science review

Fall 2002 Vol.2 no. 2

BERKELEY

BERKELEY

science review
EDITOR–IN–CHIEF

FROM

THE

E DITOR

Dear Readers, The BSR just grows and grows. A year and a half ago we were nothing but an idea and a few emails between like-minded graduate students. And here we are, 5000 copies strong, and 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 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 all world media by 2006. Domination over all that lives on this earth is only our secondary goal. Our primary aim is to bring you the best of Berkeley science in a lively and comprehensive format. Turn to page 26 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 science of bringing decimated coral reefs back to life (page 22). If you’ve only got a minute, turn to Labscope (page 4) and Biotech Beat (page 6) for snapshots of new research on and around campus. Or you can read a crackpot’s theory about how Relativity is all wrong (page 32). Enjoy the third issue of the Berkeley Science Review. And let us know if you think we’ve done something right, or done something wrong, or if you’ve got a perspective about one of our stories. Our email address is submissions@uclink.berkeley.edu. And visit us on the web at sciencereview.berkeley.edu for back issues, information about our science writing seminars, and more.

Eran Karmon
MANAGING EDITOR

Temina Madon
CURRENT BRIEFS EDITOR

Jane McGonigal
COPY EDITOR

Donna Sy
CONTENT EDITOR

Jessica Palmer
EDITORS

Joel Kamnitzer Colin McCormick Teddy Varno
ART DIRECTOR

Una Ren
ART

Aaron Golub Jessica Palmer
W EBMASTER

Tony Wilson
SPECIAL THANKS

All the best,

Evelyn Strauss
PRINTER Eran Karmon

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, the UC Berkeley College of Chemistry, and the Chancellor’s Publication Committee. 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 ASUC. Letters to the editor and story proposals are encouraged and should be e-mailed to submissions@uclink.berkeley.edu or posted to Berkeley Science Review, 10 Eshleman Hall, Berkeley, CA 94720. Advertisers, contact advertise@uclink.berkeley.edu or visit http://sciencereview.berkeley.edu.

BERKELEY

science review

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
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!

Art Meets Science

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

BSR Vol. 2 No. 2

Departments
Current Briefs
7 Splitting Heads
When it comes to brain surgery, there’s no such thing as too many cooks.

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

8

Micro Machines
Diagnosing tiny devices is tougher than it looks.

Perspective
32 Back to the Future
Does time really march on or are we just moving forward into the past?

9

Walk Like a Man
When did our ancestors first stand up for themselves?

The Back Page
36 Inside Out with Clifford Stoll
How to drink a beer without anything to put it in.

The University
26 Darwin or Dogma?
Berkeley’s surprising place in the evolution vs. creationism debate.

4

Labscope

6 11 21 35

Biotech Beat
High points of the Bay Area biotech boom.

Hawaii’s wealth of spiders. Itsy-bitsy transistors. A crystal path for photons. Modeling the Universe’s birth. Babies know what’s up.

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 identify the blue block, demonstrating that they can override perceptual cues (in this case, color) and group objects causally.
Temina Madon

Colin McCormick/BSR

BILLIONS AND BILLIONS
Courtesy/Chung-Pei Ma
BERKELEY

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

science review

4

science review

5

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 technique 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
BERKELEY

science review

6

Current Briefs SPLITTING HEADS
Collaborating towards less invasive brain surgery.
an too many doctors spoil 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. 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 intensive 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.

C

“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 cooperative 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
BERKELEY

Jane McGonigal

Learn more: Neurosurgery http://www.neurosurgery-online.com

science review

7

Current Briefs MICRO MACHINES
Tiny technology can cause big research problems.
n 1983, physicist Richard 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.

I

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 humanscale 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-ona-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.

Working the bugs out. Roya Maboudian and her students are developing 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, performance-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,
BERKELEY

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

Temina Madon

Learn More: The Maboudian Lab http://www.ccherm.berkeley.edu/~rmgrp/ The Berkeley Microfabrication Lab http://www-microlab.eecs.berkeley.edu/

science review

8

WALK LIKE A MAN
New discoveries push back the origin of bipedalism.
t has been nearly three decades 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.

I

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

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 Yohannes Haile-Selassie and colleagues date the origin of bipe(hominid) classification dalism to more than 5.5 million years ago. (Eran Karmon/BSR) relies on characteristics records were still very poor in comparison shared exclusively with later hominids. to those in the three to four millionSo my definition is less functional, and year-old range,” says White. more cladistic (i.e., relying on comparisons between ancestors and Paleontologists are now debating how to descendants).” The team has dubbed classify the find. The Berkeley team has this subspecies Ardipithecus ramidus stirred controversy by classifying the kadabba. The name kadabba is from the fossils as a new subspecies of hominid local Afar language, meaning “basal” or (a member of the human family hominidae), “founding family ancestor.” rather than as a chimpanzee. Their conclusion is based on the lone foot Classification of the fossils as hominid bone, which Haile-Selassi claims was would have important implications for used to “toe-off ” in a manner unique to theories of bipedalism. Paleontologists habitual bipeds like ourselves. Explains previously held that bipedal walking White, “As you walk, your foot touches emerged in hominids as they spread out the ground first with the heel, and rolls into open, arid savannas. Yet chemical forward onto the ball, through what we analysis in the Awash indicates that six call ‘flexion,’ and finally pushes off with million years ago it was a lush, forested, the toes. That toeing-off is the last thing upland area. Finding bipedal hominids that happens with each stride. The shape in such an environment would force of the (toe) bone in this case indicates an paleontologists to revise current adaptation to habitual bipedalism.” theories. “Previously people thought 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
BERKELEY

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]

science review

9

Current Briefs
White and Haile-Selassi are not alone in the search for early hominids. Fossil finds from the same period found by a joint Kenyan-French research team in the Tungen Hills of Kenya have a similarly complex combination of human and apelike traits. Those fossils are of Orrorin tugenensis, a primate that walked bipedally in a manner more similar to modern humans than even Lucy, who is roughly two million years younger. Could either Ardipithecus ramidus kadabba or Orrorin tugenensis have been an ancestor to us all? Wherever Ardipithecus ramidus kadabba finally settles on the evolutionary tree, White and Haile-Selassi’s finds, as well as those of their Kenyan and French counterparts, are bound to change the picture of humankind’s origin.

Noah Rolff

To learn more about White and Haile-Selassis most recent work: Nature, 418, 145 (2002)

BERKELEY

science review

10

Book Review EVOLUTION’S FEMINIST SIDE
Teddy Varno
of several different case studies that illustrate Zuk’s point. In the first section, Zuk discusses ecofeminism, motherhood, 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 important evolutionary relationships. Foremost among these myths is the belief in the 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 us to assume that we need to study 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 of the evolution of human sexuality: menstruation, homosexuality, female orgasm, and gender differences in mathematics performance. Zuk convincingly demonstrates how a feminist perspective can contribute to evolutionary theorizing, but she provides little support for the idea that
BERKELEY

Sexual Selections: What We Can and Can’t Learn about Sex from Animals, Marlene Zuk (Berkeley: University of California Press, 2002), 240 pp.

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.

eep questions lurk just beneath 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 scientifically 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.

D

TeddyVarno is a second-year graduate student in the Department of History at UC Berkeley.

Advertise in the BSR

Info at sciencereview.berkeley.edu

Sexual Selections is divided into three major sections, each of which consists

science review

11

Feature

CUTS LIKE A KNIFE
Treating brain tumors without the surgeon’s scalpel.

A

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. 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 therapy that uses precisely targeted beams of gamma radiation like a scalpel, cutting out brain tumors without the trauma and complications of conventional surgery. “Last October, I started to feel that I wasn’t quite myself. I forgot things sometimes, just the little strange things that you’re supposed to know, but nothing out of this world,” Katherine recalls. After an MRI, her doctor diagnosed multiple brain metastases. A skin cancer that doctors thought they had successfully removed from her leg had broken up and spread to the brain via her lymphatic system and bloodstream. Over twenty tumors were found in Katherine’s brain. “We were both shocked. Even my doctor said she didn’t expect to see that,” Katherine says. Conventional treatments for brain tumors involve chemotherapy, which causes fatigue and nausea, and open-skull
BERKELEY

Aubrey Lau
surgery, where risks for hemorrhage and infection always exist. With its precision, low risk of complications, and high success rate, Gamma Knife radiosurgery presents an attractive alternative. Gamma Knife targets beams of highenergy light (gamma rays) onto brain lesions. These beams converge on a point in the brain with such high intensity that they kill tumor cells, eliminating the need for a surgeon’s scalpel. Since there is no need to open the skull, virtually all patients go home on the day of treatment. Gamma Knife treatment is the final stage of a long process. After Katherine’s tumors were diagnosed, the largest metastasis, in the left frontal lobe, was surgically removed. Since then, Katherine has had ten whole-brain radiation treatments, which deliver small dosages of radiation over several sessions in the hope of killing tumor cells while sparing healthy ones.

science review

12

MEDICINE
Following the therapy, some of Katherine’s tumors stabilized, but others enlarged and spread. Her case was next brought before the radiosurgery conference, a weekly meeting of neuroradiologists, radiation oncologists, neurosurgeons, and medical physicists, to determine whether Gamma Knife would be a suitable treatment. Since Katherine’s numerous remaining tumors were small, the conference decided Katherine would make a good candidate. With the head frame secure, Katherine is brought to the scan room for magnetic resonance imaging (MRI). The scans provide detailed information about where the tumors are relative to the head frame. Unfortunately, these images have limitations: they cannot differentiate between damage caused by tumors and that caused by the radiation treatment itself. “Trying to sort out whether something is a residual disease, a recurrent disease, or just a treatment-related effect on the brain is vital,” says Nancy Fischbein, Assistant Professor of Radiology at UCSF.

S

everal weeks after the conference, Katherine is admitted for treatment. The first step of the procedure is To gather more specific information, physicians often order a fitting a frame to her head. The frame secures her skull magnetic resonance spectroscopy (MRS) scan. This twentyin place and ensures accurate targeting of brain lesions minute procedure is perduring treatment. Michael formed alongside routine McDermott, Co-neurosurMRI scans. The MRS is gical Director of the unique because it proGamma Knife radiosurgery vides infor mation on program at UCSF, adjusts specific metabolites in the frame to fit Katherine’s the brain: c holine, a head and sets up what for component of the cell most patients is the most membrane; N-acetylaspartate uncomfortable part of the (NAA), a neuronal marker; procedure—the injection and creatine, a metabolic inof local anesthesia into four dicator. High levels of chopoints of the skull via a line indicate the breakdown large needle. Katherine of cell membranes, while sticks a small piece of cloth low levels of NAA can be a into her mouth and sign of neuronal damage. clenches her teeth. She Both of these conditions makes a fist, closes her eyes, and shakes her body a Zapping tumors. 201 beam of gamma radiation converge onto the tumor. suggest the presence of tumors. little as each of the injec- Each individual beam is so weak that it can shine through healthy cells cancerous without damaging them, but the beams converge on the tumor with such Fischbein notes that MRS tions enters a different side high intensity that they damage its DNA. also has prognostic value. “I of her head. “You’re almost can easily think of plenty of examples where MRI looks stable done, it’s just like when you’re at the dentist,” consoles but the spectroscopy shows changes,” she says, “and a few months Jesse Merril, the nurse practitioner massaging Katherine’s later, the MRI catches up with the spectroscopy and it becomes shoulder. Anaesthetized, Katherine is ready for the insertion clear that the patient did have a recurrent disease.” of pins into her skull through openings in each corner of the frame. This, as McDermott explains, is the only invasive After the scans, Katherine gets a break with her family in the component of the procedure, as the titanium tips of the waiting room as neurosurgeons, medical physicists, and pins make small divots in the skull.

BERKELEY

science review

13

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 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

Surgery without a knife. The patient slides into the gamma knife treatment unit. To avoid exposure 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)

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 administered, collimators with different hole sizes are used. (Aubrey Lau/BSR)

BERKELEY

science review

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.

T

he success rate of Gamma Knife treatment is impres 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 general, tumors with the highest grade are characterized by extensive infiltration into the brain tissues and a rapid spread. As McDermott notes, high grade tumors have a remission of four to six weeks, as opposed to low grade tumors, where a remission time of ten to twelve months is observed. Gamma Knife also has limitations. The major one is that the procedure is only effective on tumors smaller than 3 cm. Radiation can kill both healthy and cancerous cells, so as the radiation dosage increases to compensate for the tumor’s size, 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 radiotherapy 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. It has been over ten hours since Katherine arrived at the hospital. The evening fog is already beginning to set in. During
BERKELEY

Frame of reference. A physician fixes a frame onto a Gamma Knife 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 system for guiding radiation beams to the tumor.

the break before the last part of her treatment, Katherine’s husband gingerly takes her hand to walk her around the waiting room. She takes a sip of water. He adjusts the ties behind her gown. Although today’s treatment has been long, Katherine is almost ready to go home. Thanks to the non-invasive nature of Gamma Knife radiosurgery, she can rest in the comfort of her own home with her family tonight.

Aubrey Lau received a BA in Integrative Biology from UC Berkeley in 2000. She is currently a research associate at UCSF.

science review

15

Feature

THE SKY’S THE LIMIT
Reviving kite aerial photography.
Temina Madon

rchitects have been mapping cities and landscapes since the 16th century, constructing imagined aerial views using the mathematical principles of perspective. It wasn’t until the 19th century that aerial photography first became possible, by way of hot air balloons and kites. Today, architects 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.

A

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.

BERKELEY

science review

16

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.”

BERKELEY

science review

17

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/.

BERKELEY

science review

18

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.

BERKELEY

science review

19

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

BERKELEY

science review

20

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 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.”

Aaron Golub/BSR

To think of all the years I wasted in school Appearing overnight in hundreds of mailboxes across campus, the 140page 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.” It’s possible a bit may have been glossed over in the name of brevity.

Aaron Golub/BSR

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!’”

BERKELEY

science review

21

Feature

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

Sneha Desai
Helen Fox

As much as half of the world’s remaining coral reefs will be lost by 2010.
BERKELEY

H

undreds of colorful fish dart chaotically in and around a canopy made of millions of branching fingers of pink, green, and brown coral. Above 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 water sprays up. In the silence that follows, a few fish carcasses float to the surface, while many more sink to the 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 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

science review

22

ENVIRONMENT
worldwide, and as many as 30%-60% of reefs in certain areas, have already been lost to sediment and nutrient pollution, over-exploitation, and mining. These rich and fragile ecosystems, which can be destroyed in a shockingly short time, may take over a hundred years to recover naturally—if they can recover at all. coral re-growth and ensure the health of a reef have barely been tested. n 1998, Helen Fox, a PhD candidate in the Department of 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. “In Komodo, there is a contrast between beautiful, incredible diving (reefs) and areas that have nothing there, just huge rubble fields,” Fox says. The close proximity of rubble fields and neighboring healthy reefs along with present-day bans on blast fishing in the area provides an ideal site for Fox’s experiments.

I

The potential economic gain for tourism industries from healthy reefs is a powerful motivation for conservation as well as restoration.
GCRMN predicts that as much as half of the world’s remaining coral reefs will be lost by 2010. The loss of these reefs would mean not only extinction for hundreds— possibly thousands—of species, but also a catastrophic loss of food and income in coastal communities and the disappearance of unique chemicals that have great potential for industrial and medical use. Researchers have only just begun to make inquiries about the basic science of coral organisms within the past five years, spurred 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 understood. 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 complicated ecosystem. Moreover, changes that could accelerate

Reefs grow layer by layer, Fox explains, as coral larvae and coralline algae first anchor on a structure of dead coral and then mature, die and leave behind their hard skeletons. But where blast fishing has been chronic, all that remains for coral larvae to settle on are small and unstable pieces of rubble, which shift with the currents and crush most of the tiny coral recruits that anchor there. In order to restore the blasted

Lost forever? Full and vibrant reefs take centuries 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) BERKELEY

science review

23

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 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 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 Oceanography 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 snowflake-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.

F

Building an artificial reef. Michae and provide habitat for adult and

In 2001, Moore patented the design and left the dot-com company 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 showing the promising results from the test site to potential clients.
Cheap fix. Integrative Biology graduate student Helen Fox hopes that inexpensive materials like rocks or netting can help rebuild damaged reefs. (Gideon Weisberg/BSR)

BERKELEY

science review

24

ENVIRONMENT
industry. Kraus believes continued conservation efforts are at least as important as developing new restoration technology. “Reefs are being destroyed so rapidly. We need to focus on keeping what’s there, stopping 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 reef restoration, Moore predicts, it will be like having to he potential economic gain for tourism industries rebuild a clear-cut forest without “knowing anything about from healthy reefs is a powerful motivation for how to plant trees.” conservation as well as restoration, according to Janine

T

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 non-governmental organization that works towards providing blast fishers with alternative livelihoods in the tourism

Sneha Desai received a BS in life sciences from Pennsylvania State University in 1997. She is currently Laptop Program Coordinator at the Urban School of San Francisco.

Learn More:
Coral Health and Monitoring Program Coral Reef Alliance Ecoreefs Komodo National Park
BERKELEY

http://www.coral.noaa.gov http://www.coralreefalliance.org http://www.ecoreefs.com http://www.komodonationalpark.org

science review

25

The University

DARWIN OR DOGMA?
Why teaching evolution is more controversial than ever.

Jessica Palmer

Y

ou can find them at PTA meetings or UC 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 fossils, 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 textbooks 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.
BERKELEY

science review

26

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.

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.”

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 redefine their goals and methods. Now, rather than arguing for creationism, critics argue against evolution—especially its

“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 unscientific: “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.”

BERKELEY

science review

27

The University
or compel student belief. Although the Alabama Disclaimer and the Kansas standards were motivated by concern over whether evolution is good science, they appropriately question A few years before the Kansas controversy, Alabama legislators what constitutes good science education in general. Science labeled their state’s biology textbooks with this disclaimer: “This is an interrogative process of critical thinking, and if it’s not taught textbook discusses evolution, a controversial theory some that way—in evolution or any scientists present as a scientific 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. Unfortunately, these aspects of and humans. No one was present You can’t repeat the experiment.” science are not emphasized when life first appeared on Earth. strongly enough or often enough in the classroom or the media. Therefore any statement about life’s origins should be considThe mainstream public doesn’t have a clear picture of what ered as theory, not fact.” scientific inquiry is. As a result, evolution’s critics get away with battling straw men, while the science community is The Alabama Disclaimer makes evolution sound like the either oblivious to the debate or baffled by it. “Where the big brainchild of a scientific lunatic fringe. But the thrust of its confusion lies is that people don’t have the basic knowledge of argument, that evolution should be taught as “theory, not how science works. They can’t look at Intelligent Design fact,” is perfectly agreeable to most scientists. Evolution is a or the old Creation Science or whatever they will come up theory. As evolutionist Dobzhansky stated, “A theory can be with next, and recognize that that’s not science,” says verified by a mass of facts, but it becomes a proven theory, UCMP’s Scotchmoor. not a fact.” In the same vein, Wells’s bookmark asks, “Why are we told that Darwin’s theory of evolution is a scientific Such attempts to confuse the issue aren’t new. In 1973, fact—even though many of its claims are based on misrepresenDobzhansky observed, “Disagreements and clashes of opinion tations of the facts?” In 2001, Kansas’s revised science standards are rife among biologists, as they should be in a living and growing outlined similar concerns: “Science studies natural science. Anti-evolutionists mistake, or pretend to mistake, phenomena by formulating explanations that can be tested these disagreements as indications of the dubiousness of against the natural world. Some scientific concepts and the entire doctrine of evolution.” It’s alarming that in three theories (e.g. cosmological and biological evolution, etc.) decades, the situation hasn’t gotten any better. may differ from the teachings of a student’s religious community or their cultural beliefs. Compelling student belief is inconsistent with the goal of education. Nothing in sciTrue 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

Theory, not fact

BERKELEY

science review

28

ten American adults are interested in learning about science and scientific discoveries. But apparently they haven’t learned much: only 54% know it takes a year for the Earth to orbit the sun. Half the American public thinks early humans had dinosaurs for neighbors.

However, the nation’s Kansas didn’t outlaw evolution, but by ensuring students would never be tested on it, the state Reductionist language is most prominent scienan alarming characteristific organizations may withdrew support for the theory. tic of popular science. If be guilty of oversimplithe public constantly hears evolution, global warming, or the fication. NSF’s surveys included 13 true/false questions. safety of prescription drugs described in yes/no, true/false Along with uncontroversial statements like “All radioactivity terms, then it’s not surprising that nearly three-quarters of is man-made (false),” NSF asked “The universe began with a American adults don’t understand the scientific process. huge explosion (true),” and “Human beings, as we know 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 backscience 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 religious 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

of science. Eager to satiate the nation’s hunger for sciencerelated stories, the news media boil each new study down to a punchline. “We simplify everything—everyone has to have a quick answer, we talk in sound bytes, and things are very black and white, but that’s not at all the way science works,” says Scotchmoor.

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

BERKELEY

science review

29

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 participants 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.

BERKELEY

science review

30

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 mentions 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 scientifically, 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 (textbooks) contain the relevant content on heredity and natural

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 curriculum. 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.

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
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

BERKELEY

science review

31

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. It moved our view of the world away from taking place in a fixed time and space and towards being, well, just relative. The question is no longer “Where is the photon?” but rather, “How far away is the photon?” Instead of “What time will the photon hit my arm?” we should ask “How long ‘til the photon hits my arm?” Instead of a law of motion, Einstein gives us a “law of distance,” which we call a “metric.” Famously, the metric is defined on a four-dimensional space, where three of the dimensions are space and the fourth is time: the metric doesn’t This is how we usually think of cause and effect. The collision only give us distances in space, but also in time. Further, the of the two particles caused the photon to be created and fly off so-called “space-time distance” to an object is dependent on in the direction that it did. My arm blocked the photon, the properties of thereby preventing it from reach- Car windows would spontaneously come back together the object in quesing the ground. and wallets would return to glove compartments. Of tion—its mass and energy. At some We would never course, the cash would still be gone. level this seems say that the reright: to figure out how far away something is in time, we’d verse was true: that my arm caused the photon, and that its better take into account how fast it’s going. More famously subsequent absorption by a particle in the Sun led to the still, though, it turns out that for objects traveling at the speed formation of two hydrogen nuclei. Why not? After all, the of light (like my arm-smashing photon) time stands still. laws of physics are (for the most part) time-symmetric. If a Viewed in this light, the notion of cause preceding effect process is allowed by the laws of physics, its reverse must also doesn’t make any sense. be allowed. So as far as I can tell, it should be possible for my 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 that the atoms crashed and interacted in a very particular way, producing a high-energy photon. Through an incredible series of coincidences, the photon managed to travel on a course that brought it all the way to the Earth, until it finally slammed into my arm. And I didn’t even feel it.

S

R

arm to make light. That it doesn’t is obvious to anyone who’s ever been in a dark room with me. People have appreciated this problem for a long time. In 1748, Scottish philosopher David Hume said that cause and effect exist only in the minds of humans and aren’t actually a part of the objective world. Cause and effect are just abstractions we use to describe events that we always see happening one after 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 same temporal order.
BERKELEY

Time is bunk. So why do we humans perceive time in the wildly mistaken, but incredibly useful way that we do? One intriguing answer is that our perception—and perhaps thus our conception—of time comes from the evolutionary benefit to having a simple way to make predictions about our environment. It’s nice to know that throwing a spear at something will probably cause it to drop dead. But are we really ready to accept that time and causality are subjective—that they arise because we view the world

science review

32

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 second 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 proceeds 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 windows 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, Australian 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.

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 matter 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 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 direction. 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.

I

I

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

BERKELEY

science review

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 particles will now spread themselves evenly over the threedimensional 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.

BERKELEY

science review

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
BERKELEY

science review

35

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 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.

T

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 handknitted 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 crawl into it,” Stoll gleefully predicts.

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

science review

36

Kiya

sh M

onse

f

Master your semester with Scribd & The New York Times

Special offer for students: Only $4.99/month.

Master your semester with Scribd & The New York Times

Cancel anytime.