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Spring 2005 Issue 8
Reach new heights with BSR
Are you fascinated by the world of science? Do you want to write
about scientific discoveries happening at Berkeley? Then join the
Berkeley Science Review! We’re a graduate student publication
created by students who are passionate about the research
happening at our university. We’re always looking for new
editors, writers, photographers and layout designers. Could
that be you? Visit us online to find out what we’re all about!
from the editor


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, then email us at
Allon Hochbaum 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

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 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

science FEATURES

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



8 In the Garden of Good and Evil

Mushroom hunters can tell the difference
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
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

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



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-

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

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).


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


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:

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,

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
—Rebecca Sutton
Want to know more? Learn more about this and other rocky
planets at



In the Garden of poisonous varieties are often

dead ringers for other edible,
Good and Evil tasty species. True mushroom
hunters know their mushroom
Mushroom hunters biology, and are well aware that
can tell the difference the size, color, texture and odor
of the stalk, cap, or gills can

T HE Bay Area is the perfect habitat for

mushroom hunters. The culture of
culinary obsession, the warm and moist
be used to distinguish between
species. Some species change
color when they are bruised or
winter climate, the abundance of conifers sliced in half and their juice
and hardwood trees, and even the region’s oxidizes. Other species can only
relaxed attitude toward experimenting be identified after microscopic
with mind-altering substances... But who spore analysis. It’s a tricky
are the mushroom hunters, and how can business, which requires more
you, the aspiring mushroom hunter, join than just a simple key or field
their ranks? guide.
Mushroom hunters come in all ages, How can you join these
with varying degrees of affinity for mushroom hunters and dine
mushroom-themed clothing. They seek on wild porcini risotto without
wild fungi for their taste, medicinal worrying about getting sick or
qualities, or psychoactive effects. For dying? The most interesting
them, mushroom hunting is more than option by far is to sign up for
a hobby. It has to be, explains Tom Tom Bruns’s course, California
Bruns, a professor in the Department of Mushrooms, PMB 3. Offered Amanita calyptrata—photo taken in the Jackson State
Plant and Microbial Biology: “Calling in the fall, the course takes advantage of Forest, on a fieldtrip for California Mushrooms, PMB 113.
them amateurs doesn’t do them justice. the early part of the mushroom season
These people are very well informed.” (which stretches from October through
Mushroom hunters must be good at March, peaking in December and wild have diverse methods of obtaining
what they do, because misidentifying a January). Students collect and learn to food. Mycorrhizal fungi form symbiotic
mushroom could be fatal. identify over 50 genera and build their relationships with trees, providing them
While the East Bay is home to edible own extensive collections throughout the with nutrients and receiving carbon in
wild chanterelles and porcinis, it is also semester. exchange. Parasitic fungi get carbon
home to a number of toxic mushrooms, Mushrooms are the fruiting bodies of from plants but give nothing in return.
which will make you sick, and poisonous fungi and exist to produce and disperse Saprophytic fungi obtain their carbon
mushrooms, which can kill you. The spores. The many types of fungi in the from dead or rotting debris.
Many species of saprophytic fungi,
Ramaria sp., Jackson State Forest. 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



perhaps not the locations of their secret off their skills in other regions: “This absolutely right.” Investigating historical
porcini patches). knowledge doesn’t travel to other places.” descriptions, herbarium specimens, and
Another way to become familiar with Perfectly edible mushrooms from the genetic data, she found that the first
mushrooms is to visit the Mycological East Coast, Europe and Asia have toxic confirmed California specimen of the
Society’s annual Fungus Fair—this year, or poisonous look-alikes here in the Bay Death Cap was collected in 945. “There
it was held at the Museum of California Area. Recently, an Oakland resident died were probably multiple introductions of
in Oakland. Here, chefs from renowned after eating Amanita phalloides, the Death this species,” she says, because Amanita
Bay Area restaurants give cooking Cap mushroom, which she mistook for phalloides in California are not genetically
demonstrations. Local mushroom experts, similar enough to have
including Bruns, give talks. There are come from a single
also booths where you can try your eye introduction.
at identifying mushrooms, peruse fabrics Because of the severe
colored with mushroom dyes, learn about consequences of a

medicinal mushrooms, and, at perhaps misidentified mushroom,

the most popular table, learn about the aspiring mushroom
psychoactive mushrooms that can be hunters are encouraged
found in nearby parks. to learn their lessons well.
One group of psychoactive mushrooms At the final exam for
contains a chemical called psilocybin, California Mushrooms,
which, when ingested, is converted to says Bruns, completely
psilocin. Psilocin is structurally similar deadpan, “the students
to serotonin, a chemical naturally present are presented with three
in the brain. It is thought that psilocin mushrooms, one of which
changes the brain’s signal-to-noise ratio. is poisonous. They have


Stimuli that the brain usually considers to eat two.”
to be noise are instead considered to
be signals, resulting in synesthesia, the JENNIFER SKENE is a graduate
simultaneous perception of more than student in integrative biology.
one sense. Two species of mushrooms
that contain psilocybin grow in the Bay Want to know more?
Visit the Mycological Society
Area: Psilocybe cyanescens and Psilocybe of San Francisco’s website at
fibrilosa. Both are small and brown, and
resemble several species of poisonous
mushrooms. Visit the Oakland Museum of
California online at
The psychoactive Amanitas, those
Alice-in-Wonderland-ish red mushrooms
with white polka dots, comprise a Good...or evil? The experts at the Mycological Society
separate group. Their active ingredient of San Francisco’s annual Fungus Fair will tell you.
is the chemical muscimol. Amanita
muscaria can be found in the Bay Area, an edible species common in her native
but they contain a small amount of Taiwan. “Posters to warn people about
muscimol and a large amount of toxic the Death Cap mushroom are printed
compounds that make people sick. in many languages to target immigrant
Amanita muscaria from Eastern Europe communities,” says Anne Pringle, a UC
contains more muscimol, resulting in Berkeley post-doctoral fellow.
stronger psychoactive effects and greater Recent work by Pringle has shown
popularity. that the Death Cap mushroom was
At a talk at this fall’s Fungus Fair, actually introduced from Europe. “There
amateur mycologist Debbie Viess warned is a great oral tradition in the amateur
that while mushroom hunters may be community here,” explains Pringle.
familiar with the species present in the “They thought Amanita phalloides was
Bay Area, they shouldn’t attempt to show introduced—and it turns out they’re




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
Second, the female fly’s egg laying organ
also has taste cells, so egg-filled mothers
can deposit their broods directly onto
air. Working under a microscope, he or bitter, but also by the location of the food sources. “Time flies like an arrow,”
dunks its feet into a spherical drop of a taste on the fly’s body. according to Groucho Marx, “and fruit
sugar solution and watches it extend its Taste ranges over only a handful flies like a banana.”
proboscis in a reflexive feeding maneuver. of “qualities”, each corresponding to Clues to how sensory perceptions are
Around the corner, PhD student a particular type of receptor protein: represented in the brain have previously
Aakanksha Singhvi examines transgenic sweet, recognizing sugars and related been found in various sensory systems
flies in which fluorescent proteins compounds; bitter, recognizing a wide in diverse animal models. The neurons
illuminate individual taste cells. This range of plant alkaloids and related at the center of the vertebrate retina, for
technique allows her to trace those cells’ compounds; salty, recognizing sodium example, make projections to the center
projections into the fly’s tiny brain and and potassium ions; and sour, recognizing of a certain brain area, while neurons
document the neural anatomy of taste in hydronium ions from acids. Mammals from the left and right edges of the retina
unprecedented detail. also have a receptor for “umami”— make connections on opposite edges
Those experiments and others—carried “yummy taste” in Japanese—recognizing of that area. Thus the brain tissues that
out in Kristin Scott’s laboratory in the amino acid glutamate, which in process visual signals embody a map of
the Department of Molecular and nature signals a protein source. the retinal image. Similarly, our sense of
Cell Biology and the Helen Wills Scott and her colleagues propose that touch is represented as a distorted map of
Neuroscience Institute and published this relatively simple system leads to a the body surface stretched over the touch
last summer in Cell—produced two simple pair of behavioral responses: to eat center of the brain. How taste circuits in
remarkable conclusions. sweet or moderately salty food sources vertebrate brains are organized remains
First, the insect taste system is and reject bitter, acid, or very salty unknown. But researchers presume that,
organized in much the same way as that food sources. But in flies there are two since the cells of the tongue are organized
of vertebrates. On any particular taste anatomical twists that Scott’s group has by taste quality, the taste center in the
neuron, the taste receptors—surface exploited. First, flies have taste neurons brain is likewise segregated anatomically
proteins that bind to small “tastant” on their wings and legs, so they taste food by taste quality. The hypothesis, in other
molecules—will bind only to bitter or at the ends of their appendages and then words, is that there are distinct brain areas
sweet tastants, for example, but never turn toward desirable sources to feed. that process sweet, bitter, salty, sour, and
to both. Flies have, in other words, (Fish, incidentally, have taste receptors umami stimuli.
dedicated sweet and bitter taste neurons, all over their bodies; taste researchers Scott’s team showed that the fly’s brain
just like we have on our tongues. like to call them “swimming tongues.”) anatomy encodes two qualities of taste



in parallel: what it tastes like, and where different compounds as bitter, without
it is on the fly’s body. They observed, for being able to tell them apart.”
example, that taste cells on the end of a Scott started her career at Berkeley
fly’s leg send projections further towards only two years ago, after a postdoctoral
the hind end of the fly’s brain than taste fellowship in the laboratory of Richard
cells on its proboscis. Furthermore, a Axel at Columbia. Axel shared last year’s
bitter and sweet cell side by side on the Nobel Prize with another former postdoc,
proboscis will project to distinct targets Linda Buck, for the identification of
within the proboscis taste area of the the genes encoding olfactory (smell)
brain. In general, each taste organ sends receptors.
nerves to distinct targets in the brain, “Our long term goal,” Scott says, “is
and within those areas, bitter and sweet to understand the neuronal circuits in
neurons seem to connect to distinct the brain” that underlie taste. In order to
groups of target neurons. begin to explain taste behavior in terms
So much for taste representation in of connected groups of neurons, they aim
the brain. How does each taste neuron to identify the individual neurons in the
genetically encode taste sensitivity? The brain that receive input from taste cells,
proboscis extension reflex Wang observes and then determine which neurons they
has been known for 30 years. But he put connect to in turn. To trace these neural
it to new use in order to characterize the circuits, postdoctoral fellow Sunanda
function of specific taste receptor genes. Marella and PhD student Walter Fischler
Sixty-eight taste receptors have been have been using transgenic flies with
identified in the sequenced genome of the neurons whose fluorescence intensity
fruit fly. Scott’s group removed specific changes when they become active. Instead
taste neurons by genetically programming of having to poke randomly around the
them for death—they drove a diphtheria tiny fly brain with electrodes, recording
toxin gene only in cells that produce taste response activity in one cell at a
that taste receptor, eliminating all cells time, their method will allow real time
that contain a certain receptor, one at a microscopic observation of the activity of
time. Then they put these flies to a sweet whole groups of neurons in the taste areas
and bitter taste test. Using this method of the fly brain—a technique known as
they characterized one bitter and one “functional imaging.”
sweet receptor. The remaining 66 gene Meanwhile, Scott’s group is screening
products are presumed to include sour for mutants with defects in taste-
and salty receptors, as well as other sweet mediated behavior. Ultimately, they hope
and bitter receptors, but none have been to identify genes required in the fly brain
characterized except the two in Scott’s for those behaviors and uncover more
studies. clues to the underlying neural circuits and
With only four taste categories, why how they function. “Functional imaging,”
does the fly genome contain so many Scott explains, “will be the platform for
taste receptor genes? Probably because all of these studies.”
of the molecular diversity of tastant
molecules. While sugars, chemically JAMES ENDRES HOWELL is a graduate student in
speaking, are a relatively simple class of molecular and cell biology.
molecules, the compounds that evolution
has dictated animals avoid—the bitter Want to know more?
Check out “Taste representations in the
tastants, in other words—are remarkably Drosophila brain”: Wang Z. et al, Cell. 117, pp.
diverse. It’s now known that in both flies 981-991 (2004).
and mice a single bitter taste cell contains
many different types of bitter receptors. Visit Kristin Scott’s lab at
“This organization,” Scott explains,
“would allow animals to recognize many



Pull My DNA other, the “trap bead,” hovers above it.

The pipette is linked to a stage Smith
Laser tweezers: a
glass micropipette
...with the world’s tiniest tweezers controls via a red trackball; the trap bead holds onto a
is held in place, not by a physical object, polystyrene bead via

M OST people take it on faith that but by light from a focused laser beam, suction. The “trap”
bead is held in
molecules exist, while a few others the heart of the laser tweezers. When place by focused
aren’t satisfied until they have seen them Smith moves the pipette bead, the trap laser beams. A
imaged by a microscope. But as Steven bead starts to follow—it’s as if an invisible strand of DNA
Smith says, “after you’ve looked at these tether is linking the beads.The tether is joins the two
molecules for a long time you really want a single strand of DNA, with its ends
to get your hands on them.” modified so that it sticks to proteins that
A fine concept, but a challenging coat the beads. While the pipette bead
task if the molecules you’re talking is solidly anchored, the laser tweezers
about are only two nanometers in hold the trap bead somewhat loosely, as
diameter ( 20,000 times smaller than a if the bead were on a spring. Researchers showed that this
human hair). Despite these minuscule observe how the DNA linking the two is possible because


dimensions, Smith, a research scientist in beads stretches when they pull on it. By the motor responsible
Carlos Bustamante’s lab in the physics, studying how the trap bead deflects the for this task is
chemistry, and molecular and cell biology laser beam, they can measure the force extremely powerful,
departments, can stretch, twist and probe on the tethered DNA in piconewtons able to work against a
all kinds of molecules with an instrument (a millionth of a millionth of the force pressure of about sixty
called laser tweezers. needed to hold a baseball) and how far it atmospheres—ten
Watching Smith work with laser stretches in nanometers. times the pressure
tweezers is like watching him play a video Laser tweezers have been especially stored in a bottle of
game. A monitor shows a view through a useful in the study of proteins that move champagne!
microscope of the two beads he controls: along DNA, doing things like reading, These experiments,
one is perched atop a pipette, and the copying, cutting, and unwinding it. Each Smith says, “take a big collaboration…
of these proteins physically You need a biologist or a biophysicist to
moves along a DNA double tell you what the problem is that’s worth
strand as it performs its solving…You need a physicist to build
function. By attaching a the optics and to interpret the data…
bead to one of these proteins, and you need an architect and a building
researchers can use laser manager to build you a basement room
tweezers to play friend or foe on bedrock.” Since laser tweezers are so
by mechanically helping or sensitive, “you have to practically build
hindering the motor’s motion. your building around [them].”
Measuring how speed varies Although on campus versions of
with force and chemical fuel Smith’s tweezers reside in the Bustamante
supply allows researchers to lab, Ignacio Tinoco’s lab in Chemistry,
investigate the fascinating and Jan Liphardt’s lab in Physics, the
coupling between the physical infrastructure requirements prohibit
mechanism and the underlying standard biology labs from using laser
biochemistry. A good example tweezers. That’s something Smith
is the “packing” motor of the wants to change, so he has built the
virus phi29, which is able to “Mini-Tweezers,” which take the 4 by 6
stuff a long strand of DNA foot optical table and associated optics

into a tiny virus shell while and cram them into a basketball-sized
preparing to infect other cells package. This portability enables your
(imagine putting a ten foot “collaborator someplace across the world
length of stiff wire in a box the to send it back to you in a box.” Smith
Steven Smith is a research scientist in Carlos Bustamante’s size of a walnut). Using laser expects a commercial version of the
lab in the Departments of Physics, MCB, and Chemistry. tweezers, Bustamante’s group instrument to cost between $00,000 and


$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

MEREK SIU is a graduate student in biophysics.

Smith’s “Mini-Tweezers” compress the essentials Want to know more?

of optical tweezers into a package the size of a Visit the Bustamante lab website at
basketball. for articles, movies, and more.

Sweeping CO2 Under the Rug

The Science of Geologic Sequestration

S ALLY BENSON was skeptical. Five 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
years ago, when the US Department impact of fossil fuels on our climate using
of Energy asked this Lawrence Berkeley existing technology from the oil and gas
National Laboratory engineer to develop industry.
a program to study geologic carbon Five years later, scientific evidence
sequestration, she described herself has created a new convert. Benson
as “agnostic.” Could the capture and easily admits, “the longer I’ve worked
underground storage of carbon dioxide on [geologic carbon sequestration], the
emitted from refineries and power plants more persuaded I’ve been that this can
really loosen the chokehold of this gas on really work.” As director of GEO-SEQ
our climate? Would it be safe? And could (pronounced “geo-seek,” for Geologic
we afford it? Sequestration), she guides public-private
Sally Benson, an LBNL engineer, coordinates
In the end, Benson could not ignore research focusing on the storage end of
joint public-private research on carbon
any means of combating global warming. this capture-and-storage technology. sequestration.
By burning fossil fuels over the last While other groups design energy
250 years, we have injected nearly 300 production facilities and gas separation carbon dioxide below ground.
billion tons of carbon, most of it carbon methods for carbon dioxide capture, the Fortunately, many good sequestration
dioxide, into our atmosphere. Carbon GEO-SEQ team explores ways to get the sites are easy to spot. Because oil and
dioxide traps the sun’s heat near the gas underground and keep it there. natural gas are buoyant, reservoirs that
Earth’s surface in a process known as The first step in carbon sequestration is store these fluids can store carbon dioxide
the greenhouse effect. In the 990s, the selection of a site with an appropriate as well. Even more carbon dioxide
record-breaking heat and devastating underground mineral formation. A good can be stored within saline formations
storms triggered international alarm formation is like a loaf of crusty bread —common mineral deposits permeated
about the effects of global warming. With —a dense, impermeable layer topping a with very old, salty water, and topped
renewable energy production still in its mass of porous material. The dense layer, by caprocks. Worldwide, depleted oil
infancy, geologic carbon sequestration known as the caprock, keeps the buoyant and gas reservoirs and saline formations




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 storage, “we are leaking 00%.” cost? If power plants used existing
carbon as carbon dioxide—six times While Benson initially questioned sequestration technology, the cost to
what we’ve produced since the rise of the security of sequestration, she is now produce electricity would increase by 30
industrialization. satisfied that storage can be quite safe. to 70%. With more advanced technology,
To study carbon sequestration, Benson It turns out that storing carbon dioxide the Department of Energy hopes to
and her team have injected 700 thousand underground is a lot like storing natural reduce the cost of storage to less than
gallons of carbon dioxide into a depleted gas underground, something industry has 0% of the cost of electricity production.
oil reservoir near the town of South been doing for decades. Existing methods Measured against the climatic disasters
Liberty, Texas. Sensors above and below to control potentially disastrous natural that may result from global warming,
ground detect trace amounts of the gas, gas leaks work just as well for carbon geologic carbon sequestration should
or minute changes in pressure, seismic dioxide, though as Benson cautions, “that prove to be an exceedingly wise
motion, or electromagnetic properties. doesn’t mean it would be cheap.” investment.
These measurements reveal the effects of And while most forms of waste disposal
natural and operational variables (like grow more dangerous as containment REBECCA SUTTON is a postdoctoral researcher in
reservoir geology and rate of injection, structures age, Benson points out that for environmental science, policy, and management.
respectively) on the flow of carbon sequestration, “it’s actually the reverse;
dioxide within the reservoir. As scientists the carbon dioxide storage actually Want to know more?
Visit the GEO-SEQ website at
improve predictions of the underground gets more and more stable over time.”
behavior of the gas, they advance their Although sequestration initially depends
ability to find and fill storage sites. on the caprock to physically trap the gas,
By testing a variety of sensors, Benson chemical reactions eventually transform
determines which can be used to detect carbon dioxide into carbonate minerals,
leaks for commercial sequestration permanent residents of the reservoir.
projects. Seepage through microfractures Benson and her GEO-SEQ team are
within caprocks presents the largest not alone. Already, three commercial
monitoring challenge, notes Scott Klara, projects each store at least a million tons
sequestration technology manager for the of carbon dioxide annually. But how
Department of Energy. However, without much does geologic carbon sequestration



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

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. During amplexus, the female frog deposits her eggs while the male frog—clasped to her
Interested in the special adaptations back—fertilizes the clutch.
amphibians must make to survive in
extreme environments, Vieites chose a frustrated, for next year. fertilized clutches. More fertilized eggs
study site high in the Spanish Pyrenees. For frogs, egg fertilization usually takes is good for mom because it means more
He worked with this population place while the male and female are in of her DNA is passed on. Second, these
throughout his undergraduate and amplexus—while the male is clasped to higher yield clutches have the advantage
graduate careers at the University of Vigo the female’s back and releases sperm on of increased genetic diversity, with some
in northwestern Spain. However, it was her eggs as she lays them. Vieites ob- portion fertilized by the original male
not until he finished with his coursework served something quite different. While and the remainder fertilized by the
as a graduate student, and finally freed some males were behaving “normally” pirate(s). This is also good for mom,
from exams in the first weeks of May, —clasping females and fertilizing eggs since a more diverse clutch will likely
that he witnessed a behavior never before in the usual way—other “pirates” were produce more fit offspring with a greater
reported among amphibians. sneaking after mating pairs and making chance of surviving to pass on her genetic
Most populations of R. temporaria off with their freshly laid egg clutches. At information.
breed at night, but the low temperatures times, the pirates banded together into The only ones who don’t seem to
at Vieites’s alpine site force these frogs to groups, patrolling the pond for unattend- benefit from the pirate behavior are the
breed during the day. This allowed Vieites ed eggs. Unsatisfied with simply grasping original males pursuing the “normal”
to take a front row seat during mating the clutch, some pirates would crawl into mating strategy. Quantifying the relative
season. the heart of an egg mass so their sperm fitness of the “normal” strategy versus the
R. temporaria is an explosive breeder. could penetrate every last egg. On aver- pirate strategy will be Vieites’s next task.
Just after the ice melts in the spring, age, pirate sperm fertilized one quarter of Only five or six other species of
enormous numbers of male frogs gather the eggs, but in some cases accounted for amphibians are known to exhibit multiple
at ponds to mate. Over the next several nearly all the fertilization in clutches. paternity, but Vieites believes that this
days, females will wander by a few at While this behavior clearly confers an number greatly underestimates the actual
a time, drawn to the cacophony of evolutionary advantage on the pirates, prevalence of this type of behavior. Very
croaks from the males. Males typically who would otherwise fail to pass on little is known about the great majority of
outnumber females by 10 to 1 which their genes, it also benefits the females amphibian species. R. temporaria is one
means only a small fraction of the males in two key ways. First, the fertilization of the best-studied species—over 4000
(10–20%) will get an opportunity rate of pirated clutches can approach scientific articles have been published
to mate. The rest will have to wait, 100% compared to just 70% in singly about it over the past 100 years—and yet


this behavior remained unknown, and it develop strategies for conserving species
would be unknown today if Vieites had when the decline is due to identifiable
not finally made it up to his study site for factors such as habitat loss. Without
that one crucial week in May. knowledge of the cause, little can be done
Unfortunately, our time to fill in the to reverse the slide. Only with further
many gaps in our knowledge about research can we hope to uncover the
amphibians may be running out. Vieites causes, and in so doing, the solutions.
emphasized that while his studies of Clearly, there is a wealth of knowledge
amphibians have resulted in many still waiting to be mined from further
interesting findings that may have much study—if behaviors such as clutch piracy
to teach us about sexual selection and are only now coming to light in our most

evolution, these are overshadowed by a well-known amphibian species, imagine

looming crisis. The World Conservation what awaits us in unfamiliar places.
Union Global Amphibian Assessment,
a major project on the conservation ALLISON DREW received her MS in
status of 5743 species of amphibians, has environmental science, policy, and management
discovered that the populations of over from UC Berkeley.
40% of species are decreasing.
Even more troubling, for almost Want to know more?
David Vietes first observed this strange mating half of the most rapidly declining Check out “Post-mating clutch piracy in an
behavior at a site high in the Spanish Pyrenees. species, populations are dwindling for amphibian”: Vieites, D. R., et al., Nature 431,
pp. 305-307 (2004).
no identifiable reason. It is possible to


it’s happening.
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

As crazy as it might at first

have seemed, SETI@home
captured people’s imaginations.
BOINC! It’s been downloaded by over 5
Do try this at home million users in 226 countries,
some 600,000 of whom still

I N THE old days, if you wanted to

be a tiny contributor to the onward
march of scientific progress, you might
remain active. Together, they’ve
contributed over 2 million
years of computing time. Its
have donated your body to science. But message boards form an online
if David Anderson has his way, you community where people can
won’t have to wait until you’re pushing socialize (several couples have
petals to advance the frontiers of human met through SETI@home and
knowledge—you just have to donate your married) and keep track of how
dead computer time. much work their computer
Anderson, a scientist at the Berkeley accounts have completed. The Is ET trying to phone home? The answer may be
Space Sciences Laboratory (SSL) and “leader board” generated so much hidden in this noise.
former professor in the Department of attention that some users began selling
Computer Science, directs BOINC—the completed units and successful accounts form. In August,
Berkeley Open Infrastructure for on eBay for as much as $275. signed up to use BOINC as well. Based
Network Computing (boinc.berkeley. While working on the original version in the UK, aims
edu). BOINC is a software platform that of SETI@home, Anderson quickly to improve long-range climate model-
makes it easier for scientists to harness discovered that he and his coworkers ing by making very small tweaks to a
the massive computing resources that were spending most of their time model’s parameters and running it again
often lie dormant in people’s homes and building infrastructure to manage the and again. Thus far, 20,000 users have
offices. In this new paradigm, called project: writing code to send out data crunched through over 2 million years
public computing, computational tasks packets to people’s computers, running of Earth’s imaginary future. Their efforts
are chopped into small pieces and sent to servers and databases, keeping track culminated in a January publication in
individual members of the public. Your of completed work sent back to the Nature showing that the Earth’s response
computer can be looking for aliens or project, and making sure that nobody to increases in greenhouse gases may be
calculating the temperature of the Indian submitted fraudulent results. They lost far more dramatic than scientists had pre-
subcontinent in the year 2050 while you a year of science in just setting up the viously expected.
sip a cup of tea or cook dinner. basics. But in the process, Anderson had As part of the World Year of Physics in
Without a doubt, the best-known a realization: “Infrastructure is totally 2005, Einstein@home has been designed
public computing project is SETI@home. independent of application. Wouldn’t it to run on BOINC to search for gravity
SETI, the Search for Extraterrestrial be better if we just developed one [system waves, the ripples in the fabric of space-
Intelligence, looks for signals from so that other] projects could start up with time predicted by Einstein’s general
intelligent extraterrestrials in data from minimal infrastructure?” And so BOINC theory of relativity. If that doesn’t interest
the Arecibo radio telescope in Puerto was born. you, you can help design magnets for the
Rico. SETI@home was created in 1995 BOINC handles all of the behind-the- Large Hadron Collider, the world’s next
by Anderson and David Gedye, then a scenes tasks so that scientists can quickly great particle accelerator at the CERN
UC Berkeley computer science graduate and easily set up public computing lab in Switzerland with LHC@home, or
student. It was the 25th anniversary of projects of their own. It’s available free of help figure out how proteins fold with the
the Apollo moon landing and Gedye was, charge for researchers and for the general Predictor@home project.
as Anderson puts it, looking for a way to public to download, and it runs on From the beginning, Anderson made
rekindle the public’s interest in science in Windows, Apple, and Linux platforms. it one of BOINC’s goals to allow users
the same way that “Apollo got the public “The goal of BOINC is that someone can to choose how to allocate their resources
really galvanized.” SETI@home was their set up one of these projects really easily,” between projects, especially with so many
answer: let people search through the Anderson says. to choose from. For example, you can
mountains of Arecibo data on their home And so far, scientists and the public choose to search for gravity waves ten
computers, a chunk at a time, and give have been quick to respond. SETI@home percent of the time and fold proteins the
them a glitzy screen saver to look at while has switched over to the BOINC plat- other ninety percent. His hope was that


BOINC could “get people to invest some Anderson cautions. While your computer

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


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.

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


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
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 new ground.
will make every effort to preserve Voters have
the choice of using biotechnology begun to legislate
in its county and encourage the scientific issues directly,
establishment of a state or national and the effects may
biotechnology policy.” Kings County, eventually ripple through
neighbor to Fresno, passed a similar UC Berkeley research
resolution, emphasizing farmer choice programs and then the
in the use of GM crops. state (and world) agricultural
As counties rush madly for one communities.
bandwagon or the other, California’s
famously chaotic, grass-roots approach The Letter of the Law
to legislation is once again breaking THE measures that made it onto No-
vember 2004 ballots in counties across scientific input was evident in such
PHOTO: GENEVIEVE SCHIFFRAR the state were a motley bunch. Some bloopers as “DNA, or deoxyribonucleic
prohibited all GMOs, while others acid, means a complex protein,” a
attempted to outlaw only GM food quote common to over half of the
crops, making exceptions for GMOs voter initiatives. (DNA is composed of
used in medicine and research. The nucleotides, not amino acids.)
penalties for contraband organisms also In other cases, the legality of some
differed, some giving the Agricultural ordinances was questionable. The
Commissioner power to dole out ap- criminalization of growing GMOs
propriate punishments. Others, like in Humboldt County’s measure was
Humboldt’s, would have punished illegal and resulted in a lack of support
offenders by “confiscation and destruc- from both sides; it failed to gain voter
tion of any organisms found to be in approval. Similar measures on the
violation,” and imposition of “a mon- November ballots in Butte and San
etary penalty and/or imprisonment,” Luis Obispo Counties, despite heavy
in essence, turning the cultivation of financial support from anti-GMO
GMOs into a criminal act. groups, also failed. In fact, the year’s
Unfortunately for their creators, these three anti-GMO successes were largely
The tassels of a GM corn plant, flowering in a measures were written without much symbolic: Marin county, for example,
research plot in northern California. scientific or legal advice. The lack of has only minimal commercial farming,


Blowin’ in the wind
Gene flow is a result of tion of Official Seed Certify- However, the chloroplast is from forming a new seed in
the pollination of one ing Agencies. But no matter naturally excluded from a the event that it does find
plant line by another. This how wide the buffer zone, plant’s pollen. This means its way to another plant.
is not normally cause for there can never be 100% that foreign DNA inserted Farmers’ rights groups
concern, but it can become certainty that no contami- into the chloroplast would were outraged at the
a problem if pollen from a nation will occur. remain only with the sta- initial introduction of this
GMO fertilizes an organic To reduce the risk of gene tionary, female portion of technology, as it was seen
plant or a native, “landrace,” flow below what a buffer the plant body, reducing as a way of maintaining
variety. Farmers have zone permits, two tech- the chance of genetically proprietary rights over GM
several options to control niques are in the pipeline. “polluting” other plants. seeds, forcing farmers to
gene flow into or out of In the first, scientists insert Currently, no commercially buy new seed each year. As
their fields. the foreign gene into a cell’s sold GM plant utilizes this a result of the outcry, the
To limit the risk of pol- chloroplast, the photosyn- technology. company that developed
len contamination, organic thetic compartment in a A second technique the terminator technology
crops are restricted to grow plant cell, rather than its nu- involves the insertion of a promised not to use it,
on land surrounded by a cleus. Transgenes inserted “terminator” gene into the even though this method
substantial buffer zone. The into this cell compartment GMO. This gene renders would drastically reduce
minimum buffer distance is can still produce the de- the pollen from a GMO the possibility of gene flow
set by the federal Associa- sired plant characteristics. plant infertile, preventing it from GMOs to other plants.

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


need to ask: are they needed, are they equivalent” to its closest classically
efficacious, and are they economic. In bred relative, no additional testing is
most cases, you’ll find they are not.” required.
Nonetheless, many companies exten-
A pound of prevention? sively test their products, regardless of
TO MANY who are concerned with government pressure, for fear of litiga-
GMO safety, one of the most tion. In fact, GMOs are tested with
significant regulatory problems is greater rigor than any classically bred
that the GMO market is dominated crop currently produced, even though
by a few very large companies like an overwhelming majority of cur-
Monsanto and DuPont. These rent peer-reviewed data indicates that
companies own not only the genetically GMOs are no more harmful than clas-
modified plants themselves, but also sically bred crops.
the technology and information used Frustrated by the success of
to create them for at least the next 20 anti-GMO initiatives, industry
years. With this monopoly and little representatives assert that the
government oversight, such companies public should be championing less
can set their own standards for product regulation, not more. Neal Gutterson,
regulation. Many people fear that as a graduate of UC Berkeley and Chief
a result, the proper tests are not done Operating Officer of Mendel, a private
and possible problems with human biotechnology research company in the
health and environmental safety are not East Bay, thinks genetically modified
agriculture (see sidebars). discovered. crops are already overregulated.
Opinion among the faculty at UC Indeed, there is very little enforced He points to a five-hundred-page
Berkeley varies as much as it does regulation by either the state or the dossier sent by Monsanto to the US
internationally. In the Departments of federal government. As long as the government in support of a new
Molecular and Cell Biology (MCB) company selling the product can product. To clear a classically bred
and Plant and Microbial Biology demonstrate that the genetically crop for sale, the government requires
(PMB), researchers regularly genetically engineered crop is “substantially far less paperwork. Gutterson argues,
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.” PHOTO: GENEVIEVE SCHIFFRAR
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 Peggy Lemaux examines some GM sorghum, engineered to be more easily digestible.


“[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

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

Old Macdonald had a right

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


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

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


Sonoma, a neighboring county, has

already collected the necessary number

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


with a

a tour of the Golub

antique microscope

by Angie Morey

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.


The Golubs in their microscope museum den.

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


1670-1680 1750-1800

c. 1745


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



c. 1890

c. 1840 1905


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 back then” and these now-common procedures required
Laboratories took the task a step further by carrying out a specialized laboratory, a niche for which Bio-Science
new research and publishing frequently in the scientific Laboratories was perfectly designed.
literature. The Laboratory rose to be a leader in the clinical Continuing with their trend of originality, the company
field and was called upon by doctors and hospitals both began to build a collection of old laboratory equipment
nationally and overseas to perform procedures such as for the aesthetic enjoyment of their clients and employees.
hormone, toxicological, and chromosomal analyses as well They envisioned that this collection would include blood
as bacteriological and immunological assays. Although counting equipment, balances, glassware, specialty books,
most of these procedures are commonplace in the medical and microscopes. As avid travelers, Golub and his wife
field today, Golub reminds us that “lab life was different 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 A life-long passion appears early: 12-year old Steve Ruzin (far right)
of eBay or Google, required more than just a few clicks on poses with his first microscope.
the Internet. Fortunately, on their many vacations abroad,
the Golubs had established the connections necessary to lined with glass shelves containing the growing collection
acquire rare specimens of historical and scientific merit. of instruments, illuminated on one side by natural light
Alain Brieux, a Parisian dealer of scientific antiquities, from an overhead skylight. The room’s den-like features
was one such connection who became instrumental included comfortable chairs, an entertainment system,
in the expansion of the Golubs’ personal microscope and a variety of books on optics and microscopy stacked
collection. The Golubs also made purchases for their on the shelves of an antique bookshelf. With a proper
personal collection from other private dealers, as well home for his microscopes, Golub continued collecting
as from Sotheby’s and other auction houses both in the microscopes even after his retirement from the Laboratory
United States and Europe. in 980. In 995, through discussions with then-Chancellor
By the late 960s the Golubs had amassed a substantial Ira Michael Heyman, Golub arranged to donate part of
the collection to UC Berkeley, to be housed in a special
Ruzin sometimes imagines “what case in the Valley Life Sciences Building. It is here that
the collection remains and continues to grow. Since
the original owner must have
its establishment, Golub has added microscopes to the
thought and felt when they used collection and plans to make other donations in the near
the instrument .” future.

number of microscopes. Luckily, the Golub family had The collection’s curator
a sizable home near the University of California, Los SINCE their arrival on the Berkeley campus, the remark-
Angeles and the time was ripe to create a dedicated space able Golub microscopes have seen several curators—but
for their prized microscopes. They hired an architect to none quite as attentive and talented as their current
redesign two spare rooms, one of which Golub had been caretaker, Steve Ruzin. Ruzin is fueled by both a gift for
using as a dark-room to develop his own photographs. gadgets and machinery and a long-standing fascination
With five children, Golub recognized that he “couldn’t do with microscopes. A photo of twelve-year-old Steve with
both—develop pictures and have a room for an extensive his first microscope eerily predicts his future as a scientist
microscope collection.” In the end, the dark-room was and innovator in the world of microscopy.
sacrificed for what could best be described as a “museum Ruzin’s affection for microscopes has found a perfect
den”. The room’s museum-like features included walls fit here on the UC Berkeley campus. He not only serves


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
Students in Dan Fletcher’s Optics and Microscopy class experience the
be pleased that their microscopes are not just gathering
Golub Collection hands-on.
dust; instead, these instruments participate in a living sci-
as curator of the Golub Collection, he is also director entific legacy, touching and shaping the minds of future
of the College of Natural Resources Biological Imaging innovators.
Facility, which functions as an instructional and research
laboratory for all aspects of modern biological light mi- ANGIE MOREY is a graduate student in the psychology department’s
croscopy and computer image processing and analysis. In program in cognition, brain, and behavior.
both arenas, Ruzin has been characteristically attentive
and detail-oriented. In curator mode, Ruzin takes apart, Want to know more?
Visit the Golub collection online at
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-, Ruzin sometimes imagines “what


Meet the Chancellor
The BSR puts the Birge back in Birgeneau
The arrival of the University’s new function like soap—that is, they form layers. The way that
chancellor last September was a detergent works is that the molecules form a film, then
greeted with much fanfare; less well-
the film surrounds the dirt particle and carries it off, so
publicized was the fact that our new
detergents are examples of smectic liquid crystals.
administrator-in-chief is a pre-eminent
physicist. In an interview earlier this
spring, Tracy Powell and Steve Bodzin In addition to being chancellor, are you an official member
asked Chancellor Birgeneau to step of the physics department?
aside, giving Professor Birgeneau a Yes, my appointment as professor of physics has been
chance to weigh in on topics ranging approved. I went through the same process that everyone
from stem cell research to the state of else goes through. I’ve already identified an office for
the physics department. 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
As a magazine devoted to science on campus, we were and valleys. Part of a department’s normal evolution is to
pleased to hear the university has a scientist at the have people who achieve a phenomenal level, as they did in
helm. How do you balance your roles as researcher and our department here at Berkeley, who then mature and are
university administrator? replaced. I think the review [you refer to] was done in the
First of all, I have to tell the truth; it is difficult to balance middle of a transition period for the department. Recently,
it all. I get paid to be a chancellor and previously as a [the department] has hired a number of really talented
president and that’s what I do most of the time. But I have young people doing nontraditional kinds of research that I
managed to maintain a research laboratory. Frankly, that think will help reestablish the preeminence of the physics
has rested strongly on having really talented postdocs. department.
Additionally, I knew the two [researchers that the
What questions do you pursue in your scientific life? department] lost personally from my research life, and they
Fundamental questions in materials physics. These days, left in good part because of limitations in the facilities here
the two main areas we work on are high-temperature on campus for the kind of research they were trying to do.
superconductivity, which remains unsolved after nearly The new facilities which we hope to build during my time
20 years, as well as something very different, which is soft as chancellor should help to solve that problem. These
condensed matter physics. This involves looking at the facilities include new, low-vibration laboratories – the
physical properties of liquid crystal materials in unusual kind of modern laboratory space that you need to do state-
environments. of-the-art research – especially of the sort that they were
doing, which was in the nano field and required extreme
Physics pop-quiz: can you give us a layman’s definition of delicacy and extreme stability.
the word “smectic”?
Smectic derives from the Greek word “smegma”, which Public-private partnerships seem to be a new trend in
means “soap”. Smectic liquid crystals are materials which 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
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 How do you address fears that this research will advance
person’s academic freedom. an era of human cloning or germline modification? Do
you have any personal ethical guidelines that you’ve
Congratulations on your appointment to the stem cell developed as a result of your particular experiences as a
advisory board created as a result of Proposition 71. As a scientist?
physicist, not a biologist, what is your role on the advisory These are very complicated issues, so of course we all have
committee? our own ethical values. I think that in the particular case
(laughing) Actually, there’s also a real estate person on the of a person who was going to use stem cell research very
board. As you can imagine, anyone who’s ended up as a directly to try to clone a human being, then we would
chancellor has a lot of experience with the organization of reject that. On the other hand, you can’t stop the progress
research. I have chaired Department of Energy panels that of science just because some person out there may try to
oversaw very large amounts of money—amounts of money use the results of science for an unethical reason; it’s just
comparable, actually, to the stem cell money. So I know not possible.
a fair amount about the organization of research, and it’s
really that part of it which our panel will be responsible for. How optimistic are you that the aims of Proposition 71 will
Our panel will review reports by expert sub-panels from be successful?
the outside; those are the people who will make technical In the long run, I’m very optimistic. I happen to have
judgments where you would have to be a biologist or a some motivations for this. One of my close friends, a
medical doctor or a life scientist of some sort. great physicist in my field, died of Lou Gehrig’s disease
last year. I watched him deteriorate over a two-year period
Much of the debate surrounding Prop. 71 concerns and he kept doing research until almost the last day. It
ethical dilemmas posed by stem cell research. As an was amazing, and it was courageous on his part that he
advisory board member, what role will you have in ethical would refuse to give in, but it’s a horrible thing to watch.
guidance? As you know, this is a neurodegenerative disease for which
I think overall that our board will be responsible for stem cells may offer a promise, and so one only needs
making sure that research is carried out ethically [and] that kind of personal experience [to be convinced] that
that there are not egregious violations of ethical standards. we really must go forward with this kind of research. Is
We already know that a particular approach to ethics has it 5 years or is it 10 years… you’re a biologist, you can
resulted in the federal government extremely constraining probably count better than I can! But certainly this is a
this area of research. We’re fortunate to be in a state with very promising approach and we need a breakthrough for
a broader viewpoint, in which the issues of human health neurodegenerative diseases. We must have a breakthrough.
are balanced against particular viewpoints that some people
have about the origins of human life. I think we’ve gotten TRACY POWELL is a graduate student in plant and microbial biology.
the balance right in California with this initiative. STEVE BODZIN is a graduate student in journalism.


Design Playing with the building blocks
by Alan Moses of biology

LTHOUGH malaria infects hundreds from S. cerevisiae (beer yeast) and then another critical
of millions of people each year and enzyme, and just like that they had bacteria that produced
kills an estimated 1.5 million, most the desired precursor. Seems like a good idea, doesn’t it? It
of whom are children, a majority seemed like a good idea to the Lawrence Berkeley National
of these cases could be cured by Lab as well: they created a whole department to encourage
combination therapy involving this kind of thinking.
the drug Artemisinin—a naturally The recent creation of the Synthetic Biology department
occurring compound extracted from the sweet wormwood at LBL, headed by Keasling, places Berkeley at the center
plant. Unfortunately, sweet wormwood takes six months of a new discipline at the interface between the life sciences
to grow to maturity, and the extraction of Artemisinin is a and engineering. Synthetic biology holds incredible promise
laborious process that itself takes several months. It seems for the solution of problems in power generation and global
incredibly frustrating that nature has provided the cure to health, but it also raises concerns that may make fears about
this terrible disease but hidden it in such an expensive and genetically modified organisms (GMOs) seem paltry by
out-of-the-way place. Why couldn’t the required chemical comparison. As usual, Berkeley will be right in the thick
precursors be produced by a fast-growing lab bacterium of it.
like E. coli? That way the drug could be produced cheaply
and quickly. Most of us might shrug our shoulders and Putting the pieces back together
go back to the hunt for sweet wormwood, but Jay Keasling, SYDNEY BRENNER, 2002 Nobel Laureate for Physiology or
UC Berkeley professor of chemical engineering, and a whole Medicine, has famously declared this era “the end of the
community of like-minded researchers think differently. beginning,” suggesting that molecular biology, which began
Rather than settle for the organisms nature provided, in earnest with the discovery of DNA as the genetic material
Keasling’s group created an organism to do exactly what and the understanding of the structural properties that allow
they wanted. Starting with E. coli, they began adding the it to serve as such, has entered a second phase. Because of
genes needed to make Artemisinin: first a pathway of genes the enormous progress of the last 50 years, we now have a


A Nobel laureate has famously is widely believed that molecular biology must follow a
similar trajectory—to begin to put the pieces back together,
declared this era as “the end finally producing a picture of the whole organism. Synthetic
of the beginning” in molecular biology sees itself as a fundamental step in this process.

biology. What’s in a name?

SO WHAT exactly is synthetic biology? Invariably, when a new
“parts list” for the cell—we have some understanding of most discipline or department is created, it faces pressure to define
of the basic molecular processes and sub-cellular structures itself. Otherwise, people might question why, in these days
found in most living organisms—as well as the ability to of tight university budgets, a department is being created
obtain complete descriptions of the genetic material for to study something they’ve never heard of. Furthermore,
virtually any organism in the form of genome sequences. A synthetic biology must differentiate itself from new research
middle period in molecular biology has arrived in which we institutes and departments that are already springing up
must begin to understand how these parts interact to form under the auspices of “systems biology”, on the one hand,
the complex systems that are living organisms. and more established departments such as bioengineering
Analogous developments occurred in the 1960’s and 1970’s on the other.
as physicists began to realize that knowledge on increasingly Perhaps it is too early for us to define the scope of
subatomic scales could not solve such seemingly simple and synthetic biology and to know whether ultimately it will
practically important problems as weather prediction. It carve itself a niche, but broadly speaking, we can say that
became clear that they had to study the complex behaviors synthetic biology aims to develop tools and methods to
that arise as the simple building blocks of nature interact; create biological molecules and cells for practical purposes.
subsequent breakthroughs in the field that became known It takes what we’ve learned over the past fifty years about the
as nonlinear dynamics and chaos theory began to offer a constituents of life and attempts to use it to solve practical
more complete picture of these complex phenomena. It problems.


Synthetic biology strives to combine (or synthesize) large cell by combining a cell membrane BioBrick and a DNA
amounts of disparate knowledge. As Keasling summarizes, sequence BioBrick with the BioBricks for transcription and
“Biology has done a great job of breaking things into pieces, translational machinery. This seemingly simple scenario is
but there has been less success in putting them back together.” far beyond today’s capabilities. While the genetic material
Like advocates of systems biology, Keasling and Graham of some model organisms (like E. coli and S. cerevisiae) can
Fleming, director of the Physical Biosciences Division at be routinely altered, the creation of an entirely new living
LBL, under which the new department was created, use thing has never been accomplished.
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
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 This possibility raises perhaps the most exciting and con-
called synthetic biology. troversial aspect of the name: the sense in which synthetic
Fleming suggests that “synthetic” is to be taken in all its means artificial. Although not artificial in the way that syn-
meanings. Another, perhaps related, meaning is “synthetic” thetic fabrics mimic the properties of cotton or silk (these
as in “synthetic chemistry”, where researchers literally could be referred to as biomimetic, according to Keasling),
synthesize more complicated compounds from their simpler, synthetic biology has its sights set on synthesizing living sys-
more available components. Thus, a goal of synthetic tems that are artificial in the sense that they have never ex-
biology is to synthesize new organisms from a set of existing, isted in nature. By combining the tricks that many different
well-understood components. Projects of this kind, such organisms have developed throughout the course of evolu-
as the “BioBricks” project at MIT, are well underway. This tion in a rational way, we will be able to generate organisms
project aims to characterize a number of biological building that perform functions not seen before. As with GMOs, the
blocks—to understand their properties as completely as impact of synthetic organisms will be felt strongly in fields
possible. Once this is done, these BioBricks will be available such as agriculture, where crops can be designed for pest
to be combined into larger and more complicated systems, or weather resistance. Synthetic organisms, however, can
and we can be confident we will understand their behavior. go much further. According to Fleming, one of the major
A future scientist will just choose the BioBricks and have reasons for the creation of the department at LBL was the
the organism made to specification. These projects will form incredibly exciting potential of synthetic biology “for im-
the fundamental tools that the synthetic biologist might use. proving human health and developing new ways to supply
“As the name suggests, the bricks are to provide a foundation,” energy.” Projects of this scope attempt to develop bacteria
says Fleming. Just as a chemist might decide to create H2O by that are redesigned to produce pharmaceuticals or swim to
combining H2 with O2, a biologist might create a free-living a tumor cell and destroy it, or synthetic viruses to be used


as HIV therapy. Although such “made-to-order” organisms synthetic biology might be, it is clear that the idea has been
may seem far in the future, projects like these are already un- gaining momentum. To get a sense of how quickly synthetic
derway in labs such as Keasling’s at LBL and on the Berkeley biology has been developing, we can take a look at the short
campus. history of the discipline. Although the ideas and research
Long-term goals for synthetic biology approach science 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
fiction: researchers supported by the Department of Energy also allows researchers and funding agencies to coordinate
at the Venter Institute (headed by Craig Venter, who led their public information efforts. Technology that seems
the private-sector effort to sequence the human genome) are poised to alter the way we look at life itself raises many
trying to develop a synthetic organism to efficiently pro- concerns both with respect to safety and also the social
duce hydrogen as a fuel source in a totally renewable way. and political consequences of such advances. For example,
Although an incredibly difficult challenge, according to Ke- Keasling points out that the synthetic biology department
asling, this type of project is the sort that synthetic biol- plans to work with the Goldman School of Public Policy
ogy should be aiming at—one that would revolutionize the and hopes to create programs to educate its scientists about
way we think about harnessing the potential of living things. public policy, to educate policymakers about science, and
In addressing how long it will be before such advances can to educate the public about both. The importance of such
make an impact on daily life, Kristen Balder-Froid, the Divi- a strategy cannot be overstated, particularly in the midst of
sion Deputy of Planning and Strategic Development for the public backlash against the use of GMOs in the agriculture
Physical Biosciences Division at LBL, points out that what industry. From the public’s perspective, when designing
will ultimately determine the time before such organisms organisms, we must realize that we may be creating life
are commonly used is what sorts of regulatory bodies they forms that God and/or evolution never dared, or—worse—
must pass—and that is very difficult to tell at this point. never dared again. Given public concerns about safety and
Regardless of how near in the future the applications of ethics, strategy about the areas on which synthetic biology


should focus research will be crucial if the new discipline is banning of GM foods in Europe and general uncertainty
to flourish. about whether GM crops might represent environmental
One main area of concern is the potential environmental dangers. As UC Berkeley anthropology professor Paul
impact of newly-designed organisms. Could synthetic Rabinow, who teaches a course called Genomics and Society
organisms escape and infiltrate the natural world? Keasling and spoke at the first synthetic biology conference this year,
argues that completely synthetic organisms really don’t puts it: “Most people think this stuff is dangerous.” Indeed,
compete well in the wild—even the most successful recent elections have led to bans on GMOs in two nearby
experimental strains are usually pathetic compared to counties and groups advocating similar measures in five
their natural counterparts. Synthetic organisms that are other counties—including Berkeley’s own Alameda (see
released either accidentally or for specific purposes would “Strange Fruit” on page 19 of this issue).
most likely die once out of the comforts of the laboratory. Fleming suggests that the ethical and social issues raised
Keasling imagines synthetic organisms growing in controlled by synthetic biology might be more relevant than the
environments and used for specific tasks. safety ones. He imagines that regulatory committees would
Although these answers may seem sufficient for now, if oversee the creation and manipulation of living organisms.
synthetic biology is successful and our ability to redesign Rabinow emphasizes that the synthetic biology community
organisms improves, our current ineptitude can’t be regarded must keep these issues in mind if their technology is to have
as a very reliable safety feature. If we are eventually to use the broad impact that seems possible. This is particularly
these organisms for clinical or industrial purposes, we must important in what he calls today’s “risk-averse” environment,
fully address questions about safety and risk. Otherwise, and given that “Americans are into values” right now.
synthetic biology may be unable to avoid a backlash similar In order to improve public perception, Rabinow suggests
to the one that has left the public demanding the labeling that focusing on world health issues such as low-cost HIV
of genetically modified (GM) products or the outright remedies might be a wiser strategy than trying to break into
the agricultural world, which is already rife with consumer
Rather than simply tinkering skepticism toward genetically modified foods. “Monsanto
was spectacularly stupid and arrogant,” says Rabinow,
with the organisms that nature referring to the manner in which they sold the first
has provided, we can begin to genetically engineered plants and the way they presented
the technology to the public. Rather than focusing on
combine their parts in radically the artificiality of genetically modified crops, they should
new ways. 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

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 While this may sound innocuous, according to Keasling
are taken out of their historical geographical context and “this means that it is easy to get copies of entire genes, or
grown organically, in a controlled way, in California and groups of genes, or even a virus.” Combined with the fact
then combined in radical and delicious concoctions that that molecular biology can be done relatively cheaply and
were never previously imagined. Rather than focusing on without too much specialized equipment—“in a garage,”
the unforeseen consequences of combining the Laurus nobilis says Keasling—one could imagine the potential for danger
(native to the Mediterranean and Turkey) with a variety if such technology falls into the wrong hands. Nevertheless,
of Fortunella (originally East Asian), we can celebrate the even with the availability of such technology, Keasling feels
triumph of human ingenuity and serendipity that brought that the likelihood that it could be used for malicious pur-
both of these to California to create a bay leaf-scented panna poses is very small: “it’s much easier for terrorists to get a
cotta with candied kumquats. truckload of fertilizer than to genetically engineer a bacteri-
um.” Terrorists have shown that they can inflict damage and
What hath man wrought? destruction with box-cutters and airline tickets—they don’t
CLEARLY synthetic biology raises all the same difficult safety need to resort to advanced technology. Molecular biology
and ethical issues GMOs do, and unfortunately it actually is still too complicated and difficult to do without an enor-
adds a new element of fear—human malice. If synthetic mous amount of technical skill and specialized knowledge.
biology is indeed to be an engineering discipline, we need Nevertheless, individuals with the right combination of skill
not only fear the unintended consequences of organisms and intent are out there—one only needs to remember the
modified slightly for benefit but also the whims of people or envelopes of anthrax spores mailed to terrible effect in 2001.
governments designing organisms with the intent to cause Rabinow reminds us that the potential exists for “one jerk…
harm. Sensationalist fears in this direction have already to spoil it for everyone,” and that scandal-mongering and
been expressed. Following the same electrical engineering malicious intentions are out there.
analogy to a perhaps inevitable conclusion, a news story on Rabinow suggests that synthetic biology follow the example, a technology news web site, suggested that of the self-regulation that was imposed by scientists during
once biological systems could be “programmed” we might the first experiments with recombinant DNA. Nearly 30
see “biohackers” or maybe even “biospammers.” Synthetic years ago at the Asilomar conference center, just south of
bacteria could give us a cold and then spell out the name of Monterey, scientists came together to discuss the safety and
a cough-syrup brand in green fluorescent protein. social issues surrounding their work on recombinant DNA,
The real risks of synthetic biology are probably much less the first “genetic engineering.” Although the moratorium
exotic. For example, Keasling points out that in the past that was eventually imposed is now regarded as overly
few years a milestone has been reached: technology now ex- cautious, the attitude of self-regulation and caution is a
ists for the rapid, cheap synthesis of long pieces of DNA. valuable example to new disciplines. Kristin Balder-Froid


points out that even if scientists than simply tinkering with the organisms that nature has
can’t predict the potential risks provided, we can begin to combine their parts in radically
of new discoveries, at least they new ways. The creation of a department of synthetic biology
can now use the example of how at LBL puts Berkeley at the forefront of this new paradigm.
to communicate seriously and Lest we forget, though, Berkeley is not only a center for
openly about the implications groundbreaking research; it’s also home to social activism
of their work. Keasling adds that such self-policing policies and liberal skepticism about the aims of big corporations and
are being put into effect already. For example, Blue Heron, government. With that duality in mind, synthetic biology,
one of the companies offering synthesis of long DNA unlike the biotech revolutions of the previous decades, seems
sequences up to 40 kilobases, long enough to synthesize to be proceeding with due deference to both the worst fears
a coronavirus like the one that causes SARS, checks all of and the most noble dreams of the community. Perhaps
the sequence synthesis orders they receive against all known as we ponder the magnitude of the act of synthesizing a
pathogenic sequences. Presumably a red flag would be completely new life form for the first time, we might realize
raised long before SARS was ever synthesized. that we would not have it any other way.
Despite the risks and fears, the promise of synthetic biology
(or at least cheap antimalarial drugs) seems hard to resist. ALAN MOSES is a graduate student in biophysics.
The Bill and Melinda Gates foundation also liked Keasling’s
approach: they donated $42 million for the development of Want to know more?
Visit the LBL Synthetic Biology Department online:
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 The Keasling Lab website:
way of thinking about the way we do biology. Rather
The BioBricks website:

Cal SCI ...get involved!

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


of the
Serving Five to Life
in Academia

by Loren
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
OW much longer do you have?” the awarding of the bachelor’s degree and the awarding of
It’s the question every graduate student dreads. Whether it’s the doctoral degree (total time to degree, TTD)—roughly
parents, friends, or new students, nobody seems to realize three years greater than RTD. Even after accounting for
how much that question hurts, or, for that matter, how these factors, the statistics can be interpreted in different
hard it is for graduate students to pin down the answer. ways. The 988 Survey of Earned Doctorates conducted by
Real statistics are not well-advertised, so most students the National Opinion Research Center (NORC) reported
don’t know the average degree time, or even the percent of that TTD had increased by approximately 30% over the
students who actually graduate. Besides this, the distribution preceding twenty years. But a subsequent study found that
seems so broad, it is hard to know if they will follow in the the decreasing number of PhDs awarded over this time
footsteps of the legendary tenth year, or replicate the feat of created a statistical bias and possibly more public concern
the whiz that finished in three-and-a-half years and already than the issue may have warranted. Calculating time to
has a job. degree based on entering, rather than graduating, class
Although many people have the vague idea that a PhD showed a more accurate—and still significant—increase of
is a roughly five-year endeavor, the actual time required to 0% over the same twenty year period.3
complete a doctoral degree is almost always longer. In 2003, Happily for most, the trend has begun to level off,
the median number of years between enrollment in graduate particularly for students in the sciences and engineering.
school and completion of the doctoral degree (elapsed time According to the 2003 national survey, the median TTD
to degree, or ETD) in all fields in the US was 7.5 years. was 0. years, or three months shorter than in 998.
The national median in the physical sciences (including
mathematics and chemistry) was 6.8 years; in engineering How long should it take?
it was 6.9 years, and in the life sciences it was 7.0 years. SO HOW long should a PhD take? The Association of
The typical time to degree for the humanities and social American Universities was formed in 900, and by 96 was
sciences is longer, and nationwide, the length of all graduate already questioning the ideal duration for post-graduate
degrees increased steadily during the late twentieth century. study, proposing three years as an appropriate length. This
The median registered time to degree (RTD or the time a number had not changed much by 964, when the Association
student is registered in a graduate program) in the United of Graduate Schools and the Council of Graduate Schools
States for students completing their degrees in 97 was 5.7 issued a joint statement that a PhD program should take
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
Real statistics are
goes back to the 960s. Berkeley’s average RTDs are shorter not well-advertised,
than the national averages, but still nowhere near five years.
In 2004, the average RTD in life sciences was 6. ± 2.3 years; so most students
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 don’t know the
Graduate Division, expresses the concern many feel about
average degree time,

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 or even the percent
time line is too long.”
Of course, the story these statistics tell isn’t as clear as it of students who
appears at first glance. It is difficult to incorporate data about
slow finishers and students who drop out. Many databases actually graduate.


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


to degree in the UC system by Maresi Nerad and Joseph a PhD in nuclear physics or nuclear chemistry has been
Cerny, who was then Berkeley’s Vice Provost for Research. 7.0 years over the last five reporting periods (998–2002).
More recently, in 200 the UC convened a Commission on Seventy percent of these PhDs then take one or more
the Growth and Support of Graduate Education. Based on (almost mandatory) postdoctoral positions lasting an
the anticipated undergraduate population and the needs of average of 3.3 years. Therefore, ten-plus years pass before
industry in California, the commission predicted a need for the ‘typical’ nuclear science PhD has a first job. This is
40,000 new faculty by 200. Consequently, they set the goal too long…We believe that the time to the PhD should be
of ,000 new graduate students in this decade. California shortened to five and a half or six years.”5
is one of only five states in which graduate enrollment has Part of the problem, according to Cerny, lies in inadequate
declined—by 2% in the last decade—while nationwide career advising: “Departments ought to be doing much
enrollment has increased. Among the commission’s proposals more career advising as to what the typical jobs actually
to reach its goal was one to “expand current efforts to reduce are.” Giving career guidance is not a high priority for
the time graduate students take to complete their programs,” many busy professors, nor are they often familiar with the
by monitoring progress closely, providing support services, many career paths their students could follow.
P H O T O : D U L A PA R K I N S O N

and increasing student financial support. A 995 report entitled “Reshaping the Graduate
Cerny, a professor of chemistry and former dean of Education of Scientists and Engineers” noted the 30%
graduate studies at Berkeley for fifteen years, feels that increase in time to degree in some fields and stated:
Berkeley’s current graduate program lengths in the sciences “Spending time in doctoral or postdoctoral activities
and engineering are reasonable for a top research institution, might not be the most effective way to use the talents
but are a factor in what he believes is the larger problem of the of young scientists and engineers for most employment
increasing time to the first job for scientists and engineers. positions. Furthermore, because of the potential financial
Cerny was recently part of a committee to study education and opportunity costs, it might discourage highly
in his field, nuclear science. Their findings included the talented people from going into or staying in science and
following: engineering.”6
“The median registered time from bachelor’s degree to 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 )


time to first job. She noted that, more than graduate student Mason’s belief, finding “that students’ aspirations to the
time to degrees, “A bigger concern in this regard are the doctorate are most affected by the relationship they have
post-doc appointments, which tend to get longer and longer with their individual faculty research advisor.”7 For both
all the time. In the biological sciences it’s not uncommon men and women who left Berkeley before finishing their
to have a five year postdoc before your first job…That’s just degrees, 54% cited a “lack of guidance from my advisor” as a
elongating the experience for everyone, which can be very factor in their decision to leave.7,8 In a multi-university study,
demoralizing, to be honest.” interviews with faculty confirmed the lack of guidance,
though the faculty view the problem from a very different
Their fates in whose hands? perspective: their most common advising attitude was one
THERE are a variety of opinions on who or what controls of an open door without making any overtures.3
the time to degree. Asking a small sample of current PhD An important influence on time to degree is the unique
students at Berkeley whether the time they would take to set of mental and emotional challenges faced by graduate
complete their degree was within their control, responses students. At Berkeley, 43% of the students seen at the
varied from “it depends on my advisor” to “[it’s] managed Counseling and Psychiatric Services are graduate students,
by the individual.” The encouragement of their advisors and though they make up less than 30% of the student body.9 A
agreement on a research plan are both contributing factors. survey by a Berkeley task force on Graduate Mental Health0
In general, students earlier in their programs felt they had found that 45% reported emotional or stress-related problems
less control, while students closer to graduation mentioned within the past twelve months that had significantly affected
the effects of unexpected problems with experiments and their well-being or academic performance. 39% reported
difficulty maintaining focus. One student said, “There feeling frequently overwhelmed, while approximately 42%
[were] way too many interesting projects that I wanted to reported feeling exhausted “frequently” or “all of the time.”
do. A good portion of the projects aren’t thesis-related, but Though personal or individual factors may determine
just too good not to investigate.” where each student falls within the range of times to degree,
When asked how students larger-scale institutional fac-
could influence their own
completion times, Cerny
In the US system, it tors—outside each student’s
control—can have much
advised that students “get
into research as early as
is possible to work greater influence on average
times to degree. Funding
possible…figure out early on your degree policy is one of the primary
what you want to do and institutional means of con-
start it.” He noted that in the until “every last trolling time to degree. Other
Department of Chemistry,
most students join a lab
ounce of interest things being equal, students
who receive fellowships or
by the middle of their first has been squeezed research assistantships have
semester. This has been true higher completion rates and
for the last half century, and, out of you.” shorter times to degree than
says Cerny, “Chemistry’s time students receiving teaching
to degree has been around 5.3 assistantships or fee waivers
years for the past forty years.” or those who are totally selfsupporting.0 “It’s a matter of
Good mentoring was described by Dean Mason as one of funding structure, and if you’re structured to finish in five
the most significant factors in graduate students’ academic and half years and then you’re cut off,” says Mason, “your
experience. “For the graduate student, having a really good professor is geared to giving you the appropriate project and
mentoring experience is probably the most important thing. to working more expeditiously with you.”
And good mentors want to get them out…which means According to Mason, a good example of the influence
they’re really concerned about the welfare of that student of funding on graduation times occurred following her
as well.” A 996 study of former doctoral students supports 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

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


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 How long will YOU be a graduate student?
they are making adequate progress toward their degrees.
But this is not necessarily the actual time required to finish actively seeking mentoring resources, writing a dissertation
doctoral studies, something only one program at Berkeley prospectus, and meeting with a dissertation committee can
(Microbiology) states clearly on their web page for current all help get the student out of the lab, into a cap and gown,
and prospective students. and then onto the streets of the real world.
Molecular and Cell Biology is one of the few programs
in which the expectation that students will complete their LOREN BENTLEY received her PhD in bioengineering from UC
degrees in five years is clearly laid out in a schedule of thesis Berkeley. She took 6.5 years.
committee meetings and progress reports, but in other Want to know more?
programs, expectations are communicated indirectly or Check out the references, or see the book “On time to doctorate:
more ambiguously. For example, the Biophysics Graduate A study of lengthening time to completion for doctorates in science
Group implies the length of its program by stating that it and engineering,” available online at
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 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
institutions and national bodies are focused on improving Chicago, 2004.
2. Summary Report 1996 Doctorate Recipients from United States Universities. National
graduate education, which includes decreasing the time Academy of Sciences, 1998.
3. Bowen, W.G. and N.L. Rudenstine, In Pursuit of the PhD. Princeton, NJ: Princeton University
to degree. But Mason points out that making these Press, 1992.
improvements is like shooting at a moving target: “Things 4. Nerad, M., Preparing for the Next Generation of Professionals and Scholars: Recent Trends
in Graduate Education in Germany and Japan. UC Berkeley, 1994.
do change so these questions can’t just be resolved once. Over 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,
the last ten years we have improved a little bit. It’s always a 2004.
6. Reshaping the Graduate Education of Scientists and Engineers. National Academy of
new set of faculty and a new set of students, so it’s a never- Sciences, National Academy of Engineers, Institute of Medicine: Washington, DC, 1995.
ending [situation].” For example, at this year’s first meeting, 7. Humphreys, S. The Role of Women Graduate Students in EECS at UCB. in Bridging the Gap.
Carnegie Mellon University, 1995.
on January 9th, the UC Regents were presented with a 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
detailed report on the importance of graduate education to (WICSE), 1996.
9. Prioritizing Mental Health, A campus Imperative: Proposal for a standing Academic Senate
California and the UC system—an effort to draw attention Subcommittee Addressing Student Mental Health. UC Berkeley, 2003.
back to important issues that had been neglected since the 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:
work of the 200 Commission. Cambridge, MA, 1992.
11. Nerad, M., Doctoral Education at the University of California and Factors Affecting Time to
For the individual graduate student, whether taking 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
courses, preparing for a qualifying exam, or planning the United States: Continuity and Change. Committee for the Study of Research Doctorate
Programs in the United States, National Research Council (US), 1995.
next experiment, it can be hard to see beyond the daily grind, 13. Golde, C.M. and T.M. Dore, “At Cross Purposes: What the experiences of doctoral students
but taking a step back and looking at the big picture can pay reveal about doctoral education.” The Pew Charitable Trusts: Philadelphia, PA, 2001.

off. Studies show that awareness of graduation requirements,


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.


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




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
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,

a thermometer, and a dimmer switch. Who needs Fisher

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.