BERKELEY

science
review
Fall 2006 Issue 11

The Aftermath of Katrina

Strung Out at Berkeley
Science’s Baby Gap


Plus: Quick Facts About Quicksand ✦ Stanley Hall Sneak Preview ✦ A Metamaterial World
 { READ — WRITE — CONTRIBUTE }
sciencereview.berkeley.edu

 BERKELEY
science
Dear Readers,

review
When the wise elders of the Berkeley Science Review gathered under the cover of night in their hooded
black robes to anoint me the next Editor-in-Chief, my first instinct was to turn tail and run. Fortunately,
they had locked the door.

At first glance, assembling some 50 pages of first class science content seemed like quite a daunting task.
Editor in Chief Luckily, the BSR’s crack team of editors and layout staff have sacrificed countless hours cranking out
another issue of Berkeley’s best general interest science magazine (extending their graduate careers in the
Michelangelo D’Agostino
process…)
Managing Editor
With all their hard work, I’d venture to say that Issue 11 is one of our best yet. Erica Spotswood tells
Wes Marner
us about Berkeley’s role in investigating the failure of the New Orleans flood protection system during
hurricane Katrina (p. 33). Meredith Carpenter takes a deep look into the world of theoretical physics
Art Director
and the role Berkeley is playing in unraveling the ball of string that may just be our universe (p. 28).
Andrew DeMond
Are you reading this issue of the BSR in your cramped basement lab, squeezed between three labmates
Copy Editor
and the storage closet? Relief is on the way, as Tracy Powell explains in her sneak preview of the soon-
Graham R. Chequer to-be-opened Stanley Hall and LBL’s new Molecular Foundry (p. 21). Letty Brown tells us about Berkeley
researchers who are busy in the field foragin’ for species (p. 25). And finally, Louis-Benoit Desroches
Editors serves up the latest in his “Who Knew?” series (back cover). Maybe you shouldn’t be so worried about
Meredith Carpenter that quicksand after all.

Jacqueline Chretien As always, we’re looking for contributions from writers, artists, designers, and editors. So if you like
Wendy Hansen what you see, think about joining us. You can always find us online at sciencereview.berkeley.edu or
email us at sciencereview@gmail.com.
Jessica Porter
Tracy Powell Enjoy the issue,
Merek Siu

Layout Editors
Jacqueline Chretien
Wendy Hansen
Matthew de la Peña Mattozzi Michelangelo D’Agostino

Jessica Porter
Kathryn Quanstrom

Contributing Artist
Jennifer Bensadoun
Printer
Sundance Press

© 2006 Berkeley Science Review. No part of this publication may be reproduced, stored, or transmitted in any form without express permission of the
publishers. Financial assistance for the 2006-2007 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; the Associated Students of the University of California (ASUC); and the Department of Mathematics. 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. All events sponsored by the BSR are handicapped accessible. For more information e-mail sciencereview@gmail.com. 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, 5A Eshelman Hall, Berkeley, CA 94720. Advertisers: contact advertise@uclink.berkeley.edu or visit http://sciencereview.berkeley.edu

Cover: Hurricane Katrina passes over the gulf coast. Read about berkeley’s involvement in investigating the aftermath on page 33. Photo 
Courtesy of NOAA.
 [Entered at the Post Office of Berkeley, C.A. as Second Class Matter.]

A bi-annual journal of practical information, art, science, mechanics, chemistry, and manufactures
Berkeley, November 2006 No. 11

21 Features page
Foundations of Excellence......................................... 21
A real estate boom is changing Berkeley’s scientific landscape. by Tracy Powell

Where the Wild Things Are....................................... 25

25 UC Berkeley researchers unearth new species. by Letty Brown

Strung Out at Berkeley.............................................. 28

Physicists ask “What are we made of?” by Meredith Carpenter

28 Flood of Criticism..................................................... 33
Berkeley engineers investigate what went wrong during Hurricane Katrina—and how to
keep it from happening again. by Erica Spotswood

Easy Glider................................................................ 41
What it takes to fly without wings by Adrienne Davich
41

Policy
Political Science..................................................................... 38
Berkeley scientists step up to the policy plate by Kayte Fischer
44

University
Mind the Gap....................................................................... 44
Studies find continued disparity in tenure rates between men and women with families.
by Jennifer Skene


 8 10 12

Current Briefs page 16

Beyond the Chalkboard........................................................... 8
Interactive learning may be a cure for ailing test scores. by Rachel Bernstein

Whose Smog Is It Anyway?................................................... 10

Tracking air pollution in one of the world’s largest megacities by Wendy Chou

It’s All Relative...................................................................... 12 14

DNA fingerprinting identifies family members—for better and for worse.
by Harish Agarwal

Taking It All In..................................................................... 14

Berkeley researchers study how the brain combines information from multiple senses.
by Pei-yi Ko
(Meta)material World............................................................ 16 17
A new class of materials promises to give scientists even greater control over Nature.
by David Strubbe
Legos of Life.......................................................................... 17
Berkeley students compete to build a better bacterium. by Jacqueline Chretien

Another One Sights the Dust................................................ 18 18

Searching for specks of cosmic dust from the comfort of home by Charlie Emrich

Departments
Labscopes................................................................................ 6
A Hitchhiker’s Guide by Ruth Murray-Clay
Fly’s Eye View by Charlie Emrich 6
Heart, Two Heart by Jesse Dill
Red Spot, Jr. by Prayrana Khadye

Book Review......................................................................... 49
The Shangri-La Diet by Seth Roberts by Alisa Gray

Who Knew?.......................................................................... 51
Quick Facts About Quicksand by Louis-Benoit Desroches


 Labscopes
LABSCOPES

a hitchhiker’s guide

A stronomers have long known that the Milky Way galaxy is

disc-shaped with spiraling arms. But just as it is easier to see
the whole UC Berkeley campus from the top of the Campanile
than from the ground, it is difficult to survey the entire Milky
Way from our location inside of it. Interstellar dust obscures vis-
ible light from the far reaches of the galaxy, blocking our view. To
overcome this problem, UC Berkeley astronomy graduate student
Evan Levine and astronomy professors Leo Blitz and Carl Heiles
have constructed a new map of the galaxy’s spiral structure us-
ing radio waves, which travel unhindered by dust. Researchers
in Leiden, Argentina, and Bonn, Germany recently completed a
survey of radio emission from neutral hydrogen across the entire
galaxy. Using their data, Levine and his colleagues picked out low
contrast spiral arms by subtracting a blurred copy of the image
from the original (a technique familiar to Photoshop users as “un-
sharp masking”). Published in the June 23 issue of Science, the
map shows that the Milky Way is an asymmetric, multi-armed
spiral galaxy, with calm gas extending much farther than was pre-
ce
ien

viously known. Furthermore, the spiral arms are pinched thinner

Sc

than the rest of the galactic disc, challenging theorists to improve

of

sy
ur te our understanding of how galaxies become spirals.
co
ge
Ima —Ruth Murray-Clay

fly’s eye view

C ameras keep getting smaller as they’re stuffed by the handful into

phones and gadgets, but making tiny lenses for them is tough, and
making tiny wide-angle lenses is nearly impossible. Fortunately, nature
has already found a solution: the compound eye, an Epcot-Center-like
collection of miniature lenses and light-sensing cells used by most insects.
Inspired, Berkeley bioengineers in Luke Lee’s group have made their own
version. Their work, published in the April 28 issue of Science, demon-
strates the creation of an artificial compound “eye” with about 8,000 in-
dividual hexagonal lenses. Ki-Hun Jeong, lead author of the study, says
that their eye is “very useful for miniature imaging systems” like the en-
doscopes used by doctors for delicate internal examinations. Insect eyes,
by virtue of their bulging shape, collect light from all directions and are
especially good at close-up vision. The artificial eyes were made from a
Image courtesy Luke Lee

light-sensitive polymer that’s able to form light guides, which precisely

mimic the way light is transmitted in insect eyes. This was the goal of the
three-year research project, says Jeong, who used a clever, flexible mold
to form the bulk of the artificial eye. A quick dose of UV light to the mold-
ed eye then activates the light guides. Jeff Goldblum would be proud.
—Charlie Emrich


 heart, two heart

LABSCOPES
W hat if—many months before you were born—the stem cells in-
tended to become your left leg had gotten confused and turned
into a spare arm instead? Beyond the unwanted comments it would bring
on the playground, this would clearly make for some problems later in
life. The complex molecular cues responsible for guiding embryonic stem
cells into specific tissues and organs are still not fully understood; how-
ever, a paper published in the November 2005 issue of Development by
Brad Davidson and Weiyang Shi (both postdoctoral researchers in Michael
Levine’s lab at UC Berkeley) has uncovered the nature of one such critical
signal. Studying a sea squirt called Ciona intestinalis, they clarified the role
of Mesp, a protein that initiates the development of heart muscle tissue in
vertebrates. In normal sea squirt embryos, two cells divide twice to form
eight grandchildren. Four of these migrate to form the organism’s heart;

Image courtesy of Brad Davidson

the other four stay put and form the tail. Davidson and Shi made mutants
of C. intestinalis in which all eight cells produce a highly active form of
Mesp. This led some cells to form a heart in the wrong location, creating
an organism with two hearts. Extending these results in an upcoming
article in Genes and Development, Davidson and Shi stimulated the growth
of a single heart with two sections—possibly articulating the evolutionary
origin of multi-chambered hearts like our own.
—Jesse Dill

red spot, jr.

J upiter’s Great Red Spot, a fierce storm twice the size
of planet Earth, has been a familiar phenomenon to
stargazers for nearly 400 years. But, as on Earth, Jupi-
ter’s climate is changing, and for the first time, detailed
images of a new red spot have been captured by UC
Berkeley Professor of Astronomy Imke de Pater and her
colleagues. The new storm, dubbed Red Spot, Jr., ma-
terialized after three white spots merged in 2000, but
appeared red only recently—a first for any spot in re-
corded Jovian history. Curiously, the source of the red
color is still a matter of debate. One theory suggests
that the storm’s hurricane-like winds, on the order of
400 miles per hour, swirl up substances from the plan-
et’s atmosphere that appear red when exposed to ultra-
violet light. “The chemistry that makes the red color
is likely to be very temperature sensitive, so a new red
spot is very interesting,” explains UC Berkeley Professor
of Fluid Dynamics Philip Marcus. “Climate is seriously
affected by the transport of heat, which is very sensitive
to the patterns of vertical storms on a planet, whether
it be Jupiter or Earth.” Though little is known about
Image courtesy of NASA

storm behavior on the giant planet, some astronomers

believe that the Great Red Spot and Red Spot, Jr. may
eventually converge to form a single titanic tempest.
—Prayrana Khadye


 Current Briefs
Beyond the Chalkboard
BRIEF

Beyond the Chalkboard

Interactive learning may be a cure for ailing test scores.

Briefly Noted S tatewide testing results from the past

academic year reveal that 30 percent of
California students graduate from high school
with a “below basic” or “far below basic”
understanding of core sciences such as biol-
Beyond the Chalkboard ogy, chemistry, and physics. Students perform
Page 8 even more poorly when the tests sample
a variety of topics instead of focusing on a
Whose Smog Is It Anyway? single discipline; in this case, the number of
Page 10 underperforming students jumps to an astro-
nomical 50 percent. Beyond falling test scores,
It’s All Relative a scientifically illiterate voting public could
Page 12 steer science policy in dangerous directions
as issues like global warming and stem cell
Taking It All In research take political center stage. To revital-
Page 14 ize science education, UC Berkeley education
researchers are developing tools that engage
(Meta)material World students with technology-based learning and
Page 16 activities outside the traditional classroom.
UC Berkeley professor of education
Legos of Life Marcia Linn founded and directs a program
Page 17 called Technology Enhanced Learning in Sci-
ence, or TELS, that uses computers to create
Another One Sights the Dust an interactive learning environment in which
Page 18 students dissect complex scientific topics.
Linn and colleagues have developed twelve
interactive, online lessons spanning topics
from global climate change to genetics that
are available at no charge to teachers across
the country. For example, in the “Airbags:
Too fast, too furious?” lesson, students
explore the physics of motion by controlling
the speed of a dummy headed for an airbag,
while a chemistry session illustrates the effect
of changing temperature on molecular mo-
tions. Animated simulations are coupled with
questions that invite students to make and
test hypotheses until they come to a logical
solution, which helps students retain these
lessons long-term. Furthermore, lesson top-
ics such as cancer medications and energy-
Illustration by Jennifer Bensadoun

efficient cars show students that science is

relevant to their everyday lives, a realization
that often spurs enthusiasm and results in
better learning. TELS benefits teachers as well
because it allows them to trace a student’s
progress through the lesson and identify
gaps in understanding. Although the lessons


 Beyond the Chalkboard
are already used in at least 30 schools across
the country, the TELS Center is continually
working to develop new ideas and improve
the program.
While computers can be excellent
learning tools inside the classroom, taking
education outdoors is another great way to

BRIEF
make science exciting. More than just idyllic
retreats, gardens are ripe with math and sci-
ence, an idea that Katharine Barrett, associate
director of education at the UC Berkeley
Botanical Garden, hopes to share through
Math in the Garden. This book of 36 fun
and educational outdoor activities for 5- to
14-year-olds, published in January 2005, is
the culmination of more than five years of
research and development by Barrett and
her coworkers. A parent or teacher leafing
through the book will find activities ranging
from a quantitative study of the various plants
and insects that make up a garden’s ecology
to nutrition activities that can even be done
in a grocery store. Another activity introduces
students to mathematical coordinate grids by
sending them on a treasure hunt. Like TELS,
Math in the Garden creates opportunities for
children to figure things out for themselves.

Photo by Lauri Twitchell/UC Botanical Garden

“Discovery learning has been maligned as
superficial,” Barrett says, “but it’s much more
powerful, more memorable, and more po-
tent. There needs to be a sensory connection.
Nobody can make somebody learn.”
Despite extensive evidence from the
TELS Center as well as many other education
research groups that supports the implemen-
tation of interactive learning activities such
as TELS and Math in the Garden, it is often
difficult for teachers to fit them into their
highly controlled curricula. “It’s all about
achieving the standards,” Barrett says, and
because science is typically not emphasized
on standardized tests until high school, it is
“relegated to smidgens of afternoon time here
and there.” On the other hand, math is an
important focus for these tests, so Math in the
Garden combines math with different facets of
the science curriculum, such as biology and
geology, simultaneously teaching students
frequently-tested material and engaging them
with hands-on science. This interdisciplinary
curriculum provides students with exposure
to basic scientific concepts in a fun environ-
ment where they can literally get their hands
dirty.
TELS faces similar obstacles regarding
class time and teacher flexibility. High school
curriculum requirements only allow about
two days to cover each of the approximately
60 required topics every year, while each
TELS module is designed to take five class
periods. The curriculum’s breakneck speed
does not allow students the time to process
what they learn and integrate it into a larger
A child investigates leaf structure and geometry during a Math in the Garden lesson at UC Botanical Garden.
context of knowledge, but when teachers
find the time to implement a TELS lesson, the
difference is clear. In August, Linn published
a study in the journal Science demonstrating
that students receiving TELS instruction
show improved knowledge integration over
peers taught by traditional methods. Interest-
ingly, the students all scored equally well on
the multiple choice portions of the assess-
ments the study is based on, but the TELS
students performed almost 20 percent better
than their counterparts on explanation items.
This result highlights the ability of the TELS
curriculum to emphasize a deep understand-
ing of science instead of the simple recall of
scientific information. Linn believes that this
positive experience will carry over into other
areas because TELS lessons give students
the tools to be productive learners in any
discipline.
Perhaps most importantly, teachers tell
Linn stories of students eagerly asking when
they are starting the TELS lesson or begging
for another one after they have been intro-
duced to the program. This sort of enthusi-
asm, not often seen in a typical high school
science classroom, highlights the potential
for science education. With the implementa-
tion of programs like Math in the Garden and
TELS, science classrooms can be transformed
from boring lecture halls to sites of exciting
personal discoveries so that the next genera-
tion of students will have a true understand-
ing and appreciation of science.
Rachel Bernstein is a graduate student in
chemistry.
Want to know more? Check out:
“Teaching and Assessing Knowledge Integra-
tion in Science”: Linn, M. et al, Science
313, 1049-1050 (2006).
TELS web site:
http://www.telscenter.org/
Math in the Garden:
http://botanicalgarden.berkeley.edu/
education/eduMIG.shtml


 Whose Smog Is It Anyway?
Tracking air pollution in one of the world’s largest megacities
BRIEF
Humans have influenced the Mexico City valley for millenia. About 25 miles northeast of Mexico
City, the Pyramid of the Sun marks the center of the ancient civilization of Teotihuacán.
S mog in crowded urban settings is nothing
new. Most Californians have probably seen
the brownish haze blanketing Los Angeles,
Bakersfield, or Fresno on a hot summer day.
Until recently, however, smog was considered
a city problem. But now the world’s leading
atmospheric scientists are asking whether
cities can generate regional pollution as well.
And how exactly does such pollution spread?
In March 2006, a group of scientists from
Ronald Cohen’s laboratory in UC Berkeley’s
College of Chemistry traveled to Mexico City,
one of the largest, most polluted cities in the
world, to explore these questions and to
examine some of the broader environmental
consequences of urbanization.
The Cohen group was part of a larger
scientific campaign, the Megacity Initiative:
Local and Global Research Observations
(MILAGRO, or “miracle” in Spanish).The cam-
paign, sponsored by both the United States
and Mexican governments, brought hundreds
of scientists to Mexico City to monitor a suite
of atmospheric contaminants. Using sampling
techniques ranging from large aircraft to
ground-based measurements, the researchers
examined sulfur oxides, carbon monoxide,
atmospheric aerosol particles such as soot,
and important smog-forming chemicals, in-
cluding volatile organic compounds (VOCs)
and nitrogen oxides. As the first researchers
to investigate air quality on such a large scale,
MILAGRO’s participants hoped to improve
understanding of the pollution emerging from
the world’s megacities, technically defined as
those with over 10 million inhabitants.
10
Air pollution in your typical megacity
comes from numerous sources, sometimes
generated by intense industrial activities, and
sometimes arising from destructive environ-
mental practices common in poor, develop-
ing communities. In Mexico City, local oil
refineries belch out hydrocarbons (one type
of VOCs) and chemical plants release benzene
and other toxins. Meanwhile, many residents
still burn wood for heating and cooking, pro-
ducing soot and carbon monoxide, and farm-
ers fertilize crops with ammonia, a volatile
form of nitrogen which can escape into the
atmosphere. On top of these anthropogenic
sources of pollution, natural conditions play
a role as well: Popocatépetl, a nearby active
volcano, spews out sulfur compounds, and
the city’s 7,300-foot elevation ensures plenty
of ultraviolet radiation to foment chemical
reactions. Finally, a ring of mountains sur-
rounds the city, trapping pollution in the
valley for long periods of time.
The Cohen lab has expertise in moni-
toring several types of nitrogen-containing
pollutants, and for their contribution to
MILAGRO, team members were active on the
ground and in the air. Two graduate students,
Delphine Farmer and Chika Minejima, and
staff scientist Paul Wooldridge made land-
based observations of air quality in Tecámac,
a Mexico City suburb about 25 miles north-
east and downwind of Mexico City’s plume of
air pollution. From this location, they could
compare their local measurements to similar
data collected elsewhere around the city to
determine the chemical changes pollutants
There’s Smoke
WhereFarmer
Photo by Delphine
undergo as they drift away from their source.
In addition, two Cohen group students
were onboard a NASA DC-8 as it flew from
Houston to Mexico City analyzing nitrogen
oxides.
It is known that certain nitrogen com-
pounds, like nitric acid (which leads to acid
rain) or the smog-forming nitrogen oxides,
are unstable, break down, and cause local
pollution. By contrast, peroxyalkyl nitrates,
secondary by-products of smog formation,
are stable enough to travel for several hours
before breaking down into nitrogen oxides,
which can then react to re-form smog. In this
fashion, peroxyalkyl nitrates can transport
smog for long distances. These peroxyalkyl
nitrates are of additional interest because
they are classified as irritants and considered
pollutants in their own right. The most com-
mon species in this category is peroxyacetyl
nitrate, or PAN.
To measure peroxyalkyl nitrates in air
samples, graduate student Delphine Farmer
rigged up a tall metal tower on the roof of
a trailer in Tecámac. Attached to this tower
were an air sampling inlet and a metal box.
Inside was her analytical instrument, which
used heat to break apart the peroxyalkyl
nitrates into nitrogen dioxide and then
detected it using a technique called laser-
induced fluorescence. However effective
at sampling air, her setup was sometimes
precarious. On one occasion, faced with an
encroaching thunderstorm, Farmer risked
becoming a human lightning rod as she
rushed to waterproof her equipment. In fact,

special on-site meteorologists had been hired
to warn MILAGRO scientists of incoming
changes in weather that might affect their
chemical measurements; unfortunately, these
predictions typically failed. What did they
use as an alternative? “Yahoo weather was
always right on,” Farmer explains.
Despite power outages and near-elec-
trocution, the Cohen lab’s month of effort
has yielded novel data on levels of PAN in
the air. Previously, no one had ever tried
to predict PAN concentrations so far away
from urban sources. Eventually, the data
collected by Farmer and her colleagues will
be entered into computer models that track
smog formation and dispersal throughout
the region. These models should be more
descriptive and accurate than any in the past
because data from the extensive campaign
can now fill in gaps that used to be left to
guesses and hand-waving. “We were able to
view the site as a giant experiment where
ideas ordinarily treated as assumptions
could actually be tested,” says Farmer. One
pattern that turned out to be more complex
than previously assumed was the behavior of
Mexico City’s plume. At the Tecámac site, the
northeast export of the Mexico City plume
was observed about 30 percent of the time.
On the remaining days, the plume followed
one of two general patterns: in one, it failed
to move because air was trapped in stagnant
layers. The second scenario, known as “loft-
ing,” occurred on days when the plume rose
above the so-called boundary layer, the layer
up to which air ordinarily mixes. During these
lofting events, the plume often wafted toward
the Gulf of Mexico rather than following the
northeast trajectory over Tecámac.
Photo by Paul Wooldridge
As Dr. Ron Cohen looks on, Delphine Farmer shuts off
her peroxyalkyl nitrate-detecting instrument before
bad weather sets in.
Helium-filled balloons carry instruments to measure
ozone and other pollutants.
The MILAGRO campaign also showed
scientists the sheer magnitude of the pollu-
tion produced by megacities. Mexico City’s
high pollution levels challenge the textbook
explanations of smog formation, which
usually involve reactions between nitrogen
oxides and hydrocarbons. According to
Farmer, “Whereas typically we might ask
‘which one is limiting, the nitrogen oxides
or the hydrocarbons?’ that type of question
isn’t easy to answer when both are so high.”
In other words, when a single pollutant type
Pollutants and dust over Tecámac scatter light,
emphasizing orange and red wavelengths at sunset.
Whose Smog Is It?
is limiting, policy measures can be directed
at minimizing the offending contaminant.
In Mexico City, there’s no easy way out, and
both types of pollutants must be decreased to
reduce smog levels.
Ultimately, by linking pollution sources
to pollution outflow, MILAGRO research will
BRIEF
help address the question of how megacities
can achieve economic development while
protecting public health. Take the issue of
transportation: one possible solution is to
cut down on the city’s four million motor
vehicles, which account for about a third of
Mexico City’s nitrogen oxides and hydrocar-
bons. Mexico did not introduce emissions
standards for new vehicles until the early
1990s, and critics claim these standards are
weakly enforced. To its credit, Mexico City
Photo by Delphine Farmer
offers some of the most affordable public
transit in the world, including a state-of-
the-art subway system and the Metrobus,
a rapid transit system launched in June of
2005. Would better models of smog forma-
tion provide the evidence needed to expand
mass transit options even further? Although
it’s still early to speculate on future policy out-
comes from MILAGRO, many view Mexico’s
enthusiastic support for the campaign, from
both a scientific and a political standpoint, as
additional proof that the city is well on the
path to reform.
Wendy Chou is a graduate student in environ-
mental science, policy, and management.
Want to know more? Check out:
http://www.windows.ucar.edu/
tour/link=/milagro/milagro_intro.html
http://www.eol.ucar.edu/
projects/milagro/media/
MILAGRO-Factsheet-Final.pdf
Photo by Dephine Farmer
11
 It’s All Relative
It’s All Relative
DNA fingerprinting identifies family members—for better and for worse.
I
BRIEF
n 1988, Lynette White was murdered in many of the ethical questions that accompany
Cardiff, Wales. The DNA evidence led its use have yet to be answered.
police to the criminal record of a 14-year-old Perhaps the most publicized use of
boy who shared a rare genetic type with the genetic fingerprinting is in the arena of
murderer, but did not exactly match the criminal justice. Since it was introduced into
genetic fingerprint. Police suspected a male the courtroom in 1985, DNA fingerprinting
relative of the boy was the real perpetrator, has become increasingly prominent in the
but a swab of his father’s DNA also yielded prosecution, and exoneration, of criminals.
a mismatch. Further investigation unearthed Crime scenes are routinely examined for
Jeffrey Gafoor, the boy’s uncle, who was an DNA evidence. These samples can then be
exact match to the crime scene evidence and compared against a DNA database. The DNA
eventually convicted of the crime. records of convicted sex offenders, as well
Taking their cue from this and similar as that of crime scene DNA, are maintained
cases, Frederick Bieber, a pathologist at Har- in a database by every state in the United
vard Medical School, David Lazer, a Harvard States. The FBI implemented the Combined
sociologist, and Charles Brenner, a visiting DNA Index System (CODIS) in 1998, which
scholar in the Forensic Science Group at organizes all of the local state records into a
UC Berkeley’s School of Public Health, pub- national database.
lished an article entitled “Finding Criminals The records do not contain the entire
Through DNA of Their Relatives” in the June three billion nucleotide sequence of a person’s
2006 edition of Science. Meanwhile, across genome; indeed, it took years to sequence
campus at Stephens Hall, Eric Stover, the a single human genome, and it is unlikely
head of the Berkeley Human Rights Centre, that anyone would be willing to wait that
works on the DNA Reunification Project. long for the result of a genetic fingerprinting
Launched in 1996, the project is an effort to test. Luckily, scientists have discovered a few
use genetic fingerprinting to reunite families tricks to expedite the process. Rather than
separated during El Salvador’s civil war, examining the entire sequence of nucleotides
which lasted from 1980 to 1992. During the (the familiar As, Gs, Cs and Ts that are the
war, many children were separated from their building blocks of DNA) in a DNA sample,
parents—some taken forcibly, others simply thirteen different spots, or loci, on the genome
put up for adoption by desperate parents. are selected. These loci are known to be the
The identification of family members and sites of short tandem repeats, or STRs, so
relatives through DNA is a new and exciting named because they contain repeats of small
application of existing technology; however, sequences (three to five nucleotides long) of
DNA. As it turns out, there
is a large variability in the
How DNA Fingerprinting Works number of repeats, called
the allele, an individual
3ECTIONOF$.!FOUNDATCRIMESCENE
may have at a locus.
REPEATSOF@!4''REPEATSOF@!44REPEATSOF@'4REPEATSOF@#'
A powerful genetic
fingerprint is obtained by
examining many different
3ECTIONOFRELATIVES$.!FOUNDINDATABASE
STR loci to identify their
REPEATSOF@!4''REPEATSOF@!44REPEATSOF@'4REPEATSOF@#' specific alleles. While a one’s genetic heritage. As a consequence, the
Graphic by Meredith Carpenter
friend may be wearing the
same color shirt as you, it
3ECTIONOFSUSPECTS$.!
is unlikely that he or she
REPEATSOF@!4''REPEATSOF@!44REPEATSOF@'4REPEATSOF@#' would be wearing the same originally restricted to sex offenders, to all ar-
Comparing the number of short tandem repeats, or STRs, at different color shirt as you both
locations in the human genome to records in the CODIS database can today and tomorrow. In the
lead investigators to relatives of the suspect.The suspect was not in the same way, although there
database, so the relative’s DNA was the top hit because it matches the is a slight chance that two
crime scene DNA at three of four loci (in reality, more loci are included). individuals share the same
This leads investigators to the suspect, whose DNA matches the crime allele at one STR locus, as
scene DNA exactly. one examines more loci,
it becomes increasingly
12
unlikely that they share the same alleles at
all loci. CODIS records the alleles at thirteen
STR loci; the odds are estimated at 1 in 1029
(that’s a 1 with 29 zeroes!) that unrelated
individuals will have an identical CODIS
record. Crime scene DNA can be compared
against these records for so-called “cold hits”,
or exact matches, with an offender’s DNA.
Bieber and his colleagues suggest that for
those cases in which CODIS does not yield a
cold-hit, the computer should generate a list
of people who may be closely related to the
individual whose DNA is being examined.
This list could then lead investigators to a
suspect, just as in the Lynette White case.
How does the computer pick out po-
tential relations from the millions of records
in CODIS? It is well-known that related
individuals have more similar genetic finger-
prints than unrelated individuals. Accord-
ingly, individuals are more likely to be related
if they have in common alleles which are very
rare in the general population, or if they have
very similar patterns of alleles. Using massive
computer simulations and previously pub-
lished data on allele frequencies, Bieber and
his colleagues were able to demonstrate that
in a database of 50,000 individuals, there is a
99 percent chance that the biological father of
a child will appear in the top 100 matches to
the child’s DNA sample. The authors suggest
a number of other familial searching methods
that can be used to improve the odds even
further. However, the search described above
can be implemented without any modifica-
tion to the existing database.
Although the familial searching tech-
nique is promising, criminal justice is not
simply a playground for forensic scientists,
no matter what CSI may have us believe. A
genetic identification record is much more
personal than a simple social security number,
because it carries with it information about
database of genetic fingerprints raises a host
of privacy issues. Some states have already
extended the law requiring DNA collection,
restees, even persons who have not yet been
convicted of a crime. Furthermore, although
the thirteen STR loci are thought to be in
regions of the human genome which are not
medically relevant, the physical DNA sample,
which contains all of the genetic information
describing an individual, is often stored for
an indefinite period of time by crime labs.
 It’s All Relative
According to Rachel
Shigekane of the UC
Berkeley Human Rights
Center, “Since 1994, Pro-
Búsqueda has registered
768 cases of missing
children,” and 316 of these
Photo Courtesy of Robert Kirschner

Eric Stover, director of the UC Berkeley Human Rights Center, takes a blood sample from a relative of a missing
child in a village in central El Salvador.
The legal framework surrounding all
of these issues is “insufficient,” according to
Erin Murphy, associate professor of law at UC
Berkeley. Some scientists are calling for the
use of more STR loci to definitively rule out
an improper match to a genetic fingerprint.
In addition, the utility of the technology itself
has not been adequately studied—while there
have been about 30,000 cold hits to date us-
ing CODIS, there has not been a systematic
study of the subsequent convictions obtained
using these hits. Finally, the sociological im-
plications of genetic
fingerprinting are
daunting. While
DNA databases
should contain a
uniform sampling
of criminal of-
fenders across the
entire population, it
may, in practice, be
Murphy.
While the use of DNA technology in the
justice system raises thorny questions, familial
searching techniques can also be played out on
less ethically ambiguous stages. Although the
El Salvadoran government has yet to address
the aftermath of its civil war, the Asociación
Pro-Búsqueda de Niñas y Niños Desaparecidos
(Association in Search of Missing Children), a
volunteer organization, has made considerable
progress in locating missing children using
conventional investigative techniques.
BRIEF
cases have been resolved.
Each of these matches
has been confirmed by
genetic fingerprints with
the help of Eric Stover at
the UC Berkeley Human
Rights Center and his DNA
Reunification Project. In
recent years, volunteers
from Pro-Búsqueda and
the Human Rights Center
have traveled throughout
El Salvador to collect DNA
samples from parents and
other family members.
These samples were then
brought to California,
where the California
Department of Justice
donated its forensic lab re-
sources during off-hours and several forensic
scientists volunteered to process the samples.
With the database complete, Pro-Búsqueda is
poised to use familial searching techniques
to match children with their families. Lost
loved ones can now avoid wading through
complicated social and bureaucratic issues in
locating adoption documents, which some-
times do not even exist, to locate each other.
The contrast between the Pro-Búsqueda
search and the use of DNA evidence in the
courtroom delineates the key to moving
forward with DNA technology: understand-
ing that while the technology itself is not
inherently unethical, the applications of
this technology must be carefully examined.
That cutting-edge technology can have social
implications is nothing new; from firearms to
the internet, human society has always had
to regulate its advances. As we continue to
innovate, it is worth keeping in mind that our
inventions do not exist in a vacuum.
Photo courtesy of Bonnie Azab Powell

more likely that an Harish Agarwal is a graduate student in

arrestee and his or physics.
her accompanying
genetic fingerprint Want to know more? Check out:
come from a poor UC Berkeley Human Rights Center :
neighborhood. www.hrcberkeley.org
Thus, familial
searching has the
potential to “further Liz Barnert (left), a UC Berkeley/UCSF medical and public health student who has
exacerbate the prob- assisted with the DNA reunification project, and Angela Fillingim (right), who was
lem of unfair polic- adopted from El Salvador by a Berkeley couple when she was six months old and
ing,” says Professor later reunited with her mother.

13
 Taking It All In
Taking It All In
Berkeley researchers study how the brain combines
information from multiple senses
BRIEF
I n a split second on the basketball court,
you make dozens of decisions based on
information from all of your senses. Your
teammate calls your name, you hear it, you
turn towards him, calculate his location and
the trajectory of the ball flying towards you.
In an instant you have judged the relative
locations and speeds of your teammate, the
ball, and your opponents using your senses
Graphic by Hanson Lee
of hearing, sight, touch, and balance. It’s a lot
to handle, but our brains perform compli-
cated sensory integrations like this every day.
Somehow, they’re able to properly match the
corresponding features reported by our dif-
ferent senses and not misjudge the direction
and degree we should turn. And they keep
us from reaching for our opponent’s head
instead of the ball.
Animals are naturally good at combin-
ing multiple sensory inputs to deal with the
dynamic flow of information, and humans are
no exception. But how is sensory information
integrated to create a unified picture of the
environment? Since we cannot possibly per-
ceive and act perfectly under all conditions,
how does the brain decide which inputs
are most important in order to optimize its
performance? UC Berkeley’s Martin Banks,
professor in the Vision Science Program and
Helen Wills Neuroscience Program, tackles
these questions in the multisensory studies
in his lab.
Sensory integration has been studied
since the early 19th century, but recent tech-
nological advances have given researchers
more tools for manipulating sensory inputs to
understand how the brain is able to combine
them. Five years ago, Banks and postdoctoral
researcher Marc Ernst, now a research scien-
tist at the Max Planck Institute for Biological
Cybernetics, acquired one such new tool, a
force-feedback device called the Phantom,
developed and marketed by the SensAble
Technology. The Phantom is used with a vir-
tual reality visual display tool and allows the
researchers to study the integration of touch
(haptic information) and vision in perceiving
the height of a virtual ridge. During a typical
Phantom experiment, the subject looks at a
visual display while placing their thumb and
index finger into metal thimbles connected to
a robotic arm which tracks and records the
fingers’ 3D location. As the fingers travel to
designated positions, the thimble/arm exerts
the proper force on the finger to simulate the
14
In a split second on the basketball court a player’s
brain must accurately combine information from
the senses of vision, hearing, balance and touch to
complete a play.
sensation of touching a ridge. In a control
condition, this force-feedback would match
the visual display; that is, the subject would
see their “virtual fingers” in the form of mouse
pointers, touching the edges of a ridge when
corresponding resistant forces are given. But
by independently manipulating the feedback
force and the visual display, the researchers
are able to introduce uncertainty or conflicts
between what the subject touches and what
he or she sees. Understanding how the brain
resolves these virtual reality-induced uncer-
tainties and conflicts can reveal underlying
computational principles of sensory integra-
tion and is of great interest to researchers in
Banks’s lab.
So, how does the brain do it? In a study
on visual-haptic integration published in the
journal Nature in 2002, Ernst explains that
the brain “use[s] information in a statistically
optimal fashion.” In other words, the brain
does what makes the most sense—it inte-
grates the information from different senses,
but weights each sensory input according to
how reliable it is. For example, if your brain
is trying to decide where the handle of the
cup is in the dark, it will weight the judgment
made by touch more highly than your visual
estimate of its location. In low light, your
brain will realize that your touch is probably
more accurate than your vision. Clearly this
doesn’t make much difference when all of
your senses are reporting the same thing,
but in conflict situations, like those that
can be created in the Phantom experiments,
this weighted integration becomes critical in
determining a person’s perceived values of
the stimuli.
This weighted combination model for
sensory integration is adapted from a math-
ematical analysis procedure, the Maximum
Likelihood Estimate (MLE) model. Accord-
ing to the MLE model, your brain statistically
determines the most likely outcome based
on a series of weighted inputs, with the
weights adjusted according to the statistical
reliabilities of the inputs. The physiological
and neural mechanisms responsible for
calculating the maximum likelihood estimate
are still not fully understood, but Ernst
and Banks have made the first step towards
modeling the process in the hope of one day
comprehending it more fully.
Having demonstrated that our brains
could be using the MLE model to integrate
visual and haptic sensory information, the
Banks lab is now working to identify whether
this principle holds across various modalities,
including visual, auditory, touch and vestibu-
lar (balance) systems. In an ideal situation,
what a person sees, hears, or feels about an
object would indicate consistently where it
is. Graduate student Carmel Levitan uses the
Phantom in conjunction with a virtual-reality
visual display and a headset to manipulate
the touch, visual, and auditory information
reaching a human subject, such that they ap-
pear to originate from different locations. She
then studies how the person deals with these
discrepancies to come up with a decision
about the object’s location.
The results indicate that when the
discrepancies between three senses are small,
we take into account the accuracy of each
sensory input and weight them accordingly,
as the MLE model would predict. However,
when the discrepancies become too large, we
entirely ignore the information that is most
erroneous and instead rely on the two that
are most consistent.
A classic example of sensory integration
is judging the direction of gravity, for which
the brain must integrate information from
the visual and vestibular systems. In the
Banks lab, graduate student Paul MacNeilage
manipulates visual and vestibular sensory in-

puts independently and tests peoples’ ability
to judge the direction of gravity. MacNeilage’s
experimental subjects are seated in a chair
that tilts slowly from side to side with the
subject’s head at the center of a wide arc.
The subject looks through a circle at a visual
scene, which may be rotating at the same or
different rate as the chair. These experiments
indicate that what we see can influence the
judgments made by our vestibular system.
When the visual input is a realistic scene such
as a living room (as opposed to random dots
like a starry sky), our perception is biased
towards the upright direction depicted in the
image, even when our vestibular system is
telling us something different.
Multisensory integration research has
many potential applications in areas like
Graduate student Paul MacNeilage
uses a tilt chair and virtual reality
display to study how the brain com-
bines visual and vestibular inputs to
tell up from down.
machine spatial navigation and the design of
ergonomic virtual reality environments. One
such example is the self-navigating car, Stan-
ley, the winner of DARPA’s Grand Challenge
2005. Designed by a team from Stanford,
the car was able to drive 132 miles across
the Mojave Desert by integrating sensory
information from radar, laser ranging, stereo
cameras, GPS, inertial guidance system,
and an odometer. The researchers designed
a guidance system that integrates all of this
information in ways that simulate human
behavior.
Video game design also aims to include
sensory information beyond just vision. Yet
there are still many challenges in virtual
environment design, such as making virtual
experiences realistic enough, or preventing
Taking It All In
disorientation as conflicting sensory messages
bombard the player. By helping to understand
how we deal with dynamic flows of informa-
tion—acquiring, learning, and forgetting the
sensations that we have experienced—Ernst’s
research may one day help to perfect such
immersive environments.
BRIEF
Pei-Yi Ko is a graduate student in vision science.
Want to know more? Check out:
Ernst M.O. & Bulthoff H.H. Merging the
senses into a robust percept. Trends Cogn Sci.
8:162-169 (2004).
Banks Lab Website:
http://bankslab.berkeley.edu/
Photo by Pey-Yi Ko
15
 (Meta)material World
(Meta)material World
A new class of materials promises to give scientists even greater control over Nature.
T oday’s materials are made from the pal-
BRIEF
ette of 116 elements known as the peri-
odic table. Select some carbon, a little sulfur,
maybe a bit of dysprosium, and voilà—a new
substance. Scientists have only scratched the
surface of the myriad chemical combinations
that can be made from the elements, but
what if you could mix up some extra colors
for the palette?
The new field of metamaterials prom-
ises to do just that: create “artificial atoms”
that can be combined into substances with
novel properties. Freed from the constraints
of nature’s building blocks, engineers can
fashion metamaterials that refract light back-
wards, that focus images of unprecedented
resolution, or that may even one day form the
basis of a cloaking device. One of the
leaders in this emerging field of meta-
materials is Professor Xiang Zhang of
UC Berkeley’s Nanoscale Science and
Engineering Center and Department
Graphic by Meredith Carpenter
of Mechanical Engineering. “We’ve
been very interested in developing
artificial materials with extraordinary
properties that do not exist in nature,”
Zhang told the Berkeley News Office.
In a recent research paper published
in Nature Materials, Professor Zhang and his
colleagues described the fabrication of the
world’s first acoustic metamaterial.
So what exactly is a metamaterial? Con-
sider a chunk of concrete the size of Manhat-
tan: that’s an ordinary material made of a more
or less uniform substance. Now consider the
real Manhattan, in which the concrete is
actually arranged into buildings arrayed on a
grid of city blocks: that’s a metamaterial. Even
though they have similar compositions, the
city with its skyscrapers has a more compli-
cated substructure than the concrete slab. As
a result, the city has different characteristics
than a concrete slab. These can be changed
by tuning the substructure—for example,
altering the height of the buildings or the size
of the city blocks.
Replace the concrete with copper and
the buildings with coils and wires, and then
shrink the whole thing down by about a
factor of a billion (think microns rather than
kilometers), and you have the basics of a
metamaterial. It is the substructure of the
metamaterial—the arrangement and sizes of
the coils and wires—that is crucial. When a
light wave or a sound wave passes through
an arrangement of structures that are much
smaller than its wavelength (the distance from
16
one wave to the next), the wave experiences
the material as though it were uniform, but
with different properties than the constituent
materials. In effect, the wave doesn’t know
about the separate substructures and “sees”
an entirely new material.
For most ordinary materials, the struc-
tures are arranged on the scale of atoms.
Metamaterial engineers, however, work with
larger-scale, more easily manipulated compo-
nents rather than settling for natural atomic
arrangements. In the case of the micron-sized
copper coils, the structure is designed to work
with microwaves. The properties of this array
are tuned so the coils naturally resonate at a
frequency very close to the frequency of the
incoming waves.
By giving them complex substructures like those
shown in the electron micrograph above, scientists can
fashion materials with new and interesting properties.
Constructed properly, a metamaterial can
achieve a negative index of refraction. When
an electromagnetic wave like light travels
from a lower-index medium to a higher-in-
dex medium (from air to water, for example)
it bends towards a line perpendicular to the
surface. However, if the light is entering
a negative-index material, it bends in the
opposite direction, as though it reflected off
the perpendicular line. This unique property
can be used to design “superlenses” that have
much higher resolution than ordinary lenses.
Last year, Zhang’s group demonstrated a silver
superlens (see “The Sharpest Image,” BSR Fall
2005). Working at a wavelength for which a
thin film of silver had a negative index, they
could resolve lines that were much thinner
than the wavelength of the ultraviolet light
they were using and surpass the “diffraction
limit” of standard optics.
Now Zhang’s lab has turned its attention
from electromagnetic waves to ultrasound
and made the first acoustic metamaterial.
If you have ever blown across the top of a
bottle to make a sound, you’re familiar with
the basic building block they used. It’s called
a Helmholtz resonator—a chamber con-
nected to the outside via a narrow neck. The
frequency of vibration is set by the volume of
the chamber and the size of the neck.
Postdoc Nicholas Fang (now a professor
at the University of Illinois at Urbana-Cham-
paign) and coworkers fabricated a linear array
of 59 aluminum resonators each about one
cm in size, tuned to vibrate at 33 kHz. The
chambers and a channel to which they were
connected were filled with water, in which
their ultrasound has a wavelength of 4.4 cm,
four times the resonator size.
Fang says he was inspired by musical
instruments. “Think about a flute,” he told
the media office at UIUC. “When we play
music, we are using some instrument that
carries sound waves, and yet each of
the buttons [is] much smaller than
the wavelengths they produce. So
here we take a similar philosophy.
We’re using very tiny elements, tiny
resonator cavities, and in an analogue
to the flute, we try to create those
structures in order to manipulate or
control the resonating frequencies of
ultrasound.”
For electromagnetic waves, the
goal had been to achieve a negative index of
refraction. For acoustic waves, Zhang’s group
achieved what’s known as a negative modu-
lus in the metamaterial, a similarly strange
property. The elastic modulus of a material
essentially answers the question, “How much
does a material compress when you push on
it?” If the modulus is negative, it doesn’t com-
press—it expands. To be sure, this is only true
if you push on it at a frequency of 33 kHz.
But negative modulus is a unique property,
not observed in any natural materials.
Zhang’s group plans to turn the linear
array into a two- or three-dimensional meta-
material which could have many interesting
applications. Current acoustic devices must
be larger than the wavelength of the waves
with which they interact, but ones with
metamaterial lenses could be much smaller
and more compact. Two possible applications
are medical ultrasound imaging and sonar
systems (the group is partially funded from
the Office of Naval Research). They also hope
to take advantage of the negative modulus to
create an acoustic superlens to beat the dif-
fraction limit, like the silver superlens.
The humble principles of the flute might
some day lead to the most science-fiction
of scenarios: a cloaking device. Research-

ers dream of wrapping an object in optical
metamaterials specially designed to bend
light around the outside and then continue
in its original direction, as though there were
nothing there at all. That’s something you just
can’t do with ordinary atoms.
David Strubbe is a graduate student in physics.
Want to know more?
Fang, N. et al, Nature Materials 5, 452-456
(2006).
Xiang Zhang’s group website at
http://xlab.me.berkeley.edu.
Legos of Life
Berkeley students compete to build a better bacterium
B acteria are wonderfully diverse and can do
some pretty amazing things, such as light
up at night and neutralize chemical waste.
But there are some things they typically can’t
do: photograph themselves, play freeze tag,
add and subtract, initiate a battle for their
petri dish, or smell like perfume instead of,
well, E. coli. The International Genetically
Engineered Machine (iGEM) competition, a
friendly contest in the field of synthetic biol-
ogy, aims to change all that.
In the iGEM competition, teams of un-
dergraduate and high school students attempt
to synthesize a useful biological device—for
example, a colony of bacteria that, through
coordinated signaling between cells, can light
up fluorescently in a regular pattern, or, in
the case of this year’s MIT project, convert
unpleasant smelling molecules to neutral or
pleasant smelling ones. In the process, the
students generate “BioBricks”, discrete pieces
of DNA that code for or regulate cellular
machinery and can be used over and over.
“The analogy of-
ten made is that these
parts are like wires,
capacitors, r esistors,
transistors, and diodes
used to make elec-
tronic circuits,” says
Chris Anderson, a
postdoctoral fellow in
Bioengineering profes-
sor Adam Arkin’s lab
and advisor to the
Berkeley iGEM team.
But instead of electri-
cal components, these Gearing up bacteria:The 2006 international Geneti-
students use (and cally Engineered Machine competition in the field of
manipulate) BioBricks synthetic biology gathers high school and undergradu-
to build their biologi- ate students to gear up bacteria with a whole host of UC Berkeley team
cal machines. new functions.
The current set of
BioBricks includes genes that encode cell sig-
naling molecules, mating factors (molecules
or small proteins that alert bacteria when
a potential partner is nearby), fluorescent
proteins, light-sensing proteins, and proteins
that provide antibiotic resistance. But the
BioBricks are hardly limited to protein-cod-
ing DNA. The toolbox also contains pieces
of regulatory DNA that act as switches to
determine whether a nearby gene is turned
on or off, or whether a gene can be translated
into protein.
Groups of BioBricks can be used to carry
out complex functions, like creating feedback
Legos of Life
loops or signal amplification. The hope is
BRIEF
that as more and more parts are added, the
machines that can be made with various
combinations will become increasingly
complex.
An analogue to robotics competitions
that get students psyched about engineering,
the iGEM competition was born in January
2003 out of an independent student project
at MIT. Since then, iGEM has evolved into an
international competition to see which group
can design the “coolest” cellular machine. UC
Berkeley has participated in the competition
for the past two years.
In 2006, 38 teams of undergraduate and
high school students from universities on ev-
ery continent except Antarctica spent three to
five months over the summer working on their
projects. The students, about half of whom
already have experience in biology, and half
of whom have backgrounds in engineering
and computer science, get a crash course in
molecular biology and lab techniques. Then
they brainstorm with
advisors about the di-
rection of the project.
After that, they spend
the majority of their
Graphic Courtesy of Matthew Mattozzi
time at the lab bench
experimenting. At UC
Berkeley, Arkin and
Chemical Engineering
professor Jay Keasling
are the project spon-
sors, with postdoctoral
fellows Chris Ander-
son and John Dueber
providing additional
guidance.
The current
is aiming to develop
an addressable two-
way communication system in bacteria.
They hope to achieve selective delivery of a
DNA message by manipulating conjugation
(the exchange of genetic material between
bacteria) in the common research organism
E. coli. Eventually, the team will be able to
manipulate this bacterial communication
to perform logic calculations or simple
mathematical functions—in effect, creating a
bacterial brain.
This year’s Berkeley team was split into
three smaller groups, each focusing on one
aspect of the larger project. One group tackled
the conjugation process, removing two genes
17

Legos of Life
BRIEF
Photos Courtesy of Melissa Li
Samantha Liang at the bench. iGEM students get a
crash course in molecular biology before spending the
summer researching.
(which signal “copy me and pass me along!”
to the bacteria) from one piece of DNA and
putting them into another. This effectively
determines which genes will be transferred
during conjugation. A second group worked
on making the conjugation process address-
able. A regulatory DNA “lock” is added to
the DNA message to prevent production of
its encoded protein. Some cells, however,
possess another piece of DNA—encoding a
Some members of the 2006 iGEM team outside their Potter Street base: (left to right) Matt Fleming, Kaitlin Davis,
Bryan Hernandez, Jennifer Lu, Samantha Liang, and advisor J. Chris Anderson.
18
molecular “key”—that enables them to read
the “locked” DNA message received during
conjugation. Finally, a third group developed
network layouts and logic circuits that use
this system to perform simple calculations.
The team will present their project at
an end of the year iGEM Jamboree, a science
fair-meets-conference to showcase their
work. After all the teams have presented,
awards both serious and light-hearted are
given. Last year’s Berkeley team won the Most
Innovative Brick Award (for a special start
site for DNA replication that is activated only
when a cell is conjugating with another cell),
as well as Best Conceptual Advance and Most
XXXtreme Presentation. The 2006 Jamboree
will be held in early November at MIT.
Ultimately, the project and even the
development of new BioBricks are secondary
aims of the iGEM competition. The main
goal, says Anderson, is “first and foremost
education,” and to spark the interest of bright
students who will lead the way in this young
field.
Still, there is a strong sense amongst
the participants that projects like iGEM are
going to change the way biology is done. “I
was struck by the sheer potential of synthetic
biology and the broad applicability of work
in the area, from pharmaceuticals, indus-
trial processes, consumer products, and basic
theoretical advances,” said Daniel Kluesing,
a senior at UC Berkeley who worked on the
2006 iGEM team. It is only a matter of time
before these BioBricks are put to work pro-
ducing hydrogen for fuel cells, churning out
anti-malarial drugs, and doing your taxes.
Jacqueline Chretien is a graduate student in
molecular and cell biology.
Want to know more? Check out:
2006 Berkeley iGEM wiki:
http://openwetware.org/wiki/IGEM:
UC Berkeley/2006
iGEM : http://parts.mit.edu/igem
Another
One Sights
the Dust
Searching for specks
of cosmic dust from the
comfort of home
I f you’ve ever aspired to be a space scientist
but wanted to skip the years of schooling
and NASA training, now is your chance,
thanks to an innovative project called
Stardust@home. Begun in early August, this
web-based program from the Berkeley Space
Sciences Lab puts ordinary people in control
of a virtual microscope to search for tiny
grains of stardust collected by a NASA space
probe.
The NASA Stardust probe, launched
in 1999, traveled halfway to Jupiter before
returning to the Utah desert last January.
During its trip, the Stardust probe deployed
a tennis-racket sized collector grid to capture
stardust for analysis back on earth.
“This is the stuff that we’re made of,” says
Andrew Westphal, leader of the Stardust@
home project. Our solar system is thought to
have been formed from gas and dust, and it’s
possible that some of the stardust returned
by the probe is actually older than the solar
system itself.
But before the stardust can be analyzed,
each of the hundred or so motes has to be
found. “That’s why we need the help of vol-
unteers,” says Westphal, “because we couldn’t
do this ourselves.” Each piece of stardust is so
tiny, according to Westphal, that finding them
is nearly impossible, but since the stardust is
zipping through space at about 45,000 miles
per hour, it blasts holes in the collector grid
that a well-trained eye can spot.
Westphal originally planned to use a
computer to find the stardust impacts, also Photo courtesy of author
NASA stardust probe.

The collector grid, made of 132 tiles of aerogel, scoops up dust in its path.
called tracks, but had limited success. “It may
be possible,” he says, “but we’re simply not
clever enough” to program a computer to
find the stardust tracks.
So with the Stardust probe still in
space, Westphal decided to enlist the help
of volunteers to search the collector grid for
stardust from the comfort of their personal
computers.
To participate in the Stardust@
home project, all volunteers simply visit
stardustathome.berkeley.edu, go through
a 15 minute training session to help them
identify stardust tracks, and then pass a 10
question test to show that they can spot
genuine tracks. (Don’t fret: if, like the author,
you don’t pass the test the first time, you can
keep taking it until you do pass.)
The ethereal aerogel is one thousand times less dense than glass, giving grid belongs to Ron Bastien,
it the appearance of solid smoke.
After passing the test, volunteers create
an account and start hunting for real stardust
tracks by looking at scenes from the actual
Stardust collector grid and adjusting the focus
of their virtual microscope to find the telltale
sign of a stardust track. A track looks “like
a little transparent carrot” growing into the
collector, says Westphal.
“If you see a track, you click on it, and if
you don’t see a track, you click on a button,”
says Westphal, adding that the process is
“kind of like a video game.”
To keep volunteers sharp and lend
a competitive aspect, the Stardust@home
team has added “fake” scenes, in much the
same way the TSA’s Threat Image Projection
system adds “fake” guns and contraband to
luggage X-rays to test the alertness of bag-
gage screeners. Volunteers who
correctly identify a track will
get co-authorship on publica-
tions from the Stardust@home
team, as well as the admiration
of more than 15,000 Stardust@
home volunteers who hail from
countries all over the world.
One of the most astounding
parts of the project is the collec-
tor grid itself, which, just like
a giant marshmallow catching
bullets, has softly captured the
precious grains of stardust.
The grid is made of 132
tiles of aerogel, a special form of
silica that is one thousand times
less dense than glass, giving each
tile the appearance of a solid
piece of smoke.
The task of scanning the
project engineer at NASA’s
Stardust@home
BRIEF
Photo courtesy of Bonnie Azab Powell
Tracks of cosmic dust.
Johnson Space Center in Texas, who antici-
pates that cutting the microscopic specks of
stardust out of the aerogel will be the next
challenge in the project, because its downy
nature makes the aerogel like “a piece of dust
with a piece of dust in it.”
Westphal’s team got help with the web
interface from fellow SSL scientist Dave
Anderson, the self described “computer geek
around the lab” who also directs the famous
SETI@home and BOINC distributed comput-
ing projects (see BSR Spring 2005). Despite
similarities in the way the two projects farm
out work to volunteers, “they’re two different
things,” says Anderson, and both can even be
run at the same time. “SETI@home uses your
processor. Stardust@home uses your brain
and eyeballs.”
Anderson hopes that Stardust@home
will help to democratize science, allowing
people of all ages and backgrounds to partici-
pate in the discovery process, and according
to Westphal, this first-of-its-kind endeavor is
money well spent.
The Stardust mission has cost $200 mil-
lion over its ten-year lifetime, which Westphal
puts into perspective as “about the salary of a
well-paid baseball player.” For science buffs,
Stardust@home is a grand slam.
Photo courtesy of Bonnie Azab Powell
Charlie Emrich is a graduate student in
biophysics.
Want to know more? Check out:
stardustathome.berkeley.edu
Parts of this story originally appeared in the
August 9, 2006 edition of The Sacramento
Bee, where the author interned under the
AAAS Mass Media Fellowship Program.
19
 A view of the East Bay from
FEATURE Foundations for Excellence

the Molecular Foundry.

20

Foundations
of Excellence
A real estate boom is changing Berkeley’s scientific landscape.
For those who’ve spent years scurry-
ing to avoid careening backhoes, hard-hat-
ted laborers, and the sweet siren song of the
jackhammer, it will come as no surprise: new
buildings are popping up all over campus.
Fortunately for the Berkeley scientific com-
munity, this construction boom includes two
major research facilities—Lawrence Berke-
ley National Laboratory (LBL)’s recently
completed Molecular Foundry and the new
Stanley Hall, scheduled to open in March.
Each promises to provide new collaborative
opportunities to scientists in and around Cal,
as the Berkeley Science Review recently saw
firsthand while touring both facilities.
Lost and foundry
A six-story, cantilevered edifice jutting
over the edge of the Berkeley hills, the new
Molecular Foundry is an imposing struc-
ture—and as a flagship facility of the National
Nanotechnology Initiative, it should be. The
federal government spent $85 million to con-
struct and equip the Foundry, which is one
of five Nanoscale Science Research Centers
funded by the Department of Energy (DOE);
beginning in 2007 this will be augmented by
an operating budget of $18–19 million per
year. The result, says Associate Director Jim
Bustillo, is “a real centerpiece of the basic en-
ergy sciences division within the DOE.”
Providing core facilities and research
space to a burgeoning community of perma-
nent and visiting researchers, the building is
intended to foster innovation and interdis-
ciplinary collaboration in nanotechnology, a
growing field that explores the properties
and uses of materials mere billionths of a
meter large. Says Bustillo, “The key is to bring
Foundations for Excellence
FEATURE
by Tracy Powell
in organic chemists and inorganic chemists
and biologists and theoreticians who are all
doing their own thing, shake it all up, and see
what happens.” To ensure a fertile mixing of
knowledge and expertise amongst Foundry
researchers, “interaction was a big theme
with the facility from the design on up,”
states building manager Joe Harkins. “We’ve
tried to make areas where paths will cross,
that are nice places to aggregate…where
people will stay and exchange ideas.”
True to this vision, coffee lounges are no
longer traditionally dismal, fluorescent-lit base-
ment affairs. Instead, the architects capitalized
on the building’s commanding hilltop views
of the East Bay, installing kitchenettes, reading
lounges, offices, and meeting rooms along the
scenic western face of the building.
But appeasing scientists who want some-
place scenic to imbibe caffeine is relatively
simple. Far more challenging is meeting the
technical and environmental requirements
of a facility that houses agonizingly precise
nanotechnological research. The minute ef-
fects of particulates in the air, imperceptible
vibrations, or even ambient electromagnetic
(EM) fields can disrupt research conduct-
ed on the scale of individual molecules. As
Bustillo points out, “One dust particle or
dandruff flake is a huge boulder compared
Photo by Tracy Powell
to the features that we’re [working with],”
and the tunneling electron microscope in a
neighboring building is reportedly sensitive
enough to record the impact of waves on the
shore miles away.
To insulate delicate instruments from
stray vibrations caused by ocean waves,
street traffic, or other environmental
sources, the Foundry’s first two floors are
21
FEATURE Foundations for Excellence
underground, surrounded by thick retaining
walls tied directly into the foundation slab.
Commenting on the eerie silence of the
lower levels, Bustillo elaborates, “All of the
pumps, all the compressors…all those things
that hum in the basement of every building
on campus—we don’t have them here.” In-
stead, basic mechanical support equipment is
housed in a separate two-story, underground
facility connected to the Foundry via a flex-
ible foamboard accordion joint that pre-
vents transmission of any vibration. Layers of
acoustic insulation paneling along the walls of
underground labs add another protective el-
ement; conversations held in the dead silence
of these basement cells sound flat and muf-
fled, robbed of the slightest reverberation.
Despite these precautions against vibra-
tion, tiny fluctuations in EM fields can also
cause trouble. For instance, says Harkins,
“even the mass of the elevator’s counter-
weight moving through the earth’s magnetic
field creates an electromagnetic disturbance
that can be problematic.” In one case, it was
a simple matter to locate the lab housing a
sensitive scanning tunneling electron micro-
scope in the center of the building, as far
away from the two elevator shafts as pos-
sible. (Researchers later decided the micro-
scope would fit better in a larger room, ten
feet closer to one of the elevator shafts. It’s
not yet clear whether additional shielding
against the elevator’s counterweight will have
to be installed.)
Other architectural tricks to minimize
unwanted EM fields are more subtle. For
instance, even when sheathed in concrete,
a building’s reinforcing steel can channel
enough ground current to disrupt sensitive
instruments. For the Foundry’s first three
floors, which house such instruments, the ar-
chitects therefore used special epoxy-coated
steel to prevent EM conduction. Directly un-
der the most sensitive equipment, the rebar
22
was replaced entirely with fiberglass rein-
forcing bars. Additionally, instead of standard
AC electrical wiring, which carries electrical
current in a single phase with a strong back-
ground signature that may show up in sensi-
tive nanoscale measurements, the architects
installed multiphase wires.These split the same
electrical current into three staggered phases,
minimizing EM “noise.” Pairs of multiphase
electrical wires were then twisted around one
another during installation, further minimizing
electromagnetic interference.
“We didn’t want to build an-
other Evans monstrosity.”
While these elaborate measures provide
the Foundry’s electron microscopes with op-
timal working conditions, a series of special
rooms on the second floor protects against
another hazard: particulate matter. Paint
flakes, bacteria, worn particles from tools or
instruments—all can disrupt nanoscale ma-
terials. As Harkins points out, however, “The
biggest contaminant in a clean room is the
people you put in there.” According to indus-
try sources, a single person sitting motionless
sheds enough skin, hair, and liquid droplets
to produce 100,000 microscopic particles
each minute; by moving around, the number
jumps to 5,000,000 particles per minute. (It’s
best not to contemplate what happens if this
hypothetical person sneezes.) Encasing re-
searchers in puffy white “bunny suits” helps
to minimize the blizzard of tiny particulates,
but it’s only part of the solution.
To scrub minute debris from the en-
vironment, the Foundry boasts a Class-100
clean room, which ensures that each cubic
foot of air has fewer than 100 particles larger
than 0.5 microns. Encased in glass and vis-
ible from the hallway through large bay win-
dows, this ultra-clean nanofabrication room
uses approximately 150 filter units to clean
and circulate air. But cleanliness comes at a
price: All those hard-working fans and filters
vibrate, disrupting sensitive equipment. Each
filter unit was therefore designed so its activ-
ity can be individually, temporarily dampened
while sensitive fabrication functions are un-
derway, then reactivated when these delicate
processes are complete.
For the truly meticulous scientist, a sec-
ond, even more stringent clean room is nest-
ed inside the first, permitting only ten 0.5-
micron particles per cubic foot of air. Built
specifically to house the Foundry’s electron
beam lithography system, which can print
features 10,000 times smaller than a human
hair, this Class-10 clean room also permits
exquisite control over humidity and tem-
perature, which can be maintained to within
0.1° F of a given target.
Above this suite of ultra-clean nanofab-
rication rooms, spacious laboratory, comput-
ing, and office areas fill the four upper levels
of the Foundry, which project out over the sur-
rounding hillside. (In this, the building embod-
ies faith in science beyond a multimillion dollar
investment: You have to really trust modern
seismic technology to sit atop the Hayward
Fault, calmly thumbing through Nature, while
cantilevered out over the edge of a cliff.)
When asked how the cantilevered lay-
out figured into the building’s design, Bustillo
laughingly recalls that “one of the premiere
characterization instruments for a nano-
technologist is an atomic force microscope
(AFM), the [essence] of which is a little sili-
con cantilever tip.The architects claimed that
the grand scheme design for this building was
symbolic of a gigantic AFM tip.” According to
Harkins, they also described the Foundry as
“a bridge to the campus and beyond.”
When a building inspires that many
overheated architectural metaphors, the

designers have probably been successful on
some level. But architecture isn’t the only
standard of success; ultimately, Bustillo as-
serts,“we’ll be measured by the quality of the
science that we do, the number of satisfied us-
ers that we have, and how nanotechnology is im-
pacting the economy.” Only time can prove the
Molecular Foundry a success on these terms.
Meanwhile, members of the LBL community can
settle into their new research space—a luxury
their on-campus colleagues, impatiently awaiting
completion of the cutting-edge Stanley Hall, are
anxious to enjoy.
Stanley 2.0
A combination of seismic instability and
outdated facilities led to the demolition of
the old Stanley Hall in 2003. Now, its copper-
tiled successor has finally been erected on
the same site as the original, near UC Berke-
ley’s East Gate. At 11 stories and 285,000
gross square feet—more than four times
larger than its predecessor—the new facility
represents a significant increase in modern
research space on campus. (So modern, in
fact, that with 6,000 control points—includ-
ing temperature sensors, alarms, and other
electronic and mechanical controls—Stanley
Hall alone accounts for a 20 percent increase
in control points on campus.)
Though the building is massive, much
of its bulk is distributed in three basement
levels; as a result, its silhouette hugs the hill-
side rather than towering over eastern cam-
pus. “We didn’t want to build another Evans
monstrosity,” says Susan Marqusee, professor
of molecular and cell biology and lead faculty
advisor throughout the building’s design and
construction. “It had to be beautiful, and we
didn’t want to give a sense of it being too
huge, too monolithic.”
Though effectively disguised from pass-
ersby, the building’s large size is necessary to
fulfill several functions. These include harbor-
ing six scientific core facilities that will serve
the campus community: mass spectrometry,
protein purification, functional genomics,
proteomics, nuclear magnetic resonance
(NMR) imaging, and a new biomolecular
nanotechnology fabrication center: Stanley
will also contain teaching laboratories, class-
rooms, and lecture halls that together will
accommodate up to 450 students. The build-
ing’s principal role, however, will be to house
the laboratories of 36 faculty members who
participate in the California Institute for
Quantitative Biomedical Research (QB3), a
cross-disciplinary organization intended to
Foundations for Excellence
spur collaboration between quantitative and
biomedical researchers.
As host to QB3, the building’s central
purpose is, like the Foundry, to foster inter-
actions between disparate scientific disci-
plines—in Stanley’s case bridging computa-
tional biology, tissue engineering, chemistry,
physics, and molecular and cellular biology.
FEATURE
Marqusee explains, “We were looking for
much more than just cohabitation—we
wanted to foster active collaboration.” To
enable these interactions, the architects in-
stalled social areas (“workrooms”) on every
floor, each complete with kitchen, computer
stations, cubicles, and whiteboard walls for
spur-of-the-moment, cross-disciplinary brain-
storming sessions. An on-site café just outside
the building’s main entryway will offer anoth-
er venue for impromptu discussions.
But beyond these social areas, Stanley’s
architects had a subtler strategy to promote
interaction: The laboratories were designed
with an emphasis on common space, placing
freezers, centrifuges, tissue culture rooms,
and other equipment in central areas away
Drawing by ZGF Partnership architects & artist Al Foerster.
from individual labs. Harry Stark, QB3’s facili-
ties and engineering director, explains, “You
give people a home, but you don’t make the
home complete, so that they need to go out
into the neighborhood in order to get their
job done. By being in the neighborhood they
bump into each other, work with each other, Facing page: Because certain wave-
communicate, and develop ideas that they lengths of light can damage photosensi-
tive materials inside, only yellow light is
might otherwise not have.” used inside clean rooms at the Molecular
This mischievous sense that scientists Foundry (left). Brand-new glove boxes,
which allow researchers to manipulate
need firm architectural prompting before experiments in an oxygen-controlled
they’ll venture forth to socialize pervades atmosphere, await use in the Molecular
Foundry (center). Snorkel exhaust fans
the designs of both Stanley and the Molecu- will act as flexible fume hoods in Stanley
lar Foundry. But do Berkeley researchers re- Hall (right). Above: An artist’s rendition
of Stanley Hall’s finished façade (top);
ally need this sort of prodding? Judging from Stanley’s current appearance (center).
the enthusiasm of Stanley’s future residents, A view from an “interaction room” at
the Molecular Foundry (bottom).
they do not. Dan Fletcher, a bioengineering
professor who will work in the new building,
asserts that “the collaborative atmosphere
is going to be very exciting…. I’m a strong
believer in proximity being a real motivator
for research, and I look forward to interact-
All photos by Tracy Powell
ing with colleagues on a much more regular
basis.” Marqusee concurs, stating, “Stanley
should create a new intellectual environ-
ment, and everyone is excited to strike up
collaborations that wouldn’t have happened
without the building.”
This enthusiasm will serve Stanley’s new
residents well, given that they will have an
extra motive to talk science with their col-
leagues: The University plans to make the
building available for outside conferences
23

FEATURE Foundations for Excellence
and meetings for part of each year. “Normal-
ly,” says Stark, “general assignment classrooms
are used year-round, so if someone wants to
All photos by Tracy Powell
have a professional conference, they can’t do
anything on campus because they don’t know
two years in advance if a room will be avail-
able.” To ease this situation, the registrar has
opted not to schedule classes in Stanley dur-
ing the summer, leaving it available for meet-
ings and symposia.
Indeed, the four-story, windowed atrium
just inside the main entrance has ample space
for poster sessions, breakout groups, or re-
ceptions after talks in the large lecture halls.
Between such special events, the entry hall’s
lofty skylights, tiered balconies, and modernist
glass chandeliers will provide an attractive hub
to the bustling building, which will eventually
house as many as 700 full-time workers. Merci-
fully, Stanley’s designers avoided the spiral-stair-
case-as-DNA motif that has become so mo-
notonously common in science building lobbies
of the past few decades. Instead, the atrium will
be graced by a series of works by contempo-
rary artist Sarah Sze in glassed recesses.
But for many researchers on campus,
these architectural niceties are beside the
point; they just want a laboratory to call
home. In a process reminiscent of sliding
block puzzles, where mobile squares are end-
lessly toggled into a single free space, faculty
members displaced from the original Stanley
(or newly arrived since its demolition) have
been shuffled around campus for years while
the new building is completed.
As Fletcher, hired four years ago in an-
ticipation of the completed QB3 facility, diplo-
matically phrases it, “We have had the oppor-
tunity to experience several of the campus’s
facilities.” Some of these proved more hospi-
table than others—at one point his lab was
housed, briefly, next to the civil engineering
department’s concrete testing facility, which
posed “some vibration issues” for the lab’s
high-resolution microscopy experiments. Re-
location to O’Brien Hall brought respite from
24
quivering concrete slabs, but Fletcher’s atomic
force microscope and suite of sensitive optical
equipment ultimately require modern, low-
vibration facilities for optimal performance.
The new Stanley’s low-vibration facilities will
therefore provide a welcome haven from the
noise of a busy campus.
As previously noted by Chancellor Birge-
neau (see BSR, Spring 2005), the lack of cut-
ting-edge facilities on campus has sometimes
hampered research efforts by scientists like
Fletcher. In part to address this problem, Stan-
ley Hall will introduce several new high-tech
features to campus. In particular, the lowest
basement level is anchored to bedrock, which,
along with antivibration shielding of mechani-
cal equipment, provides an exceptionally stable
substrate for delicate equipment. Two EM-
shielded slabs in the deepest portion of the
building are isolated from the rest of the build-
ing via flexible joints, providing an even more
sheltered environment (one of these slabs will
house Fletcher’s sensitive optics equipment).
Also found on Stanley’s lower levels is
the Central California Ultra High Field Nucle-
ar Magnetic Resonance (NMR) Imaging Facil-
ity—a huge, vaulted basement chamber nearly
as impressive as its name. Of the twelve NMR
machines to be installed there, several will be
shifted from other campus locations. Their
magnets range in strength from 150–700 MHz,
but a brand new, 900 MHz shielded NMR (one
of only 10–12 in the world) has also been
ordered. Accommodating this equipment re-
quires a large facility because the magnets are
far too massive to fit the confines of a stan-
dard floor. The powerful magnetic fields they
generate can also be a health hazard to any-
one with a medical implant; the vaulted ceiling
therefore provides enough vertical space to
buffer the upper floors from the magnets.
In addition to the NMR suite, another
new facility making its campus debut will be
the Biomolecular Nanotechnology Fabrica-
tion Center (BNC).The BNC, a series of clean
rooms equipped with equipment for generat-
Construction on Stanley
Hall nears completion (left).
A view of Stanley’s façade,
including the pavilion that
will house a coffee stand
(right).
ing minute devices and materials, will allow
manufacture of nanoscale tools for studying
the behavior of cells and molecules. The facili-
ty will share many capabilities with Cory Hall’s
Microfabrication Laboratory, but with one vi-
tal difference: the BNC will permit biological
materials, generally considered a contaminant
in traditional microfabrication facilities. This
will allow Stanley’s researchers to apply na-
noscale sensors and other fabricated materi-
als to biological systems.
Fortunately, Fletcher, Marqusee, and their
fellow researchers won’t have long to wait
for all of these new facilities. In an elaborately
choreographed migration, the first of Stanley’s
new occupants will arrive at their new home
in March 2007. Rather than contend with
hundreds of scientists stampeding into the
building (“Just cut the ribbon and everybody
runs!” quips Fletcher), different labs will arrive
in staggered shifts over subsequent months.
Final landscaping, including restoration of the
reflecting pool currently buried under por-
table construction trailers, should then be
completed by October 2007.
And for many, it’s about time. After being
blighted by years of construction (neighbor-
ing Hearst Mining Hall underwent a three-
year seismic retrofit shortly before Stanley
was demolished), Hearst Mining Circle could
do with a return to pastoral calm. Hopefully, Stan-
ley’s researchers will conclude that their new
home was worth the tumult, and the wait.
Tracy Powell is a graduate student in plant and
microbial biology.
Want to know more?
http://foundry.lbl.gov/index.html
http://qb3.org/stanleyfactsheet.htm
 Where the Wild
Things Are
H
igh above the treeline in the Tahoe
Basin’s Desolation Wilderness, Sean
Schoville crosses the snowfields,
braced against the cold. Armed with a high-
powered headlamp and insect-collecting vials,
he sweeps the snowy surface ahead searching
for beetles, as he’d done countless times be-
fore. But on this particular night, under the
moonless sky, he sees something different: an
insect, larger than any of his beetles, racing
across the snow ahead of him with astound-
ing speed. Golden and flat-bodied, with long
antennae, this is something unusual.
A rare new species?
Schoville, a graduate student in the
department of environmental science, policy,
and management (ESPM), knew immediately
that the insect belonged to a group called the
ice crawlers, members of a small order called
the Grylloblattodea. Rare and endemic to
high alpine terrain, they hunt the snowfields
at night, searching for insects blown in from
lower elevations and frozen in the snow. He
transported the ice crawler back to the lab,
attempting to determine how long it has been
isolated from other known populations. Thus
far, the data suggest that this individual, and
others Schoville has since found in the White
Mountains on the California-Nevada border,
are members of a very distinct population of
Grylloblattids, perhaps even a new species.
Species discovery rings of a bygone
era, when the likes of Charles Darwin set
course for distant lands and shipped home
proof of strange new creatures in the form
of pelts, sketches, and bones. Biologists by
trade, these men were also intrepid explor-
ers and globetrotters, and the creatures they
found were named for exotic locations of
Berkeley Critters
FEATURE
Photo Courtesy of Dan Rubinoff
Rare and found only in remote alpine terrain, this in-
sect, found by ESPM graduate student Sean Schoville,
may be a new species of ice crawler.
origin. Today, the quest for new organisms
continues, and modern-day incarnations of
Darwin exist right under our noses. Wellman
Hall and the Valley Life Sciences Building
are home base for such heroes: UC Berkeley
biologists who travel far and wide to engage
in scientific study, discovering new species in
the process.
In the field of entomology, species dis-
covery is often secondary to broader scientific
queries into evolution, ecology, behavior, and
biosystematics. For example, Schoville’s study
of the ice crawlers will focus on whether
their diversity and distribution is linked to
glacial history. Likewise, Matt Madeiros, a
graduate student in integrative biology, has
discovered several new species in the process
of investigating the evolution of flightlessness
in cave-dwelling moths. Some insect labs,
however, survey remote areas specifically
25
 Berkeley Critters

Nomenclature
When you discover a new species, you don’t get to name it—first you must describe it. To assist
you, there’s a big book of rules. The International Code of Zoological Nomenclature is a set of rules
in zoology that has one fundamental aim: to provide the maximum universality and continuity in
the naming of all animals according to taxonomic judgment. The code is meant to guide only the
nomenclature of animals, while still leaving zoologists some degree of freedom in classifying new
species and higher-level taxa. In other words, whether a species itself is or is not a real entity is a
FEATURE

subjective decision, but what name should be applied to it is not. Regarding naming after yourself: It’s
not a hard and fast rule, but some consider it poor form to bestow a new species with your name.
Better to name it so it tells something about where it lives, what it feeds on, and how it looks.

Present knowledge of these species is meager. “What qualifies as different

Humans have named 1.5-1.8 million species
to date, but only 1 percent of those have been
studied in any detail beyond basic character-
ization of habitat and anatomical features.
Discoveries of larger organisms like mammals
or birds still occur today, but they are rare.
Most new species discovered are of a smaller
ilk: fungi, bacteria, and insects. Meanwhile,
species are going extinct in record numbers,
and researchers are desperate to identify and
study novel species before they disappear for
Photo Couresy of Sean Schoville
enough?”
Determining whether a newly-discov-
ered specimen is truly a novel species is
not always easy. In the opening scene of the
movie Arachnophobia, a group of scientists
travel to a remote corner of a rainforest in
Peru: A spider falls out of a tree, and they
exclaim, “We found a new species!” Steve
Lew, a PhD student in the Will lab of ESPM,
smiles at this portrayal. “In reality, you fog
a tree in the Amazon and large numbers of

good. spiders fall out, many of which are probably

Integrative Biology graduate student
Matt Madeiros is happy to explore this
cave in his studies on the evolution of
flightless moths.
for the purpose of uncovering new species.
Recently, the Roderick and Gillespie labs in
ESPM have won grants to survey the Society
Islands near Tahiti, while Elizabeth Arias, a
postdoctoral researcher in the Gillespie lab,
Photo Couresy of Pete Oboyski
Though many new species are found in
remote places, some stories run counter to
the image of the lonely scientist far afield in
mudboots. Pete Oboyski tells one such story.
An ESPM PhD student, he studies a Hawai-
ian moth genus called Cydia, brownish-grey
moths whose larvae might be the worm you
see when you bite into an apple. To date,
Oboyski has discovered four new species of
Cydia. While working in the low elevations
of Kuaui, often dismissed by ecologists as too
degraded by humans for species discovery,
Oboyski stopped one night along the side
of a highway. As cars drove by, he set up his
moth collecting apparatus, a sheet with an
ultraviolet light attached, stringing one end to
a telephone pole and the other to a speed limit
sign. “I thought I’d have no chance,” Oboyski
said. “Imagine my surprise when within five
minutes, a new species showed up.”
ESPM graduate student Pete Oboyski has identified sev-
eral new moth species within the Hawaiian Cydia genus.
new to science. But you’re not going to know
for a long time.” The process of classifying
the individuals can be time-intensive—days
at the microscope, and weeks poring through
books and consulting experts. “There are
thousands of spiders that are new to science
sitting in jars in entomology collections
around the world, and most of them are go-
ing to stay undescribed for a while,” says Lew.
“At this point, I don’t even know how many
new species I’ve found in California.”
Further complicating matters, our no-
tions of what exactly constitutes a new spe-
cies continue to evolve. Traditionally, species
were defined as organisms that would not or
could not mate with one another to produce
fertile offspring. But this definition is not
particularly useful for species that reproduce
asexually (like fungi), or that are capable of
crossing species boundaries to breed and
form hybrids (like oak trees). Dogma also
once held that a new species would look
physically different from any other, even if
the differences were very subtle.

has received a grant to search for new organ- Now, advances in molecular biology have
isms in Chile. challenged these conventional views. Recent
research has shown that even when there
Uncharted biodiversity are no apparent morphological differences
Scientists estimate the total number of between two groups of organisms, there can
species on Earth to be around 9 to 20 million, still be molecular or behavioral differences
although the oft-cited broader range of 3 to that have great importance. These invisible
112 million better illustrates the uncertainty. differences can prevent the individuals from

26
Snail-eater

recognizing each other as mates—a key
step in the speciation process. It is unclear,
however, whether such populations qualify
as separate species. While the availability
of inexpensive DNA sequencing has made
it easier to compare potentially new species
with existing ones at the level of the genome,
Berkeley Critters
far beyond the tropics. The Bay Area native
Xerces Blue butterfly (Glaucophyche xerces),
for instance, was last seen in 1943, and is
the first butterfly in North America known to
have gone extinct due to human disturbance.
A former inhabitant of the vast sand dunes of
San Francisco, its habitat was almost entirely

there is now frequent controversy over how
much of a difference is required to draw the
species line. Oboyski cautions, “Though it
looked like the molecular revolution was go-
ing to solve our problems, we’ve now realized
that we’re still faced with questions. What
qualifies as different enough? We still have to
interpret the results.”
Get ‘em before they’re gone…
While scientists navigate the taxonomic
jungle of species identification, the urgent
need for discovery becomes all the more
clear. Species continue to go extinct in record
numbers: according to the World Resources
Institute, 100 species go extinct each day
(four every hour) due to tropical deforesta-
tion alone. Moreover, species loss extends
FEATURE
destroyed by urban development. Schoville’s
ice crawlers may represent a species whose
future is uncertain; under certain climate
change scenarios, much of California’s glacier
and snowpack is threatened. Hopefully,
Berkeley scientists will continue to unearth
new species in their quest for answers
about evolution, animal behavior, and ecol-
ogy—before the subjects they need disappear
for good.
Letty Brown is a graduate student in environ-
mental science, policy and management.
Want to know more? Check out:
The International Code of Zoological No-
menclature: www.iczn.com

Photos Courtesy of Dan Rubinoff

If it’s not a new species, it’s a new trait. Dan
Rubinoff, a professor at the University of
Hawaii (who holds his undergraduate, masters,
and doctoral degrees from UC Berkeley) and
members of his lab have discovered several species
of carnivorous caterpillars. Another Hawaiian
caterpillar, Hyposmocoma molluscivora has evolved
a novel trait: It hunts snails. In the July 2005 issue
of Science, Rubinoff describes how the caterpillar
captures its prey. Once it finds a resting snail, the
caterpillar spins a web of silk from the snail shell
to the leaf to capture and immobilize the snail.
Then it sidles up next to the trapped snail and
pursues it down the shell, Rubinoff says, literally
eating it “out of house and home.” There have
been other examples of specialized predatory
behavior in Hawaiian Lepidoptera larvae, but these
new species represent the first time a carnivorous
caterpillar has eaten anything outside its own
phylum. It is also the first case of a caterpillar using
its silk to capture prey.

27
Strung Out at Berkeley

Strung Out at Berkeley

FEATURE

by Meredith Carpenter

“From a drop of water…a logician could infer the

possibility of an Atlantic or a Niagara without having
seen or heard of one or the other. So all life is a great
chain, the nature of which is known whenever we are
shown a single link of it.”—Sir Arthur Conan Doyle

Graphic by Jennifer Bensadoun

W hat exactly are we made of? Depending on whom you ask at UC Berkeley, answers to this question could range
from “cells” (a biologist) to “atoms” (a chemist) to “I am large, I contain multitudes” (an English professor). But
ask a physicist, and you may just get the strangest answer yet: “one-dimensional vibrating strings.” Indeed, many
physicists today believe that these strings are actually the most fundamental constituents of the universe. They make up
the subatomic particles that make up the atoms that make up our bodies—and everything else in the world. Much of
the research in theoretical physics today revolves around “string theory” because of the promise it holds for explaining
everything from the foundations of matter itself to the origins of the universe. Physicists and mathematicians here at UC
Berkeley are on the cutting edge of this exploration into what has been called the “theory of everything,” studying topics
ranging from exotic types of black holes to why the universe happens to have just the right properties to sustain life.

28

It’s all relative
To understand where string theory is
going, we must first take a whirlwind tour
of the last hundred years of physics to un-
derstand where it came from. In 1905, Albert
Einstein proposed his groundbreaking theory
of special relativity. This theory contradicted
Isaac Newton’s notions of absolute space and
time—which were the paradigm in physics
for hundreds of years—by proposing that
time and space are ever-changing constructs
that are perceived differently depending on
the observer. These effects are not noticed in
everyday experience (which is why Newton’s
equations can still accurately describe how
fast a ball will roll down a ramp), but they
come into play more and more as objects ap-
proach the speed of light. Although it seems
contrary to the way we experience the world,
FORCES: Gravitational
Graphic by Meredith Carpenter
Particles experiencing:
Boson mediating:
Results in:
Fundamental forces of physics and the bosons that carry them. *Gravitons are hypothetical particles, and have not yet been observed.
an astronaut traveling in space would age
more slowly than his twin brother on Earth
because his high velocity influences the pas-
sage of time.
Special relativity was a monumental
achievement, but it had one problem: It did
not account for gravity. It took Einstein 10
more years to formulate his theory of general
relativity, which extended special relativity
to include gravity with another earthshaking
insight: Gravitation is not due to a force but
rather to the curving of space and time. For
mathematical purposes, physicists combine
the three dimensions of space and the fourth
dimension of time into a structure called
spacetime, which is often envisaged as a
stretched-out fabric. If a planet is “sitting” on
this fabric, it curves spacetime much like a
bowling ball resting on a trampoline. Moons
and planets stay in orbit because they are
trapped in the curved region of spacetime
that results from the more massive planet
or sun. As the famous American physicist
John Wheeler explained, “Spacetime grips
mass, telling it how to move, and mass grips
spacetime, telling it how to curve.”
Quantum leap
Einstein’s union of special relativity and
gravity in the theory of general relativity
works extremely well on the large size scales
of celestial bodies and the universe, but things
started to get very fishy when researchers
such as Max Planck, Werner Heisenberg,
and Erwin Schrödinger studied interactions
on smaller scales. The discovery that waves
could be measured in small packets of energy
called “quanta” led to the branch of phys-
ics known as quantum mechanics, which
describes the behavior of matter on the ex-
tremely small atomic and sub-atomic scales.
This is a strange world, where photons, the
constituents of light, have both particle-like
Weak Electromagnetic
All Quarks, Leptons
Graviton* W, Z Bosons
Gravity Radioactive decay
and wave-like properties; where Heisenberg’s
uncertainty principle states that one can
never simultaneously measure both the posi-
tion and the momentum of a subatomic par-
ticle with perfect accuracy because the act of
measurement itself makes the measurements
uncertain; and where two spatially separated
particles can be “entangled” such that their
physical properties are always correlated (this
If an atom were magnified
to the size of the solar
system, a string would be
the size of a tree.
would be like the astronaut twins always
knowing what the other is doing even when
one is in space and the other on Earth). The
landscape of the universe at the quantum
level is also quite bizarre: At such small scales
of time and space, the uncertainty principle
Strung Out at Berkeley
allows pairs of particles (matter and antimat-
ter) to briefly come into existence and then
annihilate each other again, all within the
blink of an eye. Consequently, spacetime in
this realm is often referred to as a “quantum
foam” and pictured as a turbulent, stormy sea
in which our everyday laws of physics need
not apply.
FEATURE
Despite the oddness of the universe
at the quantum level, research in quantum
mechanics has led to the development of the
Standard Model of particle physics, which
describes both the fundamental particles
and three of the four fundamental forces that
exist in nature. The particles come in two
basic sorts: fermions and bosons. Fermions
such as electrons and quarks make up all
matter, while bosons are the carriers of the
four fundamental forces in nature: the strong
Strong
Electrically charged Quarks, gluons
Photon Gluons
Electricity/magnetism Nuclei held together
force, the weak force, and the familiar elec-
tromagnetic and gravitational forces. Every
observed physical phenomenon, from the
birth of a star to the magnet sticking to your
refrigerator, can be explained by these inter-
actions. The strong force holds the nucleus
of an atom together; conversely, the weak
force (named as such because it is some 1013
times weaker than the strong force) causes
the radioactive decay of certain nuclei. The
electromagnetic force is responsible for what
we recognize as electric and magnetic fields
(including visible light), and the gravitational
force causes—surprise!—gravity.
The Standard Model accounts for three
of these forces by positing the existence of
force carrier particles: The gluon mediates the
strong force, thus gluing the nucleus together,
W and Z bosons mediate the weak force, and
photons mediate the electromagnetic force.
Consequently, two particles in a nucleus
do not interact directly, but via force carrier
particles (gluons, in this case) that keep them
from getting too far away from each other.
29
Strung Out at Berkeley
Importantly, the Standard Model does not
describe the gravitational force, though it has
been hypothesized that particles called gravi-
tons are its force carriers. The problem is that
FEATURE
gravity is much, much weaker than
the other three forces (1025 times
weaker than the weak force) and
therefore it is much more difficult
to study on a small scale, despite
the fact that its infinite range allows
it to have significant effects in the
universe.
Einstein, we have a
problem
Starting in the 1970s, theoreti-
cal physics found itself in a bit of a
predicament. “The main problem
is that Einstein’s general relativity,
while it is very successful as a theory
describing the motions of stars and
the motions of planets, is very hard
to combine with quantum mechan-
ics,” says Ori Ganor, Associate Professor of
Physics at UC Berkeley. Every time anyone
tried to mathematically combine the two
theories, the result was infinities, a sure sign
that something in the equation is wrong. In
order to describe gravity on a quantum level,
physics needed a unified theory of quantum
gravity, one that combined Einstein’s general
relativity with the Standard Model. And un-
derstanding gravity at small scales and high
energies is particularly important for address-
ing problems such as what happened during
the first moments of the Big Bang. Raphael
Bousso, Associate Professor of Physics at UC
Berkeley, explains: “We’re all after quantum
gravity. These are questions that really matter
if you want to know how the universe started
and what happens in a black hole.” The quest
for the underlying coherence of the universe
in the form of a theory of quantum gravity
has become a holy grail in physics, drawing
researchers in both mathematics and physics
to crusade on its behalf.
30
The string’s the thing Model. Strings can also split and combine,
Enter string theory, today the most which would appear as particles emitting and
viable and widely accepted, though con- absorbing other particles, thus giving rise to
troversial, theory of quantum gravity. It the known interactions between particles—
proposes that the most the fundamental forces. Hence, string theory
fundamental constitu- provides a single explanatory framework that
ents of the universe are embraces all forces and all matter.
not zero-dimensional But string theory has even stranger
point particles, as has consequences. The theory as it stands today
been believed since predicts that our universe contains a total
the time of the Greeks, of 10 or 11 dimensions, depending on the
but one-dimensional formulation of the theory (that’s six or seven
strings. These strings more than the four we observe). Where are
are indivisible, meaning these extra dimensions? Many physicists
they are not made out of believe they’re all around you, curled up
anything smaller, they so small that you could never detect them.
just…are. In equations, It is extremely difficult, if not impossible,
these strings help to even to fully comprehend this concept, even for
out the “foamy” quan- physicists themselves. A common approach
is to picture an ant crawling along
the length of a garden hose. An
observer looking at the hose from
afar can only see one dimension
of the hose, the left-right dimen-
sion. But if the ant crawls down
the side of the hose, it seems to
disappear to the observer, who is
unable to see this smaller, curled-
up dimension. The extra dimen-
sions are important to the theory
in part because they allow the
strings to vibrate in many more
patterns, determining the proper-
ties of the elementary particles.
Furthermore, string theory pre-
dicts the existence of objects such
as two-dimensional membranes
Photos by Anne Peattie (top) and Meredith Carpenter (middle and bottom)
tum landscape such that
general relativity—which
treats spacetime like a
smooth fabric—can apply.
The strings are extremely
small: roughly the size of
the Planck length, which
is 10-35 meters. Or, put
another way, if an atom
were magnified to the
size of the solar system, a
string would be the size of
a tree. As a result, strings
would appear point-like
when studied at the scales
we can access by experi-
mentation. In addition,
the strings can vibrate in First string for UC Berkeley: (top) Associate Professor of Physics Ori Ganor
different patterns, much studies the strange properties of string theory geometry. (middle) Associate
like the notes on a guitar, Professor of Physics Raphael Bousso investigates quantum gravity and other
resulting in the diverse properties of the universe. (bottom) Postdoctoral researcher Eric Gimon
fundamental “particles” studies black holes using string theory equations.
found in the Standard

Image by Ute Kraus/Tempolimit Lichtgecshwindigkeit
A simulated panoramic view of the Milky Way as it might appear near the event horizon of a black hole.This view is from a “camera” positioned 600 kilometers from a black
hole ten times as massive as the sun.
and “branes” of even higher dimensions.
These branes are just as basic as the strings
themselves, but the higher-dimensional
branes open up even more possibilities for
explaining the physical properties of the
universe.
Additionally, what has been called string
theory in the past 30 years is sometimes more
accurately called superstring theory because
it incorporates the phenomenon of “super-
symmetry.” Supersymmetry requires that, for
every fundamental fermion, there must also
exist a bosonic superpartner, and vice versa.
No superpartners have been observed so far,
but physicists hope that’s just because exist-
ing particle accelerators are not yet powerful
enough to produce these massive particles.
So is there any experimental evidence
for string theory? With all this talk of invis-
ible extra dimensions and vibrating strings,
why are physicists so convinced that they’re
on the right track? In fact, right now there is
no way to test the predictions of string theory
experimentally, and “in some ways, because
it’s not testable, it’s not a theory, it’s a model,”
says Eric Gimon, a postdoctoral researcher in
physics. Although particle accelerators like
the Stanford Linear Accelerator have detected
and characterized most of the particles of the
Standard Model, “the problem is that what
we do in our best accelerators is pretty much
at the limit of current technology, and yet
far away from what we’d need for quantum
gravity,” says Bousso. Some physicists are
optimistic that the Large Hadron Collider
currently being built at CERN in Switzerland
may provide evidence of a graviton or the su-
perpartner of some known particle, thereby
supporting the structure of string theory as it
stands today. However, even if the experimen-
tal evidence does not pan out, string theory
“is not a theory where ‘everything goes.’ It
actually has a very complicated set of tools
to verify if the things we’re coming up with
Strung Out at Berkeley
FEATURE
are consistent,” explains Ganor. Because the
theory is so constrained, “you can’t just put in
a new ingredient—you have to discover it in
the structure,” says Bousso. Thus, guided by
mathematics, string theorists can still make
meaningful contributions to the theory even
without direct experimental support.
Strings on Sproul and branes by
the Bay
Nevertheless, science isn’t science
without experimentation, so many string
theorists, including those here at UC Berkeley,
are turning to cosmology for experimental
verification of the theory. Because string
theory was originally invoked to explain what
occurs at very small distances and very high
energies, the circumstances in which general
relativity breaks down, its effects come into
play most significantly under two conditions:
at the beginning of the universe and inside a
black hole. Before the big bang, everything
31
Strung Out at Berkeley
in the universe was collapsed together in a
“singularity” of infinitely small proportions;
similarly, everything that enters a black hole
crosses the “event horizon” to reach its singu-
larity, from which not even light can escape.
In both cases, neither general relativity nor
quantum mechanics is able to explain exactly
how the singularity originates and what takes
FEATURE
place within the event horizon of a black hole.
Postdoctoral researcher Eric Gimon studies
the physics of black holes—which turn out to
be relatively common in the universe—using
the equations of string theory. In particular, he
investigates special types of black holes that
preserve supersymmetry, where particles and
their twin superpartners have the same mass.
This preservation of supersymmetry, though
not necessarily found in real black holes, is
important because it makes the equations
describing the physics at the event horizon
much easier to calculate. “We use these toy
model black holes to work out the implica-
tions of quantum gravity,” says Gimon.
Ultimately, physicists want to under-
stand more about the information content
of black holes, which turns out to be closely
related to the concept of entropy. Entropy
can be thought of as the number of different
possible configurations of a system, such as
the arrangement of air molecules in the room
in which you’re sitting. For ordinary objects,
entropy is proportional to the volume of a
space—there are more possible arrangements
of air molecules in a bigger room. However,
the well-known physicist Stephen Hawking
found that for black holes, entropy is not pro-
portional to three-dimensional volume but
rather to a two-dimensional area. In this case,
the area is the area of the event horizon—the
surface around a black hole past which noth-
ing can escape the hole’s gravity. This was
surprising to physicists, particularly when
Bousso and other researchers discovered
that this is a general property of quantum
gravity, now called the holographic principle.
Like a hologram, quantum gravity is able to
describe three-dimensional geometry with
only two-dimensions’ worth of information.
In other words, it could describe all of the
32
air molecules in the room by only taking into
account what’s happening on the walls of the
room; the volume is just an illusion. Now,
Bousso says, physics must explain “why there
is much less information in the world than
you might think.”
In addition to his work on the holo-
graphic principle, Bousso investigates another
big question in physics today: why are the
“There’s nothing sacred
about the mass of the
electron.”
properties of our universe what they are, and
why do they happen to be exactly right for
sustaining life as we know it? Even with the
sophisticated equations of modern physics,
“there’s nothing that forces you to have a cer-
tain number of fundamental particles, or to
make the masses of particles what they are,”
says Bousso. According to Bousso and others,
this problem can be resolved by picturing
the universe as a landscape rather than a
uniform field. “The Standard Model, we now
understand, is a pretty random complicated
thing that got thrown together in one part of
the universe, and things might be very differ-
ent elsewhere,” he explains. “There’s nothing
sacred about the mass of the electron.” This
conception of our corner of the universe as
only one valley in a landscape of physical
possibilities has also provided Bousso with
insight into the long-standing cosmological
constant problem in physics (see “Dark Side
of the Universe”, BSR Fall 2005).
The surprising consequences of string
theory also manifest themselves in Ganor’s
research on the geometry of string theory. “It
is possible to think of most of string theory
as a modification of classical geometry,”
says Ganor. But this modification has some
astonishing outcomes, including allowing the
application of so-called “noncommutative”
geometry. A mathematical operation is said
to be commutative when it yields the same
result forwards and backwards: 3 + 2 = 2 + 3.
Division, on the other hand, is noncommuta-
tive: 3 ÷ 2 ≠ 2 ÷ 3. In classical geometry, mul-
tiplication is required to be commutative, but
in noncommutative geometry this is not the
case. “These are things that classically seem
impossible, but string theory might allow
them,” says Ganor. One way that noncom-
mutative geometry has been applied to string
theory is in the description of branes, which
“teaches us about the structure of space and
time,” Ganor explains. He speculates that
these types of theoretical mathematical stud-
ies may eventually provide avenues by which
to experimentally test string theory, since “we
are in a position to discover an effect that is
zero in classical physics, but is nonzero in
string theory.”
Physics in the 21st century promises to
provide deeper insights into the workings of
the universe than ever before. Even before
string theory was conceived, Albert Einstein
had “deep faith that the principle of the uni-
verse will be beautiful and simple.” Whether
there is truth to the elegant idea that all the
workings of the universe are reflections of a
single grand physical principle remains to be
seen—and experimentally verified. Not ev-
eryone in the physics community accepts that
string theory is the “theory of everything.” But
as Bousso puts it, “Right now the situation is,
there’s only this one serious contender. So we
play with it until we get a prediction, or you
find something better, or you give up.” And
researchers here at Berkeley certainly are not
giving up any time soon. n
Meredith Carpenter is a graduate student in
molecular and cell biology.
Want to know more?
NOVA miniseries, “The Elegant Universe”:
www.pbs.org/wgbh/nova/elegant/
UC Berkeley Center for Theoretical Physics:
http://ctp.berkeley.edu
Flood
of Criticism
Berkeley engineers investigate what went
wrong during Hurricane Katrina—and how to
keep it from happening again
“If it had been built as it should have
been built, we would be repairing some
shingles and mopping up some wet carpets.”
Thus Dr. Robert Bea, UC Berkeley profes-
sor of civil and environmental engineering,
sums up the flood control system in New
Orleans and its failure during Hurricane Ka-
trina. But rather than merely tearing off some
shingles and soaking carpets, Katrina wreaked
its by now all-too-familiar devastation, flood-
ing around 80 percent of New Orleans, killing
over 1,500 people, displacing far more, and
causing tens of billions of dollars in damage.
Bea is part of a team of investigators based
at UC Berkeley that has spent the last year
trying to figure out exactly what went so
horribly wrong during Katrina.
The team’s conclusions, published re-
cently in a 1,300 page report, are a scathing
criticism of the engineering and organiza-
tional failures preceding the 2005 disaster—
a disaster, they argue, that could have been
prevented. Moving toward a brighter future,
they say, will require nothing less than a to-
tal overhaul of the system that creates and
maintains flood protection infrastructures
not just in New Orleans, but in the United
States as a whole.
Navigating through a catastrophe
Immediately after Hurricane Katrina tore
through New Orleans on August 29, 2005, an
aftershock of activity rumbled through the
Department of Civil and Environmental Engi-
neering (CEE) at UC Berkeley.With a pot of
emergency money mobilized by the National
Science Foundation, CEE professor Raymond
Seed hurried to organize a committee that
would become known as the Independent
Levee Investigation Team (ILIT).Their mandate
was to investigate what had happened to the
flood protection system in New Orleans
during and after the hurricane.The 34-mem-
ber team was made up of a diverse group of
Flood of Criticism
FEATURE
by Erica Spotswood
engineers, economists, lawyers, contractors,
and business people spanning 16 different
academic, private, and government institutions.
According to Dr. Seed, what really made
the team unique was not only their range
of expertise but also their sheer willingness
to work on the project on a pro bono basis.
Together, they committed thousands of hours
of their time at no cost to the government,
driven solely by the desire to provide an
independent and unbiased assessment of
what went wrong.With members who had
investigated earthquakes, dams, levees, the
space shuttles Challenger and Columbia, and
the Exxon Valdez oil spill, the team had some
impressive forensic engineering credentials.
As Bea points out, the diversity of the team
had to match the diversity of the problem,
requiring expertise in everything from soil and
structural mechanics to people mechanics.
After a month of frantic preparation
and information gathering, the team was
dispatched to New Orleans at the beginning
of October 2005.They had just three weeks
to investigate almost 200 miles of levees and
canals. Staying in a hotel in the center of town
with recently reconnected water, sewage, and
electricity, they spent the daylight hours with
the Army Corps of Engineers (or the Corps,
as it is often affectionately called) and their
nights debriefing back at the hotel. Driving
over debris large enough to necessitate a four
wheel drive vehicle, the team battled heat,
Image courtesy of NOAA
mosquitoes, and access restrictions by military
police in order to collect their data. CEE grad-
uate student Rune Storesund recounts that
the most valuable pieces of equipment during
the field work were their GPS unit and their
camera. At each point of interest, they took
a time-stamped picture and marked a GPS
point. Katrina had destroyed most reference
points, making it nearly impossible for the
team to determine precise locations, especially
in an unfamiliar city. Using the GPS to figure
33

Flood of Criticism
out where pictures were taken during the day
became a nightly ritual.
One of the original purposes of the ILIT
investigation had been simply to catalog high
water marks in order to determine how much
the levees had been “overtopped.” The Corps
FEATURE
claimed at the time that the storm had simply
been too large, causing water to flow over the
top of existing flood protection systems which
were not designed to handle such a large
storm surge. However, over the course of the
investigation, a picture began to emerge for
the team that did not match the claims of the
Corps.They saw evidence that some levees
had failed even though they had not been
overtopped, indicating that the structures had
not even withstood storm surges well within
their design standards.
Since their initial trip, the team has re-
turned many times to New Orleans to gather
more data and to witness the rebuilding effort.
These subsequent visits have confirmed their
initial suspicions that much of the damage
was caused either by errors in judgment and
engineering or by cost-cutting measures that
Image courtesy of USGS
prioritized economy over reliability. According
to the ILIT report published in July (http://
www.ce.berkeley.edu/~new_orleans), New
Orleans’s flood protection system did not
fail because of the size of the storm. Rather, it
failed due to engineering inadequacies created
by the dysfunctional organizational system in
charge of managing the infrastructure.
Photos by Rune Storesund, Leslie Harder, Rune Storesund, Rune Storesund
Shells, sand, and peat moss
The list of engineering deficiencies in
the ILIT report gives a depressing picture of
what went wrong in New Orleans. Implicat-
ing everything from canals built on swamps
to inaccurate data about the elevations of
floodwalls, the report details how multiple
sites failed for a combination of reasons (see
map on page 37).
Levees, or earthen walls, are a major
source of protection for New Orleans, provid-
ing a barrier between the city and the Gulf
of Mexico to its east. As the water in Lake
Borgne rises as a result of storm surge dur-
ing a hurricane, it runs up against the levees,
which keep it from flowing west into the city.
Because the Corps’s levee design standards
do not restrict what materials can be used to
build levees, they are usually made using what-
ever soils are present at the building site. Pre-
Katrina, the resulting system was constructed
of a wide variety of different materials. As the
team investigated how the levees had been
built, they began to notice that some soils are
34
From top to bottom: Professor Bea (far left
corner) reviews damage assessment maps pre-
pared by the Corps as part of a joint briefing to the
ILIT team in October 2005 at Corps headquarters
in New Orleans. Next: An aerial image showing
the catastrophic failure of the Lower 9th Ward “I-
wall.” A temporary berm has been constructed
to keep tidal and storm surge waters out of the
protected area while permanent repairs are made.
Next: View of the damaged concrete “I-wall” at
the Lower 9th Ward. The barge, pictured above,
was “sucked” into the Lower 9th Ward through
the floodwall breach, bending over the rebar re-
inforcement as it scraped across the top of the
wall. Next: Professor Seed, far right, measures the
depth of the scour trench that formed as a result
of the storm surge overtopping the flood protec-
tion wall at the Port of New Orleans.
much more prone to erosion and failure than
others.To the east of the city in the Mississippi
River Gulf Outlet (MRGO) area, they found
levees built out of sand and shells that had
simply washed away when Katrina hit.
Like sand and shells, the peat moss un-
derneath much of the New Orleans has been
the source of other engineering challenges
as well. Peat is a living organism, and when it
dies and decomposes, the soil breaks down
and becomes compressible.When imperme-
able structures are built on top of peat, they
are vulnerable to subsidence and seepage.This
creates persistent challenges in levee construc-
tion, where maintaining the design elevation is
a critical factor in determining how effective a
levee will be against storm surges.
Where materials were not an issue, le-
vees failed due to other errors—mistakes that
ILIT argues were overlooked by the Corps—
either in the conception of the infrastructure
projects or in their maintenance. For example,
the Corps does not require in their guide-
lines that levee designs consider the potential
impact of objects like barges against a flood
wall (something that actually happened during
the storm), and they do not design levees that
consider the impacts of overtopping. Other
phenomena such as liquefaction, which occurs
when water seeps into levees and causes
them to become waterlogged and to collapse,
were not routinely addressed.The ILIT report
points out that a considerable number of
failure modes which were not addressed in
the Corps design standards actually occurred
during Katrina.
In addition to the long system of levees
protecting New Orleans to the east and to
the north, there is also a network of canals
within the city itself. During normal conditions,
they are used to transport rainwater from

the city into Lake Ponchartrain to the north.
When Katrina hit, a number of the floodwalls
bordering these canals failed, releasing water
into the city. Several of the canals are built on
top of swamps where the foundation soils
are composed of a mixture of peat moss and
sand. As water seeped through the peat and
under the floodwalls, in some cases it caused
the walls to split and collapse. In others cases,
most notably in the catastrophic failures at the
17th Street Canal, the seepage caused the walls
to slide horizontally.The Corps previously
claimed that they could not have anticipated
the mode in which the floodwalls failed.
Mucking about in history
As the independent levee investigation
team began to understand the extent of the
engineering failures, they started to wonder
how so many errors could have been commit-
ted.To answer this question, they began look-
ing at how the levee and canal systems were
developed in the first place. As they probed,
they discovered that the reasons so many
things went wrong were rooted in history.
The flood protection system in New
Orleans is a complicated organism with a
long and tumultuous past. Built on what
was originally a swamp, floods have been
an issue in New Orleans since the city was
founded in 1718. Much of the city lies below
sea level, making it vulnerable not only to
hurricanes but also to flooding from the
From top to bottom: Professor Seed, hold-
ing the water bottle, inspects the levee materials
being used to construct the Mississippi River Gulf
Outlet (MRGO) levee. This levee was originally
constructed of sand and shell fill that “dissolved”
and washed away as the storm surge approached.
Next: A barge came to rest on top of the Bayou
Bienveue Control Structure during Hurricane Ka-
trina, leaving a visual high-water mark indicating
that the storm surge was high enough to allow the
barge to float over the 18-foot tall concrete flood
wall. Next: This house, located in the Lower 9th
Ward, was washed off its foundation as a result of
a “tidal wave” of flood waters entering the Lower
9th Ward immediately following the catastrophic
breaching of the flood protection wall. Next: The
leaning panels of the failed flood wall within the
London Avenue Drainage Canal have been sup-
ported by a temporary gravel berm/levee. The
floodwall was “pushed” over by the rising waters
in the drainage canal as a result of multiple founda-
tion failures Next: Professor Seed (Cal cap) and
Professor Bea (immediately behind Seed) strat-
egize with reconnaissance teams from the Corps
and the American Society of Civil Engineers on
which failure sites to visit next.
Flood of Criticism
Mississippi River, which runs through the
heart of the city. To cope with the floods,
New Orleans has a flood control system
nearly as old as the city itself. What began
as a series of drainage ditches has since
evolved into a complicated web of levees,
FEATURE
canals, and pumping stations. In the hands of
the Army Corps of Engineers since the early
1900s, the flood protection system has been
continuously updated, reconstructed, and
expanded over the past 100 years.
While digging into this past, the team
could not help but notice inconsisten-
cies. Some projects were started and left
unfinished, while others were started under
one set of guidelines and finished under
a second such that some parts of a single
system were stronger or higher in elevation
than others. As the team pored through
more than 3,000 agency documents and
interviews, they realized that the engineer-
ing flaws could not be removed from the
dysfunctional systems that created them.
“It was a bad plan,” says Bea, “If you try to
engineer within a bad plan you will get bad
engineering.
Photos by Rune Storesund, Leslie Harder, Rune Storesund, Rune Storesund, Rune Storesund
“It was a bad plan,” says
Bea, “If you try to engineer
within a bad plan you will
get bad engineering.”
ILIT is not alone in its opinion about
the Corps. Two other independent inves-
tigatory teams, one headed by the Uni-
versity of Louisiana and the other by the
American Society of Civil Engineers, have
also published reports that reached similar
conclusions. In the months since Katrina, as
suspicion has grown that human error was
at the heart of the failures, public outrage
directed at the Corps has increased as well.
Although the team has implicated the Corps
in a number of critical errors, they caution
against scapegoating. When asked who is to
blame, Dr. Bea responds, “Is blame appropri-
ate? I would rather call it an appropriation
of responsibility and that can’t be pinned on
any single person or organization.”
Indeed, ILIT’s focus on a whole systems
approach to the failure distinguishes it
from the two other investigatory teams.
Fundamental to their systems approach is
the idea that large infrastructures are built
not just by one organization but also by
35
 Flood of Criticism

what they call a technology delivery system,
which includes the public, the government,
and industry. With multiple organizations
involved in the construction, maintenance,
and design of different pieces of the project,
the flood protection system was left with
FEATURE
line, Storesund and Bea (among others) have
become increasingly critical of the guidelines
adopted by both the Corps and the Federal
Emergency Management Agency, in which
design standards for infrastructure projects
must be built to be able to withstand a 100-
all components of the technology delivery
system that created the flood protection
network. In short, filling levees with the shells
that washed out of them is like giving a Band-
Aid to a patient in need of a triple bypass.
In June, the Army Corps of Engineers

no one in the driver’s seat who had enough
of a handle on the big picture to manage the
system as a single unit. “The Corps focused
on the construction of projects and lost
sight of the overall system. Along the way,
there were lots of interface breakdowns,”
Bea explains.
In the ILIT report, there is plenty of
responsibility to go around. Leadership was
ineffective or changed too frequently. Risk
was inappropriately assessed and uncer-
tainties were not properly accounted for.
Maintenance was not completed as needed,
warnings went unheeded, and designs were
Filling levees with the
shells that washed out of
them is like giving a Band-
Aid to a patient in need of a
triple bypass.
not modified upon the receipt of new
information. The list goes on. In light of such
strong accusations, the inevitable question
is how the system became so dysfunctional.
In order to understand how to answer this
question, Bea has looked for examples of
high reliability institutions with low rates of
failure. He’s noticed a trend: “NASA is in a
competitive business environment now just
as [Royal Dutch] Shell is, and faces every
much as intense commercial pressure as
does [Shell]. The Corps doesn’t. This is be-
cause of the historical institutional process
that the Corps came through.”
Additionally, Storesund points out that
large infrastructure projects are difficult
beasts to tame and are somewhat differ-
ent from other kinds of projects. “One of
the big problems with large infrastructure
projects is it takes a long time to build. So,
the people who started the project aren’t
necessarily the people who will be on
board during the construction and after it is
done.” Indeed. The New Orleans Flood De-
fense System, which began after Hurricane
Betsy in 1965, had an estimated completion
date of 2018 even before Katrina hit
With such a long construction time-
year flood. “If you are designing something publicly admitted that the failures that
for the 100-year flood and it takes you 50 occurred during Katrina were related to
years to build it, is that the optimal solu- their own errors in design and engineering.
tion?” Storesund asks. They may not match Without the influence of ILIT and the other
well with the timeline of infrastructure independent investigation teams, this may
projects, but Bea adds that the standards not have happened. One step toward solving
are also too low for the associated conse- a problem is recognizing where the weak-
quences. He points out that offshore oil rigs, nesses are, and if the ILIT report is any indi-
which protect no lives, are built to with- cation, there is no shortage of information
stand a 10,000-year event. available on how those weaknesses might be
rectified. With some creative integration of
We shall rise again the independent levee investigation team’s
While ILIT was revisiting New Orleans ideas, someday New Orleans may have little
to collect more data for their investigation, more than a few broken shingles to repair
they also watched the Corps rebuilding after the next hurricane. n
many of the levees, canals, and floodwalls.
Having promised to have the city protected
by the beginning of this year’s hurricane sea- Erica Spotswood is a graduate student in envi-
ronmental science, policy, and management.
son on June 1st, the Corps has been working
in earnest since Hurricane Rita passed. Dr.
Bea is skeptical that they are doing a better Want to know more?
job. “We are trying to kill it with money, http://www.ce.berkeley.edu/~new_orleans
doing it quickly and tweaking the Corps as
little as possible so we can go to Mardi Gras
as soon as possible, and all I can do is shake
my head.” The Corps has stated that they
will get flood protection back to the level
it was before Katrina. Storesund questions
the wisdom of such a plan, arguing that if
it didn’t work the first time, it is likely to
be ineffective to rebuild to meet the same
standards. He recalls a visit in February that
was reported on the PBS News Hour. “They
were taking all the silt and shells and sand
that got washed away and putting it straight
back into the levee.”
Overall, the team has little confidence
in the rebuilding efforts of the past year.
Although the flood protection system com-
ponents that failed during Hurricane Katrina
have been replaced with much more robust,
new components, the system as a whole has
not been significantly improved. However,
they do have a lot of advice on how things
might be improved in the future. Their
recommendations would require major
restructuring of the organizations in charge
of flood protection in the US, but they argue
that nothing less will fix the problems they
identified. Fundamental to the team’s vision
is the idea that restructuring must address

36

Levees 101: A Shortcut to Major Failures
1. Lakeview Airport The transition of a
railroad from inside to outside the protected
area reduced the elevation of the levee. As
the storm surged, water traveled through the
gravel of the railroad eroding the levee at the
transition point. The scouring of the levee
then spread outward from the transition
point, eroding the levee on either side
2. Lakefront Slight overtopping causes
minor superficial damage
3. East of Hwy 11 Exceptional levee
performance and minimal damage through
both Katrina and Rita. Levee built of highly
erosion-resistant materials
4. South East corner New Orleans
East Earthen levees built of highly erodible
materials are damaged first by waves splash-
ing over the top of them, leading to massive
failure
5. Levee failures caused by overtopping and
wave splashing
6. Erosion resistant material prevents major
damage to this levee in spite of the fact that
low elevation spots along the levee caused
overtopping, which sucked a large barge
towards them. The levee resisted the impact
of the barge.
7. Bayou Bienvenue Control Struc-
ture The western half of the control
structure levee performed very well while
the eastern half was severely eroded. This
location provided a natural experiment
demonstrating the importance of materials
in levee construction. The western half, which
performed well, was built of highly resistant
materials, while the eastern half was built of ero-
sion susceptible materials
8. Mr. Go Zone Poor levee performance
due to the use of shells and sand and other
highly erosion prone materials. This area was
largely responsible for the flooding of Saint
Bernard Parish to the west. Several barges
were found deposited inland of the levee by
the storm surge.
9. Control structure Bayou Dupre
This is the site of an old bayou that was filled
in. Failure at the control structure was caused
by filling of the bayou channel with highly
erodible materials.
10. Overtopping of earthen levee causes little
damage to the levee. A fishing boat is found
Flood of Criticism
FEATURE
washed over the levee into the neighborhood
to the west.
11. Industrial Canal Metal sheet pilings
constructed to hold up the floodwalls are
not driven deeply enough to prevent water
from seeping underneath. A very large barge
was found deposited in the neighborhood
adjacent to the canal. This area responsible
for some of the flooding in the lower ninth
ward and the Orleans East Bank.
12. London Avenue Canal Canal was built
Map courtesy of the Army Corps of Engineers and ILIT
on top of swamp deposits. The canal is not
overtopped but fails anyway because water
seeping under the floodwalls.
13. Orleans Canal 200 feet of construction
on this floodwall had never been completed.
The canal was not breached, though water
easily flowed through the unfinished section
of the floodwall into the Orleans East Bank.
14. 17th Canal The floodwall slides hori-
zontally 50 feet on top of waterlogged swamp
deposit soils and eventually collapses. This
failure causes some of the most catastrophic
damage to the Orleans East Bank district.
37
Political Science
it ic al
FEATURE
Pol Science
ˆ
Berkeley scientists
M ost Berkeley students can tick off
the major science policy issues in
the news—the environment, stem cells,
energy independence, nuclear technology,
Mars exploration, and so on, but Congress
has different priorities. Following recom-
mendations from a recent National Academy
of Sciences report, the 2007 Congressional
budget focuses on improving and maintain-
ing American competitiveness in innovation
as well as supporting defense research. The
new budget leaves funding for NASA and
the National Institutes of Health at current
levels (and thus falling behind inflation),
preferring to promote basic science and
defense applications through the National
Science Foundation, National Institutes of
Science and Technology, and the Department
of Energy.
Unsatisfied by simply reading about
such policy decisions in the news, a group
of science and engineering students has em-
braced Berkeley’s activist tradition and gotten
involved in the debate over how government
spends its money. The Science, Technology,
and Engineering Policy group (STEP) formed
to allow interested students to participate in
the political process.
In its attempt to raise policy awareness
on campus, STEP has two main goals: first,
to encourage thinking about broader impacts
of science, and second, to educate students
about the impacts of scientific research at
Berkeley and elsewhere. The group hosts a
seminar series addressing a wide variety of
38
the policy plate.
step up to
issues; past topics have included innovation
in science and engineering, open source
biology, energy policy, and American scien-
tific competitiveness. Along these lines, STEP
recently held a white paper competition as a
concrete way to initiate thoughtful discussion
in the community.
White paper competition
There was a strong response to the
prompt for this year’s competition: “Describe
how a new technological innovation (or in-
novative use of an existing technology) could
either help meet an important policy goal or
raise the need for new policies.” STEP received
twenty submissions from undergraduate and
“It’s one of the things
that is very important
about this group—that
considering policy could
affect the direction of a
student’s research.”
graduate students from both engineering and
policy departments. The papers also spanned
the political landscape; the most popular top-
ics included nuclear policy, genomics, stem
cell research, health care, science education,
and energy reform.
Perhaps most importantly, the students
were encouraged to interact with STEP’s
advisers and other UC Berkeley professors.
Steve Maurer helped first place winner
Krishanu Saha refine his paper, “Navigating
to the Right Stem Cell Line.” Saha’s pro-
posal—to form a comprehensive database to
track human stem cell lines—was inspired
by problems he noticed during his doctoral
research on adult neural stem cells (from
rats). His ideas were refined at a recent Boalt
Hall conference on the ethical, legal, and
societal implications of the California stem
cell initiative, and in discussions with Maurer
about current database policy.
Beyond the current debate about the
ethical basis of human stem cell lines, there
are practical issues associated with donor
rights and ownership of biological material.
For example, in order to obtain an appropri-
ate stem cell line, scientists must commu-
nicate with other scientists or companies to
determine if a stem cell line has been stored
under the correct biological conditions,
how the cells are best grown in culture, and
what sort of proprietary rights the cell line
owner has (publishing, patenting, sales, etc).
Additionally, if a scientist chooses the wrong
cell line, legal complications may arise due to
donor concerns about what the cells are be-
ing used for or how they have been obtained.
Collecting this information is time-consum-
ing, difficult, and potentially expensive.
Saha’s database would centralize this critical
knowledge. However, Saha notes, “the first
step is to write a paper—there is still more
research to be done on how society views
biological donations and to look at what has
Continued on Page 40

Excerpts from Navigating to the Right Stem Cell
Line
Krishanu Saha, Department of Chemical Engineering
When seeking information about human embryonic stem cell
Political Science
large connected scientific projects with property rights. In hESC
research, databases have sprouted up isolated from one another,
but are currently designed to incorporate information from and to
communicate only to scientists...
Political Feasibility. Even minimal database incentives for

(hESC) lines for research, scientists do not simply peruse through
a few catalogues or journal articles. Instead, scientists find them-
selves negotiating many familiar and new relationships—with other
members of the scientific community, lawyers, advocacy groups, the
lay public, and oocyte donors. Scientists communicate the merits of
particular hESC lines. Lawyers negotiate intellectual property rights
and materials transfer agreements, while advocacy groups aspire to
guide scientists to hESC lines most pertinent to their own causes.
Simultaneously, the lay public seeks to track their investment
in hESC science while protecting public health. Lastly, [donors] may
seek to maximize usage of their hESC line in a particular field, or
for therapies in general. Ultimately, the process by which scientists
communicate their choice to all of these parties is notably varie-
gated, laborious, and guarded. In such a politically and scientifically
important arena as hESC research, every effort to make this process
transparent, inclusive, and efficient should be immediately explored.
Check the boxes for fields to display in the table. in ethical debates. By including other parties
FEATURE
input can create conflict in industry [by] pressuring trade secret
disclosure and in academia by countering the lone discovery culture
of science. …Certain segments of industry will likely welcome the
standardization and transparency from database adoption. As hESC
companies become established, they will likely want stable markets
and clearly-enforced property rights… Both donors and advocacy
groups will likely welcome the database as it provides a new mecha-
nism to influence research.
By providing a mechanism for donors to communicate to sci-
entists, the database may introduce an additional encumbrance on
scientists when choosing particular hESC lines as donor stipulations
may greatly restrict hESC research on many lines… Legislation on
donor rights likely will take years to settle, and will vary regionally.
Scientists can proactively choose to manage such legal cases via
relationships managed over the database.
Implications

Graphic by Krishanu Saha

SNP IRB Infectious Differentiation Published Chimera Price Infertility Neurology
Label Sex profile review Karyotype agent potential articles Use Range Endorsements Implications Implications
American
Click Harvard No pluripotent Science 03, $1- Cancer Yes,
HS43 F here Univ. Normal viruses (serum 3/7/05) Nature 02 Yes $10K Society Click here None

Click No pluripotent Science 03, Parkinson's Yes,

HV24 M here None Normal assay (serum 5/1/05) Nature 02 Yes $500 Foundation None Click here

Potential user interface of a proposed database to organize information on human embryonic stem cell lines for research purposes.

The wide accessibility of a web-based central database would be a
responsive mechanism to shape hESC research for greater public
benefit.
Suppliers of stem cell lines for research are increasing and di-
versifying. Suppliers currently range from purely nonprofit and public
[e.g., National Institutes of Health (NIH)], a mixture of public/private
[e.g., WiCell], and purely private [e.g., in vitro fertilization (IVF) clin-
ics and biotech companies]. In 2001 in the US, NIH supplied a large
majority of the hESC lines for research, while today there are over
200 known lines with suppliers from Korea, India, Australia, Sweden,
Canada, and U.K. growing prominently in size. Each of these suppli-
ers adheres to its own local regulations in deriving and trading hESC
lines. Harmonization of such regulations has been proven difficult
already among states in the US and is unlikely to occur soon in the
international context...
Organizing, centralizing, and standardizing not only hESC scien-
tific information, but also the legal and consent issues, could solve
many of the concerns among all parties involved. Data is generally
viewed as a public good that can not be patentable. But, the need
for databases in organizing information has long been known in
in this information exchange, the database may also have unique out-
comes in ethical debates. Donors are not forced to provide more
information than they wish and have a mechanism to define their
terms of donation. If donors collectivize into groups or charitable
trusts, such institutions can oversee the selection process and even
have a seat at the negotiation table when the supplier and scientist
negotiate the terms of trade.The lay public and advocacy groups can
scrutinize only the individuals who operate at ethical borders and
not condemn the scientific enterprise as a whole.
While scientists seek information about and new sources of
hESC lines, I have shown that a remarkably diverse assortment of
groups has similar aspirations themselves. All of these parties, with
differing interests and stakes, may gain much in the long run from ef-
fective implementation of a central database. Database management
is relatively inexpensive compared to the funding of hESC research,
and corporations are already willing to fund such an enterprise.
hESC databases have little reason to restrict the database informa-
tion and participation to only scientists, without paying attention to
the democratizing forces on science.

39
Political Science
been done in the past. Then, the next step is
to get the National Academies to think about
a good way of establishing it, if [the database
concept] remains relevant.”
Fortunately, part of the white paper
competition’s first place prize is a trip to
FEATURE
Washington, D.C. for potential meetings with
influential directors in the National Academy
Photo Courtesy of Erik Douglas
STEP student members pause for a photo opportunity with Governor Schwarzenegger’s portrait. UC Berkeley step
members Erik Douglas (left) and Lance Kim (right) and UCLA member Jay Fahlen (center) represented STEP at
the May 2006 meeting of the California Council on Science and Technology in Sacramento.
of Sciences, the American Association for the
Advancement of Science (AAAS), the NIH,
and Congress. Saha notes that the debate sur-
rounding the recent stem cell bill has done a
lot for visibility.
“One of the reasons I wrote the paper is
that the prize is really good. You’re not wast-
ing your time by writing the paper if you have
a shot at getting it implemented,” says Saha.
The feedback provided by the STEP contest
judges helped Saha to polish his arguments
for the next round of discussions.
Coming soon
According to STEP president Kate Ham-
mond, Saha’s experience embodies exactly
what STEP hopes to do for many Berkeley
students. “Ultimately, we want to provide
people with both [the] access and [the] abili-
ties to pursue interests in science policy.”
As a start, STEP hopes to improve
students’ ability to communicate complex
scientific ideas to the public. Hammond
notes that there was noticeable improvement
in the white papers where the students had
sought advice from professors in the policy
40
school. “When people with a deep science
background approached professors in policy,
they got help shaping the proposal for a
wider audience. The process was integral
because the relationship to the advisers is key
to the learning process.” Besides its monthly
seminar series, STEP offers workshops on
written and spoken communication. Ham-
mond hopes to see a wide turnout at the
kickoff meeting in October, when plans for
this year will be revealed.
In addition to the white paper competi-
tion and the seminar series, STEP plans to
Beyond the current debate
about the ethical basis of
human stem cell lines,
there are practical issues
associated with donor
rights and ownership of
biological material.
expand student involvement in legislation.
Last year, adviser Pat Windham of Stanford
University took students to sit in on nuclear
policy meetings in Sacramento. Thanks in
part to his continuing support, STEP plans
to turn toward California policy next year.
Already, a few students have contributed
advice to the California Council on Science
and Technology (CCST) for California’s
response to the National Academies’ report
“Rising Above the Gathering Storm,” which
makes recommendations on issues of glo-
balization and American competitiveness.
Hammond hopes that STEP will be able to
coordinate Berkeley involvement with CCST
on other issues as well. “We would really like
to … provide a communal meeting point and
contacts to state and federal policy makers,”
she says.
Most importantly, STEP hopes to
develop depth in specific areas of interest to
students, and prepare task forces to advise
the CCST and legislative groups. Tom Kalil,
Special Assistant to the Chancellor for Sci-
ence and Technology at Berkeley notes, “I
hope that STEP will encourage science and
engineering students to think about the
broader economic, ethical, legal, and societal
implications of their research.”
Adviser Steve Maurer goes a little
further. “It’s really valuable to think about
things engineering students can do that have
real public policy implications. STEP could
organize projects to get people involved in
real world issues.”
Though STEP may not yet be ready to
organize large-scale research projects, they
are certainly amenable to involvement from
the policy end. Current efforts aim to recruit
more graduate students from the Goldman
School of Public Policy. Hammond notes,
“I think it’s one of the things that is very
important about this group, that considering
policy could affect the direction of a student’s
research.” Scientists often think that science
and technology drives policy, but STEP
strives to highlight how policy can drive sci-
ence, too. n
Kayte Fischer is a graduate student in bioengi-
neering and a member of STEP.
Want to know more? Check out STEP’s web-
site at http://step.berkeley.edu
 A lizard of the Draco

Wingless Flight
genus suns itself in
the Western Ghats of
India. The patagium,
a skin membrane
supported by six
extended ribs, acts as
“wings” for controlled

FEATURE
gliding. Berkeley
scientists have
determined that larger
Draco species are
still capable of gliding,
despite unfavorable
surface-to-mass ratios,
by evolving larger
patagia.

Easy
Glider
Berkeley scientists
learn what it takes to
fly without wings
Photo by Jayanth Sharma, wildlifeimages.com

“T here is an art…or rather, a knack to

flying,” says Douglas Adams, the Brit-
ish writer and radio personality famous for his
Hitchhiker’s Guide to the Galaxy. “The knack
lies in learning how to throw yourself at the
ground and miss.” Curiously, Adams’ defini-
tion leaves out one element usually thought
of as essential to flying—wings. While his
intentions were clearly humorous, Adams
was perhaps more correct than he realized:
from squirrels and lizards to some tropical
ant species, a surprising number of wingless
creatures do have a knack for avoiding the
ground. They glide.
Today, researchers at UC Berkeley are
studying gliding organisms and accumulat-
ing clues as to how and why nature favored
this adaptation. Not until recently, with the
advent of high-speed, high-resolution video
cameras, was it possible to observe the move-
ment of individual body parts on an airborne
animal or insect. Armed with these innova-
tive techniques, researchers are now looking
at the specific morphologies and movements
of gliders. Such research is elucidating the
biomechanics of aerial behavior in real time,
in turn providing insight into the evolution-
ary patterns behind gliding flight.
LEAPIN’ LIZARDS
A glider is like a plane without an en-
gine, or a bird without the ability to flap its
wings. But like powered flyers, good gliders
can move a significant distance horizontally
without losing much height. To do so, they
maximize the surface area of their bodies and
adopt specific shapes, or morphologies, to
generate lift that counteracts the downward
pull of gravity. Researchers at Berkeley are
studying how body morphology contributes
to gliding flight, and how such morphologies
might have evolved in the first place.
To study the evolution of flying in a
lineage, scientists typically look at the phy-
logeny of that group—that is, they try to find
its common ancestor. Next, they determine
the group’s functional morphology, how it has
made flight possible, and how it has evolved
over time. Finally, they scour the fossil record
for empirical evidence to support their find-
ings and to formulate a theory of why flight

41
 Wingless Flight
evolved in that particular lineage.
While this conventional evolutionary
approach can be useful, when it comes to
Draco lizards, a genus of gliding arboreal
lizards from Southeast Asia, it can’t be fully
applied. Ranging in mass from three to thirty-
five grams (from the weight of, say, a pencil to
FEATURE
a plum), Dracos are the only living lizards to
have evolved elongated ribs; these ribs sup-
port a wing-like flap of skin, the patagium,
which provides the surface area needed to
glide. Unfortunately for researchers inter-
ested in the evolution of these traits, there is
no fossil record for this group (or any extant
lizards with a similar morphology), making it
difficult to chronicle how their ability to glide
evolved. Fortunately, by focusing instead on
how variation in Draco body morphology af-
fects gliding behavior, Berkeley professors of
integrative biology Jim McGuire and Robert
Dudley have been able to fill in some details
about how flight might have evolved within
this group.
When McGuire began studying Draco
in 1995, he was intrigued by the relationship
between its body size and gliding perfor-
mance. His interest was piqued in part by
the group’s incredible diversification and
coexistence: multiple species of Draco were
found in the same habitat. It made sense that
to coexist, different species must use different
types of limited resources in order to prevent
competition. Since the only major difference
across the various species was body size, Mc-
Guire wondered whether size played a role in
the type of resources each species consumed,
and whether this had anything to do with the
lizards’ gliding abilities.
At that point, he teamed up with Dudley,
and for the next several years they measured
the gliding performance of twenty-nine spe-
Photo by: Jim McGuire
cies of remote Malaysian Draco ranging across
the full size distribution. They knew from the
outset that Dracos scale isometrically—that
is, as their body mass increases, their propor-
tions stay the same. Thus, their body mass
increases at a greater rate than their surface
area. Since surface area is critical to generat-
ing lift, one would expect the big lizard spe-
cies to be relatively poor gliders compared to
the smaller ones.
To conduct gliding trials, McGuire and
A Draco melanopogon lizard glides
down from a 6-meter pole as part of
a flight experiment. Berkeley scientists
can use data on the wind speed and
animal’s velocity to determine how the
lizard directs its downward flight.
42
Dudley erected two tall poles 9.3 meters
apart—a six meter takeoff pole and a four to
five meter landing pole. They positioned the
lizards on the takeoff pole and then prodded
them, either by agitating them with a bam-
boo rod or tapping the pole, so they’d glide
toward the landing pole. A video camera
recorded each trial, and by taking into ac-
count the position of the camera relative to
the poles, McGuire and Dudley were able to
calculate the approximate height lost over a
standard horizontal glide distance and the
angle of each glide. They also used a digital
anemometer to measure wind speed and a
compass to determine wind direction. To-
gether, these measurements allowed them to
determine the velocity of each glide adjusted
for wind conditions.
“If you’re an ant falling from the
rainforest canopy, you don’t want
to land on your head.”
It turns out that the large Draco com-
pensate for their extra mass by diving faster
and farther: the first part of their glide is a
steep ballistic dive to generate velocity, and
then they level out into a flat glide. Practically
speaking, though, the larger Draco are more
limited than smaller ones in their access to
resources within the forest. Since they need a
higher initial altitude to perform a successful
glide, they are likely to remain in the upper
reaches of the rainforest canopy, whereas the
smaller Draco may scavenge far below. This
partitioning of the forest habitat may in turn
explain how multiple Draco species can coex-
ist: by living in different vertical layers of the
forest, they draw on different resource pools.
Evolutionary deductions can also be
made from the data. According to McGuire,
the original Draco gliders—the common
ancestor of those living today—were prob-
ably either large and living in really tall trees
or cliffs from where they could execute steep
ballistic dives, or they were fairly small so
they could take advantage of their higher
surface area to body mass ratio. They could
probably expand their ribs just a little bit to
create more surface area for increased lift,
but then were favored by selection such that
their patagia got larger and larger over many
generations. In the absence of a fossil record,
such evolutionary hypotheses establish a
framework for understanding how Draco
may have started gliding.
THE ANTS GO GLIDING ONE BY ONE…
Another striking example of a glider
that may shed light on the evolution of aerial
behavior is Cephalotes atratus, a species of
wingless ants living in the tropical rainforest
canopy. Remarkably, these ants are the first
documented case of wingless flight in any
living insect.
Three years ago, Robert Dudley listened
as his colleague Steve Yanoviak, a University
of Florida entomologist, told him he’d dis-
covered something amazing in the jungles
of Panama. He’d found that wingless ants,
when flicked off high tree branches, glided
back to the trunk of the tree from which
they’d fallen rather than spiraling aimlessly
to the rainforest floor. Yanoviak said he’d
witnessed the gliding behavior again, in the
same ant species, in Peru. Since there were no
documented cases of gliding flight in a living
wingless insect, the discovery indeed seemed
novel. In 2004, Dudley joined Yanoviak and

Photo by Steve Yanoviak, University of Oklahoma
Michael Kaspari, a University of Oklahoma
entomologist, in studying this phenomenon.
How were the ants maneuvering themselves,
they wondered? What about the ants’ mor-
phology facilitated aerodynamic behavior?
And what could it reveal about the evolution
of insect flight?
Dudley, Yanoviak, Kaspari, and others
spent the next year or so using high-speed,
high-resolution video cameras to document
how wingless ants in the Peruvian rainforest
glide. They used a rope and sit harness to
pull themselves up to high, treetop branches.
Sometimes they climbed with ants they’d
collected elsewhere in the forest, and other
times they resolved to find a colony once they
reached the upper reaches of the tree. They
painted the backs of the ant bodies white (for
visibility against the dark forest background),
dropped them from trees, and then recorded
the ants’ descent on video camera. The
painted ants repeatedly glided back to the
tree trunk.
Upon further study, it turns out that
these ants do what skydivers do—they use
their limbs to control their posture and orien-
tation. Their legs are slightly flattened at the
ends, so like skydivers who can initiate a spin
by slight right and left asymmetry of hand or
arm posture, the ants can initiate torque that
will rotate their bodies.
And it’s not just one ant species doing
this. Dudley says, “it’s hundreds, and they’re
not all related to each other.” Nor are ants the
only wingless insects gliding. Biologists are
now finding that many species across all insect
groups are wingless gliders. They don’t have
wings and never have—and yet, they glide.
The evolutionary pressure to adopt
gliding flight may have been as simple as ac-
cidentally falling out of a tree. Or, as Dudley
puts it, “If you’re an ant falling from the
rainforest canopy, you don’t want to land on
your head. You want to control your descent,
try to land on something so you don’t break
your antennae or another body part.” Put
this way, gliding flight sounds like a reflex,
the body and limbs responding to the force
of gravity by creating aerodynamic surfaces
that produce lift and adjust to drag. Directed
aerial descent has another possible advantage
as well—a falling ant may be able to return to
its colony as opposed to being woefully lost
on the forest floor far below.
Given how common gliding behavior
is throughout insect species, it’s natural to
ask whether these gliders fit somewhere
on the evolutionary continuum between
land-dwelling and flying insects. In other
words, did today’s flying insects evolve from
gliding ancestors? Dudley’s hypothesis is
that wingless gliding flight preceded winged
flight—that aerodynamic behavior in insects
started without wings. Admittedly, “flight
without wings” sounds a bit like putting
the chicken before the egg, but research on
Wingless Flight
FEATURE
The “flight” of the wingless ant Ceph-
alotes atratus may shed some light
on the evolution of gliding in insects
and other animals. Slow-motion video
revealed that the ants use their limbs
while airborne to control their fall.
gliding by Dudley and others has definitively
shown that it’s possible.
Furthermore, the evolutionary history of
insects offers some evidence that flying insects
evolved from gliding ancestors. According to
Dudley, the most “primitive” insects around
today—those which most closely resemble
the earliest insects on earth—are the Silverfish
(Thysanura) and Bristletails (Archaeognatha).
Both of these groups lack wings, and the
Silverfish can glide, just like the Peruvian
rainforest ants. This suggests that all modern
winged insects may have evolved the ability
to fly from wingless, gliding ancestors. So far,
however, scientists have not yet pinpointed
the transitional morphologies that would
illuminate the evolutionary steps between
skydiving silverfish and some of the earliest
winged insects.
Eventually, by understanding how glid-
ing played a role in the evolution of insect
flight, researchers hope to gain insight into
the evolution of flight in vertebrates. But in
the meantime, they continue to investigate
the mechanics of gliding, fascinated by
the many species—insect, lizard, or other-
wise—that throw themselves determinedly at
the ground, but somehow, repeatedly, miss.
Adrienne Davich is a graduate student in
journalism.
43
 MIND THE GAP:
Mind the Gap
Studies find continued disparity in tenure rates between
men and women with families.
FEATURE
“T he hardest year of my life” is how Dr.
Daniela Kaufer describes her first year
as a faculty member in the department of
integrative biology at UC Berkeley, and her
third year as a mother. Amidst the demands
of her job and her family, she says, “I had to
give up everything in life that was not essen-
tial.” No one ever said that balancing a family
and a career in academia would be easy. But
Photo (left) by Michael Shapira (right) by Peg Skorpinski
Daniela Kaufer and her daughter (left) Dean Mary Ann Mason (right)
achieving that balance is particularly chal-
lenging if an academic starts a family early
in his or her career, and if that academic is
a woman.
In the sciences, men that have early ba-
bies, born within five years of the receipt of
a PhD, achieve tenure at a rate 24 percent
higher than women with early babies. Berke-
ley Graduate Dean Mary Ann Mason calls
this gap in tenure rates the “baby gap.” She
and Graduate Division research analyst Marc
Goulden examined the family patterns of aca-
demics using data from the Survey of Doctor-
ate Recipients, a study of over 160,000 PhD
recipients from 1976 to 1999. They found
large differences in the family choices made
by men and women and the career conse-
quences of these choices. Overall, men with
tenured faculty positions are more likely than
women with tenured faculty positions to have
44
children: 70 percent of men are married with
children, compared to 44 percent of women
(1). Like many other professions, academia is
“front ended,” says Mason. “The 30s and 40s
are the make-or-break years, which are also
the most vulnerable times for women [with
respect to having children]. Children collide
with career expectations.”
The baby gap is partly due to the fact
that male faculty are much more likely than
female faculty to have a non-working spouse,
allowing them to spend more time with work
and less time with childcare. Additionally
most academic men are married to non-aca-
demic women, while most academic women
are married to academic men (2); a 1980
study of people with PhDs in science revealed
that 62 percent of women had husbands with
a PhD in science, while only 19 percent of
men had wives with a PhD in science (3).
Also, according to Mason, “Marriages in
which one spouse does not work are statisti-
cally more stable than relationships in which
both spouses work.” This may explain why
women who are married when they enter an
academic job are more likely to get divorced
or separated from their spouse than men in
the same situation. Interestingly, women who
are single when they begin their academic job
are twice as likely as men to remain single
(2). Because of these challenges, many wom-
en forego a career in academia altogether,
choosing a less demanding career that allows
time for a family.
Where are the women with PhDs?
Frequently, women slip out of the aca-
demic pipeline after graduate school. In
1998, women made up 42 percent of PhD
recipients, but constituted only 13.8 percent
of tenured faculty at research institutions (4).
Women often leave academia to take sec-
ond-tier jobs. These part-time, adjunct, and
lecture positions are becoming more com-
Marriages in which one spouse
does not work are
statistically more stable ...
mon in universities across the country; over
50 percent of undergraduate classes are now
taught by non-tenure track instructors (4, 5),
45 percent of whom are female (4). Lecture
positions are more flexible and provide more
time to spend with family, but offer lower
salaries, limited benefits, and less prestige.
Are graduate students at Berkeley con-
sidering alternate careers in order to have
time for a family? The Berkeley Science Re-
view conducted a web-based survey to find
out how graduate students at UC Berkeley
feel about career and family. Of the 146 sur-
vey respondents, 135 were graduate stu-
dents. Eighty-three respondents were female,
49 were male, and four declined to specify.
Roughly equal percentages of men and wom-
en are considering leaving academia: 38 per-
cent of the women and 34 percent of the men
are considering alternative careers. Most are
considering a shift because they want a more
flexible career that is better suited to having a
family. Many respondents also cited low pay
and low job security as reasons to look be-
yond academia.
These responses echo the sentiments ex-
pressed in a survey of over 800 UC Berkeley
postdoctoral fellows, conducted by Mason
Early Baby Gap in the Sciences
and Goulden in 2000. For single postdocs

Mind the Gap

without children, 39 percent of women and
33 percent of men indicated a career goal
shift away from academia. These numbers
were higher for married postdocs with chil-

FEATURE
dren: 59 percent of women and 39 percent of
men indicated a shift in career goals (2).

Should you have been a doctor?

Or maybe a historian?
The people who took our survey ac-
knowledged that professionals in many fields,
including medicine, law, and business, have
demanding jobs and work long hours. As in
academia, female doctors, lawyers, and cor- What stage in education/career do
porate executives are less likely to have chil- What stage in education/career do you think is the best time to have
What
you stage
think in education/career
is the best time to havedo
dren than their male counterparts. Similar to you think is thefrom
best respondents
time to have children? Answers from respondents
children? Answers
the situation in academia, women make up children? with children
with All respondents
children
far less than 50 percent of the workforce at
the top end of these professions (M.A.Mason,
Early in in
grad school Early
personal communication). Survey respon- Early grad school

dents pointed out that women in other pro- Late in in

Late grad school
grad school Late i

During
Duringpost-doc
post-doc Durin
Men with early babies Pre-tenure
Pre-tenure Pre-te
achieve tenure at a rate of
24% higher than women Post-tenure
Post-tenure Post-

with early babies. While

from
taking
While time
taking
academia
from academia
offoff
time
While
from

fessions make enough money to afford qual-
ity childcare. Says Dean Mason, “Academic
women can’t afford live-in help. And 9 to 5
childcare isn’t sufficient because academic
jobs are not 9 to 5 jobs.”
How do the family patterns of academics
in the sciences and social sciences compare?
Our survey respondents, most of whom are
graduate students in the sciences, thought
academics in the humanities might have an
easier time of balancing work and family.
Scholars in the humanities can often work
from home, they thought, unlike scientists
who are tied to their labs. Several respon-
dents expressed concern that the chemicals
they use in their research may harm a fetus,
requiring a temporary break from research
during pregnancy. Mason and Goulden’s
study shows that the baby gap is slightly
smaller in the social sciences and humanities
than in the sciences: Men with early babies
achieve tenure at a rate 20 percent higher
than women with early babies, compared to
a baby gap of 24 percent in the sciences (2).
Women in the sciences are slightly less like-
All Respondants
Responses to the BSR survey on career and family: What stage in your education/career do you think is the best
time to have children? Respondents could select more than one answer.
ly to get divorced, and less likely to remain
single, than their peers in the social sciences
and humanities. Mason speculates that there
are fewer single women in the sciences than
in the humanities because the male-to-female
ratio in the sciences is higher, meaning the
dating pool is larger. Says Mason, “There are
more men in the lab than in the library.”
Okay, so you’re a scientist. When
is the best time to have children?
Mason thinks that graduate school is a
good time to have children, because students’
schedules are more flexible. “There are not
enough graduate student parents out there,”
says Mason. She wants to attract and encour-
age graduate student parents at Berkeley, and
is trying to create grants, provide housing,
and instate a policy to provide six weeks of
Respondants with Children only
paid leave for graduate students who have
children. Of the graduate student parents
who responded to the survey, all agreed that
graduate school is one of the best times to
have children.
Daniela Kaufer had her daughter while
she was a post-doc. “There is no ‘good time’
but during a post-doc it is easier,” she says.
“You have more flexibility.” Kaufer returned
to work when her daughter was three months
old. She set up experiments in the lab in the
morning, went home in the afternoon, and
returned to the lab at night to finish the ex-
periments, often working until one in the
morning.
Dr. Rosemary Gillespie, now a tenured
faculty member in the department of envi-
ronmental science, policy and management,
had one child while she was a new faculty
member at the University of Hawaii, and one

45
 Family Status of Tenured Faculty* balances,” she says. “Universities are starting
to compete to put in place family friendly
policies, where they didn’t have them be-
Mind the Gap

fore.”
Mason also wants to develop re-entry
post-docs for women who took time off to
have children and want to return to aca-
FEATURE

demia. She has recently received a grant from

the Sloan Foundation to study re-entry to
academia.
When asked what the university could
do to make being a parent easier, Kaufer said
the university should provide more daycare
services. “There is only one place on campus,
and they take only 24 kids per year.” The sur-
Graphics (facing page) from [2] , (this page) from [1] , see cited references

vey respondents with children reiterated the

need for on-campus childcare. On-campus
daycare is preferable because it makes com-
muting more convenient, parents are nearby
in the event of an emergency, and the daycare
service offers extended hours, which are nec-
essary when faculty work late or teach early
Tips for successfully balancing career and family, classes. “Next semester, I will teach a class at
8 AM” says Kaufer, “but my daughter’s school
from Dean Mason and others:
doesn’t open that early.” Clearly, childcare is
-Never lose contact: Keep up your networks, work part time, stay on top of the literature, make contributions something that the university could improve
by writing papers and articles, go to meetings. and expand upon.
Many university policies have met with
-The women who are most successful don’t drop out for any period of time. resentment from people who have chosen
not to have kids. One survey respondent put
-If you have children, get help. Don’t try to prove that you can do everything. Hire someone to help with it very clearly:
housework and/or childcare (and worry about paying for it later).
A colleague who just had a baby said that she
- When applying for faculty jobs, consider the family-friendliness of the university. is on a kind of maternity leave where all she
has to do is her research but is free of admin
-When interviewing for an academic job, don’t voluntarily disclose your own family plans–search committee and teaching duties but still gets paid. What?
members are not even supposed to ask you. If you are asked, be straightforward. That sounds like the dream job. If true, that’s
just wrong, and unfair. Instead of rewarding
those of us who make the serious sacrifice of not
child just before tenure. Says Gillespie, “I re- at all (2). However, a second study by Mason having children for our research, it feels like we
member another faculty member saying to and Goulden shows that waiting to get ten- get penalized.
me that I was so brave to have a baby before I ure before having children is not the answer
had tenure ... not something you really want for everyone. They surveyed the entire lad- However, flexible leave options don’t
to hear, as you don’t feel at all brave!” Other der-rank faculty of the UC system, and found only benefit parents. The availability of paid
faculty members were very supportive of her that 40 percent of women said they had fewer and unpaid leave to care for family mem-
decision to have children. “I would take each children than they wanted, compared to 20 bers could be used by all faculty to care for
kid when young to meetings, and would percent of men (6). Women who wait to have an ailing spouse or relative, not just faculty
breast feed them at every meeting,” she says. children until they have tenure run the risk of with children. Likewise, a flexible part-time
“People got very used to that.” Her advice on running out of time. option could be used by any faculty in the
the best time to have children? “There never event of health problems or as they approach
is a ‘best time.’ So don’t wait until it’s too Freeze your tenure clock or freeze retirement. UC Berkeley has instated new
late.” your eggs? family-friendly policies, which allow faculty
But many women do wait, and have who have or adopt children to “freeze” their
children after they receive tenure. From a ca- Mason and Goulden have made sug- tenure clock for a semester or two. “Freezing
reer point of view, this is a good strategy. Ma- gestions that would make universities more the tenure clock is the only thing that is going
son’s study shows that women who have late equitable workplaces for male and female to make a difference,” says one mother. How-
babies have career trajectories that look more parents. Mason thinks it is up to universities ever, these options are underused, says Ma-
like those of women who don’t have children to develop “a culture that encourages family son, because people are afraid to use them.

46
Options that offer flexibility for families need Report from the National Academy of Sciences:
to be respected. Says Gillespie, “just before I Beyond Bias and Barriers: Fulfilling the Potential
had [my oldest child], I went to the Director of Women in Academic Science and Engineering

Mind the Gap

of our research unit in Hawaii and asked if I
could go part time. His response was that it http://www.nap.edu/catalog/11741.html
didn’t make a difference... So whether or not
I’d taken time off, I would have to keep up

FEATURE
productivity.” References:
What is needed is a shift in academic 1.M. A. Mason, M. Goulden, Academe 90 (2004).
culture, so that an academic’s choice to have 2.M. A. Mason, M. Goulden, Academe 88 (2002).
a family is valued and respected. Kaufer grew 3.E. Wasserman, The door in the dream: Conversa-
up in Israel, where, she says, “everyone has tions with eminent women in science (Joseph Henry
children. Therefore you are evaluated differ- Press, Washington, D.C., 2000).
ently by your peers.” It is understood that 4.J. S. White, Liberal Education 91, 22-27 (2005).
academics can be parents and can still sus- 5.American Association of University Professors,
tain successful careers. Developing family- Statement of Principles on Family Responsibilities
friendly policies is a step towards changing and Academic Work (AAUP, Washington, 2001).
academic culture. But a more open dialogue 6.M. A. Mason, M. Goulden, Annals of the American
about balancing careers and families is also Academy of Political and Social Science 596, 86-103
necessary. “People just don’t talk about this (2004).
enough,” said one woman. Fifty-three percent
of survey respondents said they did not have
a mentor with whom they feel comfortable
discussing career and family plans. Thirty-
one percent said they did not have role mod-
els who successfully balance career and fam-
ily. Said one respondent, “I’m happy to say I
can think of several woman faculty members
I’d be comfortable speaking to; unfortunately,
this survey just made me realize that none of
them has children. I don’t think I’d get much
useful feedback from such a biased sample.”
This problem has not been solved. But, says
Kaufer, “there is the story of balancing work
and family. But the bigger story is that having
kids is really fun.” The faculty parents inter-
viewed for this article said that if you pursue
an academic career and you have kids, you
make it work, and you never regret it. ■

Jennifer Skene is a graduate student in integrative

biology.

Want to know more?

For full results of the BSR’s survey, check out
our website: sciencereview .berkeley.edu.

Dean Mason’s Homepage:

www.grad.berkeley.edu/deans/mason

The UC Faculty Family Friendly Edge:

http://ucfamilyedge.berkeley.edu/
index.html

47
Reach new heights with BSR
Are you fascinated by the world of science? Do you want to write
about scientific discoveries happening at Berkeley? Then join the
Berkeley Science Review! We’re a graduate student publication
created by students who are passionate about the research
happening at our university. We’re always looking for new
editors, writers, photographers and layout designers. Could
that be you? Visit us online to find out what we’re all about!

sciencereview.berkeley.edu
 The Shangri-La Diet
The Shangri-La Diet: The No Hunger,

A Spoonful of Sugar
Eat Anything Weight Loss Plan
by Seth Roberts
Putnam Adult:2006. 208pp. $19.95

book review

P aradise might be a simple, quiet tropi-
cal island. Perhaps it’s a land where the
people are peaceful, and there is no pain
or taxes. Paradise might be right where you
are—if only you could eat whatever you
want. If this last description works for you,
then UC Berkeley psychology professor Seth
Roberts may hold the key to your Shangri-La.
The Shangri-La diet, according to Roberts’s
book, is “almost as easy as taking a pill, and a
hundred times safer and less expensive.” Even
better, it lets you eat whatever you want.
Michelle Hardesty, special to BSR
Panisse or whatever pizza is offered at The
Cheese Board, but you simply won’t have the
appetite for it.
The diet is scientific in the sense that
it is based on the theory of body weight set
point, a concept that has been around for
a while, but still stimulates debate among
metabolism researchers. The idea is that the
body actively maintains a relatively constant
weight (the set point). Hormones like leptin
and neuropeptide Y act to maintain the set
point by affecting appetite, basal metabolism,
BOOK REVIEW
The trick, then, is to learn how to reset
the set point. In The Shangri-La Diet, Roberts
postulates that the flavor of food, through
associative learning, affects the set point and
therefore weight. Roberts says that familiar,
strongly flavored foods that are digested
quickly, like soda and doughnuts, increase
the body weight set point when the body
Roberts asserts that all
you have to do to lose
weight is drink a few

In The Shangri-La Diet, Roberts asserts and body temperature.

that all you have to do to lose weight is
drink a few hundred calories’ worth of sugar
water or extra light olive oil a day. He says
that consuming flavorless, calorie-containing
foods lower an individual’s body weight set
point (the weight the body naturally “wants
to be”), thereby decreasing appetite, food
photograph by
A newer idea is that the body weight
set point system is malleable. If the set point
hundred calories worth
could be lowered, then the body would force of sugar water or extra
itself to lose weight to achieve its new set
light olive oil a day.
point. For example, if a man weighing 220 lbs
were able to lower his set point to 170 lbs, his
appetite would naturally decrease, his basal “learns” to associate the flavor of these foods

consumption, and ultimately weight. On metabolism would naturally increase, and he with calories. The more frequently the food
the Shangri-La diet you are allowed to eat would lose weight until he reached his new is consumed, the stronger the flavor, and
whatever delicious dish is presented at Chez set point of 170 lbs, with little effort. the faster the food is turned to calories, the
stronger the flavor-calorie association.
Unfamiliar, bland, or more slowly
digested foods, on the other hand,
don’t form such flavor-calorie
association in your
body. According
to Roberts, these
foods—like extra
light olive oil and
sugar water—ac-
tually lower body
weight set point.
So, to lose weight,
all anyone needs
to do is drink a
few tablespoons
of olive oil per day,
and let the body

Olive oil—the next diet supplement?

Psychology professor Seth Roberts
suggests a tablespoon of extra light olive
oil a day will keep the pounds away.

49
 The Shangri-La Diet
BOOK REVIEW
weight set point do the rest.
While the bulk of experimental evidence
for the diet comes from self-experimentation
by Roberts and several others, Roberts says
his theory explains results of previous studies
that “cannot be explained by current theories
of metabolism.” For example, one experiment
by Israel Ramirez showed that young rats
given wet food gained more weight than rats
given dry food. The Shangri-La theory says
that wetting the food “both increased its flavor
and speeded up its digestion, thereby leading
to stronger flavor-calorie associations.” But
it’s not necessarily true that this result can’t be
explained without the Shangri-La theory—if
wetting food makes it taste better, perhaps
the rats just wanted to eat more of it.
Ultimately, the book does not present as
much rigorous evidence for the diet as you
might expect from a UC Berkeley professor
who has developed a diet “based on science.”
Roberts has not conducted any controlled
experiments to show that the diet works,
nor any to support the physiological theory
behind the diet, and he has no plans to do
so. Roberts is already convinced that the diet
is effective.
50
The diet seems to have worked for him,
and for at least some of the dieters that have
weighed in at his website (sethroberts.net).
But nutrition experts remain, for the most
part, unconvinced. Nutritional biochemistry
professor and MD Marc Hellerstein said the
theory behind the diet makes “no sense,”
and there is no reason to think that flavor-
less, calorie-containing foods could affect the “This is like putting a man on the
regulators of set point. Professor Greg Aponte, moon when Southwest Airlines
an expert on satiety signal neuropeptide Y, is is already flying there every hour,
equally skeptical. But, Roberts reminds us, handing out peanuts.”
novel ways of thinking are often disregarded
at first. —Nathan Lewis, Professor of Chemistry
It comes down to this: Seth Roberts at Caltech, at the Molecular Foundry
believes the diet works, and invites you to User’s Workshop, comparing the chal-
try it. Certainly, as he points out in the book, lenge of converting solar energy to fuels
in a way that’s economically competitive
you have little to lose; neither sugar water
with cheap fossil fuels.
nor extra light olive oil pose particular health
risks. But until the diet—or the theory be-
hind it—has been tested more rigorously, it’s “Serendipity is like looking for a
unlikely that it will gain much support from needle in a haystack, and instead
biochemists or nutritionists. finding the farmer’s daughter.”
—Walter Gehring, while discussing his
Alisa Gray is a graduate of the department of famous discovery of a gene that controls
nutritional science and toxicology. eye development in fruit flies
 quick facts about
quicksand
who knew?
Y ou are walking through the jungle on an ad-
venturous trek, dodging insects and slipping
through dense foliage. The air is thick with humid-
ity, and strange sounds reverberate all around you.
You’re a little disoriented, but you persevere. And
just when you think you’ve reached your destination,
you walk into a patch of quicksand. “Aw, nuts,” you
say to yourself. The first thought that goes through
your mind is that you are likely to meet the same
fate as similar adventure-seekers in horror movies,
sinking and drowning in quicksand. But here’s the
thing: While you are certainly in some amount of
danger, it’s not quite what you expected.
What we typically think of as quicksand is a
mixture of sand, clay, salt and water—so much water,
in fact, that the sand grains are fully in suspension
and can no longer support any weight. Quicksand
typically forms near water sources, such as rivers,
swamps, lakes, and oceans. Earthquakes can also
increase underground water pressure, forcing
the formation of quicksand on the surface.
Quicksand is rarely deeper than a few feet,
though even if it were, it would be difficult
to completely sink below the surface.
Quicksand is quite dense compared with
normal water. If you jumped in a backyard pool,
you would barely float back to the surface. That’s
because the average density of the human body is
very nearly equal to the density of water (after all, hu-
mans are essentially big bags of
water). This
is how buoyancy
works; objects less dense
than the fluid they displace
will float. If you jumped into the
dense salt water of the Dead Sea, you
would float much more easily. Humans
are thus quite buoyant in quicksand
relative to normal water, which is
contrary to the common idea about
quicksand. So far so good, it seems like
you should float to the surface.
Of course, reality is a little more
complicated than that. As reported in a recent
Quicksand
Who KnEW?
Nature article by Daniel Bonn and colleagues, the
presence of salt within the quicksand mixture heavily
compromises its stability. In particular, a slight distur-
bance (such as you falling face first) causes the sand
grains to lose their stable organization and quickly
flow downwards within the quicksand mixture. Bonn
compares this action to toppling a stack of neatly ar-
ranged oranges—one small push and the pile comes
tumbling down. This downward flow segregates the
quicksand into a water-rich layer above a sand-rich
layer. It is this separation that causes the
problem—while you won’t sink in
the dense salt water, any part of you
stuck the sand-rich layer will be almost
impossible to liberate. To pull just your foot
out of quicksand, you would need a force
equivalent to lifting a midsize car!
So the danger of quicksand isn’t that
you will sink and drown, but that
you will be trapped and die
of dehydration (or if you
happen to be by the ocean,
drowned by a rising tide).
Not all is lost, however. If you
manage to remain calm and still,
the sand particles will eventually resettle
into their original organization, and you
will float to the top. At this point, your best bet
would be to grab a strong vine and very slowly
pull yourself out. Just make sure
it’s a
vine and
not an
anaconda!
Louis-Benoit Desroches
is a graduate student in
astronomy.
Want to know more? Check out
the Nature article: Khaldoun, A.,
Eiser, E., Wegdam, G.H., Bonn,
D. Nature, 437, 635 (2005).
Artwork by Jennifer Alba Bensadoun
51
 BERKELEY
science
review
sciencereview.berkeley.edu

52