCo or the University of Florida of

harming public health by inflating the cost of Gatorade. Pharmaceuticals

are an entirely different story.

2001: The Ties that Bind

With 20% of its population HIV positive, South Africa, like much

of the rest of sub-Saharan Africa, was in the throes of a crisis. The most

frequently prescribed AIDS drug on the market, a reverse transcriptase

inhibitor called “d4T”, was produced by the pharmaceutical giant

Bristol-Myers Squibb at a cost of $10 per day, per patient. With 50% of

the country living below the poverty line, the price was simply too high. In

December of 2000, Doctors Without Borders asked the South African divi-

sion of Bristol-Myers Squibb for permission to import generic forms of d4T.

Bristol-Myers Squibb told Doctors Without Borders to consult Yale,

which held the patent on d4T. Yale told Doctors Without Borders that

they would have to consult Bristol-Myers Squibb, which had an exclusive

license for the d4T patent. The terms of that license, said Yale, dictated

that only Bristol-Myers Squibb could decide whether generic forms of

d4T could be imported. At that time, Yale was making $40 million a year

from d4T royalties.

As the finger pointing continued, Yale students petitioned Yale to

relinquish its hold on the d4T patent in South Africa. They collected 600

signatures from the Yale community, and received an endorsement

from Professor William Prusoff, d4T’s original inventor. Soon after the

mainstream press got hold of the story, Yale and Bristol-Myers Squibb

announced that they would not enforce their patent rights in South

Africa, in effect allowing importation of generic d4T.

Checks and Balances“I have to be clear about this,” says M. A. Basit Khan, quickly lean-

ing forward in his seat at a table outside the Free Speech Movement Cafe.

“Our group is not entirely anti-pharma. We don’t think that’s a realistic

stance to take.”

Khan, a second-year Berkeley undergraduate, is a member of Univer-

sities for Access to Essential Medicines (UAEM), a multi-campus organiza-

tion born from the d4T student protests at Yale. UAEM has since grown

to include groups at over 25 universities in the United States and Canada.

Among the aspirations listed in UAEM’s Statement of Principles is to

persuade universities to construct licensing agreements that will “facili-

tate access in low- and middle-income countries to medicines and health

technologies originating in university research.” UAEM is understandably

interested in UC Berkeley’s socially responsible licensing program, and

word of the program has passed from the Berkeley chapter of UAEM to

other member organizations, some of which have brought the program

to the attention of their local technology transfer offices.

Although a socially responsible licensing program is clearly an op-

portunity to give UC Berkeley a public relations boost, Khan believes that

Mimura’s support of the program is not just a PR ploy. “She supports

access as much as we do,” says Khan of Mimura. “She’s totally behind it.

She’s taking a big risk.” Mimura’s liberal use of the phrase “moral impera-

tive” supports Khan’s assessment of her sincerity.

Eva Harris, an associate professor at the School of Public Health, didn’t

expect such firm support when she approached Mimura at a picnic one

Photo courtesy of Yale University

Yale Medical School administrators and Bristol-Myers Squibb officials at a ceremony celebrating their ongoing partnership.


spring day in 2002. Harris wanted to warn Mimura: she had just sent

the technology licensing office a proposal that they were not likely to

approve. Harris had just collaborated with a few electrical engineering

students to develop a tool that could be used to rapidly diagnose dengue

fever in the field. Now she had a problem. She wanted to be able to

provide the technology to developing nations at the lowest possible cost,

but on the other hand she needed to patent the technology so that no

one else would patent it and drive up the cost. In short, she needed a

royalty-free license.

Harris had a great idea,

thought Mimura. UC Berkeley had

struggled in the past to license po-

tential malaria therapies, and she

saw Harris’s proposal as a way of

enticing industry interest in tech-

nology that benefits developing

nations. Mimura was also troubled

by the recent Yale/d4T debacle.

She had expected that the pros-

pect of negative publicity would

have prompted any corporation

to act before landing on the front

page of the New York Times. “But

for some reason, they didn’t,” says

Mimura. “The checks and balanc

es we were counting on just

weren’t there. That caused us to

think—if we had that deal, how

could we have prevented that

situation?”

Prompted by Harris’s propos-

al, UC Berkeley brokered a deal

with the non-profit Sustainable Sciences Institute to provide the dengue

diagnosis technology to developing nations without royalties, while re-

serving the right to earn royalties from derivative technologies marketed to

developed countries. Since that inaugural agreement, fifteen more socially

responsible deals have followed. One deal concerns a potential new AIDS

drug; another aims to improve the nutritional content of sorghum, a staple

crop in Africa. No two contracts are identical—for example, definitions of

“developing nation” change from agreement to agreement.

UC Berkeley isn’t giving up much revenue by offering royalty-free li-

censes on technologies to detect dengue fever or to treat malaria—both of

these diseases strike developing nations that lack the economic power to

generate large royalty payments. In the meantime, incorporating equal

access clauses into some licensing agreements has attracted research

money from charitable organizations. The most lucrative example of this

is the recent research agreement between Jay Keasling’s lab in the Depart-

ment of Chemical Engineering, the nonprofit pharmaceutical company

Institute for OneWorld Health, and Amyris Biotechnologies, a for-profit

biotechnology start-up. The deal drew the interest of the Bill and Melinda

Gates Foundation, which then contributed $42.6 million dollars to fund a

cheaper method for producing the anti-malaria drug artiminisin. Ensuring

that artiminisin would be provided to developing nations at the cost of

production and distribution was the key to getting that research money.

“Gates would not fund until we could guarantee access,” says Mimura.

“I like to say that Eva Harris gave us the moral compass,” says Mimura,

“and then Jay Keasling provided the muscle.”

David Mowery, a professor in UC Berkeley’s Haas School of Business,

generally approves of the new program. “I think it makes a lot of sense,”

he says. “UC and Carol Mimura are making significant progress in

thinking more clearly about the rewards and the costs of technology

licensing.” But while he supports the royalty-free licensing approach,

limitations on drug prices worry him. Cheap drugs in Africa could

travel via the black market into more lucrative developed countries, he

points out.

Pharmaceutical companies share Mowery’s concerns. Giving up reve-

nue in developing nations is one thing, but possible intrusion into domestic

market revenue is another matter entirely. While that would not be likely

in the case of artiminisin, what about potential AIDS treatments? Mimura

and Mowery both cite the National Institute of Health’s past failed

attempts to work “reasonable pricing” clauses into licensing agreements,

and both say those clauses drove away industry investment.

Merrill Goozner, director of the Integrity in Science Project at the Center

for Science in the Public Interest, agrees that intellectual property

discussions get a lot more heated when domestic markets are involved. In

developing nations, he says, “the problem isn’t so much that intellectual

property stands in the way, it’s that the market for development just isn’t

there. Where intellectual property is much more interesting is in drugs

that go to the first world.”

IPIRA does not have a lot of leverage—generating private invest-

ment in university inventions is often an uphill struggle. “We rarely have

anything that’s truly commercial,” says Mimura. Unlike Gatorade, most

inventions that come out of a university require a great deal of further in-

vestment before producing a marketable product. In particular, the phar-

maceutical industry points to the staggering expense of clinical trials and

the equally stunning failure rate of their candidate drugs.

Mimura says that IPIRA is currently testing the waters with potential

partners in industry to find out what they are willing to accept. “We

are looking for more carrots because the stick approach is hard and can

damage corporate relationships,” says Mimura. “It’s definitely going to be

a hard sell, but definitely worth the effort.” And while Mimura searches

for ways to ensure that developing nations can access vital medicines,

one California state senator recently posed the question: Can we use

licensing to help the poor within our own country access the fruits of

university research as well?

2006: Promises, Promises

As State Senator Deborah Ortiz nears her term limit, oversight of

stem cell research ranks high on her list of priorities. In November of 2004,

Californians passed Proposition 71, a measure that allots three billion

dollars to stem cell research, after scientists and politicians promised that

the money would come back to them in the form of a flourishing biotech

industry, patent royalties, and therapies that would save them from a

myriad of diseases. Eager to ensure that Californian taxpayers will get the

promised returns on their investment, Ortiz called a hearing to discuss the

best way to license technologies derived from Prop 71 money. “We would

be remiss if we didn’t attempt to ensure that the issue of the ultimate

accessibility and affordability of stem cell therapies and treatments rely-

ing on Prop 71-funded research is addressed,” she said. “That goal has

not been addressed very well by the Bayh-Dole Act.”

On October 31, 2005, assembled experts gave opinions that were

all over the map. James Pooley, representing the Intellectual Property

Study Group of the California Council on Science and Technology,

warned against straying too far from the Bayh-Dole model. Mimura pre-

sented the details of her socially responsible licensing program. Goozner

told the panel that California should revolutionize technology licensing,

toss out the old Bayh-Dole model, and take an open-source technology

approach.

Associate Professor Eva Harris, whose royalty-free licensing proposal on a dengue fever diagnostic device kick-started UC Berkeley’s socially responsible IP licensing program.


In addition to her interest in technology licensing, Ortiz wants pro-

tections for egg donors and audits of funding distribution. For her ef-

forts, Ortiz, one of the original sponsors of Prop 71, has been accused

of hindering stem cell research, with some going so far as to say that she

has realigned herself with right-wing opponents of the program. Ortiz

defends herself, saying, “We have an obligation to the voters that goes

beyond mere science.”

The Big Boys on the Block

Scrunched down in his chair, his feet propped up on his desk, Mow-

ery rolls his eyes and winces when discussing the Prop 71 licensing hearings.

“One of the problems is that the Prop 71 work is way upstream,”

says Mowery. “We don’t have a therapy. We don’t have anything. It’s all

surrounded by layers and layers of uncertainty. And as you layer more

and more uncertainties on top of what is a fairly elastic agreement, it gets

more difficult to negotiate.”

Nevertheless, Goozner, who vehemently believes that Bayh-Dole era

patent licensing inhibits innovation and adds to the already inflated

cost of pharmaceuticals, saw in the Prop 71 hearings an opportunity to

overthrow the old system. “The Feds have always been the big boys on

the block,” says Goozner. “And now you have a case where one state is

stepping up to plate. California, because of its size, has the capacity to

show a new direction in this area.”

In the end, the licensing proposal included Mimura’s recommenda-

tions, including a few clauses that resemble those in UC Berkeley’s socially

responsible licenses. For example, the proposal requires licensees to

provide therapies derived from these discoveries to state health programs

at the lowest available commercial cost—already a common practice

among pharmaceutical companies. Licensees must also provide “a plan”

by which uninsured Californians may access those therapies. “My guess

is those plans will be pretty fuzzy because nobody knows what will come

of this research,” Mowery says.

Ortiz has clearly stated that she views the current proposal as a mini-

mal compromise, calling it “a floor for negotiation of proposed intellec-

tual property agreements.”

“You are using the taxpayer dollars of poor people, working class

people that overwhelmingly lack access to care and overwhelmingly carry

heavy disease burdens,” said Ortiz at a recent meeting on stem cell policy

at UC Berkeley’s Law School. If there are errors to be made, she added, “I

think we err on the side of society and the taxpayers who are paying for it.”

Oritz’s argument carries a lot of weight in the emotionally-charged

environment of Prop 71 discussions, but so does the counterargument:

that high licensing royalties and price limits on resulting therapies could

drive away industry investment and slow the race to find the cures

those same taxpayers were promised during the campaign. The current

proposal seems to represent a compromise between Ortiz’s vision of

accessibility and industry’s demand for flexibility. It is in essence a

miniature, state-level Bayh-Dole layered with a few socially responsible

licensing clauses.

“Bayh-Dole is not the end of the world,” says Mowery, “nor do I

think it’s transformative. But that’s what’s on the ground and people have

developed some expertise with it.” For stem cell technology, California

will likely stick to the tried-and-true licensing model rather than embrace

Goozner’s vision of a California-grown patenting revolution. But the

inclusion of socially responsible language in licensing discussions—in both

academia and state politics—is already an unprecedented step. More

tweaks to the technology licensing status quo may yet be on the horizon

as UC Berkeley cautiously expands the scope of technology licensing to

fully embrace IPIRA’s stated goal: “ to maximize the benefits of Berkeley’s

research to the economy and quality of life in the Bay Area, the State of

California, the nation, and the world.”

Heidi Ledford is a recent graduate in plant and microbial biology.

WHO WANTS SAMOA?An enticing air of adventure and romance surrounds the ethnobotanists

who travel to the remote corners of the world, harvesting indigenous knowledge about medicinal plants. Unfortunately, that image has been tarnished in many countries by abusive bioprospectors who took information and plants without regard for the dignity or natural resources of the culture that had led them to the horticultural treasure in the first place.

And so, when it came time to construct a research agreement with the country of Samoa to allow UC Berkeley Chemical Engineering Professor Jay Keasling access to the mamala tree, Samoa had a few special requests.

“They primarily wanted attribution,” says Carol Mimura, head of UC Berkeley’s technology transfer office.

In the 1980s, renowned ethnobotanist Paul Cox of Brigham Young University learned about the mamala tree from Samoan tribal healers Epenesa Mauigoa and Pela Lilo. Mauigoa and Lilo used mamala bark extract to treat viral hepatitis, but later research showed that a compound produced by the tree, prostratin, had potential anti-AIDS properties. Keasling’s lab is now looking into ways to produce prostratin in bacteria.

The research agreement between UC Berkeley and Samoa, a Pacific island nation roughly the size of the San Francisco Bay with no AIDS crisis of its own, stipulates that Keasling must get permission from villages or landowners prior to collecting material for his work. When work concerning the mamala tree is published or presented, attribution to Samoa must be given. Furthermore, the agreement states that “researchers must name any new gene, gene sequence, or gene product such that the connection to Samoa and Samoa’s national sovereignty will be clear to other researchers.”

In addition to that, Samoa will receive 50% of the royalties derived from the licensing of technologies resulting from this work. The country’s share of the royalties will be divided up: 50% of net revenue to the national government, 33% to Falealupo Village, 2% to Saipipi village, 2% to Tafua village, 8% to other villages, 2% to the lineal descendants of Epenesa Mauigoa, 2% to the lineal descendants of Pela Lilo, and 1% to Seacology, a Bay Area nonprofit that will administer the funds to Samoa.

Jay Keasling examines a Samoan mamala tree, the source of a

possible new AIDS treatment.

Photo courtesy of Jay Keasling


FE

AT

UR

ESu

sta

ina

ble

Dev

elop

men

t

Science And Sustainable

Development

by Kevin Moore


FE

AT

UR

ESu

sta

ina

ble

Dev

elop

men

t

Of the many excuses used by students at Berkeley for not turning in their homework, “it was too dark to study”

would certainly rank as one of the least believable. Globally, however, two billion people live without access

to electricity, meaning the academic lives of roughly a third of the world’s students end around 7:00 pm. Not

surprisingly, access to electricity is strongly correlated to every measurable indicator of human development,

including life expectancy, GDP per capita and, of course, adult literacy.

The problems facing developing nations are often considered to be purely governmental or policy issues with

no connection to scientific pursuits. But some scientists, including UC Berkeley physicist Marvin Cohen, hope

to change this attitude.

Leading with Physics – the World Conference on Physics and Sustainable Development

Last November, the American Physical Society (APS) and other international organizations convened the

first-ever World Conference on Physics and Sustainable Development. The meeting, held in Durban, South

Africa, brought together 500 researchers from all over the world to discuss the role of the international

physics community in the sustainable development of the world’s poorest areas.

Cohen served as the president of the APS during 2005 and played a central role at the Durban meeting. “All

the physics societies that I’ve had anything to do with over the last few years have been concerned about

developing nations,” Cohen said. “We [the APS] have tried to take a leadership role.”

The goals of the Durban meeting were two-fold. One objective was to clarify the relationship between the hard

sciences and public policy; the other to establish well-defined initiatives to address challenges in sustainable

development. The plan for future action was laid out in a set of resolutions, approved by conference attendees

at the end of the meeting.

It is too soon to tell how or even whether the proposed initiatives will be implemented. “I’m concerned that

there won’t be any action,” Cohen said after the meeting. “What we need is some motivated people to do

something, and I’d hate to see this momentum lost.” Meeting organizers hope that the prominence and

visibility of the meeting will serve as an archetype for other scientific disciplines to consider their role in

sustainable development.


FE

AT

UR

ESu

sta

ina

ble

Dev

elop

men

t Science Education and Sustainable Development

One set of goals within the Durban meeting resolution deals with

improvement of physics education in underdeveloped countries.

While worldwide access to basic education has improved greatly

over the last few decades, quality science education remains

largely elusive in much of the world. Resources for experiments

and demonstrations are scarce, and there is a severe shortage of

qualified science teachers. Too few individuals receive sufficient

training in the sciences, and those who have adequate schooling

often emigrate to industrialized countries.

The general failure of science education in underdeveloped

countries is all the more apparent when gifted students are given

the resources they need. The Abdus Salam International Centre for

Theoretical Physics (ICTP) in Trieste, Italy, another major sponsor of the

Durban meeting, recruits and trains students from all over the world with

the hope that they will take their knowledge home and put it to use.

“[Relative to] students from Egypt or Pakistan ... the [sub-Saharan]

African students coming in were way behind [in scientific knowledge].”

Cohen said after a visit to the ICTP. “At the end, the African students

were on par with the students from the other countries, and they

were so highly motivated. It was a thrill to see how well they had

done.” As scientific communities are built up in more nations around

the world, institutions like the ICTP may no longer be necessary. For

now, the ICTP serves a desperately-needed role in the education of

scientists from developing nations and could serve as a model for

similar endeavors in other industrialized nations like the U.S., where no

similar institution exists.

There is also hope that access to knowledge will be improved as

the use of the Internet increases. Mark Horner, a post-doctoral

researcher at Lawrence Berkeley National Laboratory, has used his

spare time to shape one major online resource. Horner has helped

assemble free online textbooks in physics, chemistry, biology, and

mathematics for use by high school students whose schools lack

adequate textbooks. The online texts are made up of contributions

from over 40 experts from a dozen countries (eight from UC

Berkeley), and more texts are on the way.

“I feel that education really is the key to any sort of sustainable,

peaceful future for any country,” Horner said. “The project ... isn’t

competing with other educational initiatives. I like to think we are

fulfilling a useful and fundamental niche.”

Between projects like Horner’s, the promise of widespread access to

wi-fi, and the prospect of the MIT $100 computer, it is conceivable that

a significant reduction of the vast resource gap between the world’s

educational systems is within reach.

Model Systems

One major barrier for scientists wishing to tackle sustainable

development issues has been the absence of a defined avenue for

getting involved. While the path from graduate school to post-doc to

faculty post is well-trodden, there are few resources outlining the key

steps towards joining or initiating sustainable development efforts.

The world of development funding agencies is unfamiliar territory

for scientists who are used to dealing with more traditional

research funding sources, but efforts are underway to make this

process easier. Sara Farley, a Science and Technology Strategist and

World Bank/Rockefeller Foundation consultant, addressed the topic

of funding at the Durban meeting.

“A discernable increase in support to science, technology and

innovation for development is occurring,” Farley said, citing sources

including the World Bank, USAID, and the Gates, Rockefeller and

Ford foundations. “The trick is guiding willing scientists and their

institutions toward global efforts.”

While there is no one clear path to getting involved, there are models

for contribution at many levels. Horner’s online science textbook

project is an example of a relatively small-scale project, with part-time

volunteers and a low materials cost. Large-scale projects, like the

ICTP, incur substantial operational and personnel expenses, but also

have the benefits of more established funding and defined programs.

Occasionally, an invention can motivate its own project. University

of Calgary engineering professor David Irvine-Halliday was struck by

the need for “simple, affordable, and rugged lighting” in underdevel-

oped nations. His solution was a white LED lighting unit that runs on a

fraction of the electricity of an incandescent light bulb, ideally electricity

produced by renewable energy sources. The white LED units became

the basis of the Light Up the World Foundation, which distributes the

units for use in unelectrified schools and homes around the world. The

foundation involves only a handful of people and has a potentially large

impact, but the cost to donor agencies (or recipient communities) is more

significant: each white LED system costs approximately $60.

The problem-solving style of scientists and engineers is a mindset

sorely needed for the sustainable development challenges facing

developing countries and an ever-increasingly globalized world.

Surely Angelina Jolie’s advocacy is greatly appreciated, but at

what level should we expect her and Bono to contribute to Africa’s

scientific infrastructure? The appeal of development work for the

scientific community is strong—not only is there an opportunity to

do great good, but there is also the promise of never again being

confounded by the question: “So, what’s your research worth

to society?”

KEVIN MOORE is a graduate student in physics.

Want to know more?

Check out:

The American Physical Society: www.aps.org

Resolutions from the Durban Meeting: www.wcpsd.org/outcomes.cfm

The Abdus Salam International Centre for Theoretical Physics: www.ictp.it

The Free High School Science Textbook www.nongnu.org/fhsst

The Light Up the World Foundation: www.lutw.org

Congre

ss 1

01

PO

LIC

Y


Take, for example, Vernon Ehlers, the first physicist to serve in Congress.

He began his career at UC Berkeley in the 1960s, where he received his

doctorate and later taught in the physics department. While at UC Berkeley,

he spent much of his time engaged in nuclear and atomic physics research

at the Lawrence Berkeley National Laboratory, and eventually became close

friends with the legendary Glenn Seaborg, father of radiochemistry and

discoverer of some 13 elements. At Berkeley, Ehlers met many researchers

concerned by national security policy, nuclearization, and war. He also became

aware of the lack of scientific input into the national policymaking process.

Over time, Ehlers began to venture into politics himself, initially at the

local level, addressing environmental issues in his home town of Grand Rap-

ids, Michigan. Today, he is a sixth-term member of the House of Representa-

tives (R-MI), where he chairs the Subcommittee on Environment, Technology

and Standards of the House Science Committee. His tenure in Congress has

been marked by an unwavering commitment to education and research in

science, technology, engineering, and math.

Congress 101Teaching scientists the language of policymakers

by Temina Madon

What Berkeley student hasn’t at some point felt exiled out here on the western edge of the country, isolated from the political conversations taking place in the nation’s capitol? Or frustrated at only hearing the word “academic” used pejoratively by the media? It doesn’t have to be this way; much of what goes on here is in fact relevant to

society’s larger questions. While the links between academic science and actual policy may sometimes be difficult to perceive, many people have managed to prosper in both worlds.

1859 drawing by architect Thomas U. Walter of the elevation of the Capitol dome.

Congre

ss 1

01

PO

LIC

Y


Why Washington Needs More ScientistsMany scientists drawn into the world of policy share a sense that greater

numbers of researchers should be involved in the decision-making process.

Bruce Alberts, a biochemistry professor at UC San Francisco and former

President of the National Academies, has been a strong advocate for the role

of science in policy. During his tenure at the Academies he helped establish

fellowship programs that bring scientists and engineers to Capitol Hill, with

the goal of influencing lawmakers and convincing them to embrace evidence-

based approaches in their work.

Today, there are several organizations that encourage researchers from

academia and industry to advise government on issues related to technology,

environment, health, foreign affairs, and research. One such program, admin-

istered by the American Association for the Advancement of Science (AAAS),

places early- and mid-career scientists in Congressional offices and in various

executive branch agencies—including the National Institutes of Health, Na-

tional Science Foundation, and less expected places like the State Department

and the Agency for International Development.

This year, I am serving as an AAAS fellow in the US Senate, where I

explore legislative issues that include international health, health insurance

regulation, and health information technology. While these issues draw heavily

on science and research, the results of the decision-making process can be

unexpected, because policy doesn’t always reflect reason alone—political fea-

sibility and ideology also influence outcomes. Although the average politician

may find this observation quite normal, it can surprise the uninitiated scientist.

After all, academic research communities are typically governed through self-

regulation and professional norms, with rules of conduct, ethics, and safety

determined by consensus. Because the process is transparent, data tend to

trump personal values.

However, in federal government, particularly in recent years, evidence

is less likely to dominate decisions about fundamental issues like civil rights,

diplomacy, energy policy, or social policy. Rather, these decisions can be driven

by ideology, rhetoric, and the desire to satisfy small but vocal or influential in-

terest groups. A recent example

is the decision by former Food

and Drug Administration (FDA)

Commissioner Lester Crawford

to delay over-the-counter access

to Plan B, a potent form of birth

control known as the “morn-

ing after” pill. The medication is

currently available in the United

States with a prescription, and

it has been available without a

prescription in some European

countries since 2000. Its safety

and utility—even for teenag-

ers—have been unambiguously

established by many careful clini-

cal studies.

In 2003, scientists on two

FDA advisory committees re-

viewed available data on the

drug’s safety and efficacy and

nearly unanimously recommend-

ed its approval for non-prescrip-

tion sales in the United States. In the past, the FDA has generally followed the

advice of its scientific advisory panels, yet the final approval for this drug has

been delayed for nearly three years—largely because of the moral objections

of a small minority of Americans with religious bias against birth control.

This outcome, which ultimately prompted Assistant Commissioner for

Women’s Health, Susan Wood, to resign from the FDA’s professional scientific

staff, has elicited protest from some sectors of the scientific community, in-

cluding the editorial board of the Journal of the American Medical Association.

Yet the administration has so far not responded to scientists’ concerns that

the review process obscured scientific evidence in favor of ideology.

Many organizations and professional societies have called on Congress

to restore the scientific integrity of the FDA. While lawmakers prize scientific

integrity, the values-driven arguments posed by opponents of this medication

cannot reasonably be countered by facts. There are no sound, scientific, evi-

dence-based arguments for barring over-the-counter use of this drug. In the

face of irrational arguments, what scientist or legislator would want to fight?

This is one of the great ironies of the role of science in policy: scientists

must often counter value judgments and beliefs with evidence and hypothesis-

driven data. As a scientist, it becomes a great craft to present an evidence-

based policy prescription within a framework that makes sense, even in the

context of values and morals.

Even after scientists find an entrée into Congress, they continue to face

significant barriers. For example, Congressional staffers may be too busy to

learn about the fundamental underpinnings of network structures and distrib-

uted systems before making pivotal decisions on internet regulation. Many of

these staffers have sophisticated legal backgrounds but limited experience

managing new technologies or defining research priorities. Nonetheless, these

are the people with major decision-making power and control over the na-

tion’s purse-strings. While experts are routinely brought to testify at Congres-

sional hearings and provide input into the complex policy-making process, the

selection of witnesses for hearings is carried out by those same staffers who

struggle with limited experience in science and technology. As a result, the

“expertise” brought to the Hill may be distorted, reflecting business interests

over technical information and data.

Congressman Vernon Ehlers (R-MI), left, meets with Nobel laureate the director of

the Lawrence Berkeley National Lab Steven Chu in 2005.

photo courtesy Berkeley Lab

Congre

ss 1

01

PO

LIC

Y


Bridging the GapOne organization independent of the federal government that ties

Berkeley to Washington is the National Academies (NAS). Established by

Congressional mandate in 1863, the National Academies study and report to

the government on some of the most controversial and cutting-edge issues in

science and technology. For example, with the current limitations on federal

support for embryonic stem cell research, the NAS has tried to fill the void

in providing research guidelines in this burgeoning field. Often their work

examines the interfaces between academic research, human welfare, domestic

and foreign policy, and international relations. More than 100 professors at

Berkeley serve on the Academies, providing a means for local scientific exper-

tise to be heard in Washington.

The Academies function through committees and boards, comprised of

the nation’s most respected and established scientists, engineers, and physicians.

Because of the Academies’ intellectual integrity and independence, their recom-

mendations are often acted upon by Congress. Indeed, much of the nation’s

health, economic, and foreign policy is driven by these reports. Recent reports

that are likely to trigger Congressional legislation include those on economic

competitiveness and the science workforce, terrorism and bioterrorism, the

health care crisis in developing countries, and childhood obesity. However, other

reports, such as the Academies’ recommendations to change our climate-alter-

ing ways, have not been greeted with much enthusiasm in the White House.

By staying abreast of the Academies’ latest releases, and by understanding

their content and recommendations, you have an opportunity to influence po-

litical discussion. An email to key representatives and senators, communicating

the importance of new findings from the National Academies, gives you a chance

to frame the arguments presented and influence the policymaking process.

One difference between academic science and policy is specialization.

Scientists are only expected to stay up-to-date in a narrow field of discipline,

but to be relevant to the larger community one must keep up with a much

wider range of issues. A good way to do this is to peruse the front sections of

scholarly journals with policy and news sections. Some of the best examples

are Science, Nature, and Chemical & Engineering News, which cover academic

research as well as industry and give more time to international news than

your average American newspaper. EurekAlert!, a service provided by the pub-

lishers of Science, offers online science and technology news organized by

research topic. For news and opinions on how science impacts the developing

world (which is where most humans live), read www.scidev.net or the

World Health Organization’s website. For those with some down time in

front of the computer, listen to audio files from National Public Radio (NPR),

which are available for free on the web. NPR provides comprehensive cover-

age of science and technology, often in the context of public health, global

climate change, and poverty.

Easier than hunting down the information yourself, try signing up for e-

newsletters from scholarly journals, non-governmental organizations like the

Union of Concerned Scientists, and think-tank groups like the Kaiser Family

Foundation (for news on HIV/AIDS, public health, and other health-related

policy). Many professional societies, including the American Society for Cell

Biology and the American Chemical Society, now send out “action alerts”

and legislative news of interest to researchers. Of course, you can also find

interesting science news on blogs and through RSS (Rich Site Summary) feeds;

Chris Mooney, author of the partisan book The Republican War on Science, runs

a particularly popular science blog.

Once you’ve become familiar with the issues, why not put your exper-

tise to use advising local or national policymakers? In the process of helping

politicians to make better science policy decisions, you may also help to se-

cure the future of federally funded science research. And who knows—one

day you, too, may end up running for office.

TEMINA MADON is a AAAS science and technology policy fellow and graduated from

Berkeley in 2004.

Profiles in Science Policy

Another scientist revered for his role in public policy is Joseph Roblat, a nuclear physicist who won the Nobel Peace Prize in 2005 for his leadership in

nuclear arms control. Roblat was a Polish-born Jew who left for Great Britain on a physics fellowship just as Nazi Germany began its invasion of Poland. He

later came to the United States to work on the Manhattan Project, believing the Americans’ effort could prevent an out-and-out nuclear war. However, upon

learning of the German’s failed nuclear bomb project, he returned to London to work on civilian research and to raise humanitarian concerns about nuclear

weaponization. Through a series of influential scientific gatherings known as the Pugwash conferences, Roblat would ultimately lead British and American

government officials to embrace nuclear arms control, resulting in the signing of the Nuclear Test Ban Treaty of 1963.

Physicists aren’t the only scientists to have played a role in federal policy-making. Alvin Novick, a distinguished professor of biology at Yale who died just a

year ago, is certainly remembered for his contributions to science and medical research; yet it is his leadership as an AIDS advocate that will remain his legacy.

Dr. Novick became a voice for people with AIDS in the earliest days of the epidemic, not only speaking against uninformed discrimination and stigmatization,

but also directing policymakers to use sound scientific judgment in matters of public health. He pioneered the expansion of needle exchange programs, now

recognized as one of the most effective interventions for IV drug users at risk of HIV.

The author, Temina Madon, gets first-hand experience with science policy as a Congressional Science Fellow with the American Association for the Advancement of Science.

Photo courtesy of Temina Madon

Congre

ss 1

01

PO

LIC

Y


Know what’s going on outside the ivory tower

Check out some of the public-private partnerships that exist on the edges of your research field, where findings from academia are translated into products

for popular consumption. Good places to find some of these efforts are professional schools—including law schools, medical schools, departments of public

health, and schools of public policy, but here’s a quick list to get you started.

If you’re a microbiologist, find out what the bio-security think tanks are talking about—examples include Stanford’s CISAC, the Center for International

Security and Cooperation, and the Center for Strategic and International Studies in Washington, DC.

If you’re a biophysicist working on viral replication and translation, what are the G8 countries doing to ensure that medicines for HIV/AIDS and other

viral pathogens are available in the developing world? What is the Gates Foundation doing to help alleviate the burdens of infectious disease and poverty

in sub-Saharan Africa?

If you work in database architecture, what is the Electronic Frontier Foundation, a non-profit digital rights group, working on, and what are the current

interests of open source advocates like Larry Lessig or Richard Stallman?

If you work in operations research, how is the expertise from industry being applied to social problems, like the delivery of food and drugs to remote

parts of the developing world?

Jump into the fray

Get your feet wet by trying a few of the ideas below to determine which aspects of science policy are most interesting to you.

Get informedIn addition to the resources listed above, read science policy publications like “Science and Government Report” and “Issues in Science and Technology” or

newspaper science sections like that in the New York Times.

Express yourselfWrite letters to scientific journals expressing policy views on news items, recent research articles, or academic politics. For local magazines and papers,

write a letter to the editor or an op-ed piece explaining, for example, how a recent news item such as the Patriot Act impacts researchers or your own

work by limiting international scholars’ access to visas.

Speak with deans and chairs in your department about the issues faced by researchers at your university—from problems with Department of Defense

grants or NIH study sections to issues of ethics and academic honesty, or bans on entire fields of research. Barriers to research at UC Berkeley might

include the cumbersome restrictions placed on federal funding of stem cell research, or the costly regulations required for “dual use” research, such as

the study of the anthrax genome (which, in principle, could wreak havoc in the hands of bioterrorists).

Email or write letters to members of Congress about federal and legislative issues that impact scientists—these letters actually do get read if they’re

not just “form letters.” Encourage colleagues from other institutions to sign on to a letter that you distribute by email—consensus among scientists is

powerful evidence for policy-makers.

Focus, focusKeep your letters, emails, and solicited commentary to the point and aimed at the appropriate audience. For example, don’t bring up your great arguments

for increasing the National Science Foundation’s funding at the local school board meeting—they would probably rather hear your opinion of teaching

intelligent design in science classrooms.

Be creativeStart a science policy blog or weekly digest for colleagues in your department or field of research, posting relevant news items, grant opportunities, and links

to useful laboratory resources. Encourage faculty, postdocs, and fellow students to comment and participate. Check out the synthetic biology wiki page for

a remarkably successful example at syntheticbiology.org.

Congre

ss 1

01

PO

LIC

Y


Could science policy be in your future?

It may sound strange for a student to spend a summer or a month in the nation’s Capitol, but medical students and residents do it all the time. Interning in a

Senator’s office or federal agency gives you a hands-on feeling for how policy is developed, negotiated, and implemented. Start thinking early about applying

for a science policy or science writing fellowship. There are lots of opportunities to consider at each stage of a scientist’s career.

UCDC Graduate students engaged in doctoral research and Berkeley faculty members are encouraged to contact the UC program in Washington DC for op-

portunities to speak, research, and teach in Washington. One or two advanced doctoral students work in the program as teaching assistants each semester,

while pursuing their own research and taking advantage of resources in the capitol.

Day tripParticipate in professional societies’ lobbying days—whether in DC or in Sacramento. While you may hate your first trip to the Capitol (as I did), you’re likely

to learn how little time and information members of Congress actually have when making decisions with far-reaching consequences.

Policy at homeOne of the richest experiences for the scientist interested in policy can be serving on a policy-making committee of the faculty, deans, or department heads

at Berkeley. There are also UC-wide policy committees that draw student members from all UC campuses. These committees function in much the same

way as the committees of the National Academies, the NIH, and the Congress.

Policy fellowshipsA complete listing of health policy fellowships, for doctoral students as well as senior researchers, is available at kaiseredu.org/policy_index.asp

Science and technology policy fellowships and sabbatical programs can be more difficult to locate, but here is a sample:

American Association for the Advancement of Science:

Science and Technology Policy Fellowships

fellowships.aaas.org

National Academies:

The Christine Mirzayan Science and Technology Policy Graduate

Fellowship

nationalacademies.org/policyfellowsJefferson Science Fellows and other fellowship programs

nationalacademies.org/fellowships

Princeton University, Institute for Advance Studies:

Global Science Corps

globalsciencecorps.org

National Institutes of Health, Office of Science Policy and Planning:

ospp.od.nih.gov/fellowships

Presidential Management Fellowship:

pmf.opm.gov

U.S. National Commission for UNESCO

state.gov/p/io/unesco/programs

Photo courtesy of the Electronic Frontier Foundation

Fiel

d T

rip

!O

UT

RE

AC

H

Multiple choice: A Berkeley graduate stu-

dent conducting a biodiversity survey should be

doing their research in: a) Borneo, b) an Ecuador-

ian rainforest, c) an overgrown field in Richmond

surrounded by 37 giddy seventh graders wielding

butterfly nets. Thanks to the Exploring California

Biodiversity Project, part of the National Science

Foundation’s GK-12 Program, science graduate

students all over the country are stepping out of

the lab and into the schoolyard, teaching young

students from kindergarten through the 12th

grade about science. The UC Berkeley chapter of

the project is run through the Berkeley Natural

History Museums and sends graduate students to

one middle school and three high schools in the

Bay Area. Graduate student fellows’ tuition, fees,

and stipend are provided through the project.

In addition to visiting the classroom once a

week, graduate student fellows take students on

three-day field trips to natural reserves around

California.

As one of this year’s graduate student

fellows, I work with Peg Dabel’s seventh grade

class and John Eby’s eighth grade class at Adams

Middle School in Richmond. Each week I go into

the classroom with another graduate student, Joel

Abraham, and two undergraduates, Natalie Valen-

cia and Becky Chong. We’ve learned to make our

lessons interactive and to involve every student.

Holding a class discussion is hard because there

are always a few kids with all the answers, and a

few kids who take this opportunity to tune out.

So, we’ve tried a few creative things this year. The

kids learned about California’s diverse habitats

by building dioramas. They built sea urchins out

of toothpicks, made cacti from pipe cleaners,

and learned that grizzly bears used to roam in

California’s mountains. We played “Jeopardy!” to

review the differences between birds, reptiles and

mammals. And we taught kids about how humans

can impact biodiversity through urbanization, pol-

lution and global warming by playing bingo.

But we’re not just game show hosts. Our

affiliation with the Berkeley Natural History

Museums means we can show students the

similarities among the bones in a bat wing, a bird

wing, and a seal flipper by borrowing specimens

from the Museum of Vertebrate Zoology and

bringing them into the classroom. Students can

get a close look at a diverse collection of reptiles

preserved in glass jars, and taxidermied birds and

mammals, which they can touch if they are brave

enough. We follow up these lessons with trips to

the museums on the Berkeley campus so students

can see how scientists use museum specimens,

often collected many years ago, to answer pres-

ent-day questions. Later this semester, we plan

to bring live reptiles and invertebrates into the

classroom for the kids to look at.

Of course, the best place to explore bio-

diversity is outside. After collecting insects and

plants in the yard at Adams Middle School, we

took the students to the Hastings Reservation, a

This spring several members of the BSR staff joined Jennifer, Joel, Natalie, and Becky in their Ad-ams classes for a one-day workshop on science writing and reporting. Our goal was to get the students excited about the idea of reporting on scientific discoveries and to give them a glimpse into how a science magazine is put together.

We began with a brief ‘press release’ on the sci-ence of how geckos climb walls, delivered by BSReditor Wendy Hansen. As an undergraduate at Lewis & Clark College in Oregon, Wendy was part of a research project studying the mechanisms of

adhesion underlying the gecko’s gravity defying climbing prowess.

The students’ assignment was to interview Wendy, and then write a 100-word article on the discoveries for a science maga-zine, like the Berkeley Science Re-view. While there were some off-topic but predictable questions about how poisonous geckos are, and who would win in a fight between a gecko and a scorpion; many of the questions got right to the science.

One student asked if a gecko’s sticky feet get dirty, a question it

turns out that Wendy spent much of her time at Lewis & Clark

trying to answer (apparently they don’t).After the interview session was completed, the

class broke up into small groups to write their articles. Wendy, and fellow BSR editors Charlie Koven and Jess Porter worked with the groups, getting the students to think about an exciting lead sentence, helping them decide how to explain the scientific results, and showing them examples of science articles from the BSR.

At the end of an hour, each group turned in their final draft, which we pasted into a magazine spread complete with color pictures and captions.

The workshop was fun, and it was also a dry run for the students—they will write a newsletter about their experiences with their GK-12 gradu-ate mentors, which will be published by the BSR later this spring.

JESS PORTER is a graduate student in biophysics.

BbSsRr

FIELD TRIP!Middle Schoolers learn about biodiversity in the fields of Richmond and beyond.

BSR staff (above, Jess Porter, below left, Charlie Koven) and the GK12 mentors (above, Joel Abrahom, below Becky Chong and Jen-nifer Skene) work with students on their science articles.

BSR GETS SCHOOLEDEditors talk science writing and reporting with Adams Middle School students

Anyone who asks a question about the world is a scientist.

PHOTOS BY WENDY HANSEN


OU

TR

EA

CH

Fiel

d T

rip

!

UC Natural Reserve in Carmel Valley. For three

days, the students collected plants and insects

using the methods they’d learned at Adams. We

expose students to science, and to totally new

experiences.

On the first night of the field trip, we took

the students for a night hike. In a treeless spot

along the dirt road, we convinced everyone to

turn off the flashlights and look at the sky. These

city kids had never seen so many stars. Everyone

tried to be quiet, to listen to night noises. “Was

that a mountain lion?” No, it was an owl, but

good ears. “Was that a mountain lion?” No. It

was wind in the trees. “What about that one?”

No. Please keep quiet so everyone can hear.

“Man, I could’ve sworn that was a mountain lion.”

“Yeah, I bet it was!” “We just heard a mountain

lion!” We gave up on silence, switched on the

flashlights, and kept walking.

The next day, the students were split into

teams for a scavenger hunt. First, they learned

to use a compass and a transect tape to find a

topographic map, hidden in the tall grass. Next,

they learned to read the map to discover their

next assignment: they had to climb to the lone

oak tree on Red Hill, 500

feet above their current

elevation. Students

were nervous about

the ascent—it required

hard work, and it was a

little scary. But with our

encouragement, every

student made it to the

top, where they could

all look down on the

oak woodlands and feel

proud of their accom-

plishment.

Anyone who asks

a question about the world

is a scientist. Through

the GK-12 program, the

middle and high school

students learn that science

is not intimidating or scary if you’ve got a little

self-assurance. During the field trips, the students

became more confident in their abilities to read

maps and climb steep hills, certainly, but they also

became more confident about their abilities in

the classroom. The students were always curious,

but now their curiosity is more evident because

they are not afraid to ask questions. Hopefully

their confidence and curiosity will persist, and

they’ll continue to see themselves as scientists

long after we leave their classroom.

As for us, as graduate student fellows we

learn how to talk to a new audience about sci-

ence. Communicating with the public is a critical

component of the scientific process—as evi-

denced by the many funding agencies that require

grant proposals to comment on how proposed

research will impact and involve the public—and

middle-school students provide an appropriately

challenging audience. Through our weekly trips to

the classroom, we learn how to make scientific

issues accessible and interesting to everyone.

JENNIFER SKENE is a graduate student in integrative biology.

Want to know more?

Check out:

The Exploring California Biodiversity project.

gk12calbio.berkeley.edu

Through Community Resources for Science, scientists

can visit elementary school classrooms in Alameda

County and give hands-on presentations about a variety

of science topics.

www.crscience.org

“It’s like being on an African safari looking through a pair of binoculars and seeing some water buffalo wreak-ing havoc, and then realizing they’re coming straight towards you.”

-Sir Roger Penrose describing how he felt when some of his ideas were incorporated into string theory, March 5, 2006

“When you get a thick milkshake from McDonald’s, you think that’s cream you’re drinking, but actually it’s silica nanoparticles.”

-Chancellor Robert Birgeneau, at Advanced Light Source colloquium on liquid crystal gels, March 2, 2006

“No matter what you think to the contrary, I am not a large, furless, white mouse.”

-George Whitesides speaking about the ap-plicability of model studies for pharmaceutical development, January 24, 2006

OU

TR

EA

CH

Fiel

d T

rip

!

d Hill, 500

r current

ents

bout

required

it was a

with our

t, every

t to the

y could

on the

and feel

accom-

who asks

the world“It’s like being on an African safari looking through a pair of binoculars

(Above) Birdwatch-ing at the Hastings Reservation. (Left) Students catch crickets as part of a biodiversity survey.

Photos by Jennifer Skene


BO

OK

RE

VIE

WSl

ow

Food

W hat should we eat for dinner? This is a question fraught with gastronomic

anticipation as well as complex global implications, and one that Michael Pollan tackles with gusto in his latest book, The Omnivore’s Dilemma: A Natural History of Four Meals (April 2006). Pollan, author of The Botany of Desire and director of the Knight Program in Science and Environmental Journalism at UC Berkeley, uses four meals to structure a discussion of the true cost—personal, economic, social, and environmental—of producing, preparing, and transporting the food we eat.

The first meal is the fastest food: a McDonald’s meal consumed in ten minutes at 65 mph in his car. The second and third meals are both organic, but one is industrial organic (a possible oxymoron born of modern government organic guidelines) while the other is sustainable organic. He finishes with the slowest of slow food, a meal that took months of preparation—hunting, gathering, a full day in the kitchen—but no cash transaction.

Pollan wonders, “How did we ever get to a point where we need investigative journalists to tell us where our food comes from and nutritionists to determine the dinner menu?” Part of the reason, he posits, is our “national eating disorder,” an assortment of carbophobia, lipophobia, and similar food fads invented by industries to distract and confuse consumers.

The narrative details the construction of the dysfunctional industrial food chain, where “it takes ten calories of fossil fuel energy to deliver one calorie of food energy to an American plate.” In fact, the food industry burns nearly a fifth of all the petroleum consumed in the United States; more than automobiles, more than any other industry.

Pollan also explores the social consequences of the modern food chain. For example, he cites a chilling fact: due to the ubiquity of high calorie fast food and resulting epidemic of obesity, today’s children will be the first generation of Americans whose life

expectancy will actually be shorter than that of their parents.

The book contains thoughtful explorations of vegetarianism and animal rights, as well as the human costs of the modern food chain. Pollan’s demystification of the meat industry is powerful, particularly his vivid description of the job of slaughtering 400 cattle per hour. Unfortunately, his visceral style can also occasionally be overly dramatic, which can be distracting from the ultimately important message about the origins of our food.

The Bay Area reader will take unique pleasure in reading this particular book due to the local attentions of the author. For one thing, Berkeley’s myriad food choices—thanks to our proximity to America’s richest farmland—provide an ideal starting point for this type of exploration. Local mycophiles and their mushroom collecting spots, as well as the Whole Foods on Telegraph and Ashby, play cameo roles in the author’s food adventures.

UC Berkeley scientists also contribute their expertise to the book: Integrative Biology professor Todd Dawson uses a mass spectrometer to trace the amount of corn the average American consumes and finds that “when you look at the isotope ratios, we North Americans look like corn chips with legs.”

In exploring the sources of our food,

Pollan addresses the questions of whether our plethora of food choices is real or perceived, and whether a single choice can actually affect our health or the health of the food chain. Because the intention is to inform, the account is detailed, and very long. The book includes an abundance of facts and figures suitable for arming any veggie, vegan, or foodie, some helpfully repeated at regular intervals. But other readers may find these discussions too meticulous, and may choose simply to skim these parts.

In addition to being informative, The Omnivore’s Dilemma is also a compelling read. Pollan organizes his thoughts in a way that is logical and fluid, and peppers the description of each meal with personal accounts of the people that bring each one to the table.

Throughout the book, the perspective shifts between the species’ eye view of evolution that was articulated in his previous book, A Botany of Desire, and that of the industrial food chain we have created. For example, Pollan congratulates corn for inducing humans to plant it over half of the arable United States, while enumerating the multiple uses of this versatile grain: 45 different menu items at McDonald’s are made from corn, and of the 38 ingredients it takes to make a McNugget, at least 13 are derived from corn.

Pollan’s stated agenda is solely to inform, but this book may well succeed in changing public attitudes towards food. The numerous facts and revelations—especially the annotated bibliography, which is gratifying for the serious reader—have a high impact factor, and it’s not a stretch to imagine readers changing their food purchasing and eating behavior.

This is a book that should be read by anyone interested in not just eating, but understanding the true price of any meal. As Pollan himself says, “in the end this is a book about the pleasures of eating, the kind of pleasures that are only deepened by knowing.”

Kristen DeAngelis is a graduate student in microbiology.

Want to know more? Check out michaelpollan.com

COVER REPRINTED BY PERMISSION OF PENGUIN PRESS

Slow FoodThe Omnivore’s Dilemma: A Natural History of Four Meals by Michael PollanPenguin Press: 2006. 464pp. $26.95

Reviewed by Kristen DeAngelis



It’s

Rai

ning

Yen

WH

O K

NE

W

Everyone has heard this one.

Throw a penny off a tall building

and watch in awe as it gains enough

momentum to punch through

a car on the street below. With

good enough aim you might even

hit a hapless pedestrian below.

Pennies, therefore, are supremely

dangerous. At least, that’s what I

was told as an innocent young

child, and there are certainly a few

references in popular culture to

this myth. Fortunately for us, we

have an eternal guardian protect-

ing us from these devastating penny

showers: terminal velocity.

“Terminal velocity” might

sound like a bad sci-fi action

thriller, but in the real world

it’s a very important physical

concept. Cracking open a

freshman physics textbook

will tell you that when an

object moves through a

viscous medium, it en-

counters a resistive force

that slows it down. This is

true whether the object moves

through air, water, or a vat of

maple syrup. They all have vary-

ing degrees of viscosity.

These resistive forces are

somewhat complicated math-

ematically, but for objects in free-

fall through air, the force usually

depends on the square of the

speed, the area of the object, and

the density of air. At some point

during free-fall, the force of grav-

ity accelerating you downward

will equal the resistive force,

and without any external forces,

you cruise at a constant speed,

known as the terminal velocity.

If an object starts off faster than

its terminal velocity, it will slow

down.

This concept shouldn’t be

all that foreign to us, given the

plethora of everyday examples

that incorporate it. Skydivers

certainly enjoy the bene-

fits of terminal velocity.

If you’ve ever dropped

a heavy object in water,

such as a ring or a camera,

you surely noticed it sink-

ing at a constant pace (I

certainly did—unfortunately

it was also the last time I saw

my camera).

At this point, you may de-

viously be wondering what would

happen if you dropped that penny

on its edge. Surely the

smaller cross-sectional

area would make the

penny slice through the

air and go faster. The

problem here is that a

penny falling through the

air on its side is not stable.

Given the mass and size of

the penny and the viscosity of

air, the motion of the penny will

eventually become chaotic, con-

tinuously turning end over end. The

tumbling penny now has a much

greater “effective” area, similar to

dropping a flat penny (which will also eventually

tumble).

So how fast is a penny’s terminal veloc-

ity? Richard Muller, Professor of Physics here at

Berkeley and instruc-

tor of the popular

course Physics for

Future Presidents,

estimates it to be

roughly 30 mph. The

Discovery Channel’s

“Mythbusters” inves-

tigated this myth in

an early episode and

empirically verified

a penny’s terminal veloc-

ity to be approximately

45 mph, roughly similar to

Muller’s estimate. At these speeds,

a penny doesn’t have nearly enough

kinetic energy to do any serious dam-

age—you can probably throw a penny that

fast. It might nick a small scratch

on a car. It will probably sting if it

hits you. But Armageddon

from the skies in the form

of pennies? Unlikely. So

much for those danger-

ous penny showers.

LOUIS-BENOIT DESROCHES

is a graduate student in

astronomy.

It’s Raining Yen

Who Knew?

A view from the Coit Tower: the secret fear of all sidewalk-bound pedestrians, but perhaps not so lethal after all.


It’s

Rai

ning

Yen

WH

O K

NE

W


Berkeley Science Review - Spring 2006

Documents

Transcript of Berkeley Science Review - Spring 2006