BERKELEY

science
review
Spring 2006 Issue 10

Berkeley vs. Intelligent Design

The Dawn of Multicellularity
Ethical Technology Licensing

Plus: BSR turns 10 & Origins of Chocolate & A Star is Born & Congress 101 & Pennies from Hell
B ERKELEY S CIENCE R EVIEW SPRING 2006 1
 BERKELEY DEAR READERS,

science It is my pleasure to introduce you to this, the 10th issue of the Berkeley Science Review. Beginning

review 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!

Editor in Chief 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).
Jessica Porter
New this spring, Michelangelo D’Agostino takes a hard look at UC Berkeley’s role in the
Managing Editor 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),
Wes Marner and what to expect from the world of intellectual property licensing (p.36) respectively. Jesse Dill
Art Director 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
Jack Lin legend of the lethal penny (back cover).
Copy Editor
Also new to the BSR, starting this fall we will be offering paid subscriptions to the magazine.
Tai Po Ping
So if you want to guarantee delivery of each BSR right to your door, or if you want to read our
Editors submission guidelines, peruse past issues, or check our upcoming events page, visit our website at
Meredith Carpenter sciencereview.berkeley.edu.

Michelangelo D’Agostino In the spirit of reflection brought on by this anniversary issue, I want to thank all of the editors,
Charlie Emrich 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
Wendy Hansen
exciting careers in science journalism, public policy, and academia–and we continue to rely on
Jacqueline Chretien incoming Berkeley students of all types to keep the magazine running.
Charlie Koven
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
Chief Layout Editor 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’.”
Andrew DeMond
Layout Editors Enjoy the issue,
Charlie Emrich
Wendy Hansen
Jessica Porter
Kathryn Quanstrom
Printer Jessica Porter
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 submissions@uclink.berkeley.edu or posted to the Berkeley Science Review, 10 Eshelman Hall, Berkeley, CA 94720.
Advertisers: contact advertise@uclink.berkeley.edu or visit http://sciencereview.berkeley.edu

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.
B ERKELEY S CIENCE R EVIEW SPRING 2006 3
review
Categories Current Briefs

06 We Just Turned 10 10 Like Beer for Chocolate

08 Labscopes 12 A Star is Born

12 Current Briefs 14 Mammoth Rocks

26 Main Features 16 United We Stand

48 Outreach 18 H2YDROPOWER

50 Book Review 20 Earthquake Prediction

51 Who Knew 22 Seeing Chemistry

24 Faster, Better, Smaller

Main Features Others

26 Getting Back To Nature 43 Congress 101

31 In The Matter of Berkeley 48 Field Trip

v. Berkeley

50 Slow Food
36 IP: Ideas for Purchase

51 Who Knew
40 Science And Sustainable
Development
Our 10th Issue

We’ve just turned 10!

The BSR has covered a lot of ground since we
(issues, that is)
SPECIAL

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...

O ne of NASA’s many recent science successes,

the RHESSI satellite is still taking pictures of
solar flares, four years after its 2002 launch. Designed
O ur 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
and built at the Berkeley Space Science Lab, RHESSI Python-inspired I’m not dead yet (for longevity). But one gene,
was profiled in our first issue. It has been instrumental Pokemon, has really been in the news recently. An acronym
in studying solar flares—huge bursts of energy Image Courtesy of NASA for POK Erythroid Myeloid ONtogenic, the Pokemon gene
released
r from the sun was found to be associated with some human cancers. This
that
t can wreak havoc on electronics here on ddiscovery prompted headlines like
earth.
e Despite having an original mission life ““Pokemon Causes Cancer,” leading
of
o only 2–3 years, RHESSI is still going, and has PPokémon USA to exert its legal
even
e trained its sights on Earth, imaging the rright to the trademark over the
gamma
g rays let off by lightning strikes. Pictures ccartoon character. The gene is
IS
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are
a downloaded to a dish in the Berkeley hills nnow called Zbtb7, but geneticists

ɱ during
d its six daily passes. Who knows, it might IS
SUE aare undaunted—2006 has already
be
b above you right now. —CE
ɲ wwitnessed the christening of enigma,
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sserpentine, and big bang. —MC

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N anomachines! 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
mate
I n 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
SUE
time, they had discovered over 100 SUE
IS IS
extrasolar planets orbiting 10 stars.
ɳ Marcy and his band of planet hunters ɴ
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improving their fabrication. Now were optimistic about the upcoming G 2

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
Photo courtesy of Kellar Autumn
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

STAFF AUTHORS
Aaron Golub Jessica Palmer Aaron Pierce Heidi Anderson Michelangelo D’agostino
Ainsley Seago Jinjer Larson Adam Schindler Heidi Ledford Mike Daub

O ur first 9 issues were a lot of work and a lot of fun. Just yesterday, it seems, the BSR was merely an idea. Since Amber Wise Joel Kamnitzer Ainsley Seago Jane McGonigal Nathan Bramall
Andy DeMond Josephine Lee Alan Moses Janes Endres Howell Nathanael Johnson
Angie Morey Kaspar Mossman Allison Drew Janet Fang Noah Rolff
Anna Ross Kira O’Day Alysia Marino Jeffrey Natchtigal Noam Sagiv

then, grad students from all over the Berkeley campus have been slaving away to bring you what’s now the top Antoinette Chevalier
Bryan Jackson
C. Ric Mose
Carol Hunter
Kristen DeAngelis
Letty Brown
Lisa Green
Merek Siu
Aman Singh Gill
Angie Morey
Angie Morey
Annaliese Beery
Jennie Rose
Jennifer Skeene
Jennifer Skene
Jess Porter
Padraig Murphy
Prayana Khadye
Rachel Shreter
Rachel Teukolsky

pop-sci student journal in the country. (our opinion) Carol Hunter

Charlie Emrich
Chris Weber
Christopher Weber
Michaelangelo D’agostino
Padraig Murphy
Paul Chang
Sarita Shaevitz
April Mo
Ariana Reguizzoni
Aubrey Lau
Audrey Huang
Jessica Marshall
Jessica Palmer
Jimmer Endres
Josephine Lee
Rebecca Sutton
Robert C. Froemke
Roger O’Brient
Russell Fletcher
Colin McCormick Sherry Seethaler Ben Gutman Joshua Garret Ruth Murray-Clay

Huge thanks go to everyone who helped along the way: the authors, editors, and layout people; the artists and Dan Handwerker
Delphine Farmer
Donna Sy
Tania Haddad
Teddy Varno
Temina Madon
Bill Monahan
Brendan Borrell
Carol Hunter
Julie Walters
Karen Levy
Karen Marcus
Sahelt S. R. Datta
Sarita Shaevitz
Shefa Gordon
Dula Parkinson Thomas Thomaidis Chad Heeter Kaspar Mossman Shena Gifford

photographers; all the faculty members we’ve badgered for stories; all of our advisors for “not minding” that we Elissa Preston
Eran Karmon
Heidi Ledford
Tony Le
Tony Wilson
Tracy Powell
Charlie Emrich
Charlie Koven
Cheryl Hackworth
Kira O’Day
Kristen DeAngelis
Letty Brown
Sherry Seethaler
Sheyna Gifford
Shirley Dang
Jane McGonigal Una Ren Chris Weber Lisa R. Girard Sneha Desai

weren’t in the lab; and most of all,YOU, for reading. Jess Porter
Jesse Dill
Jessica Marshall
Wendy Hansen
Wes Marner
Colin McCormick
Daisy James
Dan Roche
Loraine Lundquist
Loren Bentley
Lorraine Sadler
Stephanie Ewing
Steve Bodzin
Steven Bodzin
Delphine Farmer Louis-Benoit Desroches Teddy Varno

The totals: 428 pages, 183,971 words, 53 staffers, 96 authors. (not quite Conde Nast, but we’re getting there) Eliane Trepagnier
Elizabeth Read
Emily Singer
Eran Karmon
Marjorie James
Mark Abel
Melissa Fabros
Merek Siu
Temina Madon
Theresa Ho
Tracy Powell
Una Ren
Giovanna Guerrero Michael Downes Will Grover

6 B ERKELEY S CIENCE R EVIEW SPRING 2006

 Our 10th Issue
SPECIAL
Photo courtesy of LBL Photo courtesy of David Presti

W hen banks compete, you win, or so goes the slogan—but what about
contracts for nuclear labs? 2004 marked the first time that the
M ind over body.
This is what meditation
University of California, which has managed Lawrence Berkeley, Lawrence is supposed to achieve, and
Livermore, and Los Alamos National Labs since their formation in research by David Presti and
the 1940s and 50s, was forced to compete for their contracts. In colleagues into the physiological
April of 2005, UC received a 5-year contract to continue running effects of deep meditation in Buddhist
Lawrence Berkeley, the lab closest to home. Last December, monks seems to confirm it.When we caught
UC teamed up with industry to win a 7-year contract for Los up with Presti this spring, he had just returned
Alamos, out-competing the University of Texas ffrom another trip to the monasteries
aand Lockheed Martin. UC’s recent contract oof northern India.This time, Presti was
ssuccesses are helping to quiet rumors of lab tthere to teach, rather than to study, as
mmismanagement and bode well for the ppart of the 7th annual Science for Monks
LLivermore contract, up for competitive wworkshop. Each December since 2000, a
rrenewal in 2007. —WH ggroup of 50 Tibetan monk scholars have
IS
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ggathered at the Dehra Dun monastery to

ɶ ɷ llearn physics, mathematics, and neuroscience

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ffrom leading western experts. —JP

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I t’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
IS
computing resources that often lie dormant in
people’s homes and offices. Harness it has: over ɸ criticizing the Bush administration’s “distortion
SP
T he 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,
SUE
over 60 researchers last year signed a statement SUE
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by the Union of Concerned Scientists (UCS)
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800,000 computers are now crunching away IN
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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
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

I t’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
SUE
IS of 2005, PLoS was ranked #1 among general biology journals—with an impact factor of

ɵ 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
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B ERKELEY S CIENCE R EVIEW SPRING 2006 7

 labscopes
LABSCOPES

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

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

Richter Scale
mm ... 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
H 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

Outbreak
nyone 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,
A 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

8 B ERKELEY S CIENCE R EVIEW SPRING 2006

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B ERKELEY S CIENCE R EVIEW SPRING 2006 9

 Current Briefs
The Origins of Cacao

Like Beer for Chocolate

BRIEF

A Star is Born
Page 12
The Origins of Cacao
Earthquake Prediction othing satisfies a craving like the subtle

Page 20
N flavors of fine chocolate. Every year, over
three million tons of cacao, the raw material for
chocolate, are produced worldwide. For a food
H2ydropower loved by so many though, the origins of cacao
remain a mystery. UC Berkeley anthropologist
Page 18 Rosemary Joyce now thinks she may have found
the answer: beer.
Like Beer for Chocolate Cacao is produced from the almond-shaped
seeds of the quirky rainforest tree Theobroma cacao,
Page 10
a native of the Amazon and Orinoco river basins
(cacao is the name of the tree and its seeds while
Mammoth Rocks cocoa is the name of the defatted powder made
from the finely ground seeds). The seeds grow in
Page 14
pods hanging from the trunk of the tree. Monkeys
and other forest animals split these pods open
Seeing Chemistry to reach the sweet, juicy pulp that surrounds the
30–40 seeds inside. Raw, the seeds are bitter and
Page 22
inedible.To produce the raw material for chocolate,
they must be fermented, dried, and roasted.
United We Stand No one knows when humans first began
UC Berkeley anthropologist Rosemary Joyce has
discovered evidence of chocolate residues on Meso-
Page 16 to consume cacao. We do know that in the early american pottery from as early as 1100 BCE.
1500s, Columbus, Cortez, and other Spaniards
noted the widespread use of cacao throughout and southern Mexico that nurtured the Olmec,
Mesoamerica—the region of Central America Mayan, and Aztec civilizations. Joyce has recently
discovered chemical residues of cacao beverages
The Mayas and Aztecs believed that a feathered ser- on pottery shards dating to 1100 BCE, but the use
pent god discovered cacao and gave it to humans. of cacao could have begun even earlier.

All images courtesy of Michael Barnes

10 B ERKELEY S CIENCE R EVIEW SPRING 2006


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.
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.
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
Cacao seeds must be fermented, dried, and roasted,
like those seen here, to produce the raw material for
chocolate.
The Origins of Cacao
BRIEF
A cacao pod, broken open to reveal the fleshy pulp
surrounding the hard seeds.
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
B ERKELEY S CIENCE R EVIEW SPRING 2006 11
A Star is Born
BRIEF
A Star is Born
he night sky is an awe-inspiring sight. From the
T 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
12 B ERKELEY S CIENCE R EVIEW SPRING 2006
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
BRIEF

Photo courtesy of NASA

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

B ERKELEY S CIENCE R EVIEW SPRING 2006 13

Mammoth Rocks
BRIEF
MAMMOTH ROCKS
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A long 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
All Photos by Sarah Anne Bettelheim terior pastures during
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.
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
14 B ERKELEY S CIENCE R EVIEW SPRING 2006
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-
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
 Mammoth Rocks
BRIEF
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. O

MATTHEW BETTELHEIM is a freelance science writer, wildlife

biologist, and natural historian.
Want to know more?
Check out Mammoth Rocks at
www.parks.ca.gov/default.asp?page_
id=23566

Interested in research or volunteering?

Contact Parkman at
bparkman@parks.ca.gov

The rubbing rocks vary from smooth-worn

ridges to large sweeps of polished stone like
the rock face pictured here.

B ERKELEY S CIENCE R EVIEW SPRING 2006 15

 UNITED WE STAND
United We Stand

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.
The Origins of Multicellular Animals Instead, King focuses on choanoflagellates, a
or most of us, our common ancestry with sition to multicellularity are to the story of life, group of single-celled organisms (protozoa) that
F
BRIEF

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
Images courtesy of Melissa Motts/Current Biology (left) and Susan Young (right).
Choanoflagellates stained to show their flagella (green), collars (red), and DNA (blue). (Left) individual cells; (right)
a colony of cells.
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-
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.
choanos sponges jellyfish arthropods
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
mollusks starfish vertebrates
time

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 emergence of
non-animal we know of so far. Study of these organisms may help us understand multicellularity
which characteristics of multicellularity the single-celled ancestor of animals already
possessed and which had to evolve during the transition to multicellularity.

16 B ERKELEY S CIENCE R EVIEW SPRING 2006

 United We Stand
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

BRIEF
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.” N

AMAN SINGH GILL is a UC Berkeley graduate in environ-

mental science and policy management.

Want to know more?

Check out: 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
The King lab homepage: by the cell in vesicles. In the center is the cell’s nucleus. The King lab studies these organisms because they are
mcb.berkeley.edu/labs/king the closest single-celled relatives to multicellular animals, and therefore may help us to understand more about the
Tree of Life: tolweb.org transition to multicellularity.

B ERKELEY S CIENCE R EVIEW SPRING 2006 17

H2ydropower
H2YDROPOWER
BRIEF
Getting a grip on hydrogen to fuel tomorrow’s cars
hether it’s air quality, a desire to protect
W 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
18 B ERKELEY S CIENCE R EVIEW SPRING 2006
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
Photo by Charlie Emrich

near ambient conditions. Furthermore,e, it must be
efficient enough to offset the energy consumption
and pollution that result from usingng water or
hydrocarbons for producing the hydrogen
ydrogen in
the first place. The Department of Energy
nergy 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 d limits on
refueling time and cost.
In an effort to help meet thesee ambitious
targets, nine UC Berkeley faculty members, in
departments ranging from chemistryy 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 ch preceding
the program’s establishment, but theyy 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,”
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.
Image courtesy of the Long lab
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).
All photos by Charlie Emrich
H2ydropower
BRIEF
says Jeff Long,
Lon a chemistry professor involved in
the project.
Long hopes
hop to use synthetically-produced
solids as hydrogen storage devices. He
porous solid
currently investigating the synthesis and
is current
hydrogen-binding
h 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
Long’s ideal material is lightweight, easy
sites. Long
to produce, and able to reversibly bind hydrogen
lifetime of the car. Furthermore, it will
for the lifetim
hydrogen from the storage lattice to the
release hydro
fuel cell upon small changes in pressure. He sees
promise” in porous materials, but he also
“a lot of prom
notes that refirefining the solids so they are viable for
use is going to be a challenge.
The next few years will likely determine the
future for tthe 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
B ERKELEY S CIENCE R EVIEW SPRING 2006 19
Earthquake Prediction
BRIEF
Shake, Rattle, and Roll
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
20 B ERKELEY S CIENCE R EVIEW SPRING 2006
What if you could see 30 seconds into the future...
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
San Francisco in ruins, April 1906
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
All Photos courtesy of the Bancroft Library
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

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
Earthquake Prediction
Timeline for an ideal
earthquake warning:
0 sec. Earthquake begins. Epicenter is
BRIEF
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...
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.” N
MICHAEL ZHAO is a graduate student in journalism.
B ERKELEY S CIENCE R EVIEW SPRING 2006 21
Seeing Chemistry

Seeing Chemistry
Berkeley scientists peek into the ultra-fast
BRIEF

world of chemical reactions and discover

why the human eye works so damn well

ne of the things I learned in high-school leads to vision. This much

O chemistry class is that you can’t see atoms.
Wrong. Decades ago, researchers at IBM invented
has been known for the
better part of the last cen-
a microscope powerful enough to both see atoms tury—it led to a Nobel
and to move them around one at a time. Being able prize in 1967—but many
to see individual atoms ushered in a sea change of the specifics of this re-
in the understanding of materials like metals and action remained elusive.
ceramics. Recently, researchers at Berkeley have In particular, knowing the
upped the ante, inventing a technique that allows exact details of how retinal
them to see atoms as they move in the fastest of twists when exposed to
chemical reactions. light is key to understand-
The work, published in the November 11 ing how remarkably effi-
edition of the journal Science, sheds new light on cient the visual process is.
a very old question: How do our eyes “see”? The Retinal by itself is
retina lining the insides of our eyes brims with nowhere near as efficient
rod and cone cells that convert light into a signal at capturing light as when
that our brains interpret as vision. What makes it’s embedded in the rho-
these cells sensitive to light is the protein rho- dopsin protein. A group of
dopsin. Rod cells are packed with thousands of Berkeley researchers, led
molecules of rhodopsin, each of which contains by professor Richard Ma-
a small molecule called retinal that absorbs light. thies, found that the rho-
(Retinal, incidentally, is made from beta-carotene, dopsin protein pre-twists
lending credence to the conventional wisdom that retinal a bit, priming it to Photo by Charlie Emrich

beta-carotene-rich carrots are good for your eyes.) undergo the full twist when Graduate student Phil Kukura stands over part of the complicated optical system
When retinal absorbs light, it twists, forc- it absorbs light. As gradu- that can watch atoms move during a chemical reaction.
ing the surrounding rhodopsin protein to change ate student Phil Kukura,
shape and kicking off a long chain of events that lead author on the study,

retina

iris

“cis”
light

lens

rod cells
cornea optic nerve
“trans”

Eye diagram courtesy of the National Eye Institute/National Institutes of Health

Retinal diagram by Dan Wandschneider

(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.

22 B ERKELEY S CIENCE R EVIEW SPRING 2006


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
Photos by Charlie Emrich
(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.
Seeing Chemistry
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
BRIEF
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.” N
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).
B ERKELEY S CIENCE R EVIEW SPRING 2006 23
Hard Drives
FASTER, BETTER, SMALLER
BRIEF
One of the last moving parts in your computer is the hard drive
I magine 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
24 B ERKELEY S CIENCE R EVIEW SPRING 2006
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. The business end of a hard disk drive is the millimeter-
But if the heads get too close to the surface, Bogy long slider seen above.The surface that faces the disk
says, the head “will slap the disk,” crashing into the (above) is terraced aerodynamically to fly extremely
close to the disk surface.
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
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

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
Hard Drives
Industry Consortium (InSIC) have set themselves
a goal of reaching a tenfold greater density by the
end of 2008.
BRIEF
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.
B ERKELEY S CIENCE R EVIEW SPRING 2006 25
 GETTING
BACKTO REVISITING THE 1914 SURVEY OF CALIFORNIA WILDLIFE
by Erica Spotswood

N AT U R E
In 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.

Photo by Adam
Adam Leaché
Leaché

26 B ERKELEY S CIENCE R EVIEW SPRING 2006

 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.
Because the original database
is so complete, it is providing a
rare opportuinity for modern
researchers to get a glimpse
into the past.
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
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.
Photo byAdam
AdamLeaché
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
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.
Leaché
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-
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.
Photo by Erica Spotswood
B ERKELEY S CIENCE R EVIEW SPRING 2006 27
Back to Nature
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
FEATURE
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.
28 B ERKELEY S CIENCE R EVIEW SPRING 2006
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.”
But how do you prove
something is really not there
if you can’t find 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-
Photo by Adam Leaché
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 Leaché Photo b

Movin’ 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
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
by Jim Patton
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.
The assumption is that the
locations differ in climate, and
nothing else. In practice, nature
is never so simple.
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-
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
Photo by Adam Leaché
Back to Nature
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
FEATURE
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.
articles. The original Grinnell database consists
of over 13,000 pages of field notes and over 2,000
photographs.
Photo by Erica Spotswood
B ERKELEY S CIENCE R EVIEW SPRING 2006 29
Back to Nature

Post-doctoral fellow John Perrine has been

Genes from Drawers:
working for the last five months in the planning
In addition to shifts in distribution, the ge-
stages. Finding the sites where Grinnell originally
netic diversity of mammal populations may be
surveyed has proved much more difficult than
changing as well. Access to museum specimens
it was in Yosemite and has taken a great deal of
FEATURE

from 100 years ago with precise information on

historical sleuthing.
the locality where they were collected provides
Digging through old maps, tax records, and
a rare opportunity to study how changes in dis-
historical land tenure documents, Perrine has
tribution have influenced the genetics of mod-
managed to locate many of the sites, though he
ern populations. Emily Rubidge, PhD student in
has had to contend with quite a few obstacles:
the Department of Environmental Science, Pol-
towns that have disappeared, names that have
icy, and Management, is using new techniques
changed, railroads that have been built and then
for extracting DNA from old museum skins to
abandoned, ferries that used to transport people
compare them to the resurveyed collection.
across rivers that now have bridges, and giant cat-
Looking at a set of genetic markers to determine
tle ranches owned through land grants by Span-
variability, she will be able to determine if there
ish rancheros that no longer exist and whose
has been an overall change in the total genetic
precise locations were never defined. If his work
diversity between the two time periods.
is any indication of how the rest of the project
The way in which a species has declined
will go, the team will learn a lot about history
is expected to be reflected in the present gene
in the process. More importantly, they hope to
pool. If an entire population of alpine chipmunks
build on what they learned in Yosemite, verifying
moved up in elevation, one might expect that
or disproving the patterns they have begun to see
they would have maintained the same degree
emerging. It’s a big world out there, and with the
of genetic diversity within the contracted range.
Grinnell data and the resurvey team’s effort, we’ll
Alternatively, if the range contracted when the
be able to sneak a peek into how human activi-
lower elevation population went extinct, one
ties are changing, and will continue to change, that
would expect the current population to be less
world in the future.
genetically diverse than the original. Rubidge’s
preliminary results suggest that the alpine chip-
ERICA SPOTSWOOD is a graduate student in environmental science, munk has lost genetic diversity, suggesting the
policy, and management. latter hypothesis. As she explains, “One of the Photos by Erica Spotswood
big problems conservation biologists face is that
Want to know more?
we don’t know what things were like before. Al- Above: Both the original and the new specimens will
Check out:
though the environment obviously wasn’t unal- be stored here in the Museum of Vertebrate Zoology.
mvz.berkeley.edu/Grinnell/index.
tered in the 1900s, it is a baseline that we can Above Bottom: Brokeback Survey. Grinnell and his
html original team shown here in the field. Below left:
use to look at changes. It is exciting to be able to
Researchers prepare collected specimens at one of
ask population genetic questions about popula- the camp sites. Below right: Emily Rubige works with
tions 100 years ago.” some of the originals back in the Museum.

Photo by Chris Conroy Photo by Erica Spotswood

30 B ERKELEY S CIENCE R EVIEW SPRING 2006


In the matter of
Berkeley v. Berkeley
S tepping 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
Berkeley vs. Berkeley
FEATURE
by Michelangelo D’Agostino
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 Bear
Padian 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
Photo by Charlie Emrich
B ERKELEY S CIENCE R EVIEW SPRING 2006 31
Berkeley vs. Berkeley
FEATURE
Illustration by Colin Purrington
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- “ I think it makes people stupid.”
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]
32 B ERKELEY S CIENCE R EVIEW SPRING 2006
Exapt or Die
One 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.
Of Pandas and Professors
Ironically 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.
 Berkeley vs. Berkeley
SURVIVAL OF THE LITIGIOUS
The 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

FEATURE
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.
Reprinted by permission of evolution.berkeley.edu

Boalt From Above
Nothing 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
While supernatural explanations
may be important, and have merit,
they are not a part of science.
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.
Photo by Charlie Emrich
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,

B ERKELEY S CIENCE R EVIEW SPRING 2006 33

Berkeley vs. Berkeley
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.
FEATURE
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.
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
34 B ERKELEY S CIENCE R EVIEW SPRING 2006
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 Illustrations by Rachel Eachus
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.
interviews continued on page 
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.

Johnson interview cont’d:
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.
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
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.
Padian interview cont’d:
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
Berkeley vs. Berkeley
more about God and less about
materialism, as long as they don’t
actually have to give anything up.
You can always demonize someone
FEATURE
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.
B ERKELEY S CIENCE R EVIEW SPRING 2006 35
 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-hem-
selves freely without fear of collapse. The University of Florida receives
ves $9
million a year in trademark royalties from PepsiCo, Inc. According to the
university, royalty money is reinvested in a wide range of research. h. As
for those brave fighting gators, the Gatorade-fueled team went on to o win
the Orange Bowl for the first time in school history in 1967.
by Heidi Ledford
The Myth of the Cash Cow
For 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.”

“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 pleasantt and
professional, laughing quietly at all the right moments and just occasion-
asion-
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 n 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 g line
between university and industry, and she excels at maximizing revenue.enue.
The profound bureaucracy that she tackles is implicit in her absurdly surdly Illustration by Jennifer Bensadoun

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

ectual
Property and Industry Research Alliances (IPIRA), which means that at 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.

36 B ERKELEY S CIENCE R EVIEW SPRING 2006

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-
Photo courtesy of Yale University
Yale Medical School administrators and Bristol-Myers Squibb officials
at a ceremony celebrating their ongoing partnership.
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
B ERKELEY S CIENCE R EVIEW SPRING 2006 37
 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
Associate Professor Eva
Harris, whose royalty-free weren’t there. That caused us to
licensing proposal on a dengue think—if we had that deal, how
fever diagnostic device kick- could we have prevented that
started UC Berkeley’s socially situation?”
responsible IP licensing Prompted by Harris’s propos-
program. 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,”
38 B ERKELEY S CIENCE R EVIEW SPRING 2006
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.
 In addition to her interest in technology licensing, Ortiz wants pro- WHO WANTS SAMOA?
tections for egg donors and audits of funding distribution. For her ef- An enticing air of adventure and romance surrounds the ethnobotanists
forts, Ortiz, one of the original sponsors of Prop 71, has been accused who travel to the remote corners of the world, harvesting indigenous
of hindering stem cell research, with some going so far as to say that she knowledge about medicinal plants. Unfortunately, that image has been
has realigned herself with right-wing opponents of the program. Ortiz tarnished in many countries by abusive bioprospectors who took information
defends herself, saying, “We have an obligation to the voters that goes and plants without regard for the dignity or natural resources of the culture
beyond mere science.” 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
The Big Boys on the Block country of Samoa to allow UC Berkeley Chemical Engineering Professor Jay
Scrunched down in his chair, his feet propped up on his desk, Mow- Keasling access to the mamala tree, Samoa had a few special requests.
ery rolls his eyes and winces when discussing the Prop 71 licensing hearings. “They primarily wanted attribution,” says Carol Mimura, head of UC
“One of the problems is that the Prop 71 work is way upstream,” Berkeley’s technology transfer office.
In the 1980s, renowned ethnobotanist Paul Cox of Brigham Young
says Mowery. “We don’t have a therapy. We don’t have anything. It’s all
University learned about the mamala tree from Samoan tribal healers Epenesa
surrounded by layers and layers of uncertainty. And as you layer more
Mauigoa and Pela Lilo. Mauigoa and Lilo used mamala bark extract to treat
and more uncertainties on top of what is a fairly elastic agreement, it gets
viral hepatitis, but later research showed that a compound produced by the
more difficult to negotiate.” tree, prostratin, had potential anti-AIDS properties. Keasling’s lab is now
Nevertheless, Goozner, who vehemently believes that Bayh-Dole era looking into ways to produce prostratin in bacteria.
patent licensing inhibits innovation and adds to the already inflated The research agreement between UC Berkeley and Samoa, a Pacific
cost of pharmaceuticals, saw in the Prop 71 hearings an opportunity to island nation roughly the size of the San Francisco Bay with no AIDS
overthrow the old system. “The Feds have always been the big boys on crisis of its own, stipulates that Keasling must get permission from villages or
the block,” says Goozner. “And now you have a case where one state is landowners prior to collecting material for his work. When work concerning
stepping up to plate. California, because of its size, has the capacity to the mamala tree is published or presented, attribution to Samoa must be
show a new direction in this area.” given. Furthermore, the agreement states that “researchers must name any new
gene, gene sequence, or gene product such that the connection to Samoa and
In the end, the licensing proposal included Mimura’s recommenda-
Samoa’s national sovereignty will be clear to other researchers.”
tions, including a few clauses that resemble those in UC Berkeley’s socially
In addition to that, Samoa will receive 50% of the royalties derived
responsible licenses. For example, the proposal requires licensees to
from the licensing of technologies resulting from this work. The country’s
provide therapies derived from these discoveries to state health programs share of the royalties will be divided up: 50% of net revenue to the national
at the lowest available commercial cost—already a common practice government, 33% to Falealupo Village, 2% to Saipipi village, 2% to Tafua
among pharmaceutical companies. Licensees must also provide “a plan” village, 8% to other villages, 2% to the lineal descendants of Epenesa Mauigoa,
by which uninsured Californians may access those therapies. “My guess 2% to the lineal descendants of Pela Lilo, and 1% to Seacology, a Bay Area
is those plans will be pretty fuzzy because nobody knows what will come nonprofit that will administer the funds to Samoa.
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
Photo courtesy of Jay Keasling
think it’s transformative. But that’s what’s on the ground and people have
Jay Keasling examines a Samoan mamala tree, the source of a
developed some expertise with it.” For stem cell technology, California
possible new AIDS treatment.
will likely stick to the tried-and-true licensing model rather than embrace
Goozner’s vision of a California-grown patenting revolution. But the research to the economy and quality of life in the Bay Area, the State of
inclusion of socially responsible language in licensing discussions—in both California, the nation, and the world.”
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 Heidi Ledford is a recent graduate in plant and microbial biology.
fully embrace IPIRA’s stated goal: “ to maximize the benefits of Berkeley’s

B ERKELEY S CIENCE R EVIEW SPRING 2006 39

Sustainable Development
FEATURE

Science
And Sustainable
Development

by Kevin Moore

40 B ERKELEY S CIENCE R EVIEW SPRING 2006

 Sustainable Development
FEATURE
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.

B ERKELEY S CIENCE R EVIEW SPRING 2006 41

Sustainable Development
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
FEATURE
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.
42 B ERKELEY S CIENCE R EVIEW SPRING 2006
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
 Congress 101
Congress 101

POLICY
Teaching scientists the language of policymakers
by Temina Madon

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

hat Berkeley student hasn’t at some point felt exiled out here on the western edge of the country, isolated from

W 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.

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.

B ERKELEY S CIENCE R EVIEW SPRING 2006 43

Congress 101
POLICY
Congressman Vernon Ehlers (R-MI), left, meets with Nobel laureate the director of
the Lawrence Berkeley National Lab Steven Chu in 2005.
Why Washington Needs More Scientists
Many 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-
44 B ERKELEY S CIENCE R EVIEW SPRING 2006
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-
photo courtesy Berkeley Lab 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.
 Congress 101
Bridging the Gap
One 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-
POLICY
Photo courtesy of Temina Madon
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.
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.

B ERKELEY S CIENCE R EVIEW SPRING 2006 45

Congress 101

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.
POLICY

Get informed
In 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 yourself
Write 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, focus
Keep 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 creative
Start 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.

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?

46 B ERKELEY S CIENCE R EVIEW SPRING 2006

 Congress 101
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

POLICY
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 trip
Participate 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 home
One 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 fellowships
A 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/policyfellows
Jefferson 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

B ERKELEY S CIENCE R EVIEW SPRING 2006 47

Field Trip!

FIELD TRIP!
OUTREACH

Middle Schoolers learn about biodiversity in the fields of Richmond and beyond.
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
Anyone who asks a question
about the world is a scientist.
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

BSR GETS SCHOOLED

Editors talk science writing and reporting with Adams Middle School students
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 BSR
editor 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
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
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
PHOTOS BY WENDY HANSEN sticky feet get dirty, a question it
BSR staff (above, Jess Porter, below left, Charlie Koven) and the turns out that Wendy spent much
GK12 mentors (above, Joel Abrahom, below Becky Chong and Jen- of her time at Lewis & Clark
nifer Skene) work with students on their science articles.

48 B ERKELEY S CIENCE R EVIEW SPRING 2006


(Above) Birdwatch-
ing at the Hastings
Reservation. (Left)
Students catch
crickets as part of a
biodiversity survey.
Photos by Jennifer Skene
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
Field Trip!
oak tree on Red d Hill, 500
feet above theirr current
OUTREACH
elevation. Students
ents
were nervous aboutbout
the ascent—it required
hard work, and it was a
little scary. But with our
encouragement, t, every
student made itt to the
top, where theyy could
all look down on the
oak woodlands and feel
proud of their accom-
plishment.
Anyone who asks “It’s like being on an African safari
a question about the world looking through a pair of binoculars
is a scientist. Through and seeing some water buffalo wreak-
the GK-12 program, the ing havoc, and then realizing they’re
middle and high school coming straight towards you.”
students learn that science
is not intimidating or scary if you’ve got a little -Sir Roger Penrose describing how he felt when
self-assurance. During the field trips, the students some of his ideas were incorporated into string
became more confident in their abilities to read theory, March 5, 2006
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 “When you get a thick milkshake from
they’ll continue to see themselves as scientists McDonald’s, you think that’s cream
long after we leave their classroom. you’re drinking, but actually it’s silica
As for us, as graduate student fellows we nanoparticles.”
learn how to talk to a new audience about sci-
ence. Communicating with the public is a critical
-Chancellor Robert Birgeneau, at Advanced
Light Source colloquium on liquid crystal gels,
component of the scientific process—as evi-
March 2, 2006
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 “No matter what you think to the
issues accessible and interesting to everyone. contrary, I am not a large, furless,
white mouse.”
JENNIFER SKENE is a graduate student in integrative biology.
-George Whitesides speaking about the ap-
Want to know more? plicability of model studies for pharmaceutical
Check out: development, January 24, 2006
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
B ERKELEY S CIENCE R EVIEW SPRING 2006 49
 Slow Food
Slow Food
BOOK REVIEW
The Omnivore’s Dilemma: A Natural
History of Four Meals
by Michael Pollan
Penguin Press: 2006. 464pp. $26.95
Reviewed by Kristen DeAngelis
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
50 B ERKELEY S CIENCE R EVIEW SPRING 2006
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.
COVER REPRINTED BY PERMISSION OF
PENGUIN PRESS
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
Who Knew?
It’s Raining Yen
veryone has heard this one.
E 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.
It’s Raining Yen
WHO KNEW
This concept shouldn’t be a penny’s terminal veloc-
all that foreign to us, given the
plethora of everyday examples
ity to be approximately
45 mph, roughly similar to
that incorporate it. Skydivers Muller’s estimate. At these speeds,
certainly enjoy the bene- a penny doesn’t have nearly enough
fits of terminal velocity. kinetic energy to do any serious dam-
If you’ve ever dropped age—you can probably throw a penny that
a heavy object in water, fast. It might nick a small scratch
such as a ring or a camera, on a car. It will probably sting if it
you surely noticed it sink- hits you. But Armageddon
ing at a constant pace (I from the skies in the form
certainly did—unfortunately of pennies? Unlikely. So
it was also the last time I saw much for those danger-
my camera). ous penny showers.
At this point, you may de-
viously be wondering what would LOUIS-BENOIT DESROCHES
happen if you dropped that penny is a graduate student in
on its edge. Surely the astronomy.
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 A view from the
Coit Tower: the
course Physics for
secret fear of all
Future Presidents, sidewalk-bound
estimates it to be pedestrians, but
roughly 30 mph. The perhaps not so
lethal after all.
Discovery Channel’s
“Mythbusters” inves-
tigated this myth in
an early episode and
empirically verified
B ERKELEY S CIENCE R EVIEW SPRING 2006 51
It’s Raining Yen
WHO KNEW

BERKELEY
science
52 B ERKELEY S CIENCE R EVIEW SPRING 2006 review