Fall 2011 Issue 21

sciencereview.berkeley.edu

Digitizingthe Drawers

36 There’s a map for thatAlgorithms to ease your commute

28 Innate altruismThe psychology of good behavior

20 QB3 GarageStart-ups get a space of their own

Fall 2011 1Berkeley Science Review

Dear readers,

Welcome to the 21st issue of the Berkeley Science Review. As we saw when this year’s Nobel prizes were awarded last month, UC Berkeley research is perpetually interesting and relevant. (UC Berkeley graduate students are also interesting to Nobel laureates, as Greg Alushin describes (page 6) in his travelogue from the Lindau Meeting.) What we’d like to highlight in this issue is the driving force making science relevant and interest-ing to the public: mathematics and statistics. In our cover story Digitizing the drawers (page 46), Joan Ball relates the efforts of programmers and archivists working with Berkeley’s natural history collections to contextualize and coordinate massive numbers of specimens. In UC Berkeley’s herbaria, there are

360,000 specimens, 14 per Cal undergraduate. The number of cacti in our Botanical Garden alone is equal to the number of professors at UC Berkeley.

Tracking down every miniscule insect specimen in a museum can be a challenge, but at least pinned insects stay in one spot; some researchers on campus are trying to track all of us, every time we leave our houses. Ginger Jui, in There’s a map for that (page 36), gives us a broad view of the algorithmic and statistical analysis behind how we travel, from traffic data on a Google map to cell-phone tracking of road usage and transit time. Robert Gibboni’s Toolbox (page 56) delves into the calculations behind routing algorithms, and explains why simply choosing the faster road is sometimes a poor decision. Researchers hope that, along with taking convenience into account, understanding the costs of commuting in time and energy can drive us to make better choices. Driving more efficiently can make a tangible difference: the typical US household releases 50 tons of carbon dioxide into the atmosphere each year. A 50-ton carbon offset costs $750 on the Chicago Climate Exchange, a kind of stock exchange for greenhouse gases, but of course Berkeley puts a higher value on the environment; to purchase the same amount of carbon dioxide for a campus lab is $1532.

Statistics can also help us analyze the behavior of individuals. In The brain is half full (page 28 ), Azeen Ghorayshi investigates the Greater Good Science Center, an initiative to quantify our better nature, from altruism to collaboration. Even if our capability for good behavior may seem inextricably linked to factors outside of our control, Audrey Chang and Kristina Garfinkel report that anxiety and sleep deprivation are chemically predictable; even itchiness is attributable to a few proteins, described on page 11. Further afield from the Greater Good Science Center, UC Berkeley students are still behaving altruistically, bringing Hepatitis B vaccination to underserved communities in Alameda County, as Sharmistha Majumdar describes (page 4).

Each issue of the BSR requires the coordination of six editors, eighteen authors, seven layout editors, and a statistically significant amount of time and care. I’m overwhelmingly grateful to have Amy Orsborn as my counterpart leading the Layout team, and Mary Grace Lin keeping our resources on track, from finances to enthusiasm. We’re also lucky to have six regular authors (including one combination author and editor) on our blog team, who will keep you updated this semester on posts that tie in with some of the print articles and our second Reader’s Choice Award, where you can vote for the best feature article or brief.

Enjoy the issue,

Allison BerkeEditor in Chief

from the edito rberkeley

Fall 2011 Issue 21

sciencereview.berkeley.edu

Digitizingthe Drawers

Editor in ChiefAllison Berke

Editors Crystal Chaw

Mary Grace LinChris Holdgraf

Sebastien LounisAnna Schneider

Josh Shiode

Art DirectorAmy Orsborn

Layout StaffLeah Anderson

Marek JakubowskiAsako Miyakawa

Helene MoormanValerie O’Shea

Gregory Thomas

Copy EditorGreg Alushin

Managing EditorMary Grace Lin

Web EditorBrian Lambson

Web DirectorChris Holdgraf

PrinterSundance Press

2 Berkeley Science Review Fall 2011

features

© 2011 Berkeley Science Review. No part of this publication may be reproduced, stored, or transmitted in any form without the express permission of the publishers. Financial assistance for the 2011-2012 academic year was generously provided by the Office of the Vice Chancellor of Research, the UC Berkeley Graduate Assembly (GA), the Associated Students of the University of California (ASUC), and the Eran Karmon Memorial Fund. Berkeley Science Review is not an official publication of the University of California, Berkeley, the ASUC, the GA, or Lawrence Berkeley National Laboratory. The views expressed herein are the views of the writers and not necessarily the views of the aforementioned organizations. All events sponsored by the BSR are wheelchair accessible. For more information email sciencereview@gmail.com. Letters to the editor and story proposals are encouraged and should be emailed to sciencereview@gmail.com or posted to the Berkeley Science Review, 10 Eshleman Hall #4500, Berkeley, CA 94720. Advertisers: contact sciencereview@gmail.com or visit sciencereview.berkeley.edu.

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20 A lab space of one’s ownThe QB3 Garage: an incubator for innovationby Susanne Kassube

28 The brain is half fullThe science behind positive psychologyby Azeen Ghorayshi

36 There’s a map for thatCell phones for a better commuteby Ginger Jui

44 Digitizing the drawersMoving natural history collections onlineby Joan Ball

Fall 2011 3Berkeley Science Review

Fall 2011 Issue 21

COVER: This pinned beetle is one of 6 million invertibrate specimens in UC Berkeley’s Essig Museum of Entomology. The Calbug team is working to build databases to digitize the museum’s collection.

8 Mind over matterBrain machine interfaces come onlineby Samantha Cheung

10 Red eye scienceSleep now, learn laterby Kristina Garfinkel

11 Core issuesModeling the thermodynamic instability of planetary coresby Keith Cheveralls

12 A real head-scratcherThe molecular basis of itchby Nikki Kong

departmentsberkeley

current briefs

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CLOCKWISE FROM TOP-RIGHT: MAREK JAKUBOWSKI; ARTURO NAHUM; ASAKO MIYAKAWA; ERIC FISCHER; ELISABETH FALL; CHARLES DARWIN

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14 A perennial problemDevelopmental deficits stemming from pesticidesby Molly Sharlach

16 One small step for Cal, one giant leap for mankindAdvances in quantum computingby Zlatko Minev

17 Rising above Plateau’s problem250 years of mathematical explorationby Alireza Moharrer

1 From the Editor

4 LabscopesCan that thing fly?by Mica Smith

The frightened brainby Audrey Chang

Hyena gender rolesby Erin Jarvis

Think globally, treat locallyby Sharmistha Majumdar

6 From the fieldby Greg Alushin

52 Book reviewThe Instant PhysicistProfessor Richard A. Muller, illustrated by Joey Manfreby Erin Jarvis

54 Faculty ProfileKaren De ValoisTrue visionaryby Amanda Alvarez

56 ToolboxProbability and statisticsby Robert Gibboni

4 Berkeley Science Review Fall 2011

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Do you tend to “sweat the small stuff?” Chronic anxiety and similar neurological disorders affect over 25 million Americans, and researchers at UC Berkeley have identified two distinct pathways in the brain that can predict an individual’s susceptibility to anxiety. In this col-

laborative study between the Bishop lab at UC Berkeley and colleagues at Cambridge University, changes in blood flow to the brain were measured while subjects viewed a computer-generated

image of a person in a room just before a loud scream is heard. For some trials, the virtual figure in the room moves to cover its ears just before the scream, while in other trials the

gesture does not predict the sound, keeping subjects in a perpetual state of anticipation. Some participants with abnormal fear responses displayed a stronger reaction to

the virtual figure covering its ears—the anticipation of the loud scream led to overactivity in the amygdala region of the brain, which is known to process emotional memories. Others showed less activation in the ventral prefrontal cortex, a region responsible for decreasing the fear response. These are two separate mechanisms, but failure in either one results in a heightened fear response. This model of anxiety—activation instead of regulation—can better guide targeted therapies for anxiety disorders in the future. By understanding which mechanism is the source of an increased fear response, the success of different treatments can be better predicted.

The frightened brain

The giant hummingbird, Patagona gigas, native to the Andes, is an over-sized cousin of the Anna’s hummingbird beloved in North American backyards. It weighs about 20 grams, as much as a toothbrush, which

is twice as much as the next largest of more than 300 known hummingbird species. Professor Robert Dudley and María José Fernández of UC Berkeley’s integrative biology department analyzed the flight mechanics and metabo-lism of Patagona gigas in search of an explanation for its extreme body size.

“Muscle efficiency in general tends to be greater for larger things,” said Dudley, who wondered whether Patagona gigas evolved to take advantage of more effective energy use in the high elevation of the Chilean Altiplano. However, the giant hummingbird’s metabolic rate relative to its size cor-relates with data Dudley’s group collected for a number of smaller species. So if the giant hummingbird doesn’t expend more energy to sustain itself in flight, why haven’t hummingbirds evolved to grow even larger? Dudley cites the example of the nectar feeding bat, another vertebrate species that hovers, and can weigh up to 40 grams. “The wing design is very different,” says Dudley. “Bat wings connect to the hind legs, so they’ve got about twice the wing area. Depending on the aerodynamic mechanisms involved, the motor may be irrelevant: it’s your ability to convert that to aerodynamic force.” He speculates that the counterbalance between increasing wingspan and decreasing wingbeat frequency may place an upper limit on body size, which is represented by Patagona gigas. Though the results show that the hummingbird’s characteristically high metabolism is unaffected by size, it’ll be awhile on the evolutionary timeline before we see birds as big as falcons hovering at our feeders.

Can that thing fly?