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Spring 2005 Issue 8
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 from the editor

BERKELEY DEAR READERS,

science At a recent lab meeting, before moving on to weighty scientific matters, we were discussing
popular music. More specifically, we were discussing unpopular music.

review “Steely Dan,” said Amber, who as it happens is the BSR’s proofreader. “They’re the band
no-one likes.”
But I like Steely Dan, I said.
“You don’t count,” said Amber.
Perhaps. But as I write this I have some Steely Dan lyrics going around in my head:
Editor in Chief
“The weekend at the college didn’t turn out like you planned
Kaspar Mossman The things that pass for knowledge, I can’t understand.”
Managing Editor If you’re a graduate student, you’ve spent considerably more than a weekend in pursuit of
your degree, and you may start reeling when you contemplate the years that have passed and
Dula Parkinson
the years that remain (definitely not like you planned). You’ll find you’re in good company
Editors when you read Loren Bentley’s feature “Prisoners of the Ivory Tower,” on page 42. Every time
I look at it, I want to quit the BSR and rush back to my lab bench.
Michelangelo D’Agostino But all those weekends of research do add up to some spectacular science at UC Berkeley
Charlie Emrich and LBL, and the mission of the BSR is to bring those stories to a wide audience. Our authors
are experts in their fields and writers who excel at telling the story of Berkeley science, making
Padraig Murphy
it accessible to non-specialists like you and me. Here are just a few stories you’ll find in this
Jess Porter issue:
Tracy Powell On page 34 you can read how LBL’s new synthetic biology department may one day create
wholly new forms of life to produce medicines that cure major human diseases.
Sarita Shaevitz For all the times you wondered what it would be like to have taste receptors all over your
body (it won’t take you long to realize it’s a bad, bad idea), the story on page 10 is for you.
Art Director
Some animals do have taste receptors all over their bodies, and surprisingly, the way these
Kaspar Mossman tastes map into their brains is the same as it is in mammals.
UC Berkeley’s new chancellor Robert Birgeneau is a physicist who is still active in research
Assistant Art Director despite his administrative duties. The BSR interviewed him to find out how he balances
Stephanie Cady work and…well, more work, and to find out exactly what “smectic” means. You’ll find the
interview on page 32.
Layout Editors The BSR is still produced entirely by volunteers, most of whom are UC Berkeley
Wendy Hansen graduate students. We welcome contributions from aspiring writers, artists, designers,
and editors—check out our website at sciencereview.berkeley.edu, then email us at
Allon Hochbaum sciencereview@gmail.com. And of course, there’s no better way to support our great coverage
Bryan Jackson of Berkeley science than to send money!
Jess Porter Enjoy the issue,
Tracy Powell

Proofreader
Amber Wise

Printer Kaspar Mossman

Sundance Press
p.s. Steely Dan rocks.

© 2005 Berkeley Science Review. No part of this publication may be reproduced, stored, or transmitted in any form without express permission of the publishers.
Published with financial assistance from the Office of the Vice Chancellor of Research; Lawrence Berkeley National Lab; the Department of Physics; the Office of
the Executive Vice-Chancellor and Provost; the Graduate Division; the College of Natural Resources; the Space Sciences Laboratory; the School of Journalism; the
Biological Sciences Division, College of Letters and Sciences; and the Associated Students of the University of California (ASUC). Berkeley Science Review is not
an official publication of the University of California, Berkeley, or the ASUC. The content in this publication does not necessarily reflect the views of the University
or the ASUC. Letters to the editor and story proposals are encouraged and should be e-mailed to submissions@berkeley.edu or posted to the Berkeley Science
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C O V E R : A P E A C O C K M A N T I S S H R I M P S M A S H E S A PA N E O F G L A S S W I T H I T S T R A D E M A R K
S T R I K E . S T O R Y O N PA G E 6 . [ P H O T O : R O Y C A L D W E L L ] BERKELEY SCIENCE REVIEW 3
 SPRING 2005 ISSUE 8

BERKELEY
science FEATURES
review

26 Zoom with a View

A tour of the Golub antique
microscope collection
by Angie Morey

34 Intelligent Design
Playing with the building blocks
of biology
by Alan Moses

42 Prisoners of the
Ivory Tower
Serving five to life
in academia
by Loren Bentley

4 BERKELEY SCIENCE REVIEW

DEPARTMENTS
CURRENT BRIEFS

8 In the Garden of Good and Evil

Mushroom hunters can tell the difference
POLICY
by Jennifer Skene
19 Strange Fruit
10 Flies Taste Like Mammals California counties have a love-hate relationship
Vertebrates, invertebrates encode taste with GMOs
by Cheryl Hackworth
with the same “molecular logic”
by James Endres Howell
UNIVERSITY
12 Pull My DNA
32 Meet the Chancellor
...with the world’s smallest tweezers
The BSR puts the Birge back in Birgeneau
by Merek Siu
by Tracy Powell and Steven Bodzin

13 Sweeping CO2 Under the Rug

The science of geologic sequestration
by Rebecca Sutton

15 Who’s Your Daddy?

Survival of the fittest means
something different to frogs
by Allison Drew

17 BOINC!
Do try this at home
by Michelangelo D’Agostino

6 Labscopes 49 Read any good books lately?

Kapow! The shocking reason for the success
of The Da Vinci Code
Bold Vision
Fat is Beautiful
50 Letter From Ecuador
Like a Rock
Water, water everywhere...but
what’s the fecal coliform count?
41 Book Review
Race: the Reality of Human Differences

BERKELEY SCIENCE REVIEW 5

 LABSCOPES
Kapow! {COVER STORY}

A LTHOUGH crustaceans may get a bit punchy as they approach

their stovetop demise, few would have thought to ask the
mantis shrimp—a distant cousin of the lobster—for insight into
the fine art of the uppercut. But as Sheila Patek, Wyatt Korff,
and Roy Caldwell in the Department of Integrative Biology have
discovered, the mantis shrimp strike, which packs the equivalent
force of a .22 caliber gunshot, may be one of the fastest animal
movements ever observed. Mantis shrimp use their strike to
smash open hard-bodied prey such as snails and crabs. In order to
glimpse this feat, Patek’s group negotiated with the BBC to borrow
equipment capable of recording these animals at a whopping
5000 frames per second. The resulting observations solved the
long-standing puzzle of how these creatures are able move so
quickly: they use a unique spring-loaded click mechanism, which
PHOTO: ROY CALDWELL “looks basically like a Pringle” according to Korff, a graduate
student involved in the project. The researchers also observed a
rare phenomenon known as cavitation, which, Patek says, “occurs
when water vaporizes under low pressure, releasing both light and
sound—a consequence of the extreme speed.” Next time you stop
in at the Monterey Bay Aquarium, be sure to take a closer look at
these remarkable critters, but remember to keep your hands away
from the glass.
—Brendan Borrell
Bold Vision Want to know more? Check out movies of the shrimp strike at ist-
socrates.berkeley.edu/~patek/shrimpMechanics

L IKE couch potatoes everywhere, neuroscientists can now

grumble if they have to get up, because three Berkeley researchers
just handed them their own remote control. Rich Kramer and
Ehud Isacoff from the Department of Molecular and Cell Biology
and Dirk Trauner from the Department of Chemistry have come
up with a way to control neuron signaling from a distance, using
a synthetic ion channel that they can switch on with a beam of
light. Embedded in the cell membrane of a neuron, the channel
is blocked by a molecular gate until it’s exposed to ultraviolet
light. The gate then folds back like an accordion, triggering the
P H O T O C O U R T E S Y: PA R A M O U N T P I C T U R E S

neuron to begin signaling. Kramer, Isacoff, and Trauner will use

their invention to study the way neurons talk to each other. This
is also an exciting step toward artificial vision: in certain forms of
blindness, photoreceptors in the retina cannot respond to light,
although the rest of the vision pathway remains intact. Patients
would rely on an electronic eyepiece to translate natural light into
patterns scanned onto the retina. Synthetic channels could then be
used to restore light sensitivity to neurons in the retina, bypassing
failing photoreceptors and restoring visual function. —Jess Porter

Want to know more?

“Light-activated ion channels for remote control of neuronal firing,”
Banghard et al., Nature Neuroscience 7, pp. 1381-1386 (2004).

6 BERKELEY SCIENCE REVIEW

 LABSCOPES
Fat is Beautiful

T HOUGH reminiscent of the tie-dyed T-shirts on Telegraph

Avenue, patterns like this arise from a very different
source—interactions among proteins and fats (lipids), biological

I M A G E CO P Y R I G H T ( 2004 ) N AT I O N A L
molecules found in all living cells. Raghuveer Parthasarathy, a
Miller Postdoctoral Fellow in Jay Groves’s lab in the Department

ACADEMY OF SCIENCES, U.S.A.

of Chemistry, investigates the relationship between proteins and
cell membranes, which are double-layered lipid structures richly
studded with proteins, sugars, and other molecules. When two
cells come together—as in some types of immune responses—their
membranes interact to form a junction. To better understand these
interactions, Parthasarathy creates an artificial cell-cell junction
out of two lipid bilayers sandwiched together. Labeled proteins
within one of the layers get pushed into dense zones radiating
out from the point of contact, which can then be photographed.
The pattern formation is quick and stable, taking only about 100
milliseconds and lasting for tens of minutes. Beyond looking
cool, these patterns may help shed light on the complex protein
reorganizations that occur when real cells come together.
—Sarita Shaevitz
See more phat pictures at: groveslab.cchem.berkeley.edu

Like a Rock

L IKE a desert wanderer, UC Berkeley astronomer Geoff Marcy

seeks water, but his search is not on this planet. Using the
powerful Keck Telescope atop a dormant Hawaiian volcano,
ART: JENNIFER BENSADOUN

Marcy searches for new planets by detecting small, cyclical shifts

in the wavelengths of starlight. These “Doppler shifts” are caused
by compression and expansion of light waves that stream from
stars as they wobble, drawn ever so slightly toward an orbiting
planet. Recently, Marcy discovered a planet the size of Neptune—
small enough to have an Earth-like, rocky surface—circling a dim
red star near the constellation Leo. Planet and star are separated by
just 3% of the distance from the Earth to the Sun. Because they’re
so close, the orbiting planet exerts its own tiny gravitational tug
on the star, pulling it in small circles at just 40 mph. (Remarkably,
astronomers can distinguish subtle changes in the light of a star 33
light years away, as it wobbles at speeds too slow for our highways.)
The light side of the planet sizzles at 340°C, while the dark side
endures a chilly –100°C or below. “The most intriguing aspect,”
notes Marcy, “is the possible domain in between the hot and the
cold side, where the temperatures, as Goldilocks would say, are
just right.” Just right for liquid water, and perhaps even life, to
exist.
—Rebecca Sutton
Want to know more? Learn more about this and other rocky
planets at www.exoplanets.org

BERKELEY SCIENCE REVIEW 7


In the Garden of
Good and Evil
Mushroom hunters
can tell the difference
T HE Bay Area is the perfect habitat for
mushroom hunters. The culture of
culinary obsession, the warm and moist
winter climate, the abundance of conifers
and hardwood trees, and even the region’s
relaxed attitude toward experimenting
with mind-altering substances... But who
are the mushroom hunters, and how can
you, the aspiring mushroom hunter, join
their ranks?
Mushroom hunters come in all ages,
with varying degrees of affinity for
mushroom-themed clothing. They seek
wild fungi for their taste, medicinal
qualities, or psychoactive effects. For
them, mushroom hunting is more than
a hobby. It has to be, explains Tom
Bruns, a professor in the Department of
Plant and Microbial Biology: “Calling
them amateurs doesn’t do them justice.
These people are very well informed.”
Mushroom hunters must be good at
what they do, because misidentifying a
mushroom could be fatal.
While the East Bay is home to edible
wild chanterelles and porcinis, it is also
home to a number of toxic mushrooms,
which will make you sick, and poisonous
mushrooms, which can kill you. The
Ramaria sp., Jackson State Forest.
8 BERKELEY SCIENCE REVIEW
CURRENT
poisonous varieties are often
dead ringers for other edible,
tasty species. True mushroom
hunters know their mushroom
biology, and are well aware that
the size, color, texture and odor
of the stalk, cap, or gills can
be used to distinguish between
species. Some species change
color when they are bruised or
sliced in half and their juice
oxidizes. Other species can only
be identified after microscopic
spore analysis. It’s a tricky
business, which requires more
than just a simple key or field
guide.
How can you join these
mushroom hunters and dine
on wild porcini risotto without
worrying about getting sick or
dying? The most interesting
option by far is to sign up for
Tom Bruns’s course, California
Mushrooms, PMB 3. Offered Amanita calyptrata—photo taken in the Jackson State
in the fall, the course takes advantage of Forest, on a fieldtrip for California Mushrooms, PMB 113.
the early part of the mushroom season
(which stretches from October through
March, peaking in December and wild have diverse methods of obtaining
January). Students collect and learn to food. Mycorrhizal fungi form symbiotic
identify over 50 genera and build their relationships with trees, providing them
own extensive collections throughout the with nutrients and receiving carbon in
semester. exchange. Parasitic fungi get carbon
Mushrooms are the fruiting bodies of from plants but give nothing in return.
fungi and exist to produce and disperse Saprophytic fungi obtain their carbon
spores. The many types of fungi in the from dead or rotting debris.
Many species of saprophytic fungi,
such as oyster mushrooms and common
button mushrooms, can be easily
cultured. Mycorrhizal species, which
require a host tree, must be found in the
wild; hence the high price of chanterelles
at Monterey Market. However,
mushroom hunters who know the
locations of blewit and porcini patches
can eat like kings—for free. You can dine
with them if you join the Mycological
Society of San Francisco and attend the
Culinary Group’s monthly dinners. The
Society publishes a newsletter and hosts
forays to regional parks where seasoned
hunters pass on their knowledge (though
PHOTO COURTESY: TOM BRUNS
 BRIEFS
perhaps not the locations of their secret
porcini patches).
Another way to become familiar with
mushrooms is to visit the Mycological
Society’s annual Fungus Fair—this year,
it was held at the Museum of California
in Oakland. Here, chefs from renowned
Bay Area restaurants give cooking
demonstrations. Local mushroom experts,
including Bruns, give talks. There are
also booths where you can try your eye
at identifying mushrooms, peruse fabrics
colored with mushroom dyes, learn about
PHOTO COURTESY: TOM BRUNS
medicinal mushrooms, and, at perhaps
the most popular table, learn about the
psychoactive mushrooms that can be
found in nearby parks.
One group of psychoactive mushrooms
contains a chemical called psilocybin,
which, when ingested, is converted to
psilocin. Psilocin is structurally similar
to serotonin, a chemical naturally present
in the brain. It is thought that psilocin
changes the brain’s signal-to-noise ratio.
Stimuli that the brain usually considers
to be noise are instead considered to
be signals, resulting in synesthesia, the
simultaneous perception of more than
one sense. Two species of mushrooms
that contain psilocybin grow in the Bay
Area: Psilocybe cyanescens and Psilocybe
fibrilosa. Both are small and brown, and
resemble several species of poisonous
mushrooms.
The psychoactive Amanitas, those
Alice-in-Wonderland-ish red mushrooms
with white polka dots, comprise a
separate group. Their active ingredient
is the chemical muscimol. Amanita
muscaria can be found in the Bay Area,
but they contain a small amount of
muscimol and a large amount of toxic
compounds that make people sick.
Amanita muscaria from Eastern Europe
contains more muscimol, resulting in
stronger psychoactive effects and greater
popularity.
At a talk at this fall’s Fungus Fair,
amateur mycologist Debbie Viess warned
that while mushroom hunters may be
familiar with the species present in the
Bay Area, they shouldn’t attempt to show
off their skills in other regions: “This absolutely right.” Investigating historical
knowledge doesn’t travel to other places.” descriptions, herbarium specimens, and
Perfectly edible mushrooms from the genetic data, she found that the first
East Coast, Europe and Asia have toxic confirmed California specimen of the
or poisonous look-alikes here in the Bay Death Cap was collected in 945. “There
Area. Recently, an Oakland resident died were probably multiple introductions of
after eating Amanita phalloides, the Death this species,” she says, because Amanita
Cap mushroom, which she mistook for phalloides in California are not genetically
similar enough to have
come from a single
introduction.
Because of the severe
consequences of a
misidentified mushroom,
aspiring mushroom
hunters are encouraged
to learn their lessons well.
At the final exam for
California Mushrooms,
says Bruns, completely
deadpan, “the students
are presented with three
mushrooms, one of which
is poisonous. They have
PHOTO: JENNIFER SKENE
to eat two.”
JENNIFER SKENE is a graduate
student in integrative biology.
Want to know more?
Visit the Mycological Society
of San Francisco’s website at
www.mssf.org
Visit the Oakland Museum of
California online at
www.museumca.org
Good...or evil? The experts at the Mycological Society
of San Francisco’s annual Fungus Fair will tell you.
an edible species common in her native
Taiwan. “Posters to warn people about
the Death Cap mushroom are printed
in many languages to target immigrant
communities,” says Anne Pringle, a UC
Berkeley post-doctoral fellow.
Recent work by Pringle has shown
that the Death Cap mushroom was
actually introduced from Europe. “There
is a great oral tradition in the amateur
community here,” explains Pringle.
“They thought Amanita phalloides was
introduced—and it turns out they’re
BERKELEY SCIENCE REVIEW 9
 CURRENT

VIDEO IMAGES: ZUOREN WANG

Flies Taste
Kristin Scott and colleagues used the proboscis
extension reflex (triggered when a leg touches

Like Mammals a droplet of sugar water, right) to characterize a

sweet taste receptor gene in fruit flies.

Vertebrates, invertebrates encode

taste signals with the same
“molecular logic”

O n the second floor of LSA, postdoc

Zuoren Wang glues a fruit fly to
a glass slide, its legs wriggling in the
Moreover, the parts of the fly brain
responsible for taste perception likewise
appear to be segregated not only by sweet
air. Working under a microscope, he or bitter, but also by the location of the
dunks its feet into a spherical drop of a taste on the fly’s body.
sugar solution and watches it extend its Taste ranges over only a handful
proboscis in a reflexive feeding maneuver. of “qualities”, each corresponding to
Around the corner, PhD student a particular type of receptor protein:
Aakanksha Singhvi examines transgenic sweet, recognizing sugars and related
flies in which fluorescent proteins compounds; bitter, recognizing a wide
illuminate individual taste cells. This range of plant alkaloids and related
technique allows her to trace those cells’ compounds; salty, recognizing sodium
projections into the fly’s tiny brain and and potassium ions; and sour, recognizing
document the neural anatomy of taste in hydronium ions from acids. Mammals
unprecedented detail. also have a receptor for “umami”—
Those experiments and others—carried “yummy taste” in Japanese—recognizing
out in Kristin Scott’s laboratory in the amino acid glutamate, which in
the Department of Molecular and nature signals a protein source.
Cell Biology and the Helen Wills Scott and her colleagues propose that
Neuroscience Institute and published this relatively simple system leads to a
last summer in Cell—produced two simple pair of behavioral responses: to eat
remarkable conclusions. sweet or moderately salty food sources
First, the insect taste system is and reject bitter, acid, or very salty
organized in much the same way as that food sources. But in flies there are two
of vertebrates. On any particular taste anatomical twists that Scott’s group has
neuron, the taste receptors—surface exploited. First, flies have taste neurons
proteins that bind to small “tastant” on their wings and legs, so they taste food
molecules—will bind only to bitter or at the ends of their appendages and then
sweet tastants, for example, but never turn toward desirable sources to feed.
to both. Flies have, in other words, (Fish, incidentally, have taste receptors
dedicated sweet and bitter taste neurons, all over their bodies; taste researchers
just like we have on our tongues. like to call them “swimming tongues.”)
Second, the female fly’s egg laying organ
also has taste cells, so egg-filled mothers
can deposit their broods directly onto
food sources. “Time flies like an arrow,”
according to Groucho Marx, “and fruit
flies like a banana.”
Clues to how sensory perceptions are
represented in the brain have previously
been found in various sensory systems
in diverse animal models. The neurons
at the center of the vertebrate retina, for
example, make projections to the center
of a certain brain area, while neurons
from the left and right edges of the retina
make connections on opposite edges
of that area. Thus the brain tissues that
process visual signals embody a map of
the retinal image. Similarly, our sense of
touch is represented as a distorted map of
the body surface stretched over the touch
center of the brain. How taste circuits in
vertebrate brains are organized remains
unknown. But researchers presume that,
since the cells of the tongue are organized
by taste quality, the taste center in the
brain is likewise segregated anatomically
by taste quality. The hypothesis, in other
words, is that there are distinct brain areas
that process sweet, bitter, salty, sour, and
umami stimuli.
Scott’s team showed that the fly’s brain
anatomy encodes two qualities of taste

10 BERKELEY SCIENCE REVIEW

BRIEFS
in parallel: what it tastes like, and where
it is on the fly’s body. They observed, for
example, that taste cells on the end of a
fly’s leg send projections further towards
the hind end of the fly’s brain than taste
cells on its proboscis. Furthermore, a
bitter and sweet cell side by side on the
proboscis will project to distinct targets
within the proboscis taste area of the
brain. In general, each taste organ sends
nerves to distinct targets in the brain,
and within those areas, bitter and sweet
neurons seem to connect to distinct
groups of target neurons.
So much for taste representation in
the brain. How does each taste neuron
genetically encode taste sensitivity? The
proboscis extension reflex Wang observes
has been known for 30 years. But he put
it to new use in order to characterize the
function of specific taste receptor genes.
Sixty-eight taste receptors have been
identified in the sequenced genome of the
fruit fly. Scott’s group removed specific
taste neurons by genetically programming
them for death—they drove a diphtheria
toxin gene only in cells that produce
that taste receptor, eliminating all cells
that contain a certain receptor, one at a
time. Then they put these flies to a sweet
and bitter taste test. Using this method
they characterized one bitter and one
sweet receptor. The remaining 66 gene
products are presumed to include sour
and salty receptors, as well as other sweet
and bitter receptors, but none have been
characterized except the two in Scott’s
studies.
With only four taste categories, why
does the fly genome contain so many
taste receptor genes? Probably because
of the molecular diversity of tastant
molecules. While sugars, chemically
speaking, are a relatively simple class of
molecules, the compounds that evolution
has dictated animals avoid—the bitter
tastants, in other words—are remarkably
diverse. It’s now known that in both flies
and mice a single bitter taste cell contains
many different types of bitter receptors.
“This organization,” Scott explains,
“would allow animals to recognize many
different compounds as bitter, without
being able to tell them apart.”
Scott started her career at Berkeley
only two years ago, after a postdoctoral
fellowship in the laboratory of Richard
Axel at Columbia. Axel shared last year’s
Nobel Prize with another former postdoc,
Linda Buck, for the identification of
the genes encoding olfactory (smell)
receptors.
“Our long term goal,” Scott says, “is
to understand the neuronal circuits in
the brain” that underlie taste. In order to
begin to explain taste behavior in terms
of connected groups of neurons, they aim
to identify the individual neurons in the
brain that receive input from taste cells,
and then determine which neurons they
connect to in turn. To trace these neural
circuits, postdoctoral fellow Sunanda
Marella and PhD student Walter Fischler
have been using transgenic flies with
neurons whose fluorescence intensity
changes when they become active. Instead
of having to poke randomly around the
tiny fly brain with electrodes, recording
taste response activity in one cell at a
time, their method will allow real time
microscopic observation of the activity of
whole groups of neurons in the taste areas
of the fly brain—a technique known as
“functional imaging.”
Meanwhile, Scott’s group is screening
for mutants with defects in taste-
mediated behavior. Ultimately, they hope
to identify genes required in the fly brain
for those behaviors and uncover more
clues to the underlying neural circuits and
how they function. “Functional imaging,”
Scott explains, “will be the platform for
all of these studies.”
JAMES ENDRES HOWELL is a graduate student in
molecular and cell biology.
Want to know more?
Check out “Taste representations in the
Drosophila brain”: Wang Z. et al, Cell. 117, pp.
981-991 (2004).
Visit Kristin Scott’s lab at
mcb.berkeley.edu/labs/scott
BERKELEY SCIENCE REVIEW 11

Pull My DNA
...with the world’s tiniest tweezers
M OST people take it on faith that
molecules exist, while a few others
aren’t satisfied until they have seen them
imaged by a microscope. But as Steven
Smith says, “after you’ve looked at these
molecules for a long time you really want
to get your hands on them.”
A fine concept, but a challenging
task if the molecules you’re talking
about are only two nanometers in
diameter ( 20,000 times smaller than a
human hair). Despite these minuscule
dimensions, Smith, a research scientist in
Carlos Bustamante’s lab in the physics,
chemistry, and molecular and cell biology
departments, can stretch, twist and probe
all kinds of molecules with an instrument
called laser tweezers.
Watching Smith work with laser
tweezers is like watching him play a video
game. A monitor shows a view through a
microscope of the two beads he controls:
one is perched atop a pipette, and the
PHOTO: MEREK SIU
Steven Smith is a research scientist in Carlos Bustamante’s
lab in the Departments of Physics, MCB, and Chemistry.
12 BERKELEY SCIENCE REVIEW
other, the “trap bead,” hovers above it.
The pipette is linked to a stage Smith
controls via a red trackball; the trap bead
is held in place, not by a physical object,
but by light from a focused laser beam,
the heart of the laser tweezers. When
Smith moves the pipette bead, the trap
bead starts to follow—it’s as if an invisible
tether is linking the beads.The tether is
a single strand of DNA, with its ends
modified so that it sticks to proteins that
coat the beads. While the pipette bead
is solidly anchored, the laser tweezers
hold the trap bead somewhat loosely, as
if the bead were on a spring. Researchers
observe how the DNA linking the two
beads stretches when they pull on it. By
studying how the trap bead deflects the
laser beam, they can measure the force
on the tethered DNA in piconewtons
(a millionth of a millionth of the force
needed to hold a baseball) and how far it
stretches in nanometers.
Laser tweezers have been especially
useful in the study of proteins that move
along DNA, doing things like reading,
copying, cutting, and unwinding it. Each
of these proteins physically
moves along a DNA double
strand as it performs its
function. By attaching a
bead to one of these proteins,
researchers can use laser
tweezers to play friend or foe
by mechanically helping or
hindering the motor’s motion.
Measuring how speed varies
with force and chemical fuel
supply allows researchers to
investigate the fascinating
coupling between the physical
mechanism and the underlying
biochemistry. A good example
is the “packing” motor of the
virus phi29, which is able to
stuff a long strand of DNA
into a tiny virus shell while
preparing to infect other cells
(imagine putting a ten foot
length of stiff wire in a box the
size of a walnut). Using laser
tweezers, Bustamante’s group
CURRENT
Laser tweezers: a
glass micropipette
holds onto a
polystyrene bead via
suction. The “trap”
bead is held in
place by focused
laser beams. A
strand of DNA
joins the two
beads.
showed that this
is possible because
VIDEO IMAGE: STEVEN SMITH
the motor responsible
for this task is
extremely powerful,
able to work against a
pressure of about sixty
atmospheres—ten
times the pressure
stored in a bottle of
champagne!
These experiments,
Smith says, “take a big collaboration…
You need a biologist or a biophysicist to
tell you what the problem is that’s worth
solving…You need a physicist to build
the optics and to interpret the data…
and you need an architect and a building
manager to build you a basement room
on bedrock.” Since laser tweezers are so
sensitive, “you have to practically build
your building around [them].”
Although on campus versions of
Smith’s tweezers reside in the Bustamante
lab, Ignacio Tinoco’s lab in Chemistry,
and Jan Liphardt’s lab in Physics, the
infrastructure requirements prohibit
standard biology labs from using laser
tweezers. That’s something Smith
wants to change, so he has built the
“Mini-Tweezers,” which take the 4 by 6
foot optical table and associated optics
and cram them into a basketball-sized
package. This portability enables your
“collaborator someplace across the world
to send it back to you in a box.” Smith
expects a commercial version of the
instrument to cost between $00,000 and
 BRIEFS
PHOTO: MEREK SIU
Smith’s “Mini-Tweezers” compress the essentials
of optical tweezers into a package the size of a
basketball.
Sweeping CO2 Under the Rug
The Science of Geologic Sequestration
S ALLY BENSON was skeptical. Five
years ago, when the US Department
of Energy asked this Lawrence Berkeley
National Laboratory engineer to develop
a program to study geologic carbon
sequestration, she described herself
as “agnostic.” Could the capture and
underground storage of carbon dioxide
emitted from refineries and power plants
really loosen the chokehold of this gas on
our climate? Would it be safe? And could
we afford it?
In the end, Benson could not ignore
any means of combating global warming.
By burning fossil fuels over the last
250 years, we have injected nearly 300
billion tons of carbon, most of it carbon
dioxide, into our atmosphere. Carbon
dioxide traps the sun’s heat near the
Earth’s surface in a process known as
the greenhouse effect. In the 990s,
record-breaking heat and devastating
storms triggered international alarm
about the effects of global warming. With
renewable energy production still in its
infancy, geologic carbon sequestration
$200,000, or about the same price as an
atomic force microscope (AFM). Labs
that would consider AFMs for imaging or
high force mechanical manipulation are
the intended market. A prototype of the
Mini-Tweezers is already being used with
improved resolution and reduced drift in
what must be one of the worst rooms for
tweezers on campus. By simply dangling
from the ceiling on a single bungee cord,
the Mini-Tweezers achieves excellent
vibration isolation. Now, the key to
understanding nature’s rubber bands
is Smith’s “basketball” hanging from a
bungee.
MEREK SIU is a graduate student in biophysics.
Want to know more?
Visit the Bustamante lab website at
alice.berkeley.edu for articles, movies, and more.
has been touted as a way to reduce the
P H O T O : R O Y K A LT S C H M I D T, C O U R T E S Y O F B E R K E L E Y L A B
impact of fossil fuels on our climate using
existing technology from the oil and gas
industry.
Five years later, scientific evidence
has created a new convert. Benson
easily admits, “the longer I’ve worked
on [geologic carbon sequestration], the
more persuaded I’ve been that this can
really work.” As director of GEO-SEQ
(pronounced “geo-seek,” for Geologic
Sequestration), she guides public-private
Sally Benson, an LBNL engineer, coordinates
research focusing on the storage end of
joint public-private research on carbon
this capture-and-storage technology. sequestration.
While other groups design energy
production facilities and gas separation carbon dioxide below ground.
methods for carbon dioxide capture, the Fortunately, many good sequestration
GEO-SEQ team explores ways to get the sites are easy to spot. Because oil and
gas underground and keep it there. natural gas are buoyant, reservoirs that
The first step in carbon sequestration is store these fluids can store carbon dioxide
the selection of a site with an appropriate as well. Even more carbon dioxide
underground mineral formation. A good can be stored within saline formations
formation is like a loaf of crusty bread —common mineral deposits permeated
—a dense, impermeable layer topping a with very old, salty water, and topped
mass of porous material. The dense layer, by caprocks. Worldwide, depleted oil
known as the caprock, keeps the buoyant and gas reservoirs and saline formations
BERKELEY SCIENCE REVIEW 13
P H OTO S CO U R T E S Y: S TATO I L
Like the Texas oil reservoir that Benson studies,
underground saline formations can store CO2,
preventing this pollutant from entering our
atmosphere. Statoil’s Sleipner West natural gas
production facility (above) pumps 2800 tons of
CO2 each day into a saline formation beneath
the floor of the North Sea.
could hold nearly two trillion tons of
carbon as carbon dioxide—six times
what we’ve produced since the rise of
industrialization.
To study carbon sequestration, Benson
and her team have injected 700 thousand
gallons of carbon dioxide into a depleted
oil reservoir near the town of South
Liberty, Texas. Sensors above and below
ground detect trace amounts of the gas,
or minute changes in pressure, seismic
motion, or electromagnetic properties.
These measurements reveal the effects of
natural and operational variables (like
reservoir geology and rate of injection,
respectively) on the flow of carbon
dioxide within the reservoir. As scientists
improve predictions of the underground
behavior of the gas, they advance their
ability to find and fill storage sites.
By testing a variety of sensors, Benson
determines which can be used to detect
leaks for commercial sequestration
projects. Seepage through microfractures
within caprocks presents the largest
monitoring challenge, notes Scott Klara,
sequestration technology manager for the
Department of Energy. However, without
14 BERKELEY SCIENCE REVIEW
carbon storage, “we are leaking 00%.”
While Benson initially questioned
the security of sequestration, she is now
satisfied that storage can be quite safe.
It turns out that storing carbon dioxide
underground is a lot like storing natural
gas underground, something industry has
been doing for decades. Existing methods
to control potentially disastrous natural
gas leaks work just as well for carbon
dioxide, though as Benson cautions, “that
doesn’t mean it would be cheap.”
And while most forms of waste disposal
grow more dangerous as containment
structures age, Benson points out that for
sequestration, “it’s actually the reverse;
the carbon dioxide storage actually
gets more and more stable over time.”
Although sequestration initially depends
on the caprock to physically trap the gas,
chemical reactions eventually transform
carbon dioxide into carbonate minerals,
permanent residents of the reservoir.
Benson and her GEO-SEQ team are
not alone. Already, three commercial
projects each store at least a million tons
of carbon dioxide annually. But how
much does geologic carbon sequestration
CURRENT
cost? If power plants used existing
sequestration technology, the cost to
produce electricity would increase by 30
to 70%. With more advanced technology,
the Department of Energy hopes to
reduce the cost of storage to less than
0% of the cost of electricity production.
Measured against the climatic disasters
that may result from global warming,
geologic carbon sequestration should
prove to be an exceedingly wise
investment.
REBECCA SUTTON is a postdoctoral researcher in
environmental science, policy, and management.
Want to know more?
Visit the GEO-SEQ website at
esd.lbl.gov/GEOSEQ
 BRIEFS
Who’s Your Daddy?
Survival of the fittest means
something different to frogs
E LEVEN months of the year the
European common frog’s life is
a bit dull. But for a few weeks each
PHOTO: MIGUEL VENCES
spring some of these usually bashful
amphibians drop their mild manners
to go on a carnal free-for-all. David
Vieites, a postdoctoral fellow in UC
Berkeley’s Department of Integrative
Biology, had been studying Rana
temporaria for over ten years before he
was treated to a rare first glimpse into
their unusual sexual strategies.
Interested in the special adaptations
amphibians must make to survive in
extreme environments, Vieites chose a
study site high in the Spanish Pyrenees.
He worked with this population
throughout his undergraduate and
graduate careers at the University of Vigo
in northwestern Spain. However, it was
not until he finished with his coursework
as a graduate student, and finally freed
from exams in the first weeks of May,
that he witnessed a behavior never before
reported among amphibians.
Most populations of R. temporaria
breed at night, but the low temperatures
at Vieites’s alpine site force these frogs to
breed during the day. This allowed Vieites
to take a front row seat during mating
season.
R. temporaria is an explosive breeder.
Just after the ice melts in the spring,
enormous numbers of male frogs gather
at ponds to mate. Over the next several
days, females will wander by a few at
a time, drawn to the cacophony of
croaks from the males. Males typically
outnumber females by 10 to 1 which
means only a small fraction of the males
(10–20%) will get an opportunity
to mate. The rest will have to wait,
During amplexus, the female frog deposits her eggs while the male frog—clasped to her
back—fertilizes the clutch.
frustrated, for next year.
For frogs, egg fertilization usually takes
place while the male and female are in
amplexus—while the male is clasped to
the female’s back and releases sperm on
her eggs as she lays them. Vieites ob-
served something quite different. While
some males were behaving “normally”
—clasping females and fertilizing eggs
in the usual way—other “pirates” were
sneaking after mating pairs and making
off with their freshly laid egg clutches. At
times, the pirates banded together into
groups, patrolling the pond for unattend-
ed eggs. Unsatisfied with simply grasping
the clutch, some pirates would crawl into
the heart of an egg mass so their sperm
could penetrate every last egg. On aver-
age, pirate sperm fertilized one quarter of
the eggs, but in some cases accounted for
nearly all the fertilization in clutches.
While this behavior clearly confers an
evolutionary advantage on the pirates,
who would otherwise fail to pass on
their genes, it also benefits the females
in two key ways. First, the fertilization
rate of pirated clutches can approach
100% compared to just 70% in singly
fertilized clutches. More fertilized eggs
is good for mom because it means more
of her DNA is passed on. Second, these
higher yield clutches have the advantage
of increased genetic diversity, with some
portion fertilized by the original male
and the remainder fertilized by the
pirate(s). This is also good for mom,
since a more diverse clutch will likely
produce more fit offspring with a greater
chance of surviving to pass on her genetic
information.
The only ones who don’t seem to
benefit from the pirate behavior are the
original males pursuing the “normal”
mating strategy. Quantifying the relative
fitness of the “normal” strategy versus the
pirate strategy will be Vieites’s next task.
Only five or six other species of
amphibians are known to exhibit multiple
paternity, but Vieites believes that this
number greatly underestimates the actual
prevalence of this type of behavior. Very
little is known about the great majority of
amphibian species. R. temporaria is one
of the best-studied species—over 4000
scientific articles have been published
about it over the past 100 years—and yet
BERKELEY SCIENCE REVIEW 15

PHOTO: MIGUEL VENCES
David Vietes first observed this strange mating
behavior at a site high in the Spanish Pyrenees.
16 BERKELEY SCIENCE REVIEW
this behavior remained unknown, and it
would be unknown today if Vieites had
not finally made it up to his study site for
that one crucial week in May.
Unfortunately, our time to fill in the
many gaps in our knowledge about
amphibians may be running out. Vieites
emphasized that while his studies of
amphibians have resulted in many
interesting findings that may have much
to teach us about sexual selection and
evolution, these are overshadowed by a
looming crisis. The World Conservation
Union Global Amphibian Assessment,
a major project on the conservation
status of 5743 species of amphibians, has
discovered that the populations of over
40% of species are decreasing.
Even more troubling, for almost
half of the most rapidly declining
species, populations are dwindling for
no identifiable reason. It is possible to
CURRENT
develop strategies for conserving species
when the decline is due to identifiable
factors such as habitat loss. Without
knowledge of the cause, little can be done
to reverse the slide. Only with further
research can we hope to uncover the
causes, and in so doing, the solutions.
Clearly, there is a wealth of knowledge
still waiting to be mined from further
study—if behaviors such as clutch piracy
are only now coming to light in our most
well-known amphibian species, imagine
what awaits us in unfamiliar places.
ALLISON DREW received her MS in
environmental science, policy, and management
from UC Berkeley.
Want to know more?
Check out “Post-mating clutch piracy in an
amphibian”: Vieites, D. R., et al., Nature 431,
pp. 305-307 (2004).
 BRIEFS
S C R E E N S H O T : M I C H E L A N G E L O D ’A G O S T I N O
BOINC!
Do try this at home
I N THE old days, if you wanted to
be a tiny contributor to the onward
march of scientific progress, you might
have donated your body to science. But
if David Anderson has his way, you
won’t have to wait until you’re pushing
petals to advance the frontiers of human
knowledge—you just have to donate your
dead computer time.
Anderson, a scientist at the Berkeley
Space Sciences Laboratory (SSL) and
former professor in the Department of
Computer Science, directs BOINC—the
Berkeley Open Infrastructure for
Network Computing (boinc.berkeley.
edu). BOINC is a software platform that
makes it easier for scientists to harness
the massive computing resources that
often lie dormant in people’s homes and
offices. In this new paradigm, called
public computing, computational tasks
are chopped into small pieces and sent to
individual members of the public. Your
computer can be looking for aliens or
calculating the temperature of the Indian
subcontinent in the year 2050 while you
sip a cup of tea or cook dinner.
Without a doubt, the best-known
public computing project is SETI@home.
SETI, the Search for Extraterrestrial
Intelligence, looks for signals from
intelligent extraterrestrials in data from
the Arecibo radio telescope in Puerto
Rico. SETI@home was created in 1995
by Anderson and David Gedye, then a
UC Berkeley computer science graduate
student. It was the 25th anniversary of
the Apollo moon landing and Gedye was,
as Anderson puts it, looking for a way to
rekindle the public’s interest in science in
the same way that “Apollo got the public
really galvanized.” SETI@home was their
answer: let people search through the
mountains of Arecibo data on their home
computers, a chunk at a time, and give
them a glitzy screen saver to look at while
it’s happening.
As crazy as it might at first
have seemed, SETI@home
captured people’s imaginations.
It’s been downloaded by over 5
million users in 226 countries,
some 600,000 of whom still
remain active. Together, they’ve
contributed over 2 million
years of computing time. Its
message boards form an online
community where people can
socialize (several couples have
met through SETI@home and
married) and keep track of how
much work their computer
accounts have completed. The
“leader board” generated so much
attention that some users began selling
completed units and successful accounts
on eBay for as much as $275.
While working on the original version
of SETI@home, Anderson quickly
discovered that he and his coworkers
were spending most of their time
building infrastructure to manage the
project: writing code to send out data
packets to people’s computers, running
servers and databases, keeping track
of completed work sent back to the
project, and making sure that nobody
submitted fraudulent results. They lost
a year of science in just setting up the
basics. But in the process, Anderson had
a realization: “Infrastructure is totally
independent of application. Wouldn’t it
be better if we just developed one [system
so that other] projects could start up with
minimal infrastructure?” And so BOINC
was born.
BOINC handles all of the behind-the-
scenes tasks so that scientists can quickly
and easily set up public computing
projects of their own. It’s available free of
charge for researchers and for the general
public to download, and it runs on
Windows, Apple, and Linux platforms.
“The goal of BOINC is that someone can
set up one of these projects really easily,”
Anderson says.
And so far, scientists and the public
have been quick to respond. SETI@home
has switched over to the BOINC plat-
Is ET trying to phone home? The answer may be
hidden in this noise.
form. In August, Climateprediction.net
signed up to use BOINC as well. Based
in the UK, Climateprediction.net aims
to improve long-range climate model-
ing by making very small tweaks to a
model’s parameters and running it again
and again. Thus far, 20,000 users have
crunched through over 2 million years
of Earth’s imaginary future. Their efforts
culminated in a January publication in
Nature showing that the Earth’s response
to increases in greenhouse gases may be
far more dramatic than scientists had pre-
viously expected.
As part of the World Year of Physics in
2005, Einstein@home has been designed
to run on BOINC to search for gravity
waves, the ripples in the fabric of space-
time predicted by Einstein’s general
theory of relativity. If that doesn’t interest
you, you can help design magnets for the
Large Hadron Collider, the world’s next
great particle accelerator at the CERN
lab in Switzerland with LHC@home, or
help figure out how proteins fold with the
Predictor@home project.
From the beginning, Anderson made
it one of BOINC’s goals to allow users
to choose how to allocate their resources
between projects, especially with so many
to choose from. For example, you can
choose to search for gravity waves ten
percent of the time and fold proteins the
other ninety percent. His hope was that
BERKELEY SCIENCE REVIEW 17
 CURRENT
BOINC could “get people to invest some Anderson cautions. While your computer

thought” in the experiments they were
choosing between and ask themselves, “Is
this something beneficial to humanity?”
Dan Wertheimer, an astronomer at
SSL and chief scientist of SETI@home,
calls BOINC “a tremendous way to get
the public involved in science.” Karl
Chen, who worked on BOINC as an
undergraduate and is now a graduate
student in computer science, concurs. “I
ran SETI@home when I was a kid and
my science teacher had it at one point…
It’s good publicity and marketing.”
Individual projects work hard to put
up materials explaining their science
to participants. The Lawrence Hall of
Science has even developed a curriculum
unit for schools based on SETI@home.
Not everyone is in love with the idea of
public computing, though. To Anderson,
many in the supercomputing community
might “equate public computing with
searching for little green men” or scoff
that “you can’t get real work done that
way.” They prefer large centralized
supercomputers or national lab and
university consortia. “Livermore does
testing on nuclear weapons,” Chen says.
“That’s something they won’t run on
people’s home computers.”
“All these things have their place,”
won’t be designing next generation
nukes, it may give scientists access to
unprecedented computing power at
a very low cost, thereby breathing life
into projects that might not otherwise
have been feasible or might not have
been attractive to government funding
agencies.
As computers get faster and faster and
storage space gets cheaper and cheaper,
a larger share of the world’s computing
resources will lie scattered in homes and
offices rather than in centralized facilities.
But when it comes to harnessing this
power through public computing, as
Anderson puts it, “You can’t really buy
it—you have to convince people you
deserve it.” In this way, Anderson and
BOINC may give the public a larger
share and a larger voice in how science
gets done.
MICHELANGELO D’AGOSTINO is a graduate
student in physics.
Want to know more?
Visit BOINC:
boinc.berkeley.edu
Check out “Uncertainty in predictions of the
climate response to rising levels of greenhouse
gases”: Stainforth, D. A. et al. Nature 433, pp.
403-406 (2005).
Quanta
{heard on campus}
“Sleep with your ideas.
Don’t marry them.”
Annelise Barron of Northwestern
University. Center for Analytical
Biotechnology seminar, 1/13/2005
“Twinkling of stars may
be beautiful, but it is
very objectionable in
astronomy.”
Charles Townes, emeritus professor of
physics. IR Interferometry on Old Stars,
3/4/2005
“We built the world’s most
expensive low-fidelity
sound system.”
Steve Block of Stanford University,
explaining how he reconstructed “The
Girl From Ipanema” from angstrom-scale
oscillations of a bead in his laser trap—the
bead had picked up the signal from the
stereo playing in the next room. Optical
Tweezers: Biophysics, One Molecule at a
Time, 10/12/2004

“Those are the units

Einstein used. Dynes per
centimeter, buddy!”
Harden McConnell of Stanford University,
responding to a request that he translate
the archaic units of pressure in a phase
diagram, How Cells Handle Cholesterol,
10/26/2004

18 BERKELEY SCIENCE REVIEW

I
N SEPTEMBER 1999, a group of local activists raided UC Berkeley property. Their
mission: to save humanity and the environment from genetically modified organisms,
or GMOs. The target: two small plots of agricultural land near the university campus.
The damage: row after row of uprooted corn plants. In the end, it was an empty victory;
the guerrillas had mistakenly victimized not genetically modified crops but the innocent
offspring of traditional breeding between conventional parents. Today, the grassroots
struggle to uproot California GMOs continues, but the covert activism of five years ago
has been replaced by sweeping legislative measures voted on by the public at large.

Strange
fruit
California counties have
a love-hate relationship
with GMOs
by Cheryl Hackworth
art by Jennifer Bensadoun

Home from the GMO wars

GMOs, THOUGH broadly shunned by
the European public, are common in
the US marketplace. But even here on
the complacent side of the Atlantic,
they have become increasingly con-
troversial. Simply defined, GMOs are
organisms (most commonly bacteria
or plants) that contain genetic material
from more than one source. For ex-
ample, “Bt corn” is a corn plant with a
bacterial gene integrated into its DNA;
“Golden Rice” is a rice plant that con-
tains daffodil and bacterial genes.
Though often touted as solutions
to agricultural, nutritional, and
ecological problems, GMOs have
also inspired a variety of criticisms.
These range from ethical objections
to DNA manipulation, to concern
about the boundaries of intellectual
property rights, to fears of unintended
environmental or human health
effects. But in the end, both those
who reject these organisms and those
who defend them struggle with two
central questions: who is qualified to
evaluate the effects of GMOs, and who
is responsible for such evaluations?
On whom do we place the burden of
ensuring the safety of our Bt corn or
Golden Rice?
As it stands, no one governmental
agency regulates all aspects of GMOs.
This lack of comprehensive, mandatory
federal regulation is disquieting
to environmental and food safety
advocates. That is why, in March
2004, Mendocino County in northern
California passed Measure H, making

BERKELEY SCIENCE REVIEW 19

 it the first county in the United States
to render it “unlawful for any person,
firm, or corporation to propagate,
cultivate, raise, or grow genetically
modified organisms.” Trinity County,
also in northern California, quickly
followed suit, starting a trend in
California counties to pass this type of
measure.
To counter the anti-GMO push,
Fresno County launched a trend
of its own. Located in the center of
California’s commercial agriculture
belt, Fresno grows a large number of
genetically engineered crops; as a result,
the Fresno Board of Supervisors passed
a resolution “that the County of Fresno
will make every effort to preserve
the choice of using biotechnology
in its county and encourage the
establishment of a state or national
biotechnology policy.” Kings County,
neighbor to Fresno, passed a similar
resolution, emphasizing farmer choice
in the use of GM crops.
As counties rush madly for one
bandwagon or the other, California’s
famously chaotic, grass-roots approach
to legislation is once again breaking
PHOTO: GENEVIEVE SCHIFFRAR
The tassels of a GM corn plant, flowering in a
research plot in northern California.
20 BERKELEY SCIENCE REVIEW
new ground.
Voters have
begun to legislate
scientific issues directly,
and the effects may
eventually ripple through
UC Berkeley research
programs and then the
state (and world) agricultural
communities.
The Letter of the Law
THE measures that made it onto No-
vember 2004 ballots in counties across
the state were a motley bunch. Some
prohibited all GMOs, while others
attempted to outlaw only GM food
crops, making exceptions for GMOs
used in medicine and research. The
penalties for contraband organisms also
differed, some giving the Agricultural
Commissioner power to dole out ap-
propriate punishments. Others, like
Humboldt’s, would have punished
offenders by “confiscation and destruc-
tion of any organisms found to be in
violation,” and imposition of “a mon-
etary penalty and/or imprisonment,”
in essence, turning the cultivation of
GMOs into a criminal act.
Unfortunately for their creators, these
measures were written without much
scientific or legal advice. The lack of
PHOTO COURTESY: UCBIOTECH.ORG
scientific input was evident in such
bloopers as “DNA, or deoxyribonucleic
acid, means a complex protein,” a
quote common to over half of the
voter initiatives. (DNA is composed of
nucleotides, not amino acids.)
In other cases, the legality of some
ordinances was questionable. The
criminalization of growing GMOs
in Humboldt County’s measure was
illegal and resulted in a lack of support
from both sides; it failed to gain voter
approval. Similar measures on the
November ballots in Butte and San
Luis Obispo Counties, despite heavy
financial support from anti-GMO
groups, also failed. In fact, the year’s
three anti-GMO successes were largely
symbolic: Marin county, for example,
has only minimal commercial farming,
Blowin’ in the wind
Gene flow is a result of
the pollination of one
plant line by another. This
is not normally cause for
concern, but it can become
a problem if pollen from a
GMO fertilizes an organic
plant or a native, “landrace,”
variety. Farmers have
several options to control
gene flow into or out of
their fields.
To limit the risk of pol-
len contamination, organic
crops are restricted to grow
on land surrounded by a
substantial buffer zone. The
minimum buffer distance is
set by the federal Associa-
tion of Official Seed Certify-
ing Agencies. But no matter
how wide the buffer zone,
there can never be 100%
certainty that no contami-
nation will occur.
To reduce the risk of gene
flow below what a buffer
zone permits, two tech-
niques are in the pipeline.
In the first, scientists insert
the foreign gene into a cell’s
chloroplast, the photosyn-
thetic compartment in a
plant cell, rather than its nu-
cleus. Transgenes inserted
into this cell compartment
can still produce the de-
sired plant characteristics.
However, the chloroplast is
naturally excluded from a
plant’s pollen. This means
that foreign DNA inserted
into the chloroplast would
remain only with the sta-
tionary, female portion of
the plant body, reducing
the chance of genetically
“polluting” other plants.
Currently, no commercially
sold GM plant utilizes this
technology.
A second technique
involves the insertion of a
“terminator” gene into the
GMO. This gene renders
the pollen from a GMO
plant infertile, preventing it
from forming a new seed in
the event that it does find
its way to another plant.
Farmers’ rights groups
were outraged at the
initial introduction of this
technology, as it was seen
as a way of maintaining
proprietary rights over GM
seeds, forcing farmers to
buy new seed each year. As
a result of the outcry, the
company that developed
the terminator technology
promised not to use it,
even though this method
would drastically reduce
the possibility of gene flow
from GMOs to other plants.

almost all of which is organic. Similarly,
there were no GMOs growing in
Mendocino or Trinity Counties when
they voted to ban such organisms.
Beyond the shaky scientific wording
and legality of the California county
ordinances, questions of practicality
lurk. Whether these laws can even
successfully function on a county-by-
county basis is an open question. Peggy
Lemaux, a professor in the department
of Plant and Microbial Biology,
doesn’t think it will work at all. The
government “used to do [county-by-
county regulation] with pesticides and
it was so horrible because [the farmers’]
land would go from one county to the
next. It’s a very difficult situation for
farmers to deal with.”
But if these measures were created
quickly, with little advice from scien-
tists or lawyers, and they were passed
as a purely symbolic move, why were
people so eager to act? Lemaux thinks
the reason is because the public wants
the government to have a system in
place to regulate this new technology.
“It was born out of people’s frustration
because they don’t know…how to get
the state to move on this. This is their
way to force it.” animal characteristics for thousands of
This has some farmers in Califor- years. GMOs can also yield new crop
nia worried that this series of events lines in a much smaller time frame
has set a precedent for future action. than classical breeding. Additionally,
Sarah Hake, a professor in the Depart- many biotech companies
ment of Plant and Microbial Biology vow to engineer plants
whose husband owns an organic farm with increased nutrient
in Marin County, is disturbed by this composition and greater
trend: “I don’t think California coun- fruit yield. But op-
ties should be setting protocol in the ponents counter these
state or the nation.” She thinks these claims with vehement
laws should be created at the state level criticisms of the eco-
by legislators with help from informed nomics and ecology
scientists. of GMO-based
In the midst of this controversy, bio-
tech companies continue to produce
new genetically modified organisms,
and farmers continue to plant more
and more land with these crops. Given
a choice, with no pressure from non-
governmental organizations, farmers
choose genetically engineered crops
time and again.1
Why have most scientists and farm-
ers welcomed this technology, even in
the face of growing public opposition?
Genetic engineers claim that their new
techniques are no different from clas-
sical breeding and affirm that farmers
have been manipulating plant and

BERKELEY SCIENCE REVIEW 21


agriculture (see sidebars).
Opinion among the faculty at UC
Berkeley varies as much as it does
internationally. In the Departments of
Molecular and Cell Biology (MCB)
and Plant and Microbial Biology
(PMB), researchers regularly genetically
engineer species of bacteria, fungi, and
plants, mostly for research, but some
for eventual commercial use. Peggy
Lemaux and Sarah Hake both make it
a priority to speak to the public about
both sides of the issue. Hake, in a letter
to the residents of Marin County, wrote
that “investigating the benefits and risks
of each GM crop would be much more
prudent than simply saying no based
on fear of the unknown.”
Voicing the opposite side of the issue
are Andrew Gutierrez and Ignacio
Chapela, professors in Environmental
Science and Policy Management
(ESPM), who frequently address
the public about possible problems
with these new crops. Gutierrez, who
studies “non-target” effects of GMOs,
constantly returns to his most basic
argument against these crops: “You
22 BERKELEY SCIENCE REVIEW
need to ask: are they needed, are they
efficacious, and are they economic. In
most cases, you’ll find they are not.”
A pound of prevention?
TO MANY who are concerned with
GMO safety, one of the most
significant regulatory problems is
that the GMO market is dominated
by a few very large companies like
Monsanto and DuPont. These
companies own not only the genetically
modified plants themselves, but also
the technology and information used
to create them for at least the next 20
years. With this monopoly and little
government oversight, such companies
can set their own standards for product
regulation. Many people fear that as
a result, the proper tests are not done
and possible problems with human
health and environmental safety are not
discovered.
Indeed, there is very little enforced
regulation by either the state or the
federal government. As long as the
company selling the product can
demonstrate that the genetically
engineered crop is “substantially
Peggy Lemaux examines some GM sorghum, engineered to be more easily digestible.
equivalent” to its closest classically
bred relative, no additional testing is
required.
Nonetheless, many companies exten-
sively test their products, regardless of
government pressure, for fear of litiga-
tion. In fact, GMOs are tested with
greater rigor than any classically bred
crop currently produced, even though
an overwhelming majority of cur-
rent peer-reviewed data indicates that
GMOs are no more harmful than clas-
sically bred crops.
Frustrated by the success of
anti-GMO initiatives, industry
representatives assert that the
public should be championing less
regulation, not more. Neal Gutterson,
a graduate of UC Berkeley and Chief
Operating Officer of Mendel, a private
biotechnology research company in the
East Bay, thinks genetically modified
crops are already overregulated.
He points to a five-hundred-page
dossier sent by Monsanto to the US
government in support of a new
product. To clear a classically bred
crop for sale, the government requires
far less paperwork. Gutterson argues,
PHOTO: GENEVIEVE SCHIFFRAR
 “[introduction of GMOs to market] is
overregulated based on what is required
to demonstrate safety.” Since there has
been no verifiable demonstration of
any harm to human health,2,3 GMOs
should be regulated at the same level as
classically bred crops.
In contrast, UC Berkeley’s Andrew
Gutierrez supports the implementation
PHOTO: SARAH HAKE

of the precautionary principle,

which questions the ethics of blindly
implementing a new technology. This
principle asserts that if the effects of
a new technology are unknown but
are judged by some scientists to have
negative risks, then it is better not to
carry out the action at all rather than
risk uncertain consequences. In essence,
the precautionary principle would
thus prohibit any further development
or use of GMOs until they could be
shown to be irrefutably safe for the
environment and for human health.
Of course, the demonstration of
irrefutable safety is impossible, but
to help quiet public concerns, many
researchers continue to study the
Sarah Hake’s husband, Don Murch, at Gospel Flats, his organic farm in Marin County.
human health and environmental
safety of these crops. But, according to
Gutierrez, “it’s difficult to get resources
to do those studies. Who provides
the money? The USDA and industry
provide the money,” and these groups
have a vested interest in benign results.
Opponents of the precautionary
principle point out that the principle
can limit any technology because
there are possible negative effects
associated with any new advancement
in science. The principle ignores any
possible benefits of GMOs. Gutterson
claims, “our society would never have
gained wheels if it had been for the
precautionary principle.”
Something that both sides of the
GMO debate agree on is that the
general voting public should not

Old Macdonald had a right

Human rights groups are
concerned that the rights of
farmers, especially those in
the developing world, will
diminish as the popularity
of GMOs increases. The
ownership of these plants
remains with the company
that creates them, not with
the farmers who plant
them.
Because of patents,
farmers are prohibited from
planting saved GM seed.
Most industrial farmers
in the United States who
grow corn or other grasses
already purchase new
seed at the beginning of
every growing season. But
farmers who rely on saved
seed, many of whom are in
the developing world, may
find themselves in legal
trouble with agricultural
companies.
Percy Schmeiser, from
Saskatchewan, Canada, is
one such farmer. He blames
the Monsanto Company for
contamination of his canola
fields. During a regularly
scheduled random check,
Monsanto found that at
least 95% of Schmeiser’s
1,000 acres contained
Round-Up Ready canola
(canola that can grow in the
presence of the herbicide
Round-Up, also sold by
Monsanto).
The company promptly
sued Schmeiser for the
profit he had made on his
herbicide-resistant canola.
Schmeiser countered
Monsanto by claiming that
he gained no advantage
from the GM canola since
he had never sprayed it
with Round-Up. Schmeiser
also emphasized that
most patents do not
uncontrollably find their
way into the possession of
an unlicensed individual.
But Monsanto insisted
that regardless of how the
gene found its way into
Schmeiser’s canola, the
farmer had infringed on its
patent.
After listening to both
sides, the judge ruled that
the only way Schmeiser’s
fields could contain 95%
GM crops was if he had
in fact sprayed them with
Round-Up and then looked
for resistant plants. Even if
the crops were initially the
result of contamination,
Schmeiser had intention-
ally selected for Monsanto’s
proprietary organisms.
The precedent is clear: in
Canada, the company owns
the rights to any plant con-
taining a patented gene, re-
gardless of how it got there.

BERKELEY SCIENCE REVIEW 23

 The granules of GM sorghum tissue in this petri
dish will be treated with hormones and develop
into full-grown plants.

modified species illegally grown GM plants imported

(see sidebar “Blowin’ from the US could contaminate
in the wind”). indigenous plant lines in Central
Contamination America, where many varieties of corn
could occur if are grown on small family farms. These
a genetically plant lines, known as landraces, are
engineered genetic warehouses for traits that could
plant pollinated be classically bred into US corn lines
a non-GMO to confer desired characteristics. After
plant, thereby random sampling in the maize fields in
creating fruit or Central America, Chapela discovered
grain containing that genetically engineered traits had
a genetically already found their way into Mexican
engineered gene. landraces.
This process Although Chapela’s scientific
is known as methods have been extensively
“gene flow.” criticized, few scientists would dispute
Contaminated fruits his conclusion that contamination
or grains would be of the land races in Mexico has
grown and shipped already occurred. The extent of the
as non-genetically contamination, whether it can be
engineered stopped, and how to eliminate the
foods, and genetic pollution that exists, are all
without complex areas that require further study.
biological tests,
consumers would Closer to home
be none the wiser. THE city of Berkeley, located in
Understandably, this Alameda County, includes UC Berkeley
makes many farmers as well as a large number of private
directly decide how to regulate GMOs. uneasy, especially those who farm biotechnology companies that may
PHOTO: GENEVIEVE SCHIFFRAR

Rather, scientists and legislators should
work together to create these laws.
As Gutierrez states, “I don’t think the
public is sufficiently informed on the
issues.” Gutterson agrees, saying, “it’s
an act of democracy, so you can’t argue
with that, but you need a more expert,
informed view. The voters can be
misguided.” Instead, he thinks “we look
to the federal government to regulate
complex issues and I think that’s the
right place to go. The USDA and FDA
need to be given a mandate.”
The gene’s out of the bottle
ANOTHER major concern surrounding
GMOs is the possibility that they will
genetically contaminate other crops, be
they organic plants grown in a nearby
field or wild relatives of a genetically
organically. With even the possibility of
this contamination happening, organic
farmers stand to lose value in US and
European organic markets.
The threat to wild relatives may
be even more serious. Wild relatives
of cultivated plants are considered
unlimited reservoirs of genetic diversity
that can be bred into contemporary
crop lines. Genes stored in natural
relatives can confer traits such as
increased flavor or enhanced disease
resistance to a new pest. Farmers have
resorted to these wild relative gene
reservoirs during the entire history of
agriculture, and they continue to do so
today.
Ignacio Chapela was one of the first
scientists to address concerns over gene
flow. Chapela believed that pollen from
be affected by new laws regulating
genetically modified organisms.
Berkeley residents do not grow
genetically modified crops and most are
fairly liberal in their political leanings;
the culture in this county has more in
common with Marin than with Fresno.
This may be why groups such as GMO-
Free Alameda are taking hold here.
The main goal of GMO-Free
Alameda is to “protect the county’s
agriculture, environment, and private
property from genetic contamination
and to safeguard residents’ health
and the economy from the ill effects
of genetically modified organisms.”
GMO-Free Alameda plans to start just
as Mendocino and Marin Counties
did, with a ballot measure supported
by a collected list of supportive voters.

24 BERKELEY SCIENCE REVIEW

 Sonoma, a neighboring county, has
PHOTO: GENEVIEVE SCHIFFRAR
already collected the necessary number
of signatures to put it on the next
ballot, and Alameda County may soon
follow.
These county-based initiatives would
not directly affect research at UC
Berkeley, but the effects on private
companies and farmers in northern
California would still be felt at the
university. Peggy Lemaux conducts
research on genetically modified
grains, and some of her research is
done through contract with local
farmers. If the farmers were prohibited
from growing genetically modified
organisms, this research couldn’t be
done and, says Lemaux, “[I] couldn’t
assess the impact of GMOs because I
couldn’t do the experiment[s].”
Biotech businesses like Neal
Gutterson’s Mendel fear that local
legislation against GMOs may limit
or even reduce the financial stake the
government and private companies
have in the biotech industry and
university research in California.
Currently, California has a large
biotechnology sector in both the public
and private arenas, and a majority of
cotton farmers in California also grow
genetically modified plants. However,
all of these industries could easily
decline if California’s legislative climate
discouraged the research or use of
GMOs.
It’s a good sign that activist groups
have shifted tactics from guerrilla war-
fare to working within the legal sys-
tem—introducing ballot initiatives is a
far more civilized way to work change.
However, good democracy requires in-
formed voters, and the GMO debate is
too complex to be reduced to a simple
yes or no vote by a public generally
uneducated in science, agriculture, eco-
nomics, or technology. The people we
elect, Hollywood action heroes or oth-
erwise, should appoint qualified scien-
tists and legislators to introduce state or
Rajvinder Kavr, assistant specialist, and Erica Moehler, undergraduate, work with
GM sorghum in Peggy Lemaux’s lab.
federal laws—laws that exercise proper
caution, while still allowing farmers the The Eran Karmon Editor’s
advantages of technology. These scien-
tists and legislators need to understand
Award honors the memory
both the risks involved with gene flow of Eran Karmon, co-founder
and the social cost of patenting farm- and first editor-in-chief
ers’ seeds, while at the same time taking of the Berkeley Science
into account the tremendous benefits Review. It is donated by
this new science promises. the Karmon family, to be
awarded annually to the
CHERYL HACKWORTH is a graduate student
in molecular and cell biology.
editor-in-chief of the BSR.
The BSR would like to thank
Want to know more? the Karmon family for this
Check out the UC Biotech website: generous donation.
www.ucbiotech.org
The Pew Initiative website:
www.pewagbiotech.org
And for some activist viewpoints:
www.calgefree.org
www.organicconsumers.org
References
1. USDA-NASS Censuses; Pew Initiative on Food and
Biotechnology Study, 2004.
2. Hammond, B. G., et al., “The feeding value of soybeans
fed to rats, chickens, catfish, and dairy cattle is not altered
by genetic incorporation of glyphosate tolerance,” J.
Nutrition 126, pp. 717-727 (1996).
3. Hammond, B. G., et al., “Results of a 13 week safety
assurance study with rats fed grain from glyphosate tolerant
corn,” Food and Chemical Toxicity 42, pp. 1003-1014 (2004).
BERKELEY SCIENCE REVIEW 25
 ZOOM
with a
View
PHOTO: STEVE RUZIN

a tour of the Golub

antique microscope
collection

by Angie Morey

A
CTION figures, dolls, coins, stamps, baseball cards—hobbyists
collect all kinds of things these days. But if you’re Orville J.
Golub your hobby is anything but typical. Golub, a graduate of
UC Berkeley’s doctoral program in Bacteriology (PhD 944), has
been collecting microscopes of historic and scientific significance since the
960s. A testament to the centuries of scientific work that have preceded us,
these relics are both fascinating and aesthetically beautiful.

26 BERKELEY SCIENCE REVIEW


For years, Golub’s collection was displayed in his house,
viewable only to those who had the pleasure of visiting
him and his wife at their home in Los Angeles. However,
thanks to the generosity of the Golubs, UC Berkeley
students, affiliates, and visitors can now view a portion
of the glorious microscope collection here on campus.
The Golub Collection, bequeathed to the Regents of
the University of California by Dr. Golub and his wife,
Ellina Marx Golub (BA 939), now rests in the Onderonk
Lobby of the Valley Life Sciences Building. At last count,
the collection contained forty-eight microscopes from the
7th through 20th centuries.
PHOTO: BARRY LEVINE
The Golubs in their microscope museum den.
An affair begins
HOW does one ignite a love affair with microscopes? Like
many of its kind, this relationship began as a consequence
of circumstance. Golub entered graduate school in the
Bacteriology Department at UC Berkeley in 937, a time that
he concedes “seems prehistoric.” Perhaps not surprisingly,
Golub’s teaching assistantship in bacteriology required the
frequent use of microscopes. Gazing into the secret worlds
of tiny bacteria became a pleasant daily routine. However,
Golub’s routine was briefly interrupted when he was sud-
denly called into active duty a year before America entered
World War II. Having completed his graduate courses but
BERKELEY SCIENCE REVIEW 27
 1670-1680 1750-1800

c. 1745

A C

A. Guillaume Menard box microscope (probably from France) B. John Cuff compound microscope (England) C. Simple brass microscope (origin unknown)

not the research required for his PhD, he was fortuitously
assigned to work in the US Navy Research Unit on the
5th floor of the Valley Life Sciences Building under the
guidance of his graduate advisor, Dr. Albert Krueger.
Golub worked with the Navy Research Unit throughout
the war, managed to complete his thesis on the influenza
virus, and was awarded his PhD in 944.
After the war ended in 945, Golub accepted a position
in the Virus Division at Fort Detrick, Maryland, which
was then the headquarters for the government’s work
on biological warfare with Army, Navy, and civilian
scientists. While there, Golub became friends with three
other men who, after a couple of years, were anxious to
apply their skills and innovative minds to something
new. Their common desire to explore ideas without the
red-tape rigors of working for the government led to the
development of a Los Angeles-based company called
Bio-Science Laboratories in 948. This was not your
typical 940s lab, but rather an innovative and progressive
reference clinical laboratory. While many clinical labs

A Brief History of Microscopy

A single piece of glass, thicker 1590 Hans Janssen and his 1609 Galileo improves 1674 Anton
in the middle than around son Zacharias Janssen claim the design of the compound wenhoek create
the edges, comprised the first to invent the first compound microscope with better glass single-lens mic
“lens”, so-called because of its microscope, introducing a polishing and finer focus ad- creasing the cu
lentil shape. second lens for increased justment. glass.
magnification.

28 BERKELEY SCIENCE REVIEW

 IMAGES COURTESY: STEVE RUZIN

c. 1890

c. 1840 1905

E
D
F

D. Chevalier universal microscope (France) E. W. Watson & Sons of London compound microscope (England) F. Leitz compound microscope (Germany)

performed standard laboratory procedures, Bio-Science
Laboratories took the task a step further by carrying out
new research and publishing frequently in the scientific
literature. The Laboratory rose to be a leader in the clinical
field and was called upon by doctors and hospitals both
nationally and overseas to perform procedures such as
hormone, toxicological, and chromosomal analyses as well
as bacteriological and immunological assays. Although
most of these procedures are commonplace in the medical
field today, Golub reminds us that “lab life was different
back then” and these now-common procedures required
a specialized laboratory, a niche for which Bio-Science
Laboratories was perfectly designed.
Continuing with their trend of originality, the company
began to build a collection of old laboratory equipment
for the aesthetic enjoyment of their clients and employees.
They envisioned that this collection would include blood
counting equipment, balances, glassware, specialty books,
and microscopes. As avid travelers, Golub and his wife
were already accustomed to acquiring laboratory relics on

T I M E L I N E : A N N E P E AT T I E

van Leeu- 1757 John Dollond com- 1826 Joseph Jackson Lister 1931 Ernst Ruska builds
es a powerful bines two types of glass to (whose son pioneered anti- the first electron microscope.
croscope by in- create the first achromatic septic technique) perfects the Image resolution is now lim-
urvature of the lens. achromatic lens, reducing both ited by the wavelength of
chromatic and spherical aber- electrons, rather than visible
rations. light.
 their trips to Europe. For this reason, collecting mementos
for the Laboratory’s collection was merely an extension of
their chief diversion. However, as the “lab equipment”
collection grew, it soon became clear that the pair was
showing signs of favoritism for the microscopes. One of
Golub’s partners noticed this trend and suggested that he
P H O T O : C A R O LY N R U Z I N
“try to get more variety.” As the Laboratory’s collection
neared completion, Golub approached a crossroads. He
could either put his collecting career to rest, or continue
in his keen pursuit of rare relics. Not one to deny his
passions, Golub’s choice was simple. He “had fallen in
love with old scopes” and decided to pursue his penchant
for collecting with full force.
Collecting microscopes in the 960s, before the advent
of eBay or Google, required more than just a few clicks on
the Internet. Fortunately, on their many vacations abroad,
the Golubs had established the connections necessary to
acquire rare specimens of historical and scientific merit.
Alain Brieux, a Parisian dealer of scientific antiquities,
was one such connection who became instrumental
in the expansion of the Golubs’ personal microscope
collection. The Golubs also made purchases for their
personal collection from other private dealers, as well
as from Sotheby’s and other auction houses both in the
United States and Europe.
By the late 960s the Golubs had amassed a substantial
Ruzin sometimes imagines “what
the original owner must have
thought and felt when they used
the instrument .”
number of microscopes. Luckily, the Golub family had
a sizable home near the University of California, Los
Angeles and the time was ripe to create a dedicated space
for their prized microscopes. They hired an architect to
redesign two spare rooms, one of which Golub had been
using as a dark-room to develop his own photographs.
With five children, Golub recognized that he “couldn’t do
both—develop pictures and have a room for an extensive
microscope collection.” In the end, the dark-room was
sacrificed for what could best be described as a “museum
den”. The room’s museum-like features included walls
30 BERKELEY SCIENCE REVIEW
A life-long passion appears early: 12-year old Steve Ruzin (far right)
poses with his first microscope.
lined with glass shelves containing the growing collection
of instruments, illuminated on one side by natural light
from an overhead skylight. The room’s den-like features
included comfortable chairs, an entertainment system,
and a variety of books on optics and microscopy stacked
on the shelves of an antique bookshelf. With a proper
home for his microscopes, Golub continued collecting
microscopes even after his retirement from the Laboratory
in 980. In 995, through discussions with then-Chancellor
Ira Michael Heyman, Golub arranged to donate part of
the collection to UC Berkeley, to be housed in a special
case in the Valley Life Sciences Building. It is here that
the collection remains and continues to grow. Since
its establishment, Golub has added microscopes to the
collection and plans to make other donations in the near
future.
The collection’s curator
SINCE their arrival on the Berkeley campus, the remark-
able Golub microscopes have seen several curators—but
none quite as attentive and talented as their current
caretaker, Steve Ruzin. Ruzin is fueled by both a gift for
gadgets and machinery and a long-standing fascination
with microscopes. A photo of twelve-year-old Steve with
his first microscope eerily predicts his future as a scientist
and innovator in the world of microscopy.
Ruzin’s affection for microscopes has found a perfect
fit here on the UC Berkeley campus. He not only serves

PHOTOS: STEVE RUZIN
Students in Dan Fletcher’s Optics and Microscopy class experience the
Golub Collection hands-on.
as curator of the Golub Collection, he is also director
of the College of Natural Resources Biological Imaging
Facility, which functions as an instructional and research
laboratory for all aspects of modern biological light mi-
croscopy and computer image processing and analysis. In
both arenas, Ruzin has been characteristically attentive
and detail-oriented. In curator mode, Ruzin takes apart,
cleans, reassembles, and photographs each microscope.
He is continually astonished by the microscopes and loves
“being able to hold and study instruments that were used
by some long-deceased scientist.” As he selects one mi-
croscope each month to be showcased as the Microscope
of the Month (MOM) on the collection’s website (mi-
croscopy.berkeley.edu), Ruzin sometimes imagines “what
the original owner must have thought and felt when they
used the instrument to look at specimens they knew
nothing about.”
Hands-on experience
AS IF their presence alone were not remarkable enough,
these noteworthy relics of our scientific past have found a
place in the classroom due to the ingenuity of Steve Ruzin
and bioengineering professor Daniel Fletcher. “Bringing
the scopes into the Principle of Optics and Microscopy
course provides students with a rare and wonderful
opportunity to apply textbook and classroom lessons
to a real analysis of historically relevant microscopes.”
Fletcher goes on to describe the main project for the
course. “The students work together in groups to care-
fully analyze the functionality of their selection from the
Golub Collection.” Like photo albums made by proud
parents, the students’ final projects include pictures of
their microscopes, descriptions of their magnification
power, as well as photographs of images produced by
their microscopes.
The students’ ray diagrams, focal length estimations,
and magnification calculations are a beautiful display
of education at its best. Thanks to Golub, Ruzin, and
Fletcher, the collection’s microscopes continue to play a
role in twenty-first century science. And while researchers
from eras past may never have imagined the work that
would be done in subsequent centuries, they would likely
be pleased that their microscopes are not just gathering
dust; instead, these instruments participate in a living sci-
entific legacy, touching and shaping the minds of future
innovators.
ANGIE MOREY is a graduate student in the psychology department’s
program in cognition, brain, and behavior.
Want to know more?
Visit the Golub collection online at
golubcollection.berkeley.edu
BERKELEY SCIENCE REVIEW 31
 Meet the Chancellor
The BSR puts the Birge back in Birgeneau
The arrival of the University’s new
chancellor last September was
greeted with much fanfare; less well-
publicized was the fact that our new
administrator-in-chief is a pre-eminent
physicist. In an interview earlier this
spring, Tracy Powell and Steve Bodzin
asked Chancellor Birgeneau to step
aside, giving Professor Birgeneau a
chance to weigh in on topics ranging
from stem cell research to the state of
the physics department.
As a magazine devoted to science on campus, we were
pleased to hear the university has a scientist at the
helm. How do you balance your roles as researcher and
university administrator?
First of all, I have to tell the truth; it is difficult to balance
it all. I get paid to be a chancellor and previously as a
president and that’s what I do most of the time. But I have
managed to maintain a research laboratory. Frankly, that
has rested strongly on having really talented postdocs.
What questions do you pursue in your scientific life?
Fundamental questions in materials physics. These days,
the two main areas we work on are high-temperature
superconductivity, which remains unsolved after nearly
20 years, as well as something very different, which is soft
condensed matter physics. This involves looking at the
physical properties of liquid crystal materials in unusual
environments.
Physics pop-quiz: can you give us a layman’s definition of
the word “smectic”?
Smectic derives from the Greek word “smegma”, which
means “soap”. Smectic liquid crystals are materials which
32 BERKELEY SCIENCE REVIEW
function like soap—that is, they form layers. The way that
a detergent works is that the molecules form a film, then
the film surrounds the dirt particle and carries it off, so
detergents are examples of smectic liquid crystals.
In addition to being chancellor, are you an official member
of the physics department?
Yes, my appointment as professor of physics has been
approved. I went through the same process that everyone
else goes through. I’ve already identified an office for
myself over in Birge, which is currently being cleaned
up, as well as a couple of rooms which will become my
laboratories. I also anticipate doing some work up at LBL.
An article in the San Francisco Chronicle a year or so
ago claimed that the physics deparment was in “genteel
decline,” and was losing talented physicists to private
universities. As a physicist yourself, do have any special
plans to keep the physics department competitive?
First of all, as chancellor it would be inappropriate for me
to interfere in the workings of individual departments. Let
me just say that, generally, departments go through peaks
and valleys. Part of a department’s normal evolution is to
have people who achieve a phenomenal level, as they did in
our department here at Berkeley, who then mature and are
replaced. I think the review [you refer to] was done in the
middle of a transition period for the department. Recently,
[the department] has hired a number of really talented
young people doing nontraditional kinds of research that I
think will help reestablish the preeminence of the physics
department.
Additionally, I knew the two [researchers that the
department] lost personally from my research life, and they
left in good part because of limitations in the facilities here
on campus for the kind of research they were trying to do.
The new facilities which we hope to build during my time
as chancellor should help to solve that problem. These
facilities include new, low-vibration laboratories – the
kind of modern laboratory space that you need to do state-
of-the-art research – especially of the sort that they were
doing, which was in the nano field and required extreme
delicacy and extreme stability.
Public-private partnerships seem to be a new trend in
public university research. Some of these partnerships,
such as the Department of Plant and Microbial Biology/
Novartis agreement a few years ago, have received heated
criticism. Do you have any personal perspectives on this
trend?
Yes I do. Strong ones, actually. First of all, if you look
at the amount of research funding that comes from the
private sector in universities, it is phenomenally small, so
this [trend] has been greatly exaggerated. Number two,
although people often don’t think of it this way, I view it
at least in good part as a matter of academic freedom: if
there is an investigator who wants to do a particular kind
of research, and some private donor is willing to fund that
research, then it is that person’s right to accept that money.
[While others may] have a particular view of what a public
university should be, I think that for them to try and
prevent that person from doing that research violates that
person’s academic freedom.
Congratulations on your appointment to the stem cell
advisory board created as a result of Proposition 71. As a
physicist, not a biologist, what is your role on the advisory
committee?
(laughing) Actually, there’s also a real estate person on the
board. As you can imagine, anyone who’s ended up as a
chancellor has a lot of experience with the organization of
research. I have chaired Department of Energy panels that
oversaw very large amounts of money—amounts of money
comparable, actually, to the stem cell money. So I know
a fair amount about the organization of research, and it’s
really that part of it which our panel will be responsible for.
Our panel will review reports by expert sub-panels from
the outside; those are the people who will make technical
judgments where you would have to be a biologist or a
medical doctor or a life scientist of some sort.
Much of the debate surrounding Prop. 71 concerns
ethical dilemmas posed by stem cell research. As an
advisory board member, what role will you have in ethical
guidance?
I think overall that our board will be responsible for
making sure that research is carried out ethically [and]
that there are not egregious violations of ethical standards.
We already know that a particular approach to ethics has
resulted in the federal government extremely constraining
this area of research. We’re fortunate to be in a state with
a broader viewpoint, in which the issues of human health
are balanced against particular viewpoints that some people
have about the origins of human life. I think we’ve gotten
the balance right in California with this initiative.
PHOTOS: BONNIE POWELL
How do you address fears that this research will advance
an era of human cloning or germline modification? Do
you have any personal ethical guidelines that you’ve
developed as a result of your particular experiences as a
scientist?
These are very complicated issues, so of course we all have
our own ethical values. I think that in the particular case
of a person who was going to use stem cell research very
directly to try to clone a human being, then we would
reject that. On the other hand, you can’t stop the progress
of science just because some person out there may try to
use the results of science for an unethical reason; it’s just
not possible.
How optimistic are you that the aims of Proposition 71 will
be successful?
In the long run, I’m very optimistic. I happen to have
some motivations for this. One of my close friends, a
great physicist in my field, died of Lou Gehrig’s disease
last year. I watched him deteriorate over a two-year period
and he kept doing research until almost the last day. It
was amazing, and it was courageous on his part that he
would refuse to give in, but it’s a horrible thing to watch.
As you know, this is a neurodegenerative disease for which
stem cells may offer a promise, and so one only needs
that kind of personal experience [to be convinced] that
we really must go forward with this kind of research. Is
it 5 years or is it 10 years… you’re a biologist, you can
probably count better than I can! But certainly this is a
very promising approach and we need a breakthrough for
neurodegenerative diseases. We must have a breakthrough.
TRACY POWELL is a graduate student in plant and microbial biology.
STEVE BODZIN is a graduate student in journalism.
BERKELEY SCIENCE REVIEW 33

Intelligent
Design Playing with the building blocks
by Alan Moses
LTHOUGH malaria infects hundreds
of millions of people each year and
kills an estimated 1.5 million, most
of whom are children, a majority
of these cases could be cured by
combination therapy involving
the drug Artemisinin—a naturally
occurring compound extracted from the sweet wormwood
plant. Unfortunately, sweet wormwood takes six months
to grow to maturity, and the extraction of Artemisinin is a
laborious process that itself takes several months. It seems
incredibly frustrating that nature has provided the cure to
this terrible disease but hidden it in such an expensive and
out-of-the-way place. Why couldn’t the required chemical
precursors be produced by a fast-growing lab bacterium
like E. coli? That way the drug could be produced cheaply
and quickly. Most of us might shrug our shoulders and
go back to the hunt for sweet wormwood, but Jay Keasling,
UC Berkeley professor of chemical engineering, and a whole
community of like-minded researchers think differently.
Rather than settle for the organisms nature provided,
Keasling’s group created an organism to do exactly what
they wanted. Starting with E. coli, they began adding the
genes needed to make Artemisinin: first a pathway of genes
BERKELEY SCIENCE REVIEW
GRAPHIC: TRACY POWELL
of biology
from S. cerevisiae (beer yeast) and then another critical
enzyme, and just like that they had bacteria that produced
the desired precursor. Seems like a good idea, doesn’t it? It
seemed like a good idea to the Lawrence Berkeley National
Lab as well: they created a whole department to encourage
this kind of thinking.
The recent creation of the Synthetic Biology department
at LBL, headed by Keasling, places Berkeley at the center
of a new discipline at the interface between the life sciences
and engineering. Synthetic biology holds incredible promise
for the solution of problems in power generation and global
health, but it also raises concerns that may make fears about
genetically modified organisms (GMOs) seem paltry by
comparison. As usual, Berkeley will be right in the thick
of it.
Putting the pieces back together
SYDNEY BRENNER, 2002 Nobel Laureate for Physiology or
Medicine, has famously declared this era “the end of the
beginning,” suggesting that molecular biology, which began
in earnest with the discovery of DNA as the genetic material
and the understanding of the structural properties that allow
it to serve as such, has entered a second phase. Because of
the enormous progress of the last 50 years, we now have a
A Nobel laureate has famously
declared this era as “the end
of the beginning” in molecular
biology.
“parts list” for the cell—we have some understanding of most
of the basic molecular processes and sub-cellular structures
found in most living organisms—as well as the ability to
obtain complete descriptions of the genetic material for
virtually any organism in the form of genome sequences. A
middle period in molecular biology has arrived in which we
must begin to understand how these parts interact to form
the complex systems that are living organisms.
Analogous developments occurred in the 1960’s and 1970’s
as physicists began to realize that knowledge on increasingly
subatomic scales could not solve such seemingly simple and
practically important problems as weather prediction. It
became clear that they had to study the complex behaviors
that arise as the simple building blocks of nature interact;
subsequent breakthroughs in the field that became known
as nonlinear dynamics and chaos theory began to offer a
more complete picture of these complex phenomena. It
is widely believed that molecular biology must follow a
similar trajectory—to begin to put the pieces back together,
finally producing a picture of the whole organism. Synthetic
biology sees itself as a fundamental step in this process.
What’s in a name?
SO WHAT exactly is synthetic biology? Invariably, when a new
discipline or department is created, it faces pressure to define
itself. Otherwise, people might question why, in these days
of tight university budgets, a department is being created
to study something they’ve never heard of. Furthermore,
synthetic biology must differentiate itself from new research
institutes and departments that are already springing up
under the auspices of “systems biology”, on the one hand,
and more established departments such as bioengineering
on the other.
Perhaps it is too early for us to define the scope of
synthetic biology and to know whether ultimately it will
carve itself a niche, but broadly speaking, we can say that
synthetic biology aims to develop tools and methods to
create biological molecules and cells for practical purposes.
It takes what we’ve learned over the past fifty years about the
constituents of life and attempts to use it to solve practical
problems.
BERKELEY SCIENCE REVIEW
 Synthetic biology strives to combine (or synthesize) large
amounts of disparate knowledge. As Keasling summarizes,
“Biology has done a great job of breaking things into pieces,
but there has been less success in putting them back together.”
Like advocates of systems biology, Keasling and Graham
Fleming, director of the Physical Biosciences Division at
LBL, under which the new department was created, use
metaphors from electrical engineering. They liken cells
to circuits, and suggest that we must shift our focus from
defining basic biological “transistors” and “capacitors” to
understanding the way they interact so we can understand
the behavior of the whole computer.
The creation of an entirely new
living thing has never been
accomplished.
Synthetic biology goes even further than other similarly
holistic disciplines such as systems biology. Keasling
emphasizes that in synthetic biology the focus is not just
on understanding the way the parts interact, but on using
that understanding to help molecular biology become what
Keasling calls an “engineering discipline” that’s “focused
on applications.” Keasling argues that synthetic biology is
much more specific than systems biology, focused more at
the cellular and genetic level, although he admits that some
research that now falls under bioengineering might also be
called synthetic biology.
Fleming suggests that “synthetic” is to be taken in all its
meanings. Another, perhaps related, meaning is “synthetic”
as in “synthetic chemistry”, where researchers literally
synthesize more complicated compounds from their simpler,
more available components. Thus, a goal of synthetic
biology is to synthesize new organisms from a set of existing,
well-understood components. Projects of this kind, such
as the “BioBricks” project at MIT, are well underway. This
project aims to characterize a number of biological building
blocks—to understand their properties as completely as
possible. Once this is done, these BioBricks will be available
to be combined into larger and more complicated systems,
and we can be confident we will understand their behavior.
A future scientist will just choose the BioBricks and have
the organism made to specification. These projects will form
the fundamental tools that the synthetic biologist might use.
“As the name suggests, the bricks are to provide a foundation,”
says Fleming. Just as a chemist might decide to create H2O by
combining H2 with O2, a biologist might create a free-living
BERKELEY SCIENCE REVIEW
cell by combining a cell membrane BioBrick and a DNA
sequence BioBrick with the BioBricks for transcription and
translational machinery. This seemingly simple scenario is
far beyond today’s capabilities. While the genetic material
of some model organisms (like E. coli and S. cerevisiae) can
be routinely altered, the creation of an entirely new living
thing has never been accomplished.
This possibility raises perhaps the most exciting and con-
troversial aspect of the name: the sense in which synthetic
means artificial. Although not artificial in the way that syn-
thetic fabrics mimic the properties of cotton or silk (these
could be referred to as biomimetic, according to Keasling),
synthetic biology has its sights set on synthesizing living sys-
tems that are artificial in the sense that they have never ex-
isted in nature. By combining the tricks that many different
organisms have developed throughout the course of evolu-
tion in a rational way, we will be able to generate organisms
that perform functions not seen before. As with GMOs, the
impact of synthetic organisms will be felt strongly in fields
such as agriculture, where crops can be designed for pest
or weather resistance. Synthetic organisms, however, can
go much further. According to Fleming, one of the major
reasons for the creation of the department at LBL was the
incredibly exciting potential of synthetic biology “for im-
proving human health and developing new ways to supply
energy.” Projects of this scope attempt to develop bacteria
that are redesigned to produce pharmaceuticals or swim to
a tumor cell and destroy it, or synthetic viruses to be used
as HIV therapy. Although such “made-to-order” organisms
may seem far in the future, projects like these are already un-
derway in labs such as Keasling’s at LBL and on the Berkeley
campus.
Long-term goals for synthetic biology approach science
fiction: researchers supported by the Department of Energy
at the Venter Institute (headed by Craig Venter, who led
the private-sector effort to sequence the human genome) are
trying to develop a synthetic organism to efficiently pro-
duce hydrogen as a fuel source in a totally renewable way.
Although an incredibly difficult challenge, according to Ke-
asling, this type of project is the sort that synthetic biol-
ogy should be aiming at—one that would revolutionize the
way we think about harnessing the potential of living things.
In addressing how long it will be before such advances can
make an impact on daily life, Kristen Balder-Froid, the Divi-
sion Deputy of Planning and Strategic Development for the
Physical Biosciences Division at LBL, points out that what
will ultimately determine the time before such organisms
are commonly used is what sorts of regulatory bodies they
must pass—and that is very difficult to tell at this point.
Regardless of how near in the future the applications of
synthetic biology might be, it is clear that the idea has been
gaining momentum. To get a sense of how quickly synthetic
biology has been developing, we can take a look at the short
history of the discipline. Although the ideas and research
projects connected with synthetic biology may have been
around for some time, along with the creation of the first
department (at LBL), the first-ever conference on synthetic
biology was held at MIT this year. According to Fleming,
the decision to create a new department at LBL came out of
the realization that there were already a number of research
labs doing synthetic biology on campus, though they may
not have used the term. Creating the new department allows
Berkeley to take advantage of the lead that it already has in
the area as well as to recruit additional funding and faculty.
It will also help focus efforts by creating a community in
which the various groups can interact. Indeed, excitement
in the area is still mounting, and although it’s not official
yet, Fleming hints that another synthetic biology center or
department affiliated with the Berkeley campus is already
in the works. There have also already been several seminars
on campus sponsored by the QB3 Institute, a California
research initiative in quantitative biology, to help focus
attention on exciting work in synthetic biology that is going
on at Berkeley and elsewhere. Seminar speakers have ranged
from UCSF’s Wendell Lim on reprogramming cellular
switches to Harvard’s George Church on new methods for
ultrafast DNA sequencing.
Escaping from the lab: fear and risk
IN ADDITION to capitalizing on this growing momentum
and excitement, the formation of the new department
also allows researchers and funding agencies to coordinate
their public information efforts. Technology that seems
poised to alter the way we look at life itself raises many
concerns both with respect to safety and also the social
and political consequences of such advances. For example,
Keasling points out that the synthetic biology department
plans to work with the Goldman School of Public Policy
and hopes to create programs to educate its scientists about
public policy, to educate policymakers about science, and
to educate the public about both. The importance of such
a strategy cannot be overstated, particularly in the midst of
public backlash against the use of GMOs in the agriculture
industry. From the public’s perspective, when designing
organisms, we must realize that we may be creating life
forms that God and/or evolution never dared, or—worse—
never dared again. Given public concerns about safety and
ethics, strategy about the areas on which synthetic biology
BERKELEY SCIENCE REVIEW
 should focus research will be crucial if the new discipline is
to flourish.
One main area of concern is the potential environmental
impact of newly-designed organisms. Could synthetic
organisms escape and infiltrate the natural world? Keasling
argues that completely synthetic organisms really don’t
compete well in the wild—even the most successful
experimental strains are usually pathetic compared to
their natural counterparts. Synthetic organisms that are
released either accidentally or for specific purposes would
most likely die once out of the comforts of the laboratory.
Keasling imagines synthetic organisms growing in controlled
environments and used for specific tasks.
Although these answers may seem sufficient for now, if
synthetic biology is successful and our ability to redesign
organisms improves, our current ineptitude can’t be regarded
as a very reliable safety feature. If we are eventually to use
these organisms for clinical or industrial purposes, we must
fully address questions about safety and risk. Otherwise,
synthetic biology may be unable to avoid a backlash similar
to the one that has left the public demanding the labeling
of genetically modified (GM) products or the outright
Rather than simply tinkering
with the organisms that nature
has provided, we can begin to
combine their parts in radically
new ways.
38 BERKELEY SCIENCE REVIEW
banning of GM foods in Europe and general uncertainty
about whether GM crops might represent environmental
dangers. As UC Berkeley anthropology professor Paul
Rabinow, who teaches a course called Genomics and Society
and spoke at the first synthetic biology conference this year,
puts it: “Most people think this stuff is dangerous.” Indeed,
recent elections have led to bans on GMOs in two nearby
counties and groups advocating similar measures in five
other counties—including Berkeley’s own Alameda (see
“Strange Fruit” on page 19 of this issue).
Fleming suggests that the ethical and social issues raised
by synthetic biology might be more relevant than the
safety ones. He imagines that regulatory committees would
oversee the creation and manipulation of living organisms.
Rabinow emphasizes that the synthetic biology community
must keep these issues in mind if their technology is to have
the broad impact that seems possible. This is particularly
important in what he calls today’s “risk-averse” environment,
and given that “Americans are into values” right now.
In order to improve public perception, Rabinow suggests
that focusing on world health issues such as low-cost HIV
remedies might be a wiser strategy than trying to break into
the agricultural world, which is already rife with consumer
skepticism toward genetically modified foods. “Monsanto
was spectacularly stupid and arrogant,” says Rabinow,
referring to the manner in which they sold the first
genetically engineered plants and the way they presented
the technology to the public. Rather than focusing on
the artificiality of genetically modified crops, they should
have focused on the universality of the DNA language that
makes such manipulations possible. He further suggests
that companies should think critically about the markets
they consider: developing recombinant growth hormones
to improve milk production during the current surplus
of milk is bound to be perceived as big corporate science
hammering the last nail in the coffin of already struggling
milk farmers. Instead, efforts should be aimed at areas where
unsatisfied demand exists—such as development of cheap
medicines to combat infectious diseases in countries where
current technology is unavailable.
Critics label this type of suggestion as “experimenting on
the third world”—trying experimental crops or medicines in
poor countries where people are much more likely to accept
untested food or medicine because they are suffering. In
general acknowledgement of such safety concerns, Rabinow’s
presentation at the first synthetic biology conference was
entitled “Assembling Ethics in an Ecology of Ignorance.”
Nevertheless, given the staggering numbers of people
 suffering from diseases like AIDS and malaria, if progress
is to be made, certain risks must be taken. He argues that
we simply cannot foresee all the possible risks associated
with a new discipline—especially one with the potential of
synthetic biology. The attitude that all possible precautions
must be taken, he claims, is untenable—we can’t possibly
“MONSTERFISH”: WENXIONG LIN
know all the ramifications of any given technology, and we
just need to learn to accept that fact.
He also claims that the concerns about whether foods or
medicines are natural will fade. Agricultural plants have
always been manipulated and domesticated by humans—
they haven’t been natural for thousands of years. Rather
than thinking of synthetic biology as artificial, or unnatural,
he likens it to the creations of chef Alice Waters of Chez
Panisse, the Berkeley eatery credited with starting the
culinary revolution now referred to as “California cuisine”.
Ingredients native to environments from all over the world
are taken out of their historical geographical context and
grown organically, in a controlled way, in California and
then combined in radical and delicious concoctions that
were never previously imagined. Rather than focusing on
the unforeseen consequences of combining the Laurus nobilis
(native to the Mediterranean and Turkey) with a variety
of Fortunella (originally East Asian), we can celebrate the
triumph of human ingenuity and serendipity that brought
both of these to California to create a bay leaf-scented panna
cotta with candied kumquats.
What hath man wrought?
CLEARLY synthetic biology raises all the same difficult safety
and ethical issues GMOs do, and unfortunately it actually
adds a new element of fear—human malice. If synthetic
biology is indeed to be an engineering discipline, we need
not only fear the unintended consequences of organisms
modified slightly for benefit but also the whims of people or
governments designing organisms with the intent to cause
harm. Sensationalist fears in this direction have already
been expressed. Following the same electrical engineering
analogy to a perhaps inevitable conclusion, a news story on
Slashdot.org, a technology news web site, suggested that
once biological systems could be “programmed” we might
see “biohackers” or maybe even “biospammers.” Synthetic
bacteria could give us a cold and then spell out the name of
a cough-syrup brand in green fluorescent protein.
The real risks of synthetic biology are probably much less
exotic. For example, Keasling points out that in the past
few years a milestone has been reached: technology now ex-
ists for the rapid, cheap synthesis of long pieces of DNA.
While this may sound innocuous, according to Keasling
“this means that it is easy to get copies of entire genes, or
groups of genes, or even a virus.” Combined with the fact
that molecular biology can be done relatively cheaply and
without too much specialized equipment—“in a garage,”
says Keasling—one could imagine the potential for danger
if such technology falls into the wrong hands. Nevertheless,
even with the availability of such technology, Keasling feels
that the likelihood that it could be used for malicious pur-
poses is very small: “it’s much easier for terrorists to get a
truckload of fertilizer than to genetically engineer a bacteri-
um.” Terrorists have shown that they can inflict damage and
destruction with box-cutters and airline tickets—they don’t
need to resort to advanced technology. Molecular biology
is still too complicated and difficult to do without an enor-
mous amount of technical skill and specialized knowledge.
Nevertheless, individuals with the right combination of skill
and intent are out there—one only needs to remember the
envelopes of anthrax spores mailed to terrible effect in 2001.
Rabinow reminds us that the potential exists for “one jerk…
to spoil it for everyone,” and that scandal-mongering and
malicious intentions are out there.
Rabinow suggests that synthetic biology follow the example
of the self-regulation that was imposed by scientists during
the first experiments with recombinant DNA. Nearly 30
years ago at the Asilomar conference center, just south of
Monterey, scientists came together to discuss the safety and
social issues surrounding their work on recombinant DNA,
the first “genetic engineering.” Although the moratorium
that was eventually imposed is now regarded as overly
cautious, the attitude of self-regulation and caution is a
valuable example to new disciplines. Kristin Balder-Froid
BERKELEY SCIENCE REVIEW
 points out that even if scientists
can’t predict the potential risks
of new discoveries, at least they
can now use the example of how
to communicate seriously and
openly about the implications
of their work. Keasling adds that such self-policing policies
are being put into effect already. For example, Blue Heron,
one of the companies offering synthesis of long DNA
sequences up to 40 kilobases, long enough to synthesize
a coronavirus like the one that causes SARS, checks all of
the sequence synthesis orders they receive against all known
pathogenic sequences. Presumably a red flag would be
raised long before SARS was ever synthesized.
Despite the risks and fears, the promise of synthetic biology
(or at least cheap antimalarial drugs) seems hard to resist.
The Bill and Melinda Gates foundation also liked Keasling’s
approach: they donated $42 million for the development of
bacterially-produced Artemisinin with the goal of reducing
the cost of malaria treatment around the world.
At the very least, synthetic biology represents a new
way of thinking about the way we do biology. Rather
than simply tinkering with the organisms that nature has
provided, we can begin to combine their parts in radically
new ways. The creation of a department of synthetic biology
at LBL puts Berkeley at the forefront of this new paradigm.
Lest we forget, though, Berkeley is not only a center for
groundbreaking research; it’s also home to social activism
and liberal skepticism about the aims of big corporations and
government. With that duality in mind, synthetic biology,
unlike the biotech revolutions of the previous decades, seems
to be proceeding with due deference to both the worst fears
and the most noble dreams of the community. Perhaps
as we ponder the magnitude of the act of synthesizing a
completely new life form for the first time, we might realize
that we would not have it any other way.
ALAN MOSES is a graduate student in biophysics.
Want to know more?
Visit the LBL Synthetic Biology Department online:
www.lbl.gov/pbd/synthbio
The Keasling Lab website: www.cchem.berkeley.edu/jdkgrp
The BioBricks website: parts.mit.edu

Cal SCI ...get involved!

It’s not easy to get high
school students interested
in science, especially in Cali-
fornia, where student scores
If you would like to bring on standardized tests are
your knowledge and among the lowest in the
enthusiasm to CalSci, US. But imagine high school
please contact Steve students spending their Sat-
Andrews at urday mornings using the
sandrews.berkeley.edu
laws of thermodynamics to
design a machine that can
crush a cupcake, or engi-
neering buoyant shoes that
can support a person walk-
ing on water.
The CalSci Academy, part
of the Environmental Sci-
ences Teaching Program
(ESTP) at UC Berkeley, gives
Bay Area high school stu-
dents the chance to engage
in hands-on projects that
combine creativity with
practical science. UC Berke-
ley students work together
to develop and apply an
innovative curriculum to
support and engage high-
schoolers in science. The
program, run by Program
Coordinator Steve Andrews
and Professor William Berry
from the department of
Earth and Planetary Science,
offers undergraduate and
graduate students the op-
portunity to be both men-
tors and teachers.
—Pamela Han and Rachelle
Callenback

40 BERKELEY SCIENCE REVIEW

Prisoner
of the
S
IVORY
ToweR
Serving Five to Life
in Academia

by Loren
bentley
 “H
OW much longer do you have?”
It’s the question every graduate student dreads. Whether it’s
parents, friends, or new students, nobody seems to realize
how much that question hurts, or, for that matter, how
hard it is for graduate students to pin down the answer.
Real statistics are not well-advertised, so most students
don’t know the average degree time, or even the percent of
students who actually graduate. Besides this, the distribution
seems so broad, it is hard to know if they will follow in the
footsteps of the legendary tenth year, or replicate the feat of
the whiz that finished in three-and-a-half years and already
has a job.
Although many people have the vague idea that a PhD
is a roughly five-year endeavor, the actual time required to
complete a doctoral degree is almost always longer. In 2003,
the median number of years between enrollment in graduate
school and completion of the doctoral degree (elapsed time
to degree, or ETD) in all fields in the US was 7.5 years.
The national median in the physical sciences (including
mathematics and chemistry) was 6.8 years; in engineering
it was 6.9 years, and in the life sciences it was 7.0 years.
The typical time to degree for the humanities and social
sciences is longer, and nationwide, the length of all graduate
degrees increased steadily during the late twentieth century.
The median registered time to degree (RTD or the time a
student is registered in a graduate program) in the United
States for students completing their degrees in 97 was 5.7
years, but by 99 it had climbed to 7.0 years.2,3
At Berkeley, the Graduate Division keeps track of each
student in a database known as the “Monster” file, which
goes back to the 960s. Berkeley’s average RTDs are shorter
than the national averages, but still nowhere near five years.
In 2004, the average RTD in life sciences was 6. ± 2.3 years;
in physical sciences it was 5.7 ± 2.0 years; and in engineering it
was 5.8 ± .8 years. Mary Ann Mason, the Dean of Berkeley’s
Graduate Division, expresses the concern many feel about
GRAPHIC: TRACY POWELL
how long it takes to get a degree, noting, “It’s expensive in
time and money for the student and for the University if the
time line is too long.”
Of course, the story these statistics tell isn’t as clear as it
appears at first glance. It is difficult to incorporate data about
slow finishers and students who drop out. Many databases
only track students who complete their degrees, making it
difficult to measure attrition from doctoral programs, which
is itself a severe and complicated problem. Also, the length
of graduate programs is often reported as the time between
the awarding of the bachelor’s degree and the awarding of
the doctoral degree (total time to degree, TTD)—roughly
three years greater than RTD. Even after accounting for
these factors, the statistics can be interpreted in different
ways. The 988 Survey of Earned Doctorates conducted by
the National Opinion Research Center (NORC) reported
that TTD had increased by approximately 30% over the
preceding twenty years. But a subsequent study found that
the decreasing number of PhDs awarded over this time
created a statistical bias and possibly more public concern
than the issue may have warranted. Calculating time to
degree based on entering, rather than graduating, class
showed a more accurate—and still significant—increase of
0% over the same twenty year period.3
Happily for most, the trend has begun to level off,
particularly for students in the sciences and engineering.
According to the 2003 national survey, the median TTD
was 0. years, or three months shorter than in 998.
How long should it take?
SO HOW long should a PhD take? The Association of
American Universities was formed in 900, and by 96 was
already questioning the ideal duration for post-graduate
study, proposing three years as an appropriate length. This
number had not changed much by 964, when the Association
of Graduate Schools and the Council of Graduate Schools
issued a joint statement that a PhD program should take
Real statistics are
not well-advertised,
so most students
don’t know the
average degree time,
or even the percent
of students who
actually graduate.
BERKELEY SCIENCE REVIEW 43
 three, or at most four, years.3 This sounds great
to today’s graduate students, who have had to
come to terms with much longer degree times.
This author’s informal survey of current Berkeley
students in one graduate program showed that
most think five years is the ideal RTD and six
years is too much. Mason posed five years as
the ideal time to degree in the sciences and
engineering, and six years in the humanities and
social sciences.
Many graduate students have heard that
doctoral programs in other countries take years
less than those in the United States. The US
system was originally modeled after Germany’s,
albeit with a more structured program and
curriculum. The German degree is designed to
take around three years, though time to degree
has increased there, too.4 In England, the
Doctor of Philosophy degree (DPhil) requires a
minimum of three years of research. According
to Oxford University’s web site, DPhil students
must complete a thesis based on research, “of Suzanne Lee and Bosun Min, graduate students in MCB, are treated like
a kind which might reasonably be expected of a diligent local wildlife.
and competent student after three or at most four years of
full-time study.” This sounds attractive compared to the US on the end of a graduate program can significantly increase
system, but it is difficult to directly compare the systems students’ output in terms of research and publications, ben-
since undergraduate education is so different; for example, efiting both them and their advisors. Of course, students
German and British undergraduates focus on a specialty also have reasons for wanting to get out quickly, but surpris-
immediately. ingly, it is departments and institutions that may have the
But according to Dan Fletcher, assistant professor of biggest interest in getting students out the door. Berkeley’s
bioengineering, who received a DPhil from Oxford as well job is to produce graduates, particularly those who go on to
as a PhD from Stanford University, there can be “more notable careers. The faster they can do it, the more they can
efficiency and less frustration in British versus US PhD produce. Mason explains that time to degree is “often less
programs.” He notes that the Oxford program was more important for the graduate student than it is for the institu-
structured, with a progress assessment after the first year tion…there’s a good deal of expense and effort in training
involving both an oral exam and a plan for finishing thesis graduate students and the longer they stay, the tardier the
research in the remaining two years. In the US system, he payoff is in the sense that they are moving into the academic
says, it is possible to work on your degree until “every last pipeline and continuing on with their careers.”
ounce of interest in pursuing this field has been squeezed Without a doubt, long average TTD has broad
out of you.” repercussions. The recent summary of the Survey of Earned
Doctorates by NORC noted its impact on “the faculties and
Winners and losers administrations of the degree-granting institutions, as well
IF EVERYBODY thinks shorter is better, why does time to as national public agencies and private organizations that
degree keep increasing? One reason is obvious: the longer support doctoral study.” This wasn’t news to the University
you’re there, the more you learn, the more research you do, of California. A feared shortage of PhDs in the 980s led the
and the more productively you do it. Thus, adding a year California State Senate to commission a study of the time

44 BERKELEY SCIENCE REVIEW

 to degree in the UC system by Maresi Nerad and Joseph
Cerny, who was then Berkeley’s Vice Provost for Research.
More recently, in 200 the UC convened a Commission on
the Growth and Support of Graduate Education. Based on
the anticipated undergraduate population and the needs of
industry in California, the commission predicted a need for
40,000 new faculty by 200. Consequently, they set the goal
of ,000 new graduate students in this decade. California
is one of only five states in which graduate enrollment has
declined—by 2% in the last decade—while nationwide
enrollment has increased. Among the commission’s proposals
to reach its goal was one to “expand current efforts to reduce
the time graduate students take to complete their programs,”
by monitoring progress closely, providing support services,
P H O T O : D U L A PA R K I N S O N
and increasing student financial support.
Cerny, a professor of chemistry and former dean of
graduate studies at Berkeley for fifteen years, feels that
Berkeley’s current graduate program lengths in the sciences
and engineering are reasonable for a top research institution,
but are a factor in what he believes is the larger problem of the
increasing time to the first job for scientists and engineers.
Cerny was recently part of a committee to study education
in his field, nuclear science. Their findings included the
following:
“The median registered time from bachelor’s degree to
FIGURES: CHARLIE EMRICH
a PhD in nuclear physics or nuclear chemistry has been
7.0 years over the last five reporting periods (998–2002).
Seventy percent of these PhDs then take one or more
(almost mandatory) postdoctoral positions lasting an
average of 3.3 years. Therefore, ten-plus years pass before
the ‘typical’ nuclear science PhD has a first job. This is
too long…We believe that the time to the PhD should be
shortened to five and a half or six years.”5
Part of the problem, according to Cerny, lies in inadequate
career advising: “Departments ought to be doing much
more career advising as to what the typical jobs actually
are.” Giving career guidance is not a high priority for
many busy professors, nor are they often familiar with the
many career paths their students could follow.
A 995 report entitled “Reshaping the Graduate
Education of Scientists and Engineers” noted the 30%
increase in time to degree in some fields and stated:
“Spending time in doctoral or postdoctoral activities
might not be the most effective way to use the talents
of young scientists and engineers for most employment
positions. Furthermore, because of the potential financial
and opportunity costs, it might discourage highly
talented people from going into or staying in science and
engineering.”6
Mason also emphasizes the importance of decreasing the
S O U R C E S : D I G E S T O F E D U C AT I O N S TAT I S T I C S 2003 ( L E F T )
U C B E R K E L E Y G R A D UAT E D I V I S I O N ( R I G H T )
BERKELEY SCIENCE REVIEW 45
 time to first job. She noted that, more than graduate student
time to degrees, “A bigger concern in this regard are the
post-doc appointments, which tend to get longer and longer
all the time. In the biological sciences it’s not uncommon
to have a five year postdoc before your first job…That’s just
elongating the experience for everyone, which can be very
demoralizing, to be honest.”
Their fates in whose hands?
THERE are a variety of opinions on who or what controls
the time to degree. Asking a small sample of current PhD
students at Berkeley whether the time they would take to
complete their degree was within their control, responses
varied from “it depends on my advisor” to “[it’s] managed
by the individual.” The encouragement of their advisors and
agreement on a research plan are both contributing factors.
In general, students earlier in their programs felt they had
less control, while students closer to graduation mentioned
the effects of unexpected problems with experiments and
difficulty maintaining focus. One student said, “There
[were] way too many interesting projects that I wanted to
do. A good portion of the projects aren’t thesis-related, but
just too good not to investigate.”
When asked how students
could influence their own
completion times, Cerny
In the US system, it
advised that students “get
into research as early as
is possible to work
possible…figure out early on your degree
what you want to do and
start it.” He noted that in the until “every last
Department of Chemistry,
most students join a lab
ounce of interest
by the middle of their first has been squeezed
semester. This has been true
for the last half century, and, out of you.”
says Cerny, “Chemistry’s time
to degree has been around 5.3
years for the past forty years.”
Good mentoring was described by Dean Mason as one of
the most significant factors in graduate students’ academic
experience. “For the graduate student, having a really good
mentoring experience is probably the most important thing.
And good mentors want to get them out…which means
they’re really concerned about the welfare of that student
as well.” A 996 study of former doctoral students supports
46 BERKELEY SCIENCE REVIEW
Mason’s belief, finding “that students’ aspirations to the
doctorate are most affected by the relationship they have
with their individual faculty research advisor.”7 For both
men and women who left Berkeley before finishing their
degrees, 54% cited a “lack of guidance from my advisor” as a
factor in their decision to leave.7,8 In a multi-university study,
interviews with faculty confirmed the lack of guidance,
though the faculty view the problem from a very different
perspective: their most common advising attitude was one
of an open door without making any overtures.3
An important influence on time to degree is the unique
set of mental and emotional challenges faced by graduate
students. At Berkeley, 43% of the students seen at the
Counseling and Psychiatric Services are graduate students,
though they make up less than 30% of the student body.9 A
survey by a Berkeley task force on Graduate Mental Health0
found that 45% reported emotional or stress-related problems
within the past twelve months that had significantly affected
their well-being or academic performance. 39% reported
feeling frequently overwhelmed, while approximately 42%
reported feeling exhausted “frequently” or “all of the time.”
Though personal or individual factors may determine
where each student falls within the range of times to degree,
larger-scale institutional fac-
tors—outside each student’s
control—can have much
greater influence on average
times to degree. Funding
policy is one of the primary
institutional means of con-
trolling time to degree. Other
things being equal, students
who receive fellowships or
research assistantships have
higher completion rates and
shorter times to degree than
students receiving teaching
assistantships or fee waivers
or those who are totally selfsupporting.0 “It’s a matter of
funding structure, and if you’re structured to finish in five
and half years and then you’re cut off,” says Mason, “your
professor is geared to giving you the appropriate project and
to working more expeditiously with you.”
According to Mason, a good example of the influence
of funding on graduation times occurred following her
implementation of the Dean’s Normative Time Fellowship.
 The Usual SuspectS
There must be practical consequences when fewer than half of graduate
students have a clear picture of when they’ll graduate. We wondered what
they were, and set out to ask science graduate students at Berkeley one
very simple question: “When are you going to graduate?” Here’s what they
said.

Susan Parkinson (4th year PMB; top left): Next year. Steve Gross (4th
year PMB; top right): I don’t know. Matt Prantil (2nd year Chemistry;
bottom left): Um...I don’t know. So I got here in 2003...so like roughly
Christmas 2008. Nathan Clack (4th year Biophysics; bottom right): Um...I
think probably a year and a half.

Brad Prall (6th year Chemistry) May 2005 [cough attack]. Tomorrow? Dennis
Wylie (3rd year Biophysics): Uh...I have no idea. Suzanne Lee (4th year
MCB): Hopefully in a year and a half, maybe? In theory? Emory Chan (5th year Chemistry): I don’t know. Probably, you know,
P H O T O S : D U L A PA R K I N S O N

a year or two. Why? Christine Stuart (3rd year Chemistry): Never. Rosalie Tran (2nd year Chemistry): I don’t know. Why? Dan
Wandschneider (1st year Chemistry): What? From here? I don’t know. Philip Kukura (3rd year Chemistry): Are you recording this...
so you can make fun of me when it doesn’t happen? Robert Blazej (5th year Bioengineering): Who wants to know? Nate Beyor
(4th year Bioengineering): A long time. Why? Will Grover (6th year Chemistry): I’m not sure. I’m looking at December. Teris Liu (5th
year Chemical Engineering): I don’t know. No idea. Nick Toriello (4th year Bioengineering): I don’t know. Later than you.

This fellowship is awarded in the Social Sciences and
Humanities (where times to degree are longer, and funding
less available) and provides dissertation funding for students
who advance to candidacy within the time limit established
for their program. The program has directly decreased time
to advancement to candidacy for many students because they
need to make quick progress to qualify for the fellowship.
Six institutional factors that influence time to degree
were cited in the 99 study by Nerad and Cerny: degree
requirements; teaching requirements and means of
evaluating progress; faculty advising and departmental
guidance; student financial burden, financial support and
debt accumulation; campus facilities; and the availability of
professional job opportunities and placement support. Not
surprisingly, programs that require a dissertation prospectus
and an early start on dissertation research have shorter times
to degree. Further, programs that evaluate students’ progress
annually and provide feedback have shorter times to degree.
Teaching requirements also have an effect. At Berkeley,
students teaching for more than three years average one year
longer to graduate than students teaching less than three
years.
Program quality is a factor that has consistently emerged
as impacting time to degree. The 995 report, “Research
Programs in the United States: Continuity and Change”
found that in 993, PhD recipients whose programs ranked
in the top quartile, “typically completed their studies more
rapidly than graduates of lower ranked programs regardless
of field.”2 Another study found that, in general, better
established programs of recognized quality and of smaller
size had lower times to degree and higher completion rates.
In an analysis of TTD in math and physics at three large
(Berkeley, Chicago, Columbia) and four small (Cornell,
Harvard, Princeton, and Stanford) universities, the larger
programs averaged 6. years, while the smaller ones averaged
5.2 years (967-976 entering class). This study did not
adjust for the fact that all the small schools cited were private
institutions.3
Knowing is half the battle
THE CLARITY with which the guidelines for completing a
PhD program are set out also influences time to degree.3 A
lack of information is not just frustrating for the students—it
actually increases the time to degree. One survey found that
only 45% of the students responding said they had a very
clear understanding of the criteria for determining when
they would be ready to graduate. Similarly, only 3% said
that they clearly understood the length of time they would
be students.3
An informal survey of Berkeley graduate students in the

BERKELEY SCIENCE REVIEW 47

 sciences found that most expected to graduate after a total
of four to six years, or in other words, approximately the
same amount of time they thought was ideal. Based on
Berkeley’s statistics, a lot of them will take longer than that
to graduate.
A little digging through departmental web sites at
Berkeley usually yields one or two sentences about the
duration of the program, often citing something like,
“around five years.” Many programs list the “Normative
Time” for their program, defined in Berkeley’s Handbook of
Graduate Studies as the elapsed time students would need to
complete all requirements for the doctorate, assuming that
they are making adequate progress toward their degrees.
But this is not necessarily the actual time required to finish
doctoral studies, something only one program at Berkeley
(Microbiology) states clearly on their web page for current
and prospective students.
Molecular and Cell Biology is one of the few programs
in which the expectation that students will complete their
degrees in five years is clearly laid out in a schedule of thesis
committee meetings and progress reports, but in other
programs, expectations are communicated indirectly or
more ambiguously. For example, the Biophysics Graduate
Group implies the length of its program by stating that it
guarantees only five and a half years of funding.
Where we go from here
THOUGH many aren’t aware of it, the efforts of many
institutions and national bodies are focused on improving
graduate education, which includes decreasing the time
to degree. But Mason points out that making these
improvements is like shooting at a moving target: “Things
do change so these questions can’t just be resolved once. Over
the last ten years we have improved a little bit. It’s always a
new set of faculty and a new set of students, so it’s a never-
ending [situation].” For example, at this year’s first meeting,
on January 9th, the UC Regents were presented with a
detailed report on the importance of graduate education to
California and the UC system—an effort to draw attention
back to important issues that had been neglected since the
work of the 200 Commission.
For the individual graduate student, whether taking
courses, preparing for a qualifying exam, or planning the
next experiment, it can be hard to see beyond the daily grind,
but taking a step back and looking at the big picture can pay
off. Studies show that awareness of graduation requirements,
48 BERKELEY SCIENCE REVIEW
ART: JENNIFER BENSADOUN
How long will YOU be a graduate student?
actively seeking mentoring resources, writing a dissertation
prospectus, and meeting with a dissertation committee can
all help get the student out of the lab, into a cap and gown,
and then onto the streets of the real world.
LOREN BENTLEY received her PhD in bioengineering from UC
Berkeley. She took 6.5 years.
Want to know more?
Check out the references, or see the book “On time to doctorate:
A study of lengthening time to completion for doctorates in science
and engineering,” available online at http://www.nap.edu/books/
030904085X/html
References
1. Hoffer, S., Welch, Williams, Hess, Friedman, Reyes, Webber, Guzman-Barron, Doctorate
Recipients from United States Universities: Summary Report 2003. NORC at the University of
Chicago, 2004.
2. Summary Report 1996 Doctorate Recipients from United States Universities. National
Academy of Sciences, 1998.
3. Bowen, W.G. and N.L. Rudenstine, In Pursuit of the PhD. Princeton, NJ: Princeton University
Press, 1992.
4. Nerad, M., Preparing for the Next Generation of Professionals and Scholars: Recent Trends
in Graduate Education in Germany and Japan. UC Berkeley, 1994.
5. Education in Nuclear Science: A Status Report and Recommendations for the Beginning of
the 21st Century. DOE/NSF Nuclear Science Advisory Committee Subcommittee on Education,
2004.
6. Reshaping the Graduate Education of Scientists and Engineers. National Academy of
Sciences, National Academy of Engineers, Institute of Medicine: Washington, DC, 1995.
7. Humphreys, S. The Role of Women Graduate Students in EECS at UCB. in Bridging the Gap.
Carnegie Mellon University, 1995.
8. Kamas, L., Paxson, P., Wang. A, and Blau, R., PhD Student Attrition in the EECS Department
at the University of California at Berkeley. Women in Computer Science and Engineering
(WICSE), 1996.
9. Prioritizing Mental Health, A campus Imperative: Proposal for a standing Academic Senate
Subcommittee Addressing Student Mental Health. UC Berkeley, 2003.
10. Ehrenberg, R.G. and P.G. Mavros, Do doctoral students’ financial support patterns affect
their times- to- degree and completion probabilities? National Bureau of Economics Research:
Cambridge, MA, 1992.
11. Nerad, M., Doctoral Education at the University of California and Factors Affecting Time to
Degree. University of California, Office of the President: Oakland, CA, 1991.
12. Goldberger, M.L., B.A.Maher, and P.E. Flattau, eds. Research Doctorate Programs in the
United States: Continuity and Change. Committee for the Study of Research Doctorate
Programs in the United States, National Research Council (US), 1995.
13. Golde, C.M. and T.M. Dore, “At Cross Purposes: What the experiences of doctoral students
reveal about doctoral education.” The Pew Charitable Trusts: Philadelphia, PA, 2001.
Read any good books lately?
L OW-CARB diets. The Da Vinci Code. That must-have
Christmas toy that your little cousin just can’t live without.

PHOTOS: CHARLIE EMRICH

If you doubt the power of fads, look no further.
But how do fads start? And once they’ve started, how do they
propagate, infecting more and more people until they reach into
every nook and cranny of society? In a November issue of the
journal Physical Review Letters, a group of researchers working
in California and France, including graduate student Thomas
Gilbert of the Haas School of Business, describe how they teased
apart the complex influence of word of mouth and advertising
in the market.
The researchers investigated the sales trends of popular
books on the online retailer Amazon.com. By looking at sale
histories, they were able to trace how a book’s popularity spread
through the “complex network” formed by the “social system of
interacting buyers.”
They found two very different kinds of behaviors. The first,
termed an “exogenous shock,” starts when a book is given a large
publicity kick from a newspaper article or from mention on a
television talk show, for example. The sales histories of these
kinds of books show a sharp spike followed by a longer decline
in sales.
“Endogenous shocks,” on the other hand, result purely from
word of mouth and a grassroots-up swelling. The sales histories
of these books build up progressively
until they reach a peak, and they then
relax over a longer timescale than for
exogenous shocks.
For both types of shocks, the scientists
found that the data was best fit by a
model where each purchaser convinced,
on average, one other person to buy the
book.
Besides being of interest in marketing
circles, the research may be important for
those who study other types of complex
networks such as the stock market or
the chain of events that lead up to and follow earthquakes.

MICHELANGELO D’AGOSTINO is a graduate student in physics.


Saludos Amigos,
F rom where I’m writing, I can hear salsa music blaring
from the street below me, it feels like the heat and
humidity are turned up to max, and somewhere in the
distance roosters are crowing. Women braid each other’s
hair on the balcony of the house across the street, and a
canoe just pulled up to unload a shipment of chickens. It’s
a typical day in Borbón, the town of about 5,000 people
in northern coastal Ecuador that serves as the base of
operations for my dissertation fieldwork.
The Cayapas, Onzole, and Santiago rivers converge in
Borbón, creating an urban center supported by forest
logging. Sadly, the area is both a “biodiversity hotspot” and
deforestation front; everywhere you look you see evidence
of the booming logging industry. Huge logs float down
the rivers. Stacks of lumber ready for transport flank the
roadsides. Men pile logs and planks of wood onto flatbeds
in town. Semis haul their loads back to Quito. Chainsaws
hum. Borbón has the pulse of a frontier town—complete
with prospectors, tradesmen, Indians, drugs, street justice,
and missionaries. It’s not hard to imagine what the Wild
West must have been like from this vantage point.
Before the recent construction of a road along the coast,
the only way to reach the villages that dot these rivers was
by boat. The umbrella research project that I am working
with, funded by the National Institutes of Health and
directed by Joe Eisenberg in UC Berkeley’s School of
Public Health, is looking at the impact of road-building on
the spread of infectious waterborne diseases in the region.
I work with a team of researchers that includes 25 local
health promoters from the study villages, three technicians
from Borbón (the big city), an anthropologist and doctor
and data entry staff from Esmeraldas (the really big city, a
couple of hours south along the coast), a nurse and doctor
and microbiologist from Quito (the huge capital city),
and a gaggle of gringos who swoop in now and again to
check on us and collect some data of their own. We spend
our time traveling in dugout canoes to 2 communities
scattered along the three rivers, asking the villagers lots of
questions, and collecting their poop.
“Waterborne disease” is really just a euphemism for
diarrhea. At dinner parties I usually use the former term
50 BERKELEY SCIENCE REVIEW
LETTER FROM
No need to worry. The local kids are keeping us safe with their karate skills.
to describe my work, since the latter either grosses people
out or makes them giggle. Even though I work on these
issues, I’m always shocked to know that diarrheal disease
ranks as the third leading cause of death worldwide and is
responsible for 9% of deaths in Ecuador.
Luckily, I don’t actually have to collect poop samples
myself. Instead, for my dissertation project, I collect
water samples and test for critters in the drinking water.
My methods are actually quite simple—no two-photon
microscopy or nanotechnology here, just old-fashioned
water microbiology. I collect water samples and use
various culture-based tests to determine the level of fecal
contamination in the water. Given that these methods have
been around for ages, it’s actually quite shocking that we
still don’t know how to prevent the spread of waterborne
disease.
From laboratory studies, we know a lot about the
microorganisms that cause diarrhea and the biological
mechanisms by which they cause disease. The trouble
is that we don’t know much about how to control their
transmission in field-based settings. Throughout the course
of my research, I’ll be examining the quality of different
source waters, and comparing different water storage and
treatment techniques. My data on water quality will be
combined with diarrheal disease outcome data from the
larger study to explore how water quality affects people’s
health. I’ll also compare how villagers perceive water
quality at different times of the year with what my petri
dishes tell me about how safe the water is to drink.
ALL PHOTOS: KAREN LEVY

THE FIELD

Children often
help their parents
collect water and
bring it home (top).
The most challenging part of my work is doing I’ll be testing to see
microbiology far away from any microbiology lab. The what’s in that water
(right).
Fisher Scientific truck doesn’t deliver to Borbón, so I have
to make sure I have everything I need before heading out
to the field and improvise whatever I forget. When I was
first testing out my techniques, a fellow graduate student
and I set up a laboratorio clandestino in a hotel room, for
lack of any other place to work in Borbón. (Somehow, I
decided that locking myself up in a small room, sealing
the windows, turning off the fan and turning on a flame
when it’s 90 degrees with 90% humidity outside was a fun
way to spend the summer.) We told the staff not to clean
the room, but no doubt they peeked in to see the mattress chlorine AND boils it. When she offered me a frozen
propped up against the wall, the sheet duct-taped to the coconut popsicle made from her water, I happily ate it,
wall to cover the open windows, a table covered with filter thinking it would be quite clean. 24 hours later when
flask, forceps, examination gloves, petri dishes, parafilm, E. coli bacterial colonies grew up on the plates of her water
pipetters, etc. Gringos locos. samples, I thought better of the decision.

Now when I go out to villages along the rivers, I carry in But don’t worry, I’m staying safe and healthy and having a
the canoe with me a mobile lab to test for little critters fun time. Especially with all the amazing salsa dancing at
growing in various water sources. The portable lab includes the Borbón discos.

See you soon,

a “field hood” to try and minimize contamination and
my soon-to-be patented $0 incubator (they usually run
around $3,000-5,000), made out of a bucket, a light bulb,

Karen
a thermometer, and a dimmer switch. Who needs Fisher
Scientific?

The other big challenge to overcome is knowing when

people are giving you an honest answer versus telling you
what you want to hear. One day I collected a water sample KAREN LEVY is a graduate student in environmental science, policy,
from a woman who told me that she treats her water with and management.

BERKELEY SCIENCE REVIEW 51