Berkeley Science Review - Fall 2002

B E R K E L E YsciencereviewFall 2002 Vol.2 no. 2

FROM THE EDITORBERKELEYsciencereviewEDITOR–IN–CHIEF

Eran Karmon

MANAGING EDITOR

Temina Madon

CURRENT BRIEFS EDITOR

Jane McGonigal

COPY EDITOR

Donna Sy

CONTENT EDITOR

Jessica Palmer

EDITORS

Joel KamnitzerColin McCormick

Teddy Varno

ART DIRECTOR

Una Ren

ART

Aaron GolubJessica Palmer

WEBMASTER

Tony Wilson

SPECIAL THANKS

Evelyn Strauss

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. Publishedwith 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 encouragedand should be e-mailed to [email protected] or posted to Berkeley Science Review, 10 Eshleman Hall, Berkeley, CA 94720. Advertisers, [email protected] or visit http://sciencereview.berkeley.edu.

Dear Readers,

The BSR just grows and grows. A year and a half ago we were nothing but an idea and a fewemails between like-minded graduate students. And here we are, 5000 copies strong, andfor the first time ever, in dapper full color. This past semester, we were named Berkeley’sbest-designed student publication (thanks to our talented and dedicated art and layoutstaff). And two of this year’s 22 Mass Media Fellows of the American Association for theAdvancement of Science got their journalistic start at the BSR. At this rate, we will controlall world media by 2006.

Domination over all that lives on this earth is only our secondary goal. Our primary aim is tobring you the best of Berkeley science in a lively and comprehensive format. Turn to page 26to read all about Berkeley’s place in the evolution vs. creationism debate (you’ll be surprisedto learn that Berkeley folk fall on both sides of the fence). Or learn all about the craft andscience 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 aroundcampus. 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 donesomething right, or done something wrong, or if you’ve got a perspective about one of ourstories. Our email address is [email protected].

And visit us on the web at sciencereview.berkeley.edu for back issues, information about ourscience writing seminars, and more.

All the best,

Eran Karmon

Features

Doctors perfect a technique forcuring multiple-tumor braincancer without a single incision.

12 Cuts Like a Knife

By Aubrey Lau

MedicineMedicine

Art Meets ScienceArt Meets Science

Look! Up in the air! It’s abird! It’s a plane! Holycow, it’s a Nikon danglingon the end of a kite string!

16 The Sky’s the Limit

By Temina Madon

A pile of concrete and somenetting can mean the differencebetween a living ocean and anunderwater rubble field.

22 Constructing Coral

By Sneha Desai

EnvironmentEnvironment

BERKELEYsciencereview

Departments

BSR Vol. 2 No. 2

4 Labscope

A crystal path for photons.

Babies know what’s up.

Modeling the Universe’s birth.

Hawaii’s wealth of spiders. 6 Biotech Beat

High points of the Bay Area biotech boom.

11 Book ReviewEvolution’s feminist side.

21 Weird SciencePhoebe the Photon conquers all.

Itsy-bitsy transistors.

The Back Page 26 Darwin or Dogma?

The University

Berkeley’s surprisingplace in the evolution vs.creationism debate.

Perspective32 Back to the Future

Does time really march onor are we just movingforward into the past?

35 Quanta (heard on campus)

Current Briefs 7 Splitting Heads

When it comes to brainsurgery, there’s no suchthing as too many cooks.

Diagnosing tiny devices istougher than it looks.

8 Micro Machines

When did our ancestors firststand up for themselves?

9 Walk Like a Man

On the cover:

36 Inside Out with Clifford StollHow to drink a beer withoutanything to put it in.

Marine Patrol Officer JohnKanteley dropping a coral reefrestoration module onto a reefslope in Indonesia’s BunakenNational Marine Park.

Read about it on page 22.© www.ecoreefs.com

Labscope

Researchers led by Alex Zettl of the Department of Physics have recently created the world’s smallest transistor. The electroniccomponent, 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 nitridenanotubes. Boron nitride tubes are among the strongest and best heat-conducting materials known, according to Zettl. Boronnitride tubes were first predicted by Berkeley theorist Marvin Cohen and then synthesized in Zettl’s lab in 1997. Zettl’s group hasalso 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

In the forests of the Hawaiian Islands, Rosemary Gillespie of the Department of Environmental Science, Policy, and Managementhas 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. Incollaboration with Geoffrey Oxford of the University of York, Gillespie is also investigating the evolution of another Hawaiianarachnid, the happy-face spider (Theridion grallator). Different populations of this species exhibit strikingly varied color patternson their abdomens. Since these patterns are primarily determined genetically, they can be used as visible markers to examine hownatural selection operates on genetic differences in populations.

Teddy Varno

Jandir Hickmann and Raymond Chiao of the Department of Physics are investigating the properties of “photonic crystalwaveguides”—two-dimensional structures that can be used to guide light. Working with scaled-up models (which are easier tobuild and test than the miniature crystal versions) the group hopes to extend earlier results showing that the waveguides’ repeatedcrystal pattern prevents certain frequencies of light from traveling anywhere but along the hollow center of the crystal. Theseresults 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 tobuild high-energy particle accelerators that fit on a laboratory table.

Temina Madon

Eran Karmon

Astronomy Professor Chung-Pei Ma and her graduate students are using mathematical models to explain how the first cosmicstructures in our universe formed. Several million years after the Big Bang, small fluctuations in energy created the earliest lightand matter. Astronomers believe that, over billions of years, matter in the Universe clustered under the action of gravity, resultingin the complex cosmic structures observed today. Ma and her colleagues have simulated the billion-year evolution of fluctuationsin dark matter, photons, and neutrinos on a sub-galactic scale, illustrating the importance of complex second-order effects on thegrowth of cosmic structures. By comparing these simulations with astronomical observations, Ma hopes to unravel the past of ourearly universe—showing how intricate patterns of galaxies emerged from the cosmic ether.

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

Lisa R. Girard BLINKING BABY BLICKETS, BATMAN!

WEBS OF SPECIATION IN HAWAII

WORLD’S SMALLEST TRANSISTOR

BERKELEYs c i e n c e 5r e v i e w


Colin McCormick/BSR

Courtesy/Rosem

ary Gillespie

Cou

rtesy

/Chu

ng-P

ei M

a

GUIDING LIGHT

BILLIONS AND BILLIONS


Bayer and South San Francisco company Exelixis have completed genomesequencing of the tobacco budworm, a common insect pest. The new sequencewill allow scientists to develop novel and potent pesticides that specifically targetthe insect. Exelixis president George A. Scangos says, “This is the first timescientists can identify and screen important genetic targets derived from theagriculturally 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.

Biotech Beat

Emily Singer

Agricultural Pest Sequenced

WHAT’S HAPPENING IN BAY AREA BIOTECH

DNA-Based Drug Fights AllergiesDynavax Technologies reported a novel therapy that is effective in preventingallergic responses in mice. Researchers sensitized mice to ragweed, a commonseasonal allergen, and measured their allergic responses. The mice were then treatedwith ISS, a short immunostimulatory sequence of single-stranded DNA, combinedwith Amb a1, the main allergen component in ragweed pollen. After subsequentexposure to ragweed, mice that had undergone ISS therapy showed reducedallergic responses compared to controls. Scientists believe this drug combinationdiverts the immune system response away from harmful allergic reactions.

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

No More Morphine Jitters

Can too many doctors spoilthe surgery? Not accordingto UC Berkeley School of

Public Health graduate student MarlonMaus, whose latest paper in Neurosurgery

demonstrates the powerful benefits ofcollaboration among medical researchersfrom different fields.

“Cooperation among different specialtiesin medicine, and in science in general,often results in new ideas that are morethan the simple sum of the individualfactors,” says Maus, an oculoplasticsurgeon who has participated in such aprocess, directly witnessing its impressiveresults. Three years ago, Maus and acolleague, neurosurgeon WarrenGoldman, helped introduce the“transorbital craniotomy,” a revolutionarytechnique designed to improverecovery speed and minimize discomfortand scarring in patients undergoingbrain surgery.

The transorbital craniotomy wasdeveloped as part of a unique coopera-tive effort between neurosurgeons andophthalmologists at the NeurosensoryInstitute of the Wills Eye Hospital inPhiladelphia. There, Maus participatedin the Minimally Invasive SurgicalProgram, a group comprised primarilyof oculoplastic surgeons—specialists indiseases of the tissues that surround the

Jane McGonigal

eye, such as the optic nerve and theorbit (the opening containing the eyeand the surrounding muscle, fat andtear glands).

As an oculoplastic surgeon, Maus treatspatients afflicted by tumors that causedramatic vision loss by putting pressureon the optic nerve. “Before thetransorbital craniotomy was devised,surgery required a regular frontalcraniotomy, which involved shaving thehead, making a cut from ear to ear overthe top of the head, and peeling theforehead forward to be able to removea large portion of the frontal bone,” heexplains. In the transorbital craniotomya much smaller incision is made overthe brow. Then a small part of thefrontal bone is removed, along with theorbit. “Once the bone is removed, thebrain is retracted, or moved away from

the optic nerve, and the tumor is foundusing MRI images for guidance. Thisimage-guided approach allows a greatdeal of precision with very littleexposure of the brain itself. After thetumor is removed, the bone is replacedusing titanium screws and plates. Theincision is closed with stitches, andpatients are then taken to the intensivecare unit for recovery,” says Maus.

Maus and his collaborators studiedthe results of 72 patients on whomneurosurgeons used this surgicalapproach for various tumors of theorbit, brain, and sinuses. Accordingto Maus, transorbital craniotomyresults in shorter stays in the inten-sive care unit because there is lessunintended retraction, or dangerousbrain tissue deformation. Patientsrecover faster and in general describeless discomfort. “They are also veryhappy with the cosmetic results,since they do not have to have theirheads shaved and the scar is muchsmaller and not very noticeable onceit heals,” Maus says. He attributesthe success of the transorbitalcraniotomy to the breadth and depthof experience that interdisciplinarycollaboration has brought to theproblem of oculoplastic surgery.

SPLITTING HEADSCollaborating towards less

invasive brain surgery.

It only looks painful. The transorbitalcraniotomy removes less bone than conventionaltechniques and results in shorter hospital stays,less patient discomfort, and only a small amountof visible scarring. (Courtesy/Marlon Maus)

Current Briefs

Learn more:Neurosurgery

http://www.neurosurgery-online.com


In 1983, physicist RichardFeynman delivered a now-famousspeech challenging scientists and

engineers to think small. Twentyyears later, Feynman’s dreams ofdesigning and building of tiny machinesmade microscopic bearings, gears,flywheels, and motors have been broughtto fruition. Microelectronic mechanicalsystems (MEMS) are found everywheretoday, and the future applications arelimitless. Micro-accelerometers alreadytrigger car airbags and help steermodern jet liners. And researchers arenow developing tiny wired sensors todetect biochemical attacks, as well asmicrosurgical devices that can threadthrough capillaries.

But researchers face limitations in thedesign and implementation of MEMS.As machines get smaller, problems likefriction and “stiction” (the spontaneousand permanent adhesion of twosurfaces) arise. And technology movestowards machines on an atomic scale,researchers must grapple with theunpredictability of atomic interactions,which can make accurate and reliablemeasurements of the material propertiesof MEMS nearly impossible.

Merging the disciplines of appliedphysics, surface chemistry, and materialsengineering, UC Berkeley professorRoya Maboudian is steadily advancing the

great MEMS revolution. Her group inthe Department of Chemical Engineeringstudies material properties, perfor-mance-limiting phenomena, andperformance-enhancing coatings ofsilicon-based microdevices.

To address the problem of stiction, theMaboudian lab has pioneered thechemical modification of MEMS surfacesusing novel deposition techniques. Butresearchers must still struggle with thefact that atoms and particles interactdifferently on a small scale than on alarge scale. For example, a twelve-inchsilicon disk is brittle, and it willprobably fracture if you bend it toomuch. But apply twice as much stressto a twelve-micron silicon disk and itwon’t budge. Everything changes onthe microscale.

Measuring material properties on asmall scale is also problematic. Sincethe dawn of MEMS in the late 1980s,

Temina Madon

MICRO MACHINESTiny technology can cause

big research problems.

researchers have been trying todetermine the physical properties ofthese tiny devices. But properties likeelasticity, stress, friction, hardness, anddensity can’t be measured for amicroscopic sample using a human-scale apparatus. Even slight positioningerrors of microscopic samples in astandard lab setup can introduceenormous measurement errors.

To overcome these challenges, theMaboudian lab uses ultra-sensitivemeasurement and imaging techniqueslike electron microscopy and x-raydiffraction. Using these methods,Maboudian and her colleagues have beenable to measure the elastic modulus (theability of a material to resist bending) of asilicon lever just 125 microns long—only2.5 times the width of a human hair.

Ultimately, the Cal researchers hope toimplement complex MEMS like “lab-on-a-chip” analysis systems, biologicalimplants, and micro-power generators.With a number of exciting prototypesalready in development, they may soonbe able to shrink almost any problemdown to size.

Working the bugs out. RoyaMaboudian and her students are develop-ing techniques for testing the properties ofmicro-devices, like this tiny lock fabricatedby the Sandia National Laboratories’ MEMSdivision. A spider mite stands sentry overthe lock, showing scale.(Courtesy/Sandia National Laboratories,http://www.mems.sandia.gov)

Learn More:The Maboudian Lab

http://www.ccherm.berkeley.edu/~rmgrp/The Berkeley Microfabrication Lab

http://www-microlab.eecs.berkeley.edu/

Current Briefs



It has been nearly three decadessince the discovery of “Lucy,” achimpanzee-like primate who lived

in Ethiopia 3.6 million years ago. Yet asold as Lucy is, she lived three millionyears after the genetic split betweenchimpanzees and humans. Since Lucy’sdiscovery, paleontologists have searchedfor older protohumans in an effort tounderstand the origins of bipedalism andthe separation of early humans from theirape ancestors. In a series of recentdiscoveries, a pair of UC Berkeleyresearchers has finally begun to makeprogress on the question.

Working in the Middle Awash Valley ofEthiopia’s Afar Rift, Anthropologygraduate student Yohannes Haile-Selassi,Integrative Biology professor Tim White,and colleagues have found a series offossil deposits, the oldest group of whichcontains eleven specimens from at leastfive individuals. The specimens consist ofteeth, a partial jawbone, forearmsegments, a collarbone, one finger, andone toe. Based on nearby volcanic rockdeposits, the team dates the fossils tobetween 5.54 and 5.77 million yearsago—significantly older than Lucy. Theirfind fills an important gap in thepaleontological record. “In the early1990s we began to fill in some fossilsaround 4.4 (million years ago), but the

records were still very poor in comparisonto those in the three to four million-year-old range,” says White.

Paleontologists are now debating how toclassify the find. The Berkeley team hasstirred controversy by classifying thefossils as a new subspecies of hominid(a member of the human family hominidae),rather than as a chimpanzee. Theirconclusion is based on the lone footbone, which Haile-Selassi claims wasused to “toe-off ” in a manner unique tohabitual bipeds like ourselves. ExplainsWhite, “As you walk, your foot touchesthe ground first with the heel, and rollsforward onto the ball, through what wecall ‘flexion,’ and finally pushes off withthe toes. That toeing-off is the last thingthat happens with each stride. The shapeof the (toe) bone in this case indicates anadaptation to habitual bipedalism.”

However, the criteria for classification asa hominid are not widely agreed upon.According to White, “There are basicallytwo schools of thought as to hominid

WALK LIKE A MAN

New discoveries push backthe origin of bipedalism.

classification. One says that youshouldn’t call it a hominid without awhole suite of characteristics,

primarily bipedality.”Since Haile-Selassi andWhite’s finds exhibit amixture of primitiveapelike characteristics andevolutionarily newhumanlike traits shared bylater hominids, not allaspects of this suite arepresent. For the Berkeleyteam, says White, “The(hominid) classificationrelies on characteristics

shared exclusively with later hominids.So my definition is less functional, andmore cladistic (i.e., relying on compari-sons between ancestors anddescendants).” The team has dubbedthis subspecies Ardipithecus ramidus

kadabba. The name kadabba is from thelocal Afar language, meaning “basal” or“founding family ancestor.”

Classification of the fossils as hominidwould have important implications fortheories of bipedalism. Paleontologistspreviously held that bipedal walkingemerged in hominids as they spread outinto open, arid savannas. Yet chemicalanalysis in the Awash indicates that sixmillion years ago it was a lush, forested,upland area. Finding bipedal hominidsin such an environment would forcepaleontologists to revise currenttheories. “Previously people thoughtthat living in a savanna was an importantcorollary of the earliest hominids, butthese finds basically show that there’s nosuch correlation,” says White.

Yohannes Haile-Selassie and colleagues date the origin of bipe-dalism to more than 5.5 million years ago. (Eran Karmon/BSR)

[continued]

Noah Rolff

Current Briefs


White and Haile-Selassi are not alone inthe search for early hominids. Fossilfinds from the same period found by ajoint Kenyan-French research team inthe Tungen Hills of Kenya have asimilarly complex combination ofhuman and apelike traits. Those fossilsare of Orrorin tugenensis, a primate thatwalked bipedally in a manner moresimilar to modern humans than evenLucy, who is roughly two million yearsyounger. Could either Ardipithecus

ramidus kadabba or Orrorin tugenensis havebeen an ancestor to us all? Wherever

Ardipithecus ramidus kadabba finally settleson the evolutionary tree, White andHaile-Selassi’s finds, as well as those oftheir Kenyan and French counterparts,are bound to change the picture ofhumankind’s origin.

To learn more aboutWhite and Haile-Selassis most recentwork: Nature, 418, 145 (2002)

Book Review

Deep questions lurk just be-neath the surface of Sexual

Selections. Marlene Zuk,professor of biology at UC Riversideand a self-identified liberal feminist,challenges the idea that sociobiologyand feminist theory are by necessityideological opponents. By exposinglatent gender biases, Zuk believes,feminism can rid biology of untestedcultural assumptions that may keeplegitimate hypotheses from beingfully explored. Unlike sociobiology’smost severe critics, however, shebelieves that it is possible to scien-tifically study the evolutionary basisof human behavior. If done properly,she suggests, the comparative studyof sex in non-human animals mayeven contribute to our understandingof human sexuality.

Sexual Selections is divided into threemajor sections, each of which consists

of several different case studies thatillustrate Zuk’s point. In the first section,Zuk discusses ecofeminism, mother-hood, and sperm competition todemonstrate how a feminist perspectivemight lead evolutionary biologists toask provocative new questions. Thesecond section describes how popularbeliefs about animals and nature oftenprevent us from objectively seeing impor-tant evolutionary relationships. Foremostamong these myths is the belief in thescala naturae, the idea of an hierarchicalladder of life extending from the leastcomplicated organisms up to humans.The scala naturae, suggests Zuk, leadsus to assume that we need to studyadvanced primates and other organismsat the top rungs of the ladder to learnabout sexuality in humans. Withoutthe scala naturae, we are free to explorethe evolution of sex in response toenvironmental pressures in all organisms,particularly taking advantage of therich diversity of invertebrates. In thethird section, Zuk applies her ideas tofour controversial cases in the studyof the evolution of human sexuality:menstruation, homosexuality, femaleorgasm, and gender differences inmathematics performance.

Zuk convincingly demonstrates howa feminist perspective can contributeto evolutionary theorizing, but sheprovides little support for the idea that

EVOLUTION’S FEMINIST SIDE

Teddy Varno is a second-year graduate

student in the Department of History

at UC Berkeley.

Teddy Varno

biology has much to offer feminism.Instead, Zuk suggests that generalizingabout human sexuality based on animalexamples is a perilous undertaking bestavoided. The dissonance between Zuk’sthesis and the development of her ideasthrough the case studies gives Sexual Selections

an unfortunate ambiguity; each chapteris an interesting account in and of itself,but the three parts of the book do not buildto a coherent conclusion. Sexual Selections

is an entertaining read that covers manyintriguing topics and presents severalfertile ideas, but readers interestedprimarily in the relationship betweenfeminism and sociobiology would dobetter to look elsewhere.


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

Advertise in the BSR

Info at

sciencereview.berkeley.edu


At 6:30 AM, the fog begins to lift outside the GammaKnife Radiation Therapy Unit at the University ofCalifornia, San Francisco. Katherine lies on a gurney,

dressed in a paper-thin hospital gown. She has very little hairon her head; sutures from a past operation mark her scalp.Katherine is about to undergo Gamma Knife radiosurgery, atherapy that uses precisely targeted beams of gamma radiationlike a scalpel, cutting out brain tumors without the traumaand complications of conventional surgery.

“Last October, I started to feel that I wasn’t quite myself. Iforgot things sometimes, just the little strange things thatyou’re supposed to know, but nothing out of this world,”Katherine recalls. After an MRI, her doctor diagnosedmultiple brain metastases. A skin cancer that doctorsthought they had successfully removed from her leg had brokenup and spread to the brain via her lymphatic system and blood-stream. Over twenty tumors were found in Katherine’s brain.“We were both shocked. Even my doctor said she didn’texpect to see that,” Katherine says.

Conventional treatments for brain tumors involve chemo-therapy, which causes fatigue and nausea, and open-skull

surgery, where risks for hemorrhage and infection alwaysexist. With its precision, low risk of complications, andhigh success rate, Gamma Knife radiosurgery presents anattractive alternative. Gamma Knife targets beams of high-energy light (gamma rays) onto brain lesions. These beamsconverge on a point in the brain with such high intensity thatthey kill tumor cells, eliminating the need for a surgeon’s scalpel.Since there is no need to open the skull, virtually all patientsgo 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, whichdeliver small dosages of radiation over several sessions in thehope of killing tumor cells while sparing healthy ones.

CUTS LIKE A KNIFETreatingbrain tumorswithout thesurgeon’sscalpel.

The beams converge on a point in thebrain with such high intensity

that they kill tumor cells.

Aubrey Lau

Feature

Following the therapy, some of Katherine’s tumors stabilized,but others enlarged and spread. Her case was next broughtbefore the radiosurgery conference, a weekly meeting ofneuroradiologists, radiation oncologists, neurosurgeons, andmedical physicists, to determine whether Gamma Knifewould be a suitable treatment. Since Katherine’s numerousremaining tumors were small, the conference decidedKatherine would make a good candidate.

Several weeks after the conference, Katherine is ad-mitted for treatment. The first step of the procedure is

fitting a frame to her head. The frame secures her skullin place and ensures accurate targeting of brain lesionsduring treatment. MichaelMcDermott, Co-neurosur-gical Director of theGamma Knife radiosurgeryprogram at UCSF, adjuststhe frame to fit Katherine’shead and sets up what formost patients is the mostuncomfortable part of theprocedure—the injectionof local anesthesia into fourpoints of the skull via alarge needle. Katherinesticks a small piece of clothinto her mouth andclenches her teeth. Shemakes a fist, closes hereyes, and shakes her body alittle as each of the injec-tions enters a different sideof her head. “You’re almostdone, it’s just like when you’re at the dentist,” consolesJesse Merril, the nurse practitioner massaging Katherine’sshoulder. Anaesthetized, Katherine is ready for the insertionof pins into her skull through openings in each corner ofthe frame. This, as McDermott explains, is the only invasivecomponent of the procedure, as the titanium tips of thepins make small divots in the skull.

With the head frame secure, Katherine is brought to thescan room for magnetic resonance imaging (MRI). The scansprovide detailed information about where the tumors arerelative to the head frame. Unfortunately, these images havelimitations: they cannot differentiate between damage causedby 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 onthe brain is vital,” says Nancy Fischbein, Assistant Professorof Radiology at UCSF.

To gather more specific information, physicians often order amagnetic resonance spectroscopy (MRS) scan. This twenty-

minute procedure is per-formed alongside routineMRI scans. The MRS isunique because it pro-vides infor mation onspecific metabolites inthe bra in: chol ine, acomponent of the cellmembrane; N-acetylaspartate(NAA), a neuronal marker;and creatine, a metabolic in-dicator. High levels of cho-line indicate the breakdownof cell membranes, whilelow levels of NAA can be asign of neuronal damage.Both of these conditionssuggest the presence ofcancerous tumors.Fischbein notes that MRSalso has prognostic value. “I

can easily think of plenty of examples where MRI looks stablebut the spectroscopy shows changes,” she says, “and a few monthslater, the MRI catches up with the spectroscopy and it becomesclear that the patient did have a recurrent disease.”

After the scans, Katherine gets a break with her family in thewaiting room as neurosurgeons, medical physicists, and

MEDICINE


Zapping tumors. 201 beam of gamma radiation converge onto the tumor.Each individual beam is so weak that it can shine through healthy cellswithout damaging them, but the beams converge on the tumor with suchhigh intensity that they damage its DNA.

Feature


radiation oncologists discuss the most critical and laboriouspart of the treatment—the planning phase. The MRI imagesare entered into a computer program in the Gamma Knife TreatmentUnit. “One of the goals in treatment planning is to make theradiation dose conform to the target,” says Vernon Smith,Adjunct Professor of Radiation Oncology at UCSF. Radiationoncologists and neurosurgeons work together to decide whichareas of the brain should be targeted and which criticalstructures should be avoided. “I then use my knowledge todecide where to put what we call the ‘shot’,” Smith explains.

Since most brain lesions are irregularly shaped, multiple shotsof radiation are often needed for treatment. “You need to tryto fill the tumor up with spheres of radiation of different sizes—to decide how many spheres to use and where to put them, aswell as what dosage to use,” says Smith. Gamma Knife is uniquein its ability to target brain lesions for irradiation while sparinghealthy cells. Since the gamma rays come from 201 individualsources, a beam of radiation from a single source contributesonly approximately half a percent of the total dose. Throughstrategic 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 theirtarget that their combined energy becomes high enough todamage tissues.

After several hours of meticulous calculations, Katherine’streatment plan is ready. Because she has a large of number ofmetastases in her brain, doctors decide that only some of themcan be treated that day. Ten shots of radiation are prescribed totarget the seven largest metastases.

Katherine is led to the treatment unit. As she lies down on thetreatment couch, her head frame is attached to a collimator, acircular metal device that resembles a helmet with the topcut off. Evenly distributed over the collimator are 201 openingsthrough which gamma rays will be delivered. The head frameis attached to the collimator according to the three-dimensionalcoordinates set during planning. To minimize errors, thepositioning of Katherine’s head is checked independentlyby three different people. An intercom system allows her tocommunicate with the personnel in the control room, who

Guiding the knife. The collimator isattached to the patient’s head frame. It has201 holes that guide the gamma beams.Depending on the dose of radiation admin-istered, collimators with different hole sizesare used. (Aubrey Lau/BSR)

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 inconstant contact with the patient via a microphone and speaker system. (Aubrey Lau/BSR)

Aubrey Lau received a BA in Integrative Biology

from UC Berkeley in 2000. She is currently a

research associate at UCSF.

MEDICINE


keep her informed of the progress of the treatment. Afterall staff have left the treatment room, closing the doorbehind them, the radiation treatment commences. It lastsfor two hours, during which time collimators of various sizesare switched a few times to allow radiation beams ofdifferent size to attack the lesions.

The success rate of Gamma Knife treatment is impressive. McDermott notes that it depends on the type of

brain lesion: “For arteriovenous malformations, collections oftangled abnormal blood vessels, it depends on the size – small:80-85% (success), medium: 70-75%, large: 50%. Fortrigeminal neuralgia, a dysfunction of cranial nerve V, over90% of cases experience pain relief four to six weeks aftersurgery.” Remission time, or the length of time for whichthe tumor ceases to grow, depends on the tumor grade. Ingeneral, tumors with the highest grade are characterized byextensive infiltration into the brain tissues and a rapid spread.As McDermott notes, high grade tumors have a remissionof four to six weeks, as opposed to low grade tumors, where aremission time of ten to twelve months is observed.

Gamma Knife also has limitations. The major one is that theprocedure is only effective on tumors smaller than 3 cm.Radiation can kill both healthy and cancerous cells, so as theradiation dosage increases to compensate for the tumor’s size,more healthy cells are killed and the therapeutic value of thetreatment is reduced. “As you increase the volume of thetumor being treated, you have to decrease the dose,” notesMcDermott. “And once you get to a very large volume thedose starts to become so small that it is ineffective.” The locationand spread of the tumor are also factors. They must not beclose to critical structures like the optic chiasm, damage towhich would cause blindness, or the brainstem, which iscrossed by several critical nerve fibers. Gamma Knife radio-therapy is also not recommended for patients whose tumorshave infiltrated the ependyma, a one-cell-thick layer that linesthe ventricles of the brain. After reaching these ventricles,cancerous cells can spread along the central canal of thespinal cord, rendering radiotherapy ineffective.

It has been over ten hours since Katherine arrived at thehospital. The evening fog is already beginning to set in. During

the break before the last part of her treatment, Katherine’shusband gingerly takes her hand to walk her around the waitingroom. She takes a sip of water. He adjusts the ties behind hergown. Although today’s treatment has been long, Katherine isalmost ready to go home. Thanks to the non-invasive natureof Gamma Knife radiosurgery, she can rest in the comfort ofher own home with her family tonight.

Frame of reference. A physician fixes a frame onto a Gamma Knifepatient’s head. The frame is held in place by titanium screws in thepatient’s skull. Neuroradiologists use the frame as a precise coordinatesystem for guiding radiation beams to the tumor.


Architects have been mapping cities and land-scapes since the 16th century, constructingimagined 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 onblimps, helicopters, and satellite images to provide alook from above. But Professor Charles Benton, Chairof 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 filmfrom a kite’s-eye view. This year, he plans to organize a KAP seminar to train students and colleagues in thistechnique for aerial photography.

Benton says that KAP “gives you a view of the familiar from a place that you often can’t occupy.” Even conventionalaerial 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 willget you started for an outlay of less than $25. Of course, the rigs can quickly become elaborate, costing thousands ofdollars and incorporating video transmitters, receivers, monitors, and more.

Reviving kite aerialphotography.

Feature

Temina Madon

THE SKY’S THE LIMIT

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.”

ART MEETS SCIENCE


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/.

Feature


“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.

ART MEETS SCIENCE


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.

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

Temina Madon is a fifth-year student in the VisionScience graduate group at UC Berkeley.

Feature



Weird Science

Here at UC Berkeley we get a lot of curious correspondence. It ranges from exorbitant requests forinformation—“Please send me scientific data on quantum mechanics.”—to the oddly macabre—“I justdetected the odor of subtle error in relativity, but I’m not sure where the corpse is hidden.” Letters arrivetypewritten, handwritten, and even (according to legend) written in blood. A brief selection of the moreinteresting 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 Lightfor sure !!!” because a basic assumption of Einstein’s relativity “istotally WRONG!” In fact, “There exists NO relativity. The wholetheories of relativities are totally artificially man-made. Thank youvery 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 understandthe universe in terms of elementary particle physics and quantummechanics one will be illiterate.” Bad news for the English majors. Italso sums up “All of Physics” in just 28 words: “Right Hand and LeftHand branes and quarks inventory and exchange the N-particle. A quarkis 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.

Fiat Lux

In further relativity news, longtime Berkeley resident “Pastor Glen” recently distributed his magnum opus,

Adventures With Phebe The Photon, or, Having Fun With Time Dilation! at select locations on campus. It openswith 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’sspace-time diagrams? “‘Besides,’ Phebe sniffs, ‘that diagram is ALL WRONG about me!’”

Colin McCormick

MAIL CALL

Aaron Golub/BSR

Aaron G

olub/BSR


Hundreds of colorful fish dart chaotically in andaround a canopy made of millions of branchingfingers of pink, green, and brown coral. Above the

surface, an Indonesian man in a small wooden boat throws ahomemade bomb overboard. It arcs through the air and hitsthe warm blue water. A moment passes, then a fountain ofwater sprays up. In the silence that follows, a few fishcarcasses float to the surface, while many more sink to theocean floor, blanketing a crater in the shattered coral reef.Blast fishing, as this illegal practice is known, earns thisfisherman about eight dollars a day—five times theaverage daily wage in Indonesia.

Blast fishing is just one of many human activities that arerapidly destroying coral reefs. Studies by the Global CoralReef Monitoring Network (GCRMN) show than 11% of reefs

CONSTRUCTING CORALThe world’s reefsare disappearing.How do we stem

the tide?

As much as half of theworld’s remaining

coral reefs will be lostby 2010.

Sneha Desai

Feature

Helen Fox

worldwide, and as many as 30%-60% of reefs in certainareas, 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 takeover a hundred years to recover naturally—if they canrecover at all.

GCRMN predicts that as much as half of the world’sremaining coral reefs will be lost by 2010. The loss ofthese reefs would mean not only extinction for hundreds—possibly thousands—of species, but also a catastrophic lossof food and income in coastal communities and the disappear-ance of unique chemicals that have great potential for in-dustrial and medical use.

Researchers have only just begun to make inquiries about thebasic science of coral organisms within the past five years, spurredin part by increased awareness ofthe rapid destruction of reefs. Butcoral reef restoration and thecomplex factors that impact areef’s health are still poorly under-stood. The reef ecosystem iscomprised not only of coral, butalso of 32 of the 34 known phylaof animals. Their mutuallydependent interactions, as wellas seasonal and climatic effects,generate an immensely compli-cated ecosystem. Moreover,changes that could accelerate

coral re-growth and ensure the health of a reef have barelybeen tested.

In 1998, Helen Fox, a PhD candidate in the Department ofIntegrative Biology, began testing several low-cost methods

for providing coral reef restoration in eastern Indonesia’sKomodo National Park, where blast fishing had been practiced

regularly until 1996.“In Komodo, there is acontrast between beautiful,

incredible diving (reefs) and areasthat have nothing there, just huge rubble fields,”

Fox says. The close proximity of rubble fields andneighboring healthy reefs along with present-day bans on blast fish-ing in the area provides an ideal site for Fox’s experiments.

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

The potential economic gain for tourism industriesfrom healthy reefs is a powerful motivation forconservation as well as restoration.

ENVIRONMENT


Lost forever? Full and vibrant reefs take cen-turies to form and are being destroyed at analarming pace. Conservation alone may notbe enough to reverse the trend; artificial reefrebuilding may be necessary, too.(©2001 www.ecoreefs.com; Helen Fox)


Featurereef, a stable anchoring place for the larvae must beartificially created.

Fox’s experiments tested low-tech, inexpensive, and locallyavailable materials as stabilizers for the shifting coral rubbleand as substrate for larval recruits. She prepared several smallrubble field sites, each with three different stabilizationmethods: rock piles, netting over the rubble, and cement slabs.After revisiting the sites over two seasons, Fox found that therock piles most successfully attracted and maintained recruits,so she started a larger trial. Her research has attractedsupport from the Nature Conservancy and funding from thePackard Foundation. The Nature Conservancy is currentlyundertaking a large-scale study of Fox’s rock pile substrateover two hectares of ocean floor.

Former Berkeley graduate student Michael Moore istrying a different strategy: targeting the tourism industry.

Moore recently founded EcoReefs, a company that developsreef-restoration technologies. Fox serves as an informalscience advisor for Ecoreefs. Moore, who received his PhD

in Integrative Biology in 1995, hopes tosell his patented coral reef restorationmethod to dive operators, beachfronthotels, and local governments worldwide.

Coral reef restoration became a concernof Moore’s in the late 1980s, when he wasconducting oceanographic research inIndonesia and saw that reefs were beingannihilated. After graduate school Mooreworked at the Scripps Institute of Ocean-ography in San Diego, and then joinedthe 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. Asa marine researcher, he had been awarethat coral scientists use ceramic tiles,which are pH neutral, to attract corallarvae and measure local coral population.Moore’s innovation was to create a 3Dhexagonal ceramic module that couldbe mass-produced and assembled at arestoration site.

In 2001, Moore patented the design and left the dot-com com-pany to devote his time to EcoReefs. “Most of my engineerfriends 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 smallarea of damaged reef in Bunaken National Park, which is nearKomodo. The design successfully mimicked the complexarchitecture of a natural reef and provided habitat for adultand juvenile fish—especially herbivorous fish that eat the algaeand soft coral that compete with reef-building coral larvae forsettlement space. The ceramic modules also quickly attractedred crustose algae, an important precursor species that signalsto the larvae that substrate is available. Moore is currently show-ing the promising results from the test site to potential clients.

Cheap fix. Integrative Biology graduate student Helen Fox hopesthat inexpensive materials like rocks or netting can help rebuilddamaged reefs. (Gideon Weisberg/BSR)

Building an artificial reef. Michaeand provide habitat for adult and

Learn More:

Coral Health and Monitoring Program http://www.coral.noaa.govCoral Reef Alliance http://www.coralreefalliance.orgEcoreefs http://www.ecoreefs.comKomodo National Park http://www.komodonationalpark.org

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.

ENVIRONMENT


el Moore places one of his reef restoration modules in a bed of damaged coral. The modules attract coral larvaed juvenile fish. (©2001 www.ecoreefs.com)

The potential economic gain for tourism industriesfrom healthy reefs is a powerful motivation for

conservation as well as restoration, according to JanineKraus, Managing Director for the Coral Reef Alliance(CORAL), a non-profit organization that works with thedive industry and other constituents to conserve coral reefs.CORAL recently gave a micro-grant to an Indonesiannon-governmental organization that works towards providingblast fishers with alternative livelihoods in the tourism

industry. Kraus believes continuedconservation efforts are at least asimportant as developing new resto-ration technology. “Reefs are beingdestroyed so rapidly. We need tofocus on keeping what’s there, stop-ping this bleeding. There is a role forrestoration, but it’s very expensive,and we choose to focus our resourceselsewhere,” she says.

There is some tension between thereef conservation and reef restorationcamps, but this should hopefullyproduce a variety of strategies fordealing with what everyone agreesis a dire situation. While decreasingthe rate of destruction remains thetop priority for Kraus, Fox andMoore are laying a foundation that willbe sorely needed once conservationalone becomes insufficient. “If wedon’t start doing research now onthe tools we need to restore reefs,we won’t be ready,” says Moore.Without more research on coral

reef restoration, Moore predicts, it will be like having torebuild a clear-cut forest without “knowing anything abouthow to plant trees.”


DARWIN OR DOGMA?

Y ou can find them at PTA meetings or UCBerkeley seminars: pink and blue bookmarks entitled “Ten Questions to Ask Your Biology

Teacher About Evolution.” These colorful little freebies seemdesigned to excite kids about science fairs and collecting fos-sils, but they’re actually the latest salvo in an escalating battleto keep evolutionary theory out of public schools.

The Ten Questions have a clear bias against evolution: “Why dotextbooks use pictures of peppered moths camouflaged on treetrunks as evidence for natural selection—when biologists haveknown since the 1980s that the moths don’t normally rest ontree trunks, and all the pictures have been staged? Why do text-books use drawings of similarities in vertebrate embryos asevidence for their common ancestry—even though biologists haveknown for over a century that vertebrate embryos are not most similarin their early stages, and the drawings are faked?”

Even biologists may find it tough to marshal specific evidence to refutethese accusations—not surprising, since a biologist wrote them. Thebookmark’s creator is Jonathan Wells, author of Icons of Evolution, whoholds a PhD in Molecular and Cell Biology from UC Berkeley and also aPhD in Religious Studies from Yale University.

Judy Scotchmoor, Director of Museum Relations at Berkeley’s UC Museumof 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 teachersrespond to the Ten Questions, and other questions like them, UCMP is collaborating with the NationalScience 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.

Why teaching evolutionis more controversialthan ever.

The University

Jessica Palmer

When it debuts in 2003, http://evolution.berkeley.edu will be aone-stop shopping center for science teachers, saysScotchmoor. It will offer background information, lessonplans, and other tools to deal with the controversy surroundingevolution education, including the NCSE’s rebuttal ofWells’s Ten Questions.

The mess in Kansas

During the past few decades, evolution’s place in publicschool curricula has seemed secure. It’s difficult to teachgeology, biochemistry, or ecology without mentioning Darwinor the theory he founded. As renowned geneticist TheodosiusDobzhansky noted in a 1973 essay, “Nothing in biology makessense except in the light of evolution.”

Then, in 1999, the Kansas State Board of Education cutevolution from the state science curriculum. Kansas didn’toutlaw evolution, but by ensuring students would never betested on it, the state withdrew support for the theory. Anoutcry from the science community immediately followed.“We can thank the mess in Kansas for opening our eyes thatsomething had to be done,” says UCMP’s Scotchmoor.

At the time of the Kansas controversy, it had been severaldecades since the teaching of evolution was seriously threatenedin the US. Tennessee’s Butler Act of 1925, which precipitatedthe Scopes Trial, explicitly banned from the classroom “anytheory that denies the divine creation of man and teachesinstead that man has descended from a lower order of animals.”In a 1968 case, the US Supreme Court ruled all bans on teachingevolution unconstitutional. In 1987, it struck down a lawmandating equal time for creationism in the classroom.

These legal decisions forced evolution’s opponents to rede-fine their goals and methods. Now, rather than arguingfor creationism, critics argue against evolution—especially its

role in the origin of life on Earth. Just like Wells’s little bluebookmark, they object to evidence of evolution, to the way itis taught, and to its philosophical and religious implications.In Kansas, and most recently in Ohio, these groups are makingthemselves heard.

The most vocal anti-evolution movement, which calls itselfIntelligent Design (ID), began at UC Berkeley. Professor ofLaw Phillip Johnson argued in his 1991 book Darwin On Trial

that evolutionary theory was “pseudoscience.” Johnson judgesnatural selection to have a real, but overvalued, effect. “Theappearance of innovations like new complex organs or bodyplans,” he says, “cannot be explained adequately withoutallowing for intelligent causes”—that is, an intelligentdesign or blueprint for life.

Darwin himself had been amazed by the power of naturalselection to assemble a complex eye, not just once, but severaltimes in different animal lineages. Many scientists privatelyreconcile 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 alternativetheory to evolution in state science curricula.

Science educators hold that there is no scientific alternativeto evolution. ID, they say, is just another variation oncreationism. But Johnson insists that the evolution campitself has a religious agenda, because it promotes a “naturalisticworldview,” and that educators must “teach the controversy.”

Vocal critics like Gary Demar, president of the creationistorganization American Vision, say evolution is also unscien-tific: “You can’t apply the scientific method to evolution. It’snever been observed. You can’t repeat the experiment. Andso what’s being sold as science, in terms of evolution, reallyisn’t science in terms of the way they define it.”

The Alabama Disclaimer makesevolution sound like the brainchild

of a scientific lunatic fringe.

“Where the big confusion lies isthat people don’t have the basic

knowledge of how science works.”


“You can’t apply the scientific methodto evolution. It’s never been observed.

You can’t repeat the experiment.”


Theory, not fact

A few years before the Kansas controversy, Alabama legislatorslabeled their state’s biology textbooks with this disclaimer: “Thistextbook discusses evolution, a controversial theory somescientists present as a scientificexplanation for the origin of liv-ing things, such as plants, animals,and humans. No one was presentwhen life first appeared on Earth.Therefore any statement about life’s origins should be consid-ered as theory, not fact.”

The Alabama Disclaimer makes evolution sound like thebrainchild of a scientific lunatic fringe. But the thrust of itsargument, that evolution should be taught as “theory, notfact,” is perfectly agreeable to most scientists. Evolution is atheory. As evolutionist Dobzhansky stated, “A theory can beverified by a mass of facts, but it becomes a proven theory,not a fact.” In the same vein, Wells’s bookmark asks, “Whyare we told that Darwin’s theory of evolution is a scientificfact—even though many of its claims are based on misrepresen-tations of the facts?” In 2001, Kansas’s revised science standardsoutlined similar concerns: “Science studies naturalphenomena by formulating explanations that can be testedagainst the natural world. Some scientific concepts andtheories (e.g. cosmological and biological evolution, etc.)may differ from the teachings of a student’s religious com-munity or their cultural beliefs. Compelling student beliefis inconsistent with the goal of education. Nothing in sci-ence or any other field should be taught dogmatically.”

No qualified scientist or educator would teach dogmatically,

or compel student belief. Although the Alabama Disclaimerand the Kansas standards were motivated by concern overwhether evolution is good science, they appropriately questionwhat constitutes good science education in general. Scienceis an interrogative process of critical thinking, and if it’s not taught

that way—in evolution or anyother area—it’s a problem.

Unfortunately, these aspects ofscience are not emphasized

strongly enough or often enough in the classroom or the media.The mainstream public doesn’t have a clear picture of whatscientific inquiry is. As a result, evolution’s critics get awaywith battling straw men, while the science community iseither oblivious to the debate or baffled by it. “Where the bigconfusion lies is that people don’t have the basic knowledge ofhow science works. They can’t look at Intelligent Designor the old Creation Science or whatever they will come upwith next, and recognize that that’s not science,” saysUCMP’s Scotchmoor.

Such attempts to confuse the issue aren’t new. In 1973,Dobzhansky observed, “Disagreements and clashes of opinionare rife among biologists, as they should be in a living and growingscience. Anti-evolutionists mistake, or pretend to mistake,these disagreements as indications of the dubiousness ofthe entire doctrine of evolution.” It’s alarming that in threedecades, the situation hasn’t gotten any better.

True or False?

According to the National Science Foundation’s latest biennialreport, Science and Engineering Indicators 2002, nine out of

The University

Kansas didn’t outlaw evolution, but by ensuringstudents would never be tested on it, the state

withdrew support for the theory.


ten American adults are interested in learning about scienceand scientific discoveries. But apparently they haven’t learnedmuch: only 54% know it takes a year for the Earth to orbitthe sun. Half the American public thinks early humans haddinosaurs for neighbors.

However, the nation’smost prominent scien-tific organizations maybe guilty of oversimpli-fication. NSF’s surveys included 13 true/false questions.Along with uncontroversial statements like “All radioactivityis man-made (false),” NSF asked “The universe began with ahuge explosion (true),” and “Human beings, as we knowthem today, developed from earlier species of animals(true).” Adults with a high level of science education whootherwise did well (92% answered the radioactivity questioncorrectly) performed much worse on the latter two questions(50% and 69% correct, respectively). And 2001 was the firstyear that the majority of American adults of all educational back-grounds answered the evolution question correctly (53%, upfrom 45% in 1999).

So what can we learn from the NSF survey results? NSF hassuggested, “Responses to these two questions may reflect reli-gious beliefs rather than actual knowledge about science.”Perhaps, but in addition, because true/false questions imposeartificial dichotomies, they are arguably an inappropriate wayto discuss theories, which can never become facts. If theoriescan never be facts, shouldn’t we be careful about describingthem as true or false?

Oversimplification is part of the problem in public education

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

says Scotchmoor.

Reductionist language isan alarming characteris-tic of popular science. If

the public constantly hears evolution, global warming, or thesafety of prescription drugs described in yes/no, true/falseterms, then it’s not surprising that nearly three-quarters ofAmerican adults don’t understand the scientific process.

What did T. rex taste like?

Al Janulaw, former President of the California Science TeachersAssociation and a middle school teacher with 32 years ofscience teaching experience, thinks the problem can be fixedin the schools. “We have a very scientifically illiterate public,and today’s high school students are tomorrow’s public.”

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 elementaryteachers, these teachers harbor the same misconceptionsabout the history of the Earth and mechanisms of evolutionthat the average citizen does. It’s not going to serve the teachersor their students well if they don’t understand it any better thanthe kids and their parents do.”

Jessica Palmer/BSR


The Designer’s Advocate

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

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

Phillip Johnson: Yes, very often. Our educators teach science as a process of learning facts, rather than applyingcritical thinking skills to scientific claims, which in many cases are speculative and linked with ideology. Sciencejournalists have the same education, and cannot afford to lose access to the most influential scientists, so theyreport 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 maynot consider all the possibilities, but must restrict themselves to those which are consistent with a strict philosophicalnaturalism.” 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 witha naturalistic worldview. What I most object to is that they conceal their philosophical assumptions and claimimmense creative power for the Darwinian mechanism, for example, as if this claim were based on empiricaltesting, 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 evidencewherever it leads, even if it leads to conclusions they do not welcome. As it is, they promulgate naturalism andDarwinism 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 educationstatute states an excellent principle for science education that should be followed even if it did not have the effectof law. It says that a good science education should teach students to distinguish between the testable theories ofscience and religious or philosophical claims made in the name of science. Where controversial subjects likebiological 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 thesesound 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 anydebate. They seem to be afraid of what will happen if the subject is not kept safely within their own professionalterritory, where they control the definitions and assumptions.

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

The University


The key to teaching evolution right, says Janulaw, is teachingcritical thinking first. “This is about thinking scientifically. Thenwhen the students arrive in sixth grade and someone men-tions the ‘E-word,’ or the idea of evolution or the history ofthe planet, these kids are already doing critical thinking. They’realready empiricists. The truth is, I can’t tell a seven-year-oldthe history of life on Earth without telling it dogmatically. Sowe don’t do it. What we try to do is build these skills, so thekid can understand it when it comes along.”

To do this, the Understanding Evolution project builds onthe pedagogical resources of an earlier NSF/UCMP project,“Explorations Through Time,” which provides field-testedteaching 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 ideais 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. TheAmerican Association for the Advancement of Science’s Project2061 found in 2000 that even high school biology textbooksdon’t cover central concepts like the nature of science insufficient depth. Scotchmoor agrees: “A lot of us teachershave this pet peeve about the way the scientific method is shownin textbooks: steps one, two, three, four, five, conclusion, jobdone. 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 EllenRoseman, director of Project 2061, says “While most (text-books) contain the relevant content on heredity and natural

selection, they don’t help students learn it or help teachersteach it.” Wells’s 10 Questions bookmark, though strident,makes an excellent point—textbooks do present the same oldstories and figures over and over, often in a misleading way orwithout context. Wells’s mistake lies in equating the theory ofevolution with the poor way in which it is often taught.

Janulaw concludes, “To get kids to deal with the tentativenessand open-endedness and need for further study—the natureof science—first you need to get the teachers there. And Idon’t think they are.” The American public isn’t “there” either.It’s frustrating for scientists when the media misrepresents astudy or when parents object to evolution in their child’s cur-riculum. But who, if not the scientific community, is ultimatelyresponsible for informing the public about science? Scotchmoorsays, “We, the scientists, are not very good at this, you know—we’re still learning. We need to be more proactive and realizethat sharing research and science with the public is essential.”

It may be hard to take, but scientists and science educatorshave a lot to learn from evolution’s critics. We must reconsiderhow science is taught in schools and explained to the public. Weneed to weed bad science out of textbooks, teach children tothink critically, and learn to answer those Ten Questionsourselves—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 http://www.natcenscied.orgNSF Science and Engineering Indicators 2002 http://www.nsf.gov/sbe/srs/seind02/start.htmUC Museum of Paleontology http://www.ucmp.berkeley.eduUnderstanding Evolution http://evolution.berkeley.eduWells’s Ten Questions http://www.iconsofevolution.com/tools/questions.php3


Some time ago, in the center of the Sun, two hydrogenatoms traveling at enormous velocities were headed ona 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 incredibleseries of coincidences, the photon managed to travel on acourse that brought it all the way to the Earth, until it finallyslammed into my arm. And I didn’t even feel it.

This is how we usually think of cause and effect. The collisionof the two particles caused the photon to be created and fly offin the direction that it did. My arm blocked the photon,thereby prevent-ing it from reach-ing the ground.We would neversay that the re-verse was true: that my arm caused the photon, and that itssubsequent absorption by a particle in the Sun led to theformation of two hydrogen nuclei. Why not? After all, thelaws of physics are (for the most part) time-symmetric. If aprocess is allowed by the laws of physics, its reverse must alsobe allowed. So as far as I can tell, it should be possible for myarm to make light. That it doesn’t is obvious to anyone who’sever 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 effectexist only in the minds of humans and aren’t actually a part ofthe objective world. Cause and effect are just abstractions weuse to describe events that we always see happening one afterthe other, and never the other after one. All we need to do,then, is explain why there are events that always occur in thesame temporal order.

Relativity 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 thephoton hit my arm?” we should ask “How long ‘til the photonhits my arm?” Instead of a law of motion, Einstein gives us a“law of distance,” which we call a “metric.” Famously, the met-ric is defined on a four-dimensional space, where three of thedimensions are space and the fourth is time: the metric doesn’tonly give us distances in space, but also in time. Further, theso-called “space-time distance” to an object is dependent on

the properties ofthe object in ques-tion—its mass andenergy. At somelevel this seems

right: to figure out how far away something is in time, we’dbetter take into account how fast it’s going. More famouslystill, though, it turns out that for objects traveling at the speedof light (like my arm-smashing photon) time stands still.Viewed in this light, the notion of cause preceding effectdoesn’t make any sense.

Time is bunk. So why do we humans perceive time in thewildly mistaken, but incredibly useful way that we do? Oneintriguing answer is that our perception—and perhaps thusour conception—of time comes from the evolutionary benefitto having a simple way to make predictions about ourenvironment. It’s nice to know that throwing a spear at some-thing will probably cause it to drop dead.

But are we really ready to accept that time and causalityare subjective—that they arise because we view the world

BACK TO THE FUTUREThe last angry man travels through time.

Perspective

Alan Moses

Car windows would spontaneously come back togetherand wallets would return to glove compartments. Of

course, the cash would still be gone.

from a limited perspective? I don’t think we should giveup so easily. All we need to do is find some process thatoccurs in accordance with the objective laws of physics butshows bias towards either the future or the past. Itshouldn’t be that hard.

Let’s consider obviously temporal processes. Let’s also forgetabout photons for a minute just to keep us from getting fouledup by relativity—or worse, relativism. Processes that go oneway but don’t happen the other way are called “irreversible.”Most irreversible processes fall under a less elegant, almostpractical branch of physics called thermodynamics. The sec-ond law of thermodynamics gives processes directionality intime by stipulating the eventual increase of a pesky quantitycalled entropy. There are several competing interpretationsof what this magic quantity is, and it hasbeen loosely translated as “disorder” oreven “chaos.” Any of these gives thesecond law in its pop form: order pro-ceeds to chaos. My car window can besmashed into tiny pieces, but the tinypieces will never get up and re-form intomy car window. You can’t go from a moredisordered state to an ordered one—it’s against the law. Otherwise car win-dows could spontaneously come back together and walletswould return to glove compartments. Of course, the cashwould still be gone.

In his 1996 book, Time’s Arrow and Archimedes’ Point, Austra-lian philosopher Huw Price suggests we take a closer look

at what the second law actually says before jumping on thesecond-law-gives-objective-direction-of-time bandwagon. Inthe form most widely accepted by physicists, the second lawsays that if all the particles of the window are simply followingthe laws of motion, they are much more likely to end up in anarrangement (or configuration) that corresponds to a “shattered”state. The argument is simply probabilistic: shattered statesare the overwhelming majority of the possible configurationsfor the particles that make up the window, and the particlesdon’t have any preference to whether their bulk macroscopicstate is shattered or not. So, says physics, it’s not that it’simpossible for shattered windows to re-form, it’s justvery unlikely.

Price, however, points out the following oversight: Entropycertainly increases towards the future—the second law andall of our experience says so, but what about the past? Whydoes entropy seem to decrease as we look back in time? Runthe tape backwards, and disordered piles of smashed glassturn 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 tothe search-for-objectivity drawing board.

In Order out of Chaos, Ilya Prigogine describes what he callsthe “subjective interpretation of irreversibility.” The

reason that there are so few microscopic configurations inthe past—in other words, that theentropy was low—is because we candescribe the past with relative certainty.We saw it happen or there’s some sort ofevidence that points us in the right direc-tion. As we try to predict the future, thelimited information we have becomes lessand less adequate. Finally, we just cutbait and concede that all the microscopicstates are equally probable—the entropy

is maximal. Ask me if it rained yesterday, and I can give youa decent answer. But will it rain a week from today? A month?A year? Hell, you got me. Anything could happen. So thereason the past looks nice and tidy and the future looksentropic and jumbly is that our knowledge of the futureis 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 thelittle hooligan did my previously tidily arranged windowparticles start spending all their time in shattered configurations!OK, I’m getting a little agitated thinking about the repairbill, so let’s put that smashed window out of our minds. Let’sjust think about a simple two-dimensional square that’s fullof particles bouncing around (but with all their motionconfined to the plane). Further, let’s put the whole thing in asealed box. The particles on the plane will spread themselvesout evenly because there are vastly more configurations that


Alan Moses is a third-year student in the Biophysics GraduateGroup at UC Berkeley.


Perspectivecorrespond to spread-out distributions than clumped ones(that’s why the air in most rooms is usually not all bunchedup in one corner). The “window” (plane) seems to be inequilibrium, and it should remain in that state indefinitely.

Now, let’s go ahead and replace the punk kid with a tiny wingeddemon that’s capable of manipulating particles with extremecare. The demon walks around for a bit and then chooses aparticle at random and gives it the tiniest, smallest, mostminute push up out of the plane. Then the demon picksanother particle and gives that one the tiniest, smallest, mostminute push down out of the plane. We’ll call that tiny amounte, so that the demon added e momentum to the first particleand subtracted e momentum from the second particle, leavingthe total momentum in the box completely unchanged.If the box that we have the window in is small and its wallsare perfectly bouncy, those first two particles that the demonset bouncing around will collide with other particles in theplane and pretty soon the box is going to be full of particleswhizzing every which way. The original equilibrium—whenthe particles were spread out over the plane—is disruptedand the system approaches a new equilibrium, where the

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 goback 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 entropywas high. But the demon, very simply, was able to presentthe particles with previously unreachable configurations.Once available, the particles had no choice but to explorethem. I don’t think there’s anything subjective here: thepast is pulled into the future by the vast expanse of newpossibilities. So maybe we humans aren’t so misled. Afterall, time is money.


Quanta (heard on campus)

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

Neal Lane, ProfessorDepartment of Physics and AstronomyRice UniversityFormer Director of the NSF andthe White House Office of Science and Technology PolicyApril 18, 2002

“If you’ve developed a theory of cosmology or of atomic physics that makessense, it’s probably wrong. I doubt that you could bring up a child in a wayso that it would feel comfortable with quantum mechanics. I think (the kid)would be insane.”

Gunther Stent, ProfessorDepartment of Molecular and Cellular BiologyUC BerkeleyAuthor of Nazis, Women, and Molecular BiologyMay 8, 2002

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

Jeffrey Sachs, DirectorCenter for International DevelopmentHarvard UniversityApril 21, 2002

Got a great story?Write for the Review.Submission guidelines are at sciencereview.berkeley.edu

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The Back Page

Take a narrow piece of paper, twist it, tape together the ends, and you’vechanged 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 specializesin 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 tocheating slightly. “A true Klein bottle can only exist infour dimensions, and alas, our universe has only three spatialdimensions.” Stohl really makes a “3-D immersion” of the4-D shape. Just as a photograph is a 2-D immersion of a3-D object, Stoll explains, “our Klein bottle is a 3-Dphotograph of a true Klein bottle.” Fortunately forKlein enthusiasts, the most paradoxical quality of thebottle survives this dimensional transformation. “Ithas no edge. It’s boundary-free, and an ant canwalk across the entire surface without evercrossing an edge.”

So far, Stoll’s backyard business has soldmore than 300 bottles and awarded fourannual Klein Bottle Awards to researchersin the field of topology. Acme’s latesteffort is a collaboration to build theworld’s largest Klein bottle, whichwill stand one meter high. “It will be thesize of a five-year old child and a ferret will be able tocrawl into it,” Stoll gleefully predicts.

INSIDE OUT WITHCLIFFORD STOLL

Mobius madness overtakes a local scientist.

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

Jane McGonigal

Berkeley Science Review - Fall 2002

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Transcript of Berkeley Science Review - Fall 2002