BERKELEY

science
review
Fall 2002 Vol.2 no. 2
 BERKELEY
science FROM THE E DITOR
review
EDITOR–IN–CHIEF Dear Readers,
Eran Karmon
The BSR just grows and grows. A year and a half ago we were nothing but an idea and a few
MANAGING EDITOR
emails between like-minded graduate students. And here we are, 5000 copies strong, and
Temina Madon
for the first time ever, in dapper full color. This past semester, we were named Berkeley’s
best-designed student publication (thanks to our talented and dedicated art and layout
CURRENT BRIEFS EDITOR
Jane McGonigal staff). And two of this year’s 22 Mass Media Fellows of the American Association for the
Advancement of Science got their journalistic start at the BSR. At this rate, we will control
COPY EDITOR all world media by 2006.
Donna Sy
Domination over all that lives on this earth is only our secondary goal. Our primary aim is to
CONTENT EDITOR bring you the best of Berkeley science in a lively and comprehensive format. Turn to page 26
Jessica Palmer to read all about Berkeley’s place in the evolution vs. creationism debate (you’ll be surprised
to learn that Berkeley folk fall on both sides of the fence). Or learn all about the craft and
EDITORS science of bringing decimated coral reefs back to life (page 22). If you’ve only got a minute,
Joel Kamnitzer turn to Labscope (page 4) and Biotech Beat (page 6) for snapshots of new research on and around
Colin McCormick campus. Or you can read a crackpot’s theory about how Relativity is all wrong (page 32).
Teddy Varno
Enjoy the third issue of the Berkeley Science Review. And let us know if you think we’ve done
ART DIRECTOR
something right, or done something wrong, or if you’ve got a perspective about one of our
Una Ren
stories. Our email address is submissions@uclink.berkeley.edu.
ART
Aaron Golub And visit us on the web at sciencereview.berkeley.edu for back issues, information about our
Jessica Palmer science writing seminars, and more.

W EBMASTER
Tony Wilson All the best,

SPECIAL THANKS
Evelyn Strauss
Eran Karmon
PRINTER
UC Press

©2002 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 College of Letters and Science at UC Berkeley, the UC Berkeley Graduate Assembly, the Associated Students of the University of California,
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BERKELEY
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Features
Medicine 12 Cuts Like a Knife
Doctors perfect a technique for
curing multiple-tumor brain
cancer without a single incision.

By Aubrey Lau

16 The Sky’s the Limit Art Meets Science

Look! Up in the air! It’s a

bird! It’s a plane! Holy
cow, it’s a Nikon dangling
on the end of a kite string!
By Temina Madon

Environment 22 Constructing Coral

A pile of concrete and some
netting can mean the difference
between a living ocean and an
underwater rubble field.
By Sneha Desai

Departments
Current Briefs
7 Splitting Heads
When it comes to brain
surgery, there’s no such
thing as too many cooks.
8 Micro Machines Perspective
Diagnosing tiny devices is
tougher than it looks. 32
9 Walk Like a Man
When did our ancestors first
stand up for themselves?
The University
The Back Page 26
36 Inside Out with Clifford Stoll
How to drink a beer without
anything to put it in.
4 Labscope 6 Biotech Beat
Hawaii’s wealth of spiders.
Itsy-bitsy transistors. 11
A crystal path for photons.
Modeling the Universe’s birth. 21
Babies know what’s up.
35
BSR Vol. 2 No. 2
On the cover:
Marine Patrol Officer John
Kanteley dropping a coral reef
restoration module onto a reef
slope in Indonesia’s Bunaken
National Marine Park.
Read about it on page 22.
© www.ecoreefs.com
Back to the Future
Does time really march on
or are we just moving
forward into the past?
Darwin or Dogma?
Berkeley’s surprising
place in the evolution vs.
creationism debate.
High points of the Bay Area biotech boom.
Book Review
Evolution’s feminist side.
Weird Science
Phoebe the Photon conquers all.
Quanta (heard on campus)
 Labscope

Courtesy/Rosemary Gillespie
Teddy Varno WEBS OF SPECIATION IN HAWAII
In the forests of the Hawaiian Islands, Rosemary Gillespie of the Department of Environmental Science, Policy, and Management
has discovered 19 new species of spider. The spiders all belong to the genus Tetragnatha and display a wide range of shapes, colors,
and behaviors, making them ideal subjects for studies on the role of physical appearance and behavior in patterns of speciation. In
collaboration with Geoffrey Oxford of the University of York, Gillespie is also investigating the evolution of another Hawaiian
arachnid, the happy-face spider (Theridion grallator). Different populations of this species exhibit strikingly varied color patterns
on their abdomens. Since these patterns are primarily determined genetically, they can be used as visible markers to examine how
natural selection operates on genetic differences in populations.

Eran Karmon WORLD’S SMALLEST TRANSISTOR

Researchers led by Alex Zettl of the Department of Physics have recently created the world’s smallest transistor. The electronic
component, 100 times smaller than the smallest feature on commercially available microchips, is made out of carbon nanotubes—
small cylindrical structures about a billionth of a meter in diameter. To make the tiny device, the researchers crossed two nanotubes.
The junction, which is only a few atoms wide, acts like a transistor. Similar structures are being fabricated from boron nitride
nanotubes. Boron nitride tubes are among the strongest and best heat-conducting materials known, according to Zettl. Boron
nitride tubes were first predicted by Berkeley theorist Marvin Cohen and then synthesized in Zettl’s lab in 1997. Zettl’s group has
also made atomic bearings and is working on nano-scale motors.
Learn more about the group’s work at http://physics.berkeley.edu/research/zettl/.

Colin McCormick GUIDING LIGHT

Jandir Hickmann and Raymond Chiao of the Department of Physics are investigating the properties of “photonic crystal
waveguides”—two-dimensional structures that can be used to guide light. Working with scaled-up models (which are easier to
build and test than the miniature crystal versions) the group hopes to extend earlier results showing that the waveguides’ repeated
crystal pattern prevents certain frequencies of light from traveling anywhere but along the hollow center of the crystal. These
results suggest that waveguides may be a nearly zero-loss way of transmitting information. If the experiments prove successful,
photonic crystals could eventually replace conventional fiber optics as a means of guiding light, and might ultimately be used to
build high-energy particle accelerators that fit on a laboratory table.

Lisa R. Girard BLINKING BABY BLICKETS, BATMAN!

Experiments in Alison Gopnik’s lab in the Department of Psychology are revealing young children’s remarkable understanding of
cause and effect. The group’s experiments involve a “blicket detector”—a creation of Gopnik’s—that lights up when certain
objects, “blickets,” are placed on it. In one experiment, children are shown four blocks, two red and two blue, which are placed
one at a time into the blicket detector. Only one block of each color lights up the detector. The children are told that the red block
that lights up the device is a blicket and are then asked to identify the other blicket. Children as young as 30 months correctly
Colin McCormick/BSR
identify the blue block, demonstrating that they can override perceptual cues (in this case, color) and group objects causally.

Temina Madon BILLIONS AND BILLIONS

Astronomy Professor Chung-Pei Ma and her graduate students are using mathematical models to explain how the first cosmic

Courtesy/Chung-Pei Ma
structures in our universe formed. Several million years after the Big Bang, small fluctuations in energy created the earliest light
and matter. Astronomers believe that, over billions of years, matter in the Universe clustered under the action of gravity, resulting
in the complex cosmic structures observed today. Ma and her colleagues have simulated the billion-year evolution of fluctuations
in dark matter, photons, and neutrinos on a sub-galactic scale, illustrating the importance of complex second-order effects on the
growth of cosmic structures. By comparing these simulations with astronomical observations, Ma hopes to unravel the past of our
early universe—showing how intricate patterns of galaxies emerged from the cosmic ether.
BERKELEY BERKELEY
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Biotech Beat

WHAT’S HAPPENING IN BAY AREA BIOTECH

Agricultural Pest Sequenced

Bayer and South San Francisco company Exelixis have completed genome
sequencing of the tobacco budworm, a common insect pest. The new sequence
will allow scientists to develop novel and potent pesticides that specifically target
the insect. Exelixis president George A. Scangos says, “This is the first time
scientists can identify and screen important genetic targets derived from the
agriculturally relevant insect, rather than from a closely related model system.”
Pesticide developers previously relied on genetic information from the fruit fly.
The joint project took a year to complete using the “shotgun” sequencing tech-
nique made famous by the Human Genome Project.

No More Morphine Jitters

South San Francisco-based Pain Therapeutics announced preclinical results on
two novel opioid painkillers—Oxytrex™ and MorViva™. The company’s
study shows that mice treated with the new drugs do not suffer from the side
effects usually caused by opioids like morphine. Ten days of treatment with the
new drugs did not result in the drug tolerance and impaired pain reduction
associated with a morphine regimen of similar length. The animals also did not
show any typical opioid withdrawal behaviors.

DNA-Based Drug Fights Allergies

Dynavax Technologies reported a novel therapy that is effective in preventing
allergic responses in mice. Researchers sensitized mice to ragweed, a common
seasonal allergen, and measured their allergic responses. The mice were then treated
with ISS, a short immunostimulatory sequence of single-stranded DNA, combined
with Amb a1, the main allergen component in ragweed pollen. After subsequent
exposure to ragweed, mice that had undergone ISS therapy showed reduced
allergic responses compared to controls. Scientists believe this drug combination
diverts the immune system response away from harmful allergic reactions.

Emily Singer
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 Current Briefs
SPLITTING HEADS
Collaborating towards less
invasive brain surgery.
an too many doctors spoil
C the surgery? Not according
to UC Berkeley School of
Public Health graduate student Marlon
Maus, whose latest paper in Neurosurgery
demonstrates the powerful benefits of
collaboration among medical researchers
from different fields.
“Cooperation among different specialties
in medicine, and in science in general,
often results in new ideas that are more
than the simple sum of the individual
factors,” says Maus, an oculoplastic
surgeon who has participated in such a
process, directly witnessing its impressive
results. Three years ago, Maus and a
colleague, neurosurgeon Warren
Goldman, helped introduce the
“transorbital craniotomy,” a revolutionary
technique designed to improve
recovery speed and minimize discomfort
and scarring in patients undergoing
brain surgery.
The transorbital craniotomy was
developed as part of a unique coopera-
tive effort between neurosurgeons and
ophthalmologists at the Neurosensory
Institute of the Wills Eye Hospital in
Philadelphia. There, Maus participated
in the Minimally Invasive Surgical
Program, a group comprised primarily
of oculoplastic surgeons—specialists in
diseases of the tissues that surround the
It only looks painful. The transorbital
craniotomy removes less bone than conventional
techniques and results in shorter hospital stays,
less patient discomfort, and only a small amount
of visible scarring. (Courtesy/Marlon Maus)
eye, such as the optic nerve and the
orbit (the opening containing the eye
and the surrounding muscle, fat and
tear glands).
As an oculoplastic surgeon, Maus treats
patients afflicted by tumors that cause
dramatic vision loss by putting pressure
on the optic nerve. “Before the
transorbital craniotomy was devised,
surgery required a regular frontal
craniotomy, which involved shaving the
head, making a cut from ear to ear over
the top of the head, and peeling the
forehead forward to be able to remove
a large portion of the frontal bone,” he
explains. In the transorbital craniotomy
a much smaller incision is made over
the brow. Then a small part of the
frontal bone is removed, along with the
orbit. “Once the bone is removed, the
brain is retracted, or moved away from
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the optic nerve, and the tumor is found
using MRI images for guidance. This
image-guided approach allows a great
deal of precision with very little
exposure of the brain itself. After the
tumor is removed, the bone is replaced
using titanium screws and plates. The
incision is closed with stitches, and
patients are then taken to the intensive
care unit for recovery,” says Maus.
Maus and his collaborators studied
the results of 72 patients on whom
neurosurgeons used this surgical
approach for various tumors of the
orbit, brain, and sinuses. According
to Maus, transorbital craniotomy
results in shorter stays in the inten-
sive care unit because there is less
unintended retraction, or dangerous
brain tissue deformation. Patients
recover faster and in general describe
less discomfort. “They are also very
happy with the cosmetic results,
since they do not have to have their
heads shaved and the scar is much
smaller and not very noticeable once
it heals,” Maus says. He attributes
the success of the transorbital
craniotomy to the breadth and depth
of experience that interdisciplinary
collaboration has brought to the
problem of oculoplastic surgery.
Jane McGonigal
Learn more:
Neurosurgery
http://www.neurosurgery-online.com
Current Briefs
MICRO MACHINES
Tiny technology can cause
big research problems.
n 1983, physicist Richard
I
Feynman delivered a now-famous
speech challenging scientists and
engineers to think small. Twenty
years later, Feynman’s dreams of
designing and building of tiny machines
made microscopic bearings, gears,
flywheels, and motors have been brought
to fruition. Microelectronic mechanical
systems (MEMS) are found everywhere
today, and the future applications are
limitless. Micro-accelerometers already
trigger car airbags and help steer
modern jet liners. And researchers are
now developing tiny wired sensors to
detect biochemical attacks, as well as
microsurgical devices that can thread
through capillaries.
But researchers face limitations in the
design and implementation of MEMS.
As machines get smaller, problems like
friction and “stiction” (the spontaneous
and permanent adhesion of two
surfaces) arise. And technology moves
towards machines on an atomic scale,
researchers must grapple with the
unpredictability of atomic interactions,
which can make accurate and reliable
measurements of the material properties
of MEMS nearly impossible.
Merging the disciplines of applied
physics, surface chemistry, and materials
engineering, UC Berkeley professor
Roya Maboudian is steadily advancing the
Working the bugs out. Roya
Maboudian and her students are develop-
ing techniques for testing the properties of
micro-devices, like this tiny lock fabricated
by the Sandia National Laboratories’ MEMS
division. A spider mite stands sentry over
the lock, showing scale.
(Courtesy/Sandia National Laboratories,
http://www.mems.sandia.gov)
great MEMS revolution. Her group in
the Department of Chemical Engineering
studies material properties, perfor-
mance-limiting phenomena, and
performance-enhancing coatings of
silicon-based microdevices.
To address the problem of stiction, the
Maboudian lab has pioneered the
chemical modification of MEMS surfaces
using novel deposition techniques. But
researchers must still struggle with the
fact that atoms and particles interact
differently on a small scale than on a
large scale. For example, a twelve-inch
silicon disk is brittle, and it will
probably fracture if you bend it too
much. But apply twice as much stress
to a twelve-micron silicon disk and it
won’t budge. Everything changes on
the microscale.
Measuring material properties on a
small scale is also problematic. Since
the dawn of MEMS in the late 1980s,
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researchers have been trying to
determine the physical properties of
these tiny devices. But properties like
elasticity, stress, friction, hardness, and
density can’t be measured for a
microscopic sample using a human-
scale apparatus. Even slight positioning
errors of microscopic samples in a
standard lab setup can introduce
enormous measurement errors.
To overcome these challenges, the
Maboudian lab uses ultra-sensitive
measurement and imaging techniques
like electron microscopy and x-ray
diffraction. Using these methods,
Maboudian and her colleagues have been
able to measure the elastic modulus (the
ability of a material to resist bending) of a
silicon lever just 125 microns long—only
2.5 times the width of a human hair.
Ultimately, the Cal researchers hope to
implement complex MEMS like “lab-on-
a-chip” analysis systems, biological
implants, and micro-power generators.
With a number of exciting prototypes
already in development, they may soon
be able to shrink almost any problem
down to size.
Temina Madon
Learn More:
The Maboudian Lab
http://www.ccherm.berkeley.edu/~rmgrp/
The Berkeley Microfabrication Lab
http://www-microlab.eecs.berkeley.edu/

WALK LIKE A MAN
New discoveries push back
the origin of bipedalism.
t has been nearly three decades
I since the discovery of “Lucy,” a
chimpanzee-like primate who lived
in Ethiopia 3.6 million years ago. Yet as
old as Lucy is, she lived three million
years after the genetic split between
chimpanzees and humans. Since Lucy’s
discovery, paleontologists have searched
for older protohumans in an effort to
understand the origins of bipedalism and
the separation of early humans from their
ape ancestors. In a series of recent
discoveries, a pair of UC Berkeley
researchers has finally begun to make
progress on the question.
Working in the Middle Awash Valley of
Ethiopia’s Afar Rift, Anthropology
graduate studentYohannes Haile-Selassi,
Integrative Biology professor Tim White,
and colleagues have found a series of
fossil deposits, the oldest group of which
contains eleven specimens from at least
five individuals. The specimens consist of
teeth, a partial jawbone, forearm
segments, a collarbone, one finger, and
one toe. Based on nearby volcanic rock
deposits, the team dates the fossils to
between 5.54 and 5.77 million years
ago—significantly older than Lucy. Their
find fills an important gap in the
paleontological record. “In the early
1990s we began to fill in some fossils
around 4.4 (million years ago), but the
Yohannes Haile-Selassie and colleagues date the origin of bipe-
dalism to more than 5.5 million years ago. (Eran Karmon/BSR)
records were still very poor in comparison
to those in the three to four million-
year-old range,” says White.
Paleontologists are now debating how to
classify the find. The Berkeley team has
stirred controversy by classifying the
fossils as a new subspecies of hominid
(a member of the human family hominidae),
rather than as a chimpanzee. Their
conclusion is based on the lone foot
bone, which Haile-Selassi claims was
used to “toe-off ” in a manner unique to
habitual bipeds like ourselves. Explains
White, “As you walk, your foot touches
the ground first with the heel, and rolls
forward onto the ball, through what we
call ‘flexion,’ and finally pushes off with
the toes. That toeing-off is the last thing
that happens with each stride. The shape
of the (toe) bone in this case indicates an
adaptation to habitual bipedalism.”
However, the criteria for classification as
a hominid are not widely agreed upon.
According to White, “There are basically
two schools of thought as to hominid
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classification. One says that you
shouldn’t call it a hominid without a
whole suite of characteristics,
primarily bipedality.”
Since Haile-Selassi and
White’s finds exhibit a
mixture of primitive
apelike characteristics and
evolutionarily new
humanlike traits shared by
later hominids, not all
aspects of this suite are
present. For the Berkeley
team, says White, “The
(hominid) classification
relies on characteristics
shared exclusively with later hominids.
So my definition is less functional, and
more cladistic (i.e., relying on compari-
sons between ancestors and
descendants).” The team has dubbed
this subspecies Ardipithecus ramidus
kadabba. The name kadabba is from the
local Afar language, meaning “basal” or
“founding family ancestor.”
Classification of the fossils as hominid
would have important implications for
theories of bipedalism. Paleontologists
previously held that bipedal walking
emerged in hominids as they spread out
into open, arid savannas. Yet chemical
analysis in the Awash indicates that six
million years ago it was a lush, forested,
upland area. Finding bipedal hominids
in such an environment would force
paleontologists to revise current
theories. “Previously people thought
that living in a savanna was an important
corollary of the earliest hominids, but
these finds basically show that there’s no
such correlation,” says White.
[continued]
 Current Briefs
White and Haile-Selassi are not alone in Ardipithecus ramidus kadabba finally settles
the search for early hominids. Fossil on the evolutionary tree, White and
finds from the same period found by a Haile-Selassi’s finds, as well as those of
joint Kenyan-French research team in their Kenyan and French counterparts,
the Tungen Hills of Kenya have a are bound to change the picture of
similarly complex combination of humankind’s origin.
human and apelike traits. Those fossils
are of Orrorin tugenensis, a primate that Noah Rolff
walked bipedally in a manner more
similar to modern humans than even
Lucy, who is roughly two million years
To learn more about
younger. Could either Ardipithecus
White and Haile-Selassis most recent
ramidus kadabba or Orrorin tugenensis have
work: Nature, 418, 145 (2002)
been an ancestor to us all? Wherever

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 Book Review
EVOLUTION’S FEMINIST SIDE
Sexual Selections: What We Can
and Can’t Learn about Sex from
Animals, Marlene Zuk (Berkeley:
University of California Press,
2002), 240 pp.
eep questions lurk just be-
Teddy Varno
of several different case studies that
illustrate Zuk’s point. In the first section,
Zuk discusses ecofeminism, mother-
hood, and sperm competition to
demonstrate how a feminist perspective
might lead evolutionary biologists to
ask provocative new questions. The
second section describes how popular
beliefs about animals and nature often
prevent us from objectively seeing impor-
tant evolutionary relationships. Foremost
among these myths is the belief in the
biology has much to offer feminism.
Instead, Zuk suggests that generalizing
about human sexuality based on animal
examples is a perilous undertaking best
avoided. The dissonance between Zuk’s
thesis and the development of her ideas
through the case studies gives Sexual Selections
an unfortunate ambiguity; each chapter
is an interesting account in and of itself,
but the three parts of the book do not build
to a coherent conclusion. Sexual Selections
is an entertaining read that covers many
intriguing topics and presents several
fertile ideas, but readers interested
primarily in the relationship between
feminism and sociobiology would do
better to look elsewhere.

D neath the surface of Sexual

Selections. Marlene Zuk,
professor of biology at UC Riverside
and a self-identified liberal feminist,
challenges the idea that sociobiology
and feminist theory are by necessity
ideological opponents. By exposing
latent gender biases, Zuk believes,
feminism can rid biology of untested
cultural assumptions that may keep
legitimate hypotheses from being
fully explored. Unlike sociobiology’s
most severe critics, however, she
believes that it is possible to scien-
tifically study the evolutionary basis
of human behavior. If done properly,
she suggests, the comparative study
of sex in non-human animals may
even contribute to our understanding
of human sexuality.
Sexual Selections is divided into three
major sections, each of which consists
scala naturae, the idea of an hierarchical
ladder of life extending from the least
complicated organisms up to humans.
The scala naturae, suggests Zuk, leads
TeddyVarno is a second-year graduate
student in the Department of History
us to assume that we need to study at UC Berkeley.
advanced primates and other organisms
at the top rungs of the ladder to learn
about sexuality in humans. Without
the scala naturae, we are free to explore
the evolution of sex in response to
environmental pressures in all organisms,
particularly taking advantage of the
rich diversity of invertebrates. In the
third section, Zuk applies her ideas to
four controversial cases in the study Advertise in the BSR
of the evolution of human sexuality:
menstruation, homosexuality, female
orgasm, and gender differences in
mathematics performance.
Info at
Zuk convincingly demonstrates how
a feminist perspective can contribute
to evolutionary theorizing, but she
sciencereview.berkeley.edu
provides little support for the idea that

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Feature

CUTS LIKE A KNIFE

Treating
brain tumors
without the
surgeon’s
scalpel.
The beams converge on a point in the
brain with such high intensity
t 6:30 AM, the fog begins to lift outside the Gamma
that they kill tumor cells.
A Knife Radiation Therapy Unit at the University of
California, San Francisco. Katherine lies on a gurney,
dressed in a paper-thin hospital gown. She has very little hair
on her head; sutures from a past operation mark her scalp.
Katherine is about to undergo Gamma Knife radiosurgery, a
Aubrey Lau
therapy that uses precisely targeted beams of gamma radiation
like a scalpel, cutting out brain tumors without the trauma surgery, where risks for hemorrhage and infection always
and complications of conventional surgery. exist. With its precision, low risk of complications, and
high success rate, Gamma Knife radiosurgery presents an
“Last October, I started to feel that I wasn’t quite myself. I attractive alternative. Gamma Knife targets beams of high-
forgot things sometimes, just the little strange things that energy light (gamma rays) onto brain lesions. These beams
you’re supposed to know, but nothing out of this world,” converge on a point in the brain with such high intensity that
Katherine recalls. After an MRI, her doctor diagnosed they kill tumor cells, eliminating the need for a surgeon’s scalpel.
multiple brain metastases. A skin cancer that doctors Since there is no need to open the skull, virtually all patients
thought they had successfully removed from her leg had broken go home on the day of treatment.
up and spread to the brain via her lymphatic system and blood-
stream. Over twenty tumors were found in Katherine’s brain. Gamma Knife treatment is the final stage of a long process.
“We were both shocked. Even my doctor said she didn’t After Katherine’s tumors were diagnosed, the largest metastasis,
expect to see that,” Katherine says. in the left frontal lobe, was surgically removed. Since then,
Katherine has had ten whole-brain radiation treatments, which
Conventional treatments for brain tumors involve chemo- deliver small dosages of radiation over several sessions in the
therapy, which causes fatigue and nausea, and open-skull hope of killing tumor cells while sparing healthy ones.

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 MEDICINE
Following the therapy, some of Katherine’s tumors stabilized, With the head frame secure, Katherine is brought to the
but others enlarged and spread. Her case was next brought scan room for magnetic resonance imaging (MRI). The scans
before the radiosurgery conference, a weekly meeting of provide detailed information about where the tumors are
neuroradiologists, radiation oncologists, neurosurgeons, and relative to the head frame. Unfortunately, these images have
medical physicists, to determine whether Gamma Knife limitations: they cannot differentiate between damage caused
would be a suitable treatment. Since Katherine’s numerous by tumors and that caused by the radiation treatment itself.
remaining tumors were small, the conference decided “Trying to sort out whether something is a residual disease,
Katherine would make a good candidate. a recurrent disease, or just a treatment-related effect on
the brain is vital,” says Nancy Fischbein, Assistant Professor
everal weeks after the conference, Katherine is ad- of Radiology at UCSF.
S mitted for treatment. The first step of the procedure is
fitting a frame to her head. The frame secures her skull To gather more specific information, physicians often order a
in place and ensures accurate targeting of brain lesions magnetic resonance spectroscopy (MRS) scan. This twenty-
during treatment. Michael minute procedure is per-
McDermott, Co-neurosur- formed alongside routine
gical Director of the MRI scans. The MRS is
Gamma Knife radiosurgery unique because it pro-
program at UCSF, adjusts vides infor mation on
the frame to fit Katherine’s specific metabolites in
head and sets up what for the brain: c holine, a
most patients is the most component of the cell
uncomfortable part of the membrane; N-acetylaspartate
procedure—the injection (NAA), a neuronal marker;
of local anesthesia into four and creatine, a metabolic in-
points of the skull via a dicator. High levels of cho-
large needle. Katherine line indicate the breakdown
sticks a small piece of cloth of cell membranes, while
into her mouth and low levels of NAA can be a
clenches her teeth. She sign of neuronal damage.
makes a fist, closes her Both of these conditions
eyes, and shakes her body a Zapping tumors. 201 beam of gamma radiation converge onto the tumor. suggest the presence of
little as each of the injec- Each individual beam is so weak that it can shine through healthy cells cancerous tumors.
without damaging them, but the beams converge on the tumor with such
tions enters a different side high intensity that they damage its DNA. Fischbein notes that MRS
of her head. “You’re almost also has prognostic value. “I
done, it’s just like when you’re at the dentist,” consoles can easily think of plenty of examples where MRI looks stable
Jesse Merril, the nurse practitioner massaging Katherine’s but the spectroscopy shows changes,” she says, “and a few months
shoulder. Anaesthetized, Katherine is ready for the insertion later, the MRI catches up with the spectroscopy and it becomes
of pins into her skull through openings in each corner of clear that the patient did have a recurrent disease.”
the frame. This, as McDermott explains, is the only invasive
component of the procedure, as the titanium tips of the After the scans, Katherine gets a break with her family in the
pins make small divots in the skull. waiting room as neurosurgeons, medical physicists, and

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 Feature
radiation oncologists discuss the most critical and laborious
part of the treatment—the planning phase. The MRI images
are entered into a computer program in the Gamma KnifeTreatment
Unit. “One of the goals in treatment planning is to make the
radiation dose conform to the target,” says Vernon Smith,
Adjunct Professor of Radiation Oncology at UCSF. Radiation
oncologists and neurosurgeons work together to decide which
areas of the brain should be targeted and which critical
structures should be avoided. “I then use my knowledge to
decide where to put what we call the ‘shot’,” Smith explains.
Since most brain lesions are irregularly shaped, multiple shots
of radiation are often needed for treatment. “You need to try
to fill the tumor up with spheres of radiation of different sizes—
to decide how many spheres to use and where to put them, as
well as what dosage to use,” says Smith. Gamma Knife is unique
in its ability to target brain lesions for irradiation while sparing
healthy cells. Since the gamma rays come from 201 individual
sources, a beam of radiation from a single source contributes
only approximately half a percent of the total dose. Through
strategic targeting, the radiation dosage of individual beams is
Surgery without a knife. The patient slides into the gamma knife treatment unit. To avoid expo-
sure to radiation, physicians and technicians control the surgery from another room, but are in
constant contact with the patient via a microphone and speaker system. (Aubrey Lau/BSR)
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not high enough to harm the healthy tissues they pass through.
It is not until the beams converge when they are close to their
target that their combined energy becomes high enough to
damage tissues.
After several hours of meticulous calculations, Katherine’s
treatment plan is ready. Because she has a large of number of
metastases in her brain, doctors decide that only some of them
can be treated that day.Ten shots of radiation are prescribed to
target the seven largest metastases.
Katherine is led to the treatment unit. As she lies down on the
treatment couch, her head frame is attached to a collimator, a
circular metal device that resembles a helmet with the top
cut off. Evenly distributed over the collimator are 201 openings
through which gamma rays will be delivered. The head frame
is attached to the collimator according to the three-dimensional
coordinates set during planning. To minimize errors, the
positioning of Katherine’s head is checked independently
by three different people. An intercom system allows her to
communicate with the personnel in the control room, who
Guiding the knife. The collimator is
attached to the patient’s head frame. It has
201 holes that guide the gamma beams.
Depending on the dose of radiation admin-
istered, collimators with different hole sizes
are used. (Aubrey Lau/BSR)
14
 MEDICINE
keep her informed of the progress of the treatment. After
all staff have left the treatment room, closing the door
behind them, the radiation treatment commences. It lasts
for two hours, during which time collimators of various sizes
are switched a few times to allow radiation beams of
different size to attack the lesions.

he success rate of Gamma Knife treatment is impres

T sive. McDermott notes that it depends on the type of
brain lesion: “For arteriovenous malformations, collections of
tangled abnormal blood vessels, it depends on the size – small:
80-85% (success), medium: 70-75%, large: 50%. For
trigeminal neuralgia, a dysfunction of cranial nerve V, over
90% of cases experience pain relief four to six weeks after
surgery.” Remission time, or the length of time for which
the tumor ceases to grow, depends on the tumor grade. In Frame of reference. A physician fixes a frame onto a Gamma Knife
general, tumors with the highest grade are characterized by patient’s head. The frame is held in place by titanium screws in the
patient’s skull. Neuroradiologists use the frame as a precise coordinate
extensive infiltration into the brain tissues and a rapid spread. system for guiding radiation beams to the tumor.
As McDermott notes, high grade tumors have a remission
of four to six weeks, as opposed to low grade tumors, where a the break before the last part of her treatment, Katherine’s
remission time of ten to twelve months is observed. husband gingerly takes her hand to walk her around the waiting
room. She takes a sip of water. He adjusts the ties behind her
Gamma Knife also has limitations. The major one is that the gown. Although today’s treatment has been long, Katherine is
procedure is only effective on tumors smaller than 3 cm. almost ready to go home. Thanks to the non-invasive nature
Radiation can kill both healthy and cancerous cells, so as the of Gamma Knife radiosurgery, she can rest in the comfort of
radiation dosage increases to compensate for the tumor’s size, her own home with her family tonight.
more healthy cells are killed and the therapeutic value of the
treatment is reduced. “As you increase the volume of the
tumor being treated, you have to decrease the dose,” notes
McDermott. “And once you get to a very large volume the
dose starts to become so small that it is ineffective.” The location
and spread of the tumor are also factors. They must not be
close to critical structures like the optic chiasm, damage to
which would cause blindness, or the brainstem, which is
crossed by several critical nerve fibers. Gamma Knife radio-
therapy is also not recommended for patients whose tumors
have infiltrated the ependyma, a one-cell-thick layer that lines
the ventricles of the brain. After reaching these ventricles,
cancerous cells can spread along the central canal of the
spinal cord, rendering radiotherapy ineffective.
Aubrey Lau received a BA in Integrative Biology
It has been over ten hours since Katherine arrived at the from UC Berkeley in 2000. She is currently a
hospital. The evening fog is already beginning to set in. During research associate at UCSF.
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Feature

THE SKY’S THE LIMIT

Reviving kite aerial
photography.

Temina Madon

rchitects have been mapping cities and land-

A scapes since the 16th century, constructing

imagined aerial views using the mathemati-
cal principles of perspective. It wasn’t until the 19th
century that aerial photography first became pos-
sible, by way of hot air balloons and kites. Today, ar-
chitects and geographers rely almost exclusively on
blimps, helicopters, and satellite images to provide a
look from above. But Professor Charles Benton, Chair
of the Department of Architecture at UC Berkeley, is
leading a revival of kite aerial photography (KAP). In the last ten years, Benton has snapped over 550 rolls of film
from a kite’s-eye view. This year, he plans to organize a KAP seminar to train students and colleagues in this
technique for aerial photography.

Benton says that KAP “gives you a view of the familiar from a place that you often can’t occupy.” Even conventional
aerial photographers—strapped to helicopters, holding on for dear life—can’t offer the perspective of a lightweight,
compact kite rig. KAP rigs can be remarkably simple: a kite, disposable camera, kitchen timer, and some kite line will
get you started for an outlay of less than $25. Of course, the rigs can quickly become elaborate, costing thousands of
dollars and incorporating video transmitters, receivers, monitors, and more.

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 ART MEETS SCIENCE

Restoration of Hearst Mining. The original design for Hearst

Mining Building included two open courtyards and a centerline

skylight. These features admitted sunlight into adjoining office

spaces—a necessity as the building was designed to function without

electric lamps. Over many years of redesign and restructuring, the

light courts and skylights were filled in with office space. Benton

says, “It’s about time for us to rediscover these features. It’s time to turn

the lights off and start taking advantage of that borrowed light again.”

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Feature

KAP can be a useful tool for anthropologists, archeologists,

computer scientists, and ecologists seeking unconventional representations

of their research subjects. Benton teamed up with Berkeley computer

scientist Paul Debevec (PhD ’96) to generate a 3D computer model of

the Campanile, using kite aerial photographs like this one to develop

the model. A computer-generated movie of the campanile is available

at http://www.cs.berkeley.edu/~debevec/Campanile/.

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 ART MEETS SCIENCE

“Composition in Absentia.” In order to capture an image

with a kite rig, Benton must first compose the image mentally,

then translate that image into the kite’s position and the timing

of the camera’s shutter. For this photograph of Doe Library’s

reading room, he had to maneuver his camera rig within a few

feet of the building’s edge. Kite flying in the midst of urban

landscapes is a challenge, but Benton points out that airflow

around buildings can be used to his advantage. Unpredictable

local accelerations, vortices, and other flow patterns near a

building can actually provide lift for a kite—though of course

they also create regions of turbulence that must be avoided.

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Feature

All Plugged Up. Benton says that it took at least a dozen tries

to capture this image of Wellman Hall. This structure, like Hearst

Mining Building, was once illuminated by natural light admitted

by large windows and a central skylight. Sadly, these original

features have been covered over by hastily-constructed ventilation

retrofits and a suspended acoustical ceiling.

Temina Madon is a fifth-year student in theVision

Science graduate group at UC Berkeley.

To see more of Benton’s work visit http://arch.ced.berkeley.edu/kap

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Weird Science
MAIL CALL
Colin McCormick

Here at UC Berkeley we get a lot of curious correspondence. It ranges from exorbitant requests for
information—“Please send me scientific data on quantum mechanics.”—to the oddly macabre—“I just
detected the odor of subtle error in relativity, but I’m not sure where the corpse is hidden.” Letters arrive
typewritten, handwritten, and even (according to legend) written in blood. A brief selection of the more
interesting contents of our inboxes:

Thank God someone’s checking our work

A recent email from one C. Wang breathlessly informed Berkeley
physics faculty and students that “!!! We can pass the Speed of Light
for sure !!!” because a basic assumption of Einstein’s relativity “is

Aaron Golub/BSR
totally WRONG!” In fact, “There exists NO relativity. The whole
theories of relativities are totally artificially man-made. Thank you
very much and have a nice day.”

To think of all the years I wasted in school

Appearing overnight in hundreds of mailboxes across campus, the 140-
page N-Particle Model—published at the personal expense of its author,
D. M. Degner—explains, “In the 21st century if one does not understand
the universe in terms of elementary particle physics and quantum
mechanics one will be illiterate.” Bad news for the English majors. It
also sums up “All of Physics” in just 28 words: “Right Hand and Left
Hand branes and quarks inventory and exchange the N-particle. A quark
is an integer fraction of a brane. Quarks are only found inside atoms.”
Aaron Golub/BSR
It’s possible a bit may have been glossed over in the name of brevity.

Fiat Lux
In further relativity news, longtime Berkeley resident “Pastor Glen” recently distributed his magnum opus,
AdventuresWith Phebe The Photon, or, Having FunWith Time Dilation! at select locations on campus. It opens
with a poem, Hymn to Light: “WHO ARE YOU, LIGHT? You tourist from pinpoint galaxies! You stranger!”
We are then introduced to “that imperious PHOTON (!)—her name is PHEBE.” And as for Einstein’s
space-time diagrams? “‘Besides,’ Phebe sniffs, ‘that diagram is ALL WRONG about me!’”

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 Feature

CONSTRUCTING CORAL
The world’s reefs
are disappearing.
How do we stem
the tide?

Sneha Desai
Helen Fox

undreds of colorful fish dart chaotically in and

H around a canopy made of millions of branching

fingers of pink, green, and brown coral. Above the

As much as half of the

surface, an Indonesian man in a small wooden boat throws a
homemade bomb overboard. It arcs through the air and hits
the warm blue water. A moment passes, then a fountain of

world’s remaining water sprays up. In the silence that follows, a few fish
carcasses float to the surface, while many more sink to the

coral reefs will be lost ocean floor, blanketing a crater in the shattered coral reef.
Blast fishing, as this illegal practice is known, earns this
fisherman about eight dollars a day—five times the
by 2010. average daily wage in Indonesia.

Blast fishing is just one of many human activities that are

rapidly destroying coral reefs. Studies by the Global Coral
Reef Monitoring Network (GCRMN) show than 11% of reefs
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 ENVIRONMENT
worldwide, and as many as 30%-60% of reefs in certain coral re-growth and ensure the health of a reef have barely
areas, have already been lost to sediment and nutrient pollution, been tested.
over-exploitation, and mining. These rich and fragile ecosystems,
which can be destroyed in a shockingly short time, may take n 1998, Helen Fox, a PhD candidate in the Department of
over a hundred years to recover naturally—if they can
recover at all.
I Integrative Biology, began testing several low-cost methods
for providing coral reef restoration in eastern Indonesia’s
Komodo National Park, where blast fishing had been practiced
regularly until 1996.
The potential economic gain for tourism industries “In Komodo, there is a
from healthy reefs is a powerful motivation for contrast between beautiful,
incredible diving (reefs) and areas
conservation as well as restoration. that have nothing there, just huge rubble fields,”
Fox says. The close proximity of rubble fields and
GCRMN predicts that as much as half of the world’s neighboring healthy reefs along with present-day bans on blast fish-
remaining coral reefs will be lost by 2010. The loss of ing in the area provides an ideal site for Fox’s experiments.
these reefs would mean not only extinction for hundreds—
possibly thousands—of species, but also a catastrophic loss Reefs grow layer by layer, Fox explains, as coral larvae and
of food and income in coastal communities and the disappear- coralline algae first anchor on a structure of dead coral and
ance of unique chemicals that have great potential for in- then mature, die and leave behind their hard skeletons. But
dustrial and medical use. where blast fishing has been chronic, all that remains for coral
larvae to settle on are small and unstable pieces of rubble,
Researchers have only just begun to make inquiries about the which shift with the currents and crush most of the tiny coral
basic science of coral organisms within the past five years, spurred recruits that anchor there. In order to restore the blasted
in part by increased awareness of
the rapid destruction of reefs. But
coral reef restoration and the
complex factors that impact a
reef’s health are still poorly under-
stood. The reef ecosystem is
comprised not only of coral, but
also of 32 of the 34 known phyla
of animals. Their mutually
dependent interactions, as well
as seasonal and climatic effects,
generate an immensely compli-
cated ecosystem. Moreover,
changes that could accelerate

Lost forever? Full and vibrant reefs take cen-

turies to form and are being destroyed at an
alarming pace. Conservation alone may not
be enough to reverse the trend; artificial reef
rebuilding may be necessary, too.
(©2001 www.ecoreefs.com; Helen Fox)

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Feature
reef, a stable anchoring place for the larvae must be
artificially created.
Fox’s experiments tested low-tech, inexpensive, and locally
available materials as stabilizers for the shifting coral rubble
and as substrate for larval recruits. She prepared several small
rubble field sites, each with three different stabilization
methods: rock piles, netting over the rubble, and cement slabs.
After revisiting the sites over two seasons, Fox found that the
rock piles most successfully attracted and maintained recruits,
so she started a larger trial. Her research has attracted
support from the Nature Conservancy and funding from the
Packard Foundation. The Nature Conservancy is currently
undertaking a large-scale study of Fox’s rock pile substrate
over two hectares of ocean floor.
ormer Berkeley graduate student Michael Moore is
F trying a different strategy: targeting the tourism industry.
Moore recently founded EcoReefs, a company that develops
reef-restoration technologies. Fox serves as an informal
science advisor for Ecoreefs. Moore, who received his PhD
Cheap fix. Integrative Biology graduate student Helen Fox hopes
that inexpensive materials like rocks or netting can help rebuild
damaged reefs. (Gideon Weisberg/BSR)
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in Integrative Biology in 1995, hopes to
sell his patented coral reef restoration
method to dive operators, beachfront
hotels, and local governments worldwide.
Coral reef restoration became a concern
of Moore’s in the late 1980s, when he was
conducting oceanographic research in
Indonesia and saw that reefs were being
annihilated. After graduate school Moore
worked at the Scripps Institute of Ocean-
ography in San Diego, and then joined
the dot-com world in San Francisco.
While working for a dot-com company,
Moore hit upon the design of his snow-
flake-like reef restoration modules. As
a marine researcher, he had been aware
that coral scientists use ceramic tiles,
which are pH neutral, to attract coral
larvae and measure local coral population.
Moore’s innovation was to create a 3D
hexagonal ceramic module that could
be mass-produced and assembled at a
restoration site. Building an artificial reef. Michae
and provide habitat for adult and
In 2001, Moore patented the design and left the dot-com com-
pany to devote his time to EcoReefs. “Most of my engineer
friends took their $40,000 and bought BMWs. I took my
$40,000 and started EcoReefs,” he says. In October 2001,
Moore installed a demonstration restoration structure in a small
area of damaged reef in Bunaken National Park, which is near
Komodo. The design successfully mimicked the complex
architecture of a natural reef and provided habitat for adult
and juvenile fish—especially herbivorous fish that eat the algae
and soft coral that compete with reef-building coral larvae for
settlement space. The ceramic modules also quickly attracted
red crustose algae, an important precursor species that signals
to the larvae that substrate is available. Moore is currently show-
ing the promising results from the test site to potential clients.
24
 ENVIRONMENT
industry. Kraus believes continued
conservation efforts are at least as
important as developing new resto-
ration technology. “Reefs are being
destroyed so rapidly. We need to
focus on keeping what’s there, stop-
ping this bleeding. There is a role for
restoration, but it’s very expensive,
and we choose to focus our resources
elsewhere,” she says.

There is some tension between the

reef conservation and reef restoration
camps, but this should hopefully
produce a variety of strategies for
dealing with what everyone agrees
is a dire situation. While decreasing
the rate of destruction remains the
top priority for Kraus, Fox and
Moore are laying a foundation that will
be sorely needed once conservation
alone becomes insufficient. “If we
don’t start doing research now on
the tools we need to restore reefs,
el Moore places one of his reef restoration modules in a bed of damaged coral. The modules attract coral larvae we won’t be ready,” says Moore.
d juvenile fish. (©2001 www.ecoreefs.com)
Without more research on coral
he potential economic gain for tourism industries reef restoration, Moore predicts, it will be like having to
T from healthy reefs is a powerful motivation for
conservation as well as restoration, according to Janine
rebuild a clear-cut forest without “knowing anything about
how to plant trees.”
Kraus, Managing Director for the Coral Reef Alliance
(CORAL), a non-profit organization that works with the
dive industry and other constituents to conserve coral reefs.
CORAL recently gave a micro-grant to an Indonesian Sneha Desai received a BS in life sciences from Pennsylvania
non-governmental organization that works towards providing State University in 1997. She is currently Laptop Program
blast fishers with alternative livelihoods in the tourism Coordinator at the Urban School of San Francisco.

Learn More:

Coral Health and Monitoring Program http://www.coral.noaa.gov

Coral Reef Alliance http://www.coralreefalliance.org
Ecoreefs http://www.ecoreefs.com
Komodo National Park http://www.komodonationalpark.org

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The University

DARWIN OR DOGMA?
Why teaching evolution
is more controversial
than ever.
Jessica Palmer
ou can find them at PTA meetings or UC

Y Berkeley seminars: pink and blue book

marks entitled “Ten Questions to Ask Your Biology
Teacher About Evolution.” These colorful little freebies seem
designed to excite kids about science fairs and collecting fos-
sils, but they’re actually the latest salvo in an escalating battle
to keep evolutionary theory out of public schools.

The Ten Questions have a clear bias against evolution: “Why do

textbooks use pictures of peppered moths camouflaged on tree
trunks as evidence for natural selection—when biologists have
known since the 1980s that the moths don’t normally rest on
tree trunks, and all the pictures have been staged? Why do text-
books use drawings of similarities in vertebrate embryos as
evidence for their common ancestry—even though biologists have
known for over a century that vertebrate embryos are not most similar
in their early stages, and the drawings are faked?”

Even biologists may find it tough to marshal specific evidence to refute

these accusations—not surprising, since a biologist wrote them. The
bookmark’s creator is Jonathan Wells, author of Icons of Evolution, who
holds a PhD in Molecular and Cell Biology from UC Berkeley and also a
PhD in Religious Studies from Yale University.

Judy Scotchmoor, Director of Museum Relations at Berkeley’s UC Museum

of Paleontology (UCMP) and a former science teacher, calls the Ten Questions “very in-your-face,
purposeful challenges. Most teachers simply don’t have the tools to respond to them.” To help teachers
respond to the Ten Questions, and other questions like them, UCMP is collaborating with the National
Science Foundation, the Howard Hughes Medical Institute, and the National Center for Science Education
(NCSE) to build a teacher’s toolbox: the “Understanding Evolution” web site.

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The Alabama Disclaimer makes
evolution sound like the brainchild
of a scientific lunatic fringe.
When it debuts in 2003, http://evolution.berkeley.edu will be a
one-stop shopping center for science teachers, says
Scotchmoor. It will offer background information, lesson
plans, and other tools to deal with the controversy surrounding
evolution education, including the NCSE’s rebuttal of
Wells’s Ten Questions.
The mess in Kansas
During the past few decades, evolution’s place in public
school curricula has seemed secure. It’s difficult to teach
geology, biochemistry, or ecology without mentioning Darwin
or the theory he founded. As renowned geneticist Theodosius
Dobzhansky noted in a 1973 essay, “Nothing in biology makes
sense except in the light of evolution.”
Then, in 1999, the Kansas State Board of Education cut
evolution from the state science curriculum. Kansas didn’t
outlaw evolution, but by ensuring students would never be
tested on it, the state withdrew support for the theory. An
outcry from the science community immediately followed.
“We can thank the mess in Kansas for opening our eyes that
something had to be done,” says UCMP’s Scotchmoor.
At the time of the Kansas controversy, it had been several
decades since the teaching of evolution was seriously threatened
in the US. Tennessee’s Butler Act of 1925, which precipitated
the Scopes Trial, explicitly banned from the classroom “any
theory that denies the divine creation of man and teaches
instead that man has descended from a lower order of animals.”
In a 1968 case, the US Supreme Court ruled all bans on teaching
evolution unconstitutional. In 1987, it struck down a law
mandating equal time for creationism in the classroom.
These legal decisions forced evolution’s opponents to rede-
fine their goals and methods. Now, rather than arguing
for creationism, critics argue against evolution—especially its
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role in the origin of life on Earth. Just like Wells’s little blue
bookmark, they object to evidence of evolution, to the way it
is taught, and to its philosophical and religious implications.
In Kansas, and most recently in Ohio, these groups are making
themselves heard.
The most vocal anti-evolution movement, which calls itself
Intelligent Design (ID), began at UC Berkeley. Professor of
Law Phillip Johnson argued in his 1991 book Darwin On Trial
that evolutionary theory was “pseudoscience.” Johnson judges
natural selection to have a real, but overvalued, effect. “The
appearance of innovations like new complex organs or body
plans,” he says, “cannot be explained adequately without
allowing for intelligent causes”—that is, an intelligent
design or blueprint for life.
Darwin himself had been amazed by the power of natural
selection to assemble a complex eye, not just once, but several
times in different animal lineages. Many scientists privately
reconcile religion, and the idea of a Creator, with evolution.
But Johnson’s contingent wants the debate out in the open,
and inside the classroom, with ID presented as an alternative
theory to evolution in state science curricula.
Science educators hold that there is no scientific alternative
to evolution. ID, they say, is just another variation on
creationism. But Johnson insists that the evolution camp
itself has a religious agenda, because it promotes a “naturalistic
worldview,” and that educators must “teach the controversy.”
“Where the big confusion lies is
that people don’t have the basic
knowledge of how science works.”
Vocal critics like Gary Demar, president of the creationist
organization American Vision, say evolution is also unscien-
tific: “You can’t apply the scientific method to evolution. It’s
never been observed. You can’t repeat the experiment. And
so what’s being sold as science, in terms of evolution, really
isn’t science in terms of the way they define it.”
27
The University
Theory, not fact or compel student belief. Although the Alabama Disclaimer
and the Kansas standards were motivated by concern over
A few years before the Kansas controversy, Alabama legislators whether evolution is good science, they appropriately question
labeled their state’s biology textbooks with this disclaimer: “This what constitutes good science education in general. Science
textbook discusses evolution, a controversial theory some is an interrogative process of critical thinking, and if it’s not taught
scientists present as a scientific that way—in evolution or any
explanation for the origin of liv- “You can’t apply the scientific method other area—it’s a problem.
ing things, such as plants, animals, to evolution. It’s never been observed.
and humans. No one was present You can’t repeat the experiment.” Unfortunately, these aspects of
when life first appeared on Earth. science are not emphasized
Therefore any statement about life’s origins should be consid- strongly enough or often enough in the classroom or the media.
ered as theory, not fact.” The mainstream public doesn’t have a clear picture of what
scientific inquiry is. As a result, evolution’s critics get away
The Alabama Disclaimer makes evolution sound like the with battling straw men, while the science community is
brainchild of a scientific lunatic fringe. But the thrust of its either oblivious to the debate or baffled by it. “Where the big
argument, that evolution should be taught as “theory, not confusion lies is that people don’t have the basic knowledge of
fact,” is perfectly agreeable to most scientists. Evolution is a how science works. They can’t look at Intelligent Design
theory. As evolutionist Dobzhansky stated, “A theory can be or the old Creation Science or whatever they will come up
verified by a mass of facts, but it becomes a proven theory, with next, and recognize that that’s not science,” says
not a fact.” In the same vein, Wells’s bookmark asks, “Why UCMP’s Scotchmoor.
are we told that Darwin’s theory of evolution is a scientific
fact—even though many of its claims are based on misrepresen- Such attempts to confuse the issue aren’t new. In 1973,
tations of the facts?” In 2001, Kansas’s revised science standards Dobzhansky observed, “Disagreements and clashes of opinion
outlined similar concerns: “Science studies natural are rife among biologists, as they should be in a living and growing
phenomena by formulating explanations that can be tested science. Anti-evolutionists mistake, or pretend to mistake,
against the natural world. Some scientific concepts and these disagreements as indications of the dubiousness of
theories (e.g. cosmological and biological evolution, etc.) the entire doctrine of evolution.” It’s alarming that in three
may differ from the teachings of a student’s religious com- decades, the situation hasn’t gotten any better.
munity or their cultural beliefs. Compelling student belief
is inconsistent with the goal of education. Nothing in sci- True or False?
ence or any other field should be taught dogmatically.”
According to the National Science Foundation’s latest biennial
No qualified scientist or educator would teach dogmatically, report, Science and Engineering Indicators 2002, nine out of

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ten American adults are interested in learning about science of science. Eager to satiate the nation’s hunger for science-
and scientific discoveries. But apparently they haven’t learned related stories, the news media boil each new study down to
much: only 54% know it takes a year for the Earth to orbit a punchline. “We simplify everything—everyone has to have
the sun. Half the American public thinks early humans had a quick answer, we talk in sound bytes, and things are very
dinosaurs for neighbors. black and white, but that’s not at all the way science works,”
says Scotchmoor.
However, the nation’s Kansas didn’t outlaw evolution, but by ensuring
most prominent scien- students would never be tested on it, the state Reductionist language is
tific organizations may withdrew support for the theory. an alarming characteris-
be guilty of oversimpli- tic of popular science. If
fication. NSF’s surveys included 13 true/false questions. the public constantly hears evolution, global warming, or the
Along with uncontroversial statements like “All radioactivity safety of prescription drugs described in yes/no, true/false
is man-made (false),” NSF asked “The universe began with a terms, then it’s not surprising that nearly three-quarters of
huge explosion (true),” and “Human beings, as we know American adults don’t understand the scientific process.
them today, developed from earlier species of animals
(true).” Adults with a high level of science education who What did T. rex taste like?
otherwise did well (92% answered the radioactivity question
correctly) performed much worse on the latter two questions Al Janulaw, former President of the California Science Teachers
(50% and 69% correct, respectively). And 2001 was the first Association and a middle school teacher with 32 years of
year that the majority of American adults of all educational back- science teaching experience, thinks the problem can be fixed
grounds answered the evolution question correctly (53%, up in the schools. “We have a very scientifically illiterate public,
from 45% in 1999). and today’s high school students are tomorrow’s public.”

So what can we learn from the NSF survey results? NSF has
suggested, “Responses to these two questions may reflect reli-
gious beliefs rather than actual knowledge about science.”
Perhaps, but in addition, because true/false questions impose
artificial dichotomies, they are arguably an inappropriate way
to discuss theories, which can never become facts. If theories
can never be facts, shouldn’t we be careful about describing
them as true or false?
Oversimplification is part of the problem in public education
Janulaw is lending his expertise to the Understanding Evolution
web project. He believes science literacy among teachers,
particularly at the lower grade levels, is an essential first step.
“In my experience working with non-science-major elementary
teachers, these teachers harbor the same misconceptions
about the history of the Earth and mechanisms of evolution
that the average citizen does. It’s not going to serve the teachers
or their students well if they don’t understand it any better than
the kids and their parents do.”

Jessica Palmer/BSR

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The University

The Designer’s Advocate

For more on the Intelligent Design position, the BSR went straight to the source: Berkeley Professor of Law Emeritus
Phillip Johnson, author of Darwin on Trial.

Berkeley Science Review: Do you think that the American public is too accepting of scientific ideas, without thinking
critically about them?

Phillip Johnson: Yes, very often. Our educators teach science as a process of learning facts, rather than applying
critical thinking skills to scientific claims, which in many cases are speculative and linked with ideology. Science
journalists have the same education, and cannot afford to lose access to the most influential scientists, so they
report what they are told with endorsements like “experts say.”

BSR: In Darwin On Trial, you state that Darwinism gives rise to a “naturalist philosophy” in which “scientists may
not consider all the possibilities, but must restrict themselves to those which are consistent with a strict philosophical
naturalism.” Isn’t that restriction necessary for science to function as the limited tool that it is?

PJ: I wish our scientific leaders really did admit that science is merely a “limited tool” rather than identifying it with
a naturalistic worldview. What I most object to is that they conceal their philosophical assumptions and claim
immense creative power for the Darwinian mechanism, for example, as if this claim were based on empirical
testing, when in fact it is based only on philosophy.

BSR: Do you think that science can be an effective analytical tool without promulgating this “naturalist philosophy?”

PJ: Yes. Scientists and science educators should be willing to consider all the evidence, and to follow the evidence
wherever it leads, even if it leads to conclusions they do not welcome. As it is, they promulgate naturalism and
Darwinism regardless of the evidence.

BSR: What would you see as the perfect policy resolution to the evolution controversy in public schools?

PJ: The "Santorum Amendment" language in the Conference Committee Report attached to the new federal education
statute states an excellent principle for science education that should be followed even if it did not have the effect
of law. It says that a good science education should teach students to distinguish between the testable theories of
science and religious or philosophical claims made in the name of science. Where controversial subjects like
biological evolution are taught, educators should teach the controversy, preparing students to be informed partici-
pants in public debates. The important question is why scientific organizations are bitterly opposed to these
sound educational principles.

BSR: In your experience, has the Berkeley community been supportive of debate on this topic?

PJ: The campus has been good to me in matters such as academic promotions, but biologists have fled from any
debate. They seem to be afraid of what will happen if the subject is not kept safely within their own professional
territory, where they control the definitions and assumptions.

Johnson recommends Signs of Intelligence by Demski & Kushiner for more essays on Intelligent Design.

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The key to teaching evolution right, says Janulaw, is teaching
critical thinking first. “This is about thinking scientifically. Then
when the students arrive in sixth grade and someone men-
tions the ‘E-word,’ or the idea of evolution or the history of
the planet, these kids are already doing critical thinking. They’re
already empiricists. The truth is, I can’t tell a seven-year-old
the history of life on Earth without telling it dogmatically. So
we don’t do it. What we try to do is build these skills, so the
kid can understand it when it comes along.”
To do this, the Understanding Evolution project builds on
the pedagogical resources of an earlier NSF/UCMP project,
“Explorations Through Time,” which provides field-tested
teaching exercises on topics like fossils and geologic time.
“What Did T. rex Taste Like?” is an introduction to cladistics
(hierarchical organization on the basis of common ancestry)
that never uses a word more technical than “lineage.” The idea
is to help students get in-depth experience thinking scien-
tifically, rather than emphasizing details, definitions, and facts.
Unfortunately, most K-12 science textbooks don’t do this. The
American Association for the Advancement of Science’s Project
2061 found in 2000 that even high school biology textbooks
don’t cover central concepts like the nature of science in
sufficient depth. Scotchmoor agrees: “A lot of us teachers
have this pet peeve about the way the scientific method is shown
in textbooks: steps one, two, three, four, five, conclusion, job
done. When does science ever say, ‘Ok, that’s over with’?”
Project 2061 also found that all textbooks examined did a “poor”
job of addressing commonly held beliefs about evolution. Jo Ellen
Roseman, director of Project 2061, says “While most (text-
books) contain the relevant content on heredity and natural
Learn more about science education and evolution:
The National Center for Science Education
NSF Science and Engineering Indicators 2002
UC Museum of Paleontology
Understanding Evolution
Wells’s Ten Questions
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selection, they don’t help students learn it or help teachers
teach it.” Wells’s 10 Questions bookmark, though strident,
makes an excellent point—textbooks do present the same old
stories and figures over and over, often in a misleading way or
without context. Wells’s mistake lies in equating the theory of
evolution with the poor way in which it is often taught.
Janulaw concludes, “To get kids to deal with the tentativeness
and open-endedness and need for further study—the nature
of science—first you need to get the teachers there. And I
don’t think they are.” The American public isn’t “there” either.
It’s frustrating for scientists when the media misrepresents a
study or when parents object to evolution in their child’s cur-
riculum. But who, if not the scientific community, is ultimately
responsible for informing the public about science? Scotchmoor
says, “We, the scientists, are not very good at this, you know—
we’re still learning. We need to be more proactive and realize
that sharing research and science with the public is essential.”
It may be hard to take, but scientists and science educators
have a lot to learn from evolution’s critics. We must reconsider
how science is taught in schools and explained to the public. We
need to weed bad science out of textbooks, teach children to
think critically, and learn to answer those Ten Questions
ourselves—one way or another.
Jessica Palmer is a fifth-year graduate student in the
Department of Molecular and Cell Biology at UC Berkeley.
http://www.natcenscied.org
http://www.nsf.gov/sbe/srs/seind02/start.htm
http://www.ucmp.berkeley.edu
http://evolution.berkeley.edu
http://www.iconsofevolution.com/tools/questions.php3
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Perspective
BACK TO THE FUTURE
The last angry man travels through time.
Alan Moses

elativity isn’t popular just because it has a catchy name.

S
ome time ago, in the center of the Sun, two hydrogen
atoms traveling at enormous velocities were headed on
a collision course. The conditions were just right so
R It moved our view of the world away from taking place
in a fixed time and space and towards being, well, just relative.
that the atoms crashed and interacted in a very particular way, The question is no longer “Where is the photon?” but rather,
producing a high-energy photon. Through an incredible “How far away is the photon?” Instead of “What time will the
series of coincidences, the photon managed to travel on a photon hit my arm?” we should ask “How long ‘til the photon
course that brought it all the way to the Earth, until it finally hits my arm?” Instead of a law of motion, Einstein gives us a
slammed into my arm. And I didn’t even feel it. “law of distance,” which we call a “metric.” Famously, the met-
ric is defined on a four-dimensional space, where three of the
This is how we usually think of cause and effect. The collision dimensions are space and the fourth is time: the metric doesn’t
of the two particles caused the photon to be created and fly off only give us distances in space, but also in time. Further, the
in the direction that it did. My arm blocked the photon, so-called “space-time distance” to an object is dependent on
thereby prevent- the properties of
ing it from reach- Car windows would spontaneously come back together the object in ques-
ing the ground. and wallets would return to glove compartments. Of tion—its mass and
We would never course, the cash would still be gone. energy. At some
say that the re- level this seems
verse was true: that my arm caused the photon, and that its right: to figure out how far away something is in time, we’d
subsequent absorption by a particle in the Sun led to the better take into account how fast it’s going. More famously
formation of two hydrogen nuclei. Why not? After all, the still, though, it turns out that for objects traveling at the speed
laws of physics are (for the most part) time-symmetric. If a of light (like my arm-smashing photon) time stands still.
process is allowed by the laws of physics, its reverse must also Viewed in this light, the notion of cause preceding effect
be allowed. So as far as I can tell, it should be possible for my doesn’t make any sense.
arm to make light. That it doesn’t is obvious to anyone who’s
ever been in a dark room with me. Time is bunk. So why do we humans perceive time in the
wildly mistaken, but incredibly useful way that we do? One
People have appreciated this problem for a long time. In 1748, intriguing answer is that our perception—and perhaps thus
Scottish philosopher David Hume said that cause and effect our conception—of time comes from the evolutionary benefit
exist only in the minds of humans and aren’t actually a part of to having a simple way to make predictions about our
the objective world. Cause and effect are just abstractions we environment. It’s nice to know that throwing a spear at some-
use to describe events that we always see happening one after thing will probably cause it to drop dead.
the other, and never the other after one. All we need to do,
then, is explain why there are events that always occur in the But are we really ready to accept that time and causality
same temporal order. are subjective—that they arise because we view the world

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from a limited perspective? I don’t think we should give
up so easily. All we need to do is find some process that
occurs in accordance with the objective laws of physics but
shows bias towards either the future or the past. It
shouldn’t be that hard.
Let’s consider obviously temporal processes. Let’s also forget
about photons for a minute just to keep us from getting fouled
up by relativity—or worse, relativism. Processes that go one
way but don’t happen the other way are called “irreversible.”
Most irreversible processes fall under a less elegant, almost
practical branch of physics called thermodynamics. The sec-
ond law of thermodynamics gives processes directionality in
time by stipulating the eventual increase of a pesky quantity
called entropy. There are several competing interpretations
of what this magic quantity is, and it has
been loosely translated as “disorder” or
even “chaos.” Any of these gives the
second law in its pop form: order pro-
ceeds to chaos. My car window can be
smashed into tiny pieces, but the tiny
pieces will never get up and re-form into
my car window. You can’t go from a more
disordered state to an ordered one—
it’s against the law. Otherwise car win-
dows could spontaneously come back together and wallets
would return to glove compartments. Of course, the cash
would still be gone.
n his 1996 book, Time’s Arrow and Archimedes’ Point, Austra-
I lian philosopher Huw Price suggests we take a closer look
at what the second law actually says before jumping on the
second-law-gives-objective-direction-of-time bandwagon. In
the form most widely accepted by physicists, the second law
says that if all the particles of the window are simply following
the laws of motion, they are much more likely to end up in an
arrangement (or configuration) that corresponds to a “shattered”
state. The argument is simply probabilistic: shattered states
are the overwhelming majority of the possible configurations
for the particles that make up the window, and the particles
don’t have any preference to whether their bulk macroscopic
state is shattered or not. So, says physics, it’s not that it’s
impossible for shattered windows to re-form, it’s just
very unlikely.
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Price, however, points out the following oversight: Entropy
certainly increases towards the future—the second law and
all of our experience says so, but what about the past? Why
does entropy seem to decrease as we look back in time? Run
the tape backwards, and disordered piles of smashed glass
turn into ordered car windows. Since the laws of physics are
(mostly) time-symmetric, entropy should increase no mat-
ter which way we play the tape. The question isn’t why entropy
will be high in the future, but rather, how did it get to be low in the
past? And the answer is going to send us scrambling back to
the search-for-objectivity drawing board.
n Order out of Chaos, Ilya Prigogine describes what he calls
I the “subjective interpretation of irreversibility.” The
reason that there are so few microscopic configurations in
the past—in other words, that the
entropy was low—is because we can
describe the past with relative certainty.
We saw it happen or there’s some sort of
evidence that points us in the right direc-
tion. As we try to predict the future, the
limited information we have becomes less
and less adequate. Finally, we just cut
bait and concede that all the microscopic
states are equally probable—the entropy
is maximal. Ask me if it rained yesterday, and I can give you
a decent answer. But will it rain a week from today? A month?
A year? Hell, you got me. Anything could happen. So the
reason the past looks nice and tidy and the future looks
entropic and jumbly is that our knowledge of the future
is incomplete.
But hang on: my window didn’t just shatter out of the blue.
Some punk kid hit it with a crowbar! Only after they met the
little hooligan did my previously tidily arranged window
particles start spending all their time in shattered configurations!
OK, I’m getting a little agitated thinking about the repair
bill, so let’s put that smashed window out of our minds. Let’s
just think about a simple two-dimensional square that’s full
of particles bouncing around (but with all their motion
confined to the plane). Further, let’s put the whole thing in a
sealed box. The particles on the plane will spread themselves
out evenly because there are vastly more configurations that
33
Perspective
correspond to spread-out distributions than clumped ones
(that’s why the air in most rooms is usually not all bunched
up in one corner). The “window” (plane) seems to be in
equilibrium, and it should remain in that state indefinitely.
Now, let’s go ahead and replace the punk kid with a tiny winged
demon that’s capable of manipulating particles with extreme
care. The demon walks around for a bit and then chooses a
particle at random and gives it the tiniest, smallest, most
minute push up out of the plane. Then the demon picks
another particle and gives that one the tiniest, smallest, most
minute push down out of the plane. We’ll call that tiny amount
e, so that the demon added e momentum to the first particle
and subtracted e momentum from the second particle, leaving
the total momentum in the box completely unchanged.
If the box that we have the window in is small and its walls
are perfectly bouncy, those first two particles that the demon
set bouncing around will collide with other particles in the
plane and pretty soon the box is going to be full of particles
whizzing every which way. The original equilibrium—when
the particles were spread out over the plane—is disrupted
and the system approaches a new equilibrium, where the
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particles will now spread themselves evenly over the three-
dimensional volume of the box. Although I present no proof,
I claim that this is an irreversible process. The demon can’t go
back and put the particles back in the plane.
In our thought experiment, the past is not low entropy.
The particles were all jumbled up in the plane and entropy
was high. But the demon, very simply, was able to present
the particles with previously unreachable configurations.
Once available, the particles had no choice but to explore
them. I don’t think there’s anything subjective here: the
past is pulled into the future by the vast expanse of new
possibilities. So maybe we humans aren’t so misled. After
all, time is money.
Alan Moses is a third-year student in the Biophysics Graduate
Group at UC Berkeley.
34
Quanta (heard on campus)
“If you’ve developed a theory of cosmology or of atomic physics that makes
sense, it’s probably wrong. I doubt that you could bring up a child in a way
so that it would feel comfortable with quantum mechanics. I think (the kid)
would be insane.”

Gunther Stent, Professor

Department of Molecular and Cellular Biology
UC Berkeley
Author of Nazis, Women, and Molecular Biology
May 8, 2002

“Physicists can read Jane Eyre and be moved to laughter and tears. An English professor
doesn’t feel that way about Maxwell’s equations—except maybe the tears.”

Neal Lane, Professor

Department of Physics and Astronomy
Rice University
Former Director of the NSF and
the White House Office of Science and Technology Policy
April 18, 2002

“Privatization misses the basic point of the dynamic of the world’s poorest people. Don’t send in the
World Bank and the IMF. Send in the epidemiologists, send in the agronomists.”

Jeffrey Sachs, Director

Center for International Development
Harvard University
April 21, 2002

Got a great story?

Write for the Review.
Submission guidelines are at sciencereview.berkeley.edu

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 The Back Page

INSIDE OUT WITH

CLIFFORD STOLL
Mobius madness overtakes a local scientist.
ake a narrow piece of paper, twist it, tape together the ends, and you’ve
T changed your two-sided piece of paper into a one-sided Mobius strip. Wild. But
it gets even weirder. Sew multiple strips together, and you’ve built German mathematician Felix Klein’s 1882 invention,
the Klein bottle, a vessel that has zero volume but can hold beer just fine.

Oakland resident and former Lawrence Berkeley Lab astronomer Clifford Stoll has a one-man company that specializes
in building Klein bottles. Acme Klein Bottles makes Klein wine bottles, Klein flasks to liven up the lab, and Klein steins
(perfect for that zero-volume beer). For those who prefer to wear their Klein bottles, Stoll has created a hand-
knitted Klein bottle hat.

Sound too strange to be true? Well, Stoll admits to

cheating slightly. “A true Klein bottle can only exist in
four dimensions, and alas, our universe has only three spatial
dimensions.” Stohl really makes a “3-D immersion” of the
4-D shape. Just as a photograph is a 2-D immersion of a
3-D object, Stoll explains, “our Klein bottle is a 3-D
photograph of a true Klein bottle.” Fortunately for
Klein enthusiasts, the most paradoxical quality of the
bottle survives this dimensional transformation. “It
has no edge. It’s boundary-free, and an ant can
walk across the entire surface without ever
crossing an edge.”

So far, Stoll’s backyard business has sold

more than 300 bottles and awarded four
annual Klein Bottle Awards to researchers
in the field of topology. Acme’s latest
effort is a collaboration to build the
world’s largest Klein bottle, which
will stand one meter high. “It will be the
size of a five-year old child and a ferret will be able to
f
onse

crawl into it,” Stoll gleefully predicts.

sh M
Kiya

Jane McGonigal
To learn more, visit Acme Klein Bottle’s website at http://www.kleinbottle.com.
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