YSM Issue 87.2

yalescientific

Yale Scientific

Established in 1894

THE NATION’S OLDEST COLLEGE SCIENCE PUBLICATION

MARCH 2014 VOL. 87 NO. 2

cancer breakthrough

Genetic technology revolutionizes treatment

our water footprint

A new look at sustainability

Global demand strains resources


q a

&

BY MARI KAWAKATSU

All stars die, but not all stars

“explode.” A supernova is a violent

explosion that marks the end of a

star’s life cycle. But our sun, the most

famous star in our sky, is destined for

a gentler death.

Astronomers estimate that in

approximately five billion years, the

Sun will begin to die when its core

runs out of hydrogen, its primary

fuel source. As the core collapses,

temperatures will increase until

helium starts burning to carbon. In

the shell around the core, the rising

temperature will result in hydrogen

nuclei combining into more massive

helium nuclei.

Gaining energy from this nuclear

fusion in its shell, the Sun’s outer layers

will expand. As the outer layers get

IMAGE COURTESY OF NASA

Our sun is the size of over one million Earths.

Will the Sun explode?

further away from the energy source,

their temperature will decrease. At

this point, the Sun will be a red giant

— a relatively cool star with a surface

temperature of approximately 3500K,

still large enough to envelop the

current orbits of Earth and Mars.

However, the Sun is not sufficiently

massive to explode in a type II

supernova, which requires at least

eight solar masses. Instead, the core

will turn into a white dwarf, a small,

dense stellar remnant that slowly cools

down while shining. Meanwhile, the

Sun’s outer layers will turn into a cloud

of dust and gas that gradually drifts

off into space.

Our sun’s final exit, therefore, will be

surprisingly undramatic. While more

massive stars go out with a bang, the

centerpiece of our solar system will

go out with a sigh.

What causes differences between identical twins?

BY CAROLINE AYINON

Identical twins share exactly the

same genome, and are usually raised

under the same conditions during the

early parts of their lives. Thus, it is not

surprising that identical twins share

strikingly similar physical features.

However, twins often find themselves

dealing with rather different health

situations as adults. An ongoing study

at King’s College in London has found

that the surprising differences in the

lives of identical twins are largely due

to the effects of a mechanism known

as epigenetics.

Epigenetics functions through

methylation, the process in which a

chemical add-on called a methyl group

binds to our DNA. Since methylation

inhibits a gene from producing a

certain protein, genes that would

IMAGE COURTESY OF MARTIN SCHOELLER

Identical twins share the same DNA, and thus

share very similar physical features.

otherwise regulate illnesses such as

obesity, cancer, and depression may be

limited or no longer expressed due to

epigenetics.

Differences in the behavioral

tendencies of twins, such as smoking,

stress, and diet, can cause changes

in the methylation patterns of the

epigenome. Studies have suggested

that pain tolerance, for example, is not

very heritable, but is instead related

to variation in one’s methylation

states. Ultimately, it is differences

in life patterns, coupled with other

environmental factors, that cause

epigenetic changes and lead to striking

health inconsistencies between

identical twins. From these discoveries,

scientists can now better judge which

health conditions are purely heritable,

and which are primarily influenced by

behaviors and epigenetics.


5

NEWS

Letter from the Editor

Yale Scientific

Established 1894

CONTENTS

MARCH 2014 VOL. 87 ISSUE NO. 2

ON THE COVER

6

6

7

7

8

9

10

11

25

26

28

29

30

32

33

34

36

Lifton Wins Breakthrough Prize

People, Policy, and Locusts

Student Expedition to Arecibo

Oxytocin Ameliorates Autism

Personalized Cancer Treatment

Quantum Computing

Computer-Aided Enzyme Design

Overcoming Friction

FEATURES

Cell Biology

New Properties of Bacterial Cytoplasm

Medicine

Effects of Cold on the Human Body

Public Health

Lightning: More Than Just a Shock

Biology

Love at Second Sight

Environmental Science

Our Water Footprint

Undergraduate Profile

Parker Liautaud DC ’16

Alumni Profile

Robert Needlman YC ’81, YSM ’85

Essay Contest

Breaking Convention

Debunking Science

Limitations of Brain Imaging

16

12

18

Metal Fever

Are we running out of metals in this digital era? According to

scientists at the Yale Center for Industrial Ecology, not exactly —

but the more important questions lie elsewhere.

Using Life’s

Code to Rewrite

the Genome

A recent study is pushing

new frontiers in the field

of synthetic biology.

Scientists have been able

to successfully recode the

entire genome of an E. coli

bacterium, opening up vast

commercial applications.

Tiny Guts, Big

Consequences

Disrupting the bacteria

inside the guts of ticks can

have big ramifications for

this feared vector of Lyme

disease. Yale researchers

share interdisciplinary

perspectives on these

interactions in the context

of immunity.

20

IMAGE COURTESY OF BUSINESS INSIDER

PHOTO BY CHANTHIA MA

Immortal Neurons: Is Neuron

Loss Inevitable?

37

38

Unsolved Mysteries

The Science of Identity

Science in the Spotlight

Book Reviews:

Gulp, Newton’s Football

IMAGE COURTESY OF THE

AGRICULTURAL RESEARCH SERVICE

22

IMAGE COURTESY OF YALE OFFICE OF SUSTAINABILITY

Sustainability in Flight: Yale’s

Citizen Science Program

More articles available online at www.yalescientific.org

www.yalescientific.org

March 2014

Yale Scientific Magazine

3


Citizen Science

New programs empower the individual

to engage in scientific inquiry.

pg. 22

“What is genius but the

power of expressing a

new individuality?

—Elizabeth Barrett Browning

Exploring

Identity

Identity: an expression of uniqueness;

a reflection of self; a scientific mystery.

pg. 37

Personalized

Medicine

The media, arts, and sciences have

long celebrated individuality. And

now, thanks to genetic sequencing,

medicine is following suit.

pg. 8

ART BY RACHEL LAWRENCE


F R O M T H E E D I T O R

Science and the Individual

Every now and then, we come across scientific discoveries that earn a collective doubletake

from humanity. The first man on the moon. The discovery of the Higgs Boson. The

earliest, shadowy X-ray images of DNA’s double helix. Breakthroughs like these are the

ones that answer sweeping questions about who we are and where we came from. They

resonate with all of mankind by exploring the universal.

But by zooming in, we find that some of the most fascinating mysteries in science lie at

the individual level—a single, rare case of liver cancer, for instance, or a phenotypic quirk

that appears in one identical twin and not the other. By straying from the average, these

outliers can provide telling clues about the sample as a whole. With this in mind, the Yale

Scientific will devote its first issue of 2014 to exploring “Science and the Individual.” From

advances in personalized medicine (pg. 8) to debates on the biological basis of identity (pg.

37), we have much to learn from probing the myriad factors that make each of us unique.

This issue will also examine the intimate relationship between science and the individual.

It’s easy to assume that science is locked away in ivory towers, when in fact it pervades nearly

every aspect of daily life; the wide array of topics in this issue suggests that science calls out

to each of us in strikingly different ways. To the 65-year-old with advanced Alzheimer’s, the

most important scientific contribution may be pending research on neuron regeneration

(pg. 20). To a woman in rural South Africa, it could be a shelter that protects her family

from lightning strikes (pg. 28). And to that Yalie from southern California, it may simply be

a deeper understanding of how cold affects the human body (pg. 26).

Thanks to the growing citizen science movement, even those without formal training

can now contribute to groundbreaking scientific research by gathering and analyzing data

on their own. The investigative article on page 22 highlights the trajectory of Yale’s own

citizen science program, a joint effort between the Yale Office of Sustainability and Peabody

Museum of Natural History. Through training students and staff to track biodiversity on

campus, the growing initiative draws science and the average person even closer together.

And so, in this issue we invite you to join us in celebrating the individual. With more

frequent online articles, brand new outreach initiatives, and a redesigned layout, the Yale

Scientific aims to convey the resounding impact of scientific discovery — on the world, on

the research community, and perhaps most importantly, on the individual. In these pages, I

hope that you will discover an aspect of science that resonates with you.

Editor-in-Chief

Publisher

Yale Scientific

M A G A Z I N E

Established in 1894

MARCH 2014 VOL. 87 NO. 2

Managing Editors

News Editor

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Senior Editorial Advisor

Staff Writers

Renee Wu

Theresa Steinmeyer

Blake Smith

Grace Pan

Contributing Writers

Lisa Zheng

Lorraine James

Emmy Yang

Rain Tsong

Mari Kawakatsu

Mariana Do Carmo

Rebecca Su

Aurora Xu

Chanthia Ma

Naaman Mehta

Andrew Qi

Payal Marathe

Julia Rothchild

Grace Cao

Christina de Fontnouvelle

Jiahe Gu

Kevin Wang

Carrie Cao

Rachel Lawrence

Aparna Nathan

Nicole Tsai

Claudia Shin

Elena Malloy

Adam Pissaris

Mina Himwich

Emma Graham

Somin Lee

Zachary Mankoff

Claudia Shin

Karthik Ardhanareeswaran

Jessica Hahne

Taryn Laubenstein

Zachary Miller

Ameya Mahajan

Henry (Fangyi) Li

Mari Kawakatsu

Tessa Adler

Caroline Ayinon

Audrey Luo

Zachary Gardner

Austin Igelman

A B O U T T H E A R T

Rebecca Su

Editor-in-Chief

Advisory Board

Sean Barrett, Chair

Priyamvada Natarajan

Kurt Zilm

Fred Volkmar

Stanley Eisenstat

James Duncan

Melinda Smith

Peter Kindlmann

Werner Wolf

John Wettlaufer

William Summers

Jeremiah Quinlan

Carl Seefried

Physics

Astronomy

Chemistry

Child Study Center

Computer Science

Diagnostic Radiology

Ecology & Evolutionary Biology

Electrical Engineering

Emeritus

Geology & Geophysics

History of Science, Medicine, & Public Health

Undergraduate Admissions

Yale Science & Engineering Association

Yale Scientific

Established in 1894

THE NATION’S OLDEST COLLEGE SCIENCE PUBLICATION

MARCH 2014 VOL. 87 NO. 2

cancer breakthrough

Genetic technology revolutionizes treatment

our water footprint

A new look at sustainability

Global demand strains resources

The cover art, designed by Arts Editor Nicole Tsai, illustrates

the world’s surging demand for metals used to create hightech

products. In the foreground, molten metal is squeezed out

of the Earth to form an array of electronic gadgets. A scene

from a metal mine emerges from the background. Contributing

artists for this issue were Rachel Lawrence (page 4), Nicole

Tsai (pages 12, 20), Jason Liu (page 16), Jeremy Puthumana

(page 18), Audrey Luo (page 22), Casey McLaughlin (pages

26-27), Danielle Carrol (page 28), Grace Pan (page 29),

Christina Zhang (page 30), Carrie Cao (pages 35, 37), and

Celina Chiodo (page 39).

The Yale Scientific Magazine (YSM) is published four times a year

by Yale Scientific Publications, Inc. Third class postage paid in New

Haven, CT 06520. Non-profit postage permit number 01106 paid

for May 19, 1927 under the act of August 1912. ISN:0091-287. We

reserve the right to edit any submissions, solicited or unsolicited, for

publication. This magazine is published by Yale College students,

and Yale University is not responsible for its contents. Perspectives

expressed by authors do not necessarily reflect the opinions of YSM.

We retain the right to reprint contributions, both text and graphics,

in future issues as well as a non-exclusive right to reproduce these

in electronic form. The YSM welcomes comments and feedback.

Letters to the editor should be under 200 words and should include

the author’s name and contact information. We reserve the right to

edit letters before publication. Please send questions and comments

to ysm@yale.edu.


NEWS

in brief

awards & accolades

Lifton Wins $3 Million Breakthrough Prize

IMAGE COURTESY OF PAUL FETTERS PHOTOGRAPHY

Richard Lifton, Sterling Professor

and Chair of Genetics at Yale

University, won the 2014 Breakthrough

Prize in the Life Sciences.

BY AUSTIN IGELMAN

On December 12, 2013, Sterling

Professor and Chair of Genetics

Richard Lifton was awarded a $3 million

Breakthrough Prize in Life Sciences for

his work studying the genetic causes of

hypertension. Sponsored by Silicon Valley

entrepreneurs including Mark Zuckerberg,

Priscilla Chan, Sergey Brin, Yuri Milner,

and Anne Wojcicki, the Breakthrough

Prize “recognizes excellence in research

aimed at curing intractable diseases and

extending human life.”

Hypertension, or high blood pressure,

is a key risk factor for a wide range of

cardiovascular diseases and disorders.

Over 20 years ago, Lifton proposed

that hypertension might be linked to

single genes. At the time, the causes of

hypertension were poorly understood

and were thought to be too complicated

for this analysis. However, drawing upon

his experience studying fruit fly genetics,

Lifton knew that single gene mutations

in flies could “change one body part

into another.” He then hypothesized that

more complex diseases like hypertension

could also be caused by a set of genetic

mutations.

To identify specific genes affecting

blood pressure, Lifton “scoured the

planet looking for extreme outliers in the

population with either extremely high

or extremely low blood pressure.” He

discovered around 20 gene mutations

associated with hypertension. After

analyzing the data, he found that the

mutated genes were “not distributed

across the physiological landscape,” but

rather converged on salt management

in the kidneys. Lifton’s work, now the

cornerstone for understanding blood

pressure regulation, has led to improved

methods of treating and preventing

hypertension worldwide.

environment

IMAGE COURTESY OF DEVIANTART

Eli Fenichel, Assistant Professor

of Bioeconomics and Ecosystem

Management, seeks to model locust

outbreaks as well as human responses

to these outbreaks.

NSF Connects People, Policy, and Locusts

BY ZACHARY GARDNER

Capable of devastating agricultural

and food security in over 60 countries

worldwide, locust swarms threaten the

livelihoods of over one-tenth of the

world’s population. And now, there is

reason to believe that figures may be

on the rise. A recent study found that

widespread nitrogen depletion in soil due

to overgrazing might be key in causing

solitary locusts to aggregate into swarms.

The lower protein content of plants

grown in nitrogen-depleted soil provides

locusts with a carbohydrate-rich diet that

stimulates swarm formation.

In response to the study and to growing

concern over the threat that locusts pose

to the global food supply, the National

Science Foundation granted a team of six

researchers $955,000 to investigate this

phenomenon. One of these researchers

is Eli Fenichel, Assistant Professor

of Bioeconomics and Ecosystem

Management at the Yale School of

Forestry & Environmental Studies.

Fenichel’s research lies at the intersection

of economics and ecology. He plans to

use mathematical modeling to explore the

links between insect nutrition, national

land rights policies, and livestock markets

to evaluate countries’ abilities to respond

to increasingly destructive swarms.

“Overall, we want to connect ecological

dynamics to people who respond to locust

outbreaks and build models of the systems

of the locust outbreaks as well as models

of how people respond,” said Fenichel in

an interview with the Yale Daily News.

Locust swarms will likely continue to

pose a threat to agriculture worldwide.

However, by collaborating with

agricultural and agronomic organizations,

the research team will use the insights

they gain to develop more effective locust

management strategies.

6 Yale Scientific Magazine March 2014 www.yalescientific.org


astronomy

Student Expedition to the Arecibo Observatory

in brief

NEWS

BY HENRY (FANGYI ) LI

Last semester, the students in “ASTR

255: Astrophysics Research Methods”

embarked on an four-day trip to the

Arecibo Observatory in Puerto Rico. Led

by Marla Geha, Associate Professor of

Astronomy and Physics, their visit marked

the first time an undergraduate group

observed on the site in the context of a

class. In three-hour blocks, each student

directed the telescope at selected targets

and took data home for further analysis.

“The trip to Arecibo is part of a final

project for ASTR 255 where students

design and conduct their own research,”

said Professor Geha. “One of their goals

is to study isolated dwarf galaxies by their

atomic hydrogen emission lines.”

As an introduction to the Astrophysics

major, ASTR 255 aims to equip students

with the analytical tools necessary for

professional astronomical research. It is a

highly intensive course that encompasses

diverse topics from high-level programming

to experimental design.

Nevertheless, Geha emphasized the

course’s accessibility to all interested

students: “You aren’t expected to know

anything coming in, but we really hit the

ground running.”

Despite the rigorous pace of the class

material, students responded positively

on their overall class experience. Former

student Kareem El-Badry describes the

trip as “the highlight of [his] semester,” as

he recalls climbing across catwalks hanging

high over the telescope.

Although this was the course’s first year,

Geha envisions ASTR 255 as an integral

part of the Astrophysics curriculum in

future years. “Science is never about doing

problem sets. It’s about creative thinking

— novel ideas. Arecibo is where students

learn to design and conduct their own

experiments.”

IMAGE COURTESY OF MARLA GEHA

Marla Geha, Professor of Astronomy

and Physics, led her students on a

research trip to Puerto Rico’s Arecibo

Observatory this past summer.

pharmacology

Oxytocin Observed to Ameliorate Autism

BY JIAHE GU

Autism spectral disorder (ASD) is an

increasingly common disorder that causes

reduced social interaction and other

abnormalities, especially in children. While

psychological counseling can sometimes

be effective, a proven pharmacological

treatment for ASD does not yet exist. A

study recently published by researchers

at the Yale School of Medicine in the

Proceedings of the National Academy of

Sciences aims to change this.

Led by Ilanit Gordon, Adjunct Assistant

Professor at the Yale Child Study Center,

the group conducted a double-blind,

placebo-controlled test in which oxytocin

was administered as a nasal spray to 17

children and adolescents afflicted with

ASD.

Oxytocin, a hormone traditionally

known to induce intimacy as well as a

variety of physical changes, has previously

been shown to enhance processing of

social stimuli in both healthy adults and

those affected by ASD.

Gordon and her colleagues demonstrated

that younger patients with ASD responded

in a similar manner. When presented with

pictures of eyes and asked to deduce the

emotional state expressed, subjects given

intranasal oxytocin exhibited significantly

greater activity in the parts of the brain

associated with social processing than

subjects given a placebo spray.

These results suggest that oxytocin may

hold promise as a treatment for the social

impairment caused by ASD. Because ASD

is as much a developmental disease as it

is a neurological one, administration of

such a treatment from infancy could lead

to a compounding effect as improvements

are magnified with each successive stage

of social development. Oxytocin therapy

could therefore lead to considerably

improved social ability by adulthood.

PHOTO BY JIAHE GU

Autism awareness is growing

as more is understood about the

disorder. Here, Harkness tower is lit

up for World Autism Awareness Day.

www.yalescientific.org

March 2014

Yale Scientific Magazine

7


NEWS

genetics

Unlocking New Potential:

Gunel team revolutionizes personalized cancer care

BY MARIANA DO CARMO

Recently, a team of Yale researchers led by Dr. Murat Gunel,

Nixdorff-German Professor of Neurosurgery and Professor of

Genetics and Neurobiology, was able to diagnose an 18-month-old

girl from Turkey with a rare form of liver cancer using breakthrough

genetic technology. By mapping out her individual genetic sequence,

Gunel proceeded to develop a personalized cure.

When she was eight months old, Derin began to show strange

signs of discomfort and a lack of desire to eat, drink, and sleep.

Worried by these severe and persistent symptoms, her parents

immediately looked to the medical community for answers. It took

Turkish doctors ten months to discover the source of Derin’s illness,

a tumor in her liver. This tumor, however, turned out to be a rare

form of liver cancer with only ten known reported cases, leaving

the doctors perplexed and uncertain about how to treat it. They

proposed performing a liver transplant, a stressful and dangerous

procedure for a toddler to undergo.

Seeking further and immediate medical attention, Derin’s parents

brought her to the Yale-New Haven Children’s Hospital, where

Gunel and his colleagues rapidly diagnosed her and set to work on

developing a cure. Unlike most standardized cancer treatments such

as surgery, chemotherapy, and radiation, where all patients receive

the same methods and therapies, Gunel turned to a personalized

approach to treat Derin’s rare cancer.

Gunel extracted a 1-mm by 3-mm slice of Derin’s parenchymal

tissue from her liver and used it to map out her genetic code. In

only five days, doctors found a mutation in the DNA sequence that

encodes for a protein responsible for bile salt secretion. Bile salts are

synthesized in the liver from cholesterol and help remove lipids from

the body. Derin’s mutation led to these bile salts accumulating in her

liver, creating a harmful build-up that led to her cancer.

Professor David F. Stern, Professor of Pathology at the Yale

School of Medicine and a member of the Yale Cancer Center who

was not affiliated with Gunel’s research, elaborated on the process

of identifying the mutations. “Dr. Gunel’s approach was to sequence

the tumor cell DNA and compare it to the DNA found on a normal,

Close-up of parenchymal tissue extracted from liver.

IMAGE COURTESY OF WTNH

IMAGE COURTESY OF WTNH

Derin, the 18-month-old girl diagnosed with and treated for a rare

case of liver cancer.

healthy liver cell,” said Stern. “Researchers detected a number

of differences, focused on the ones that were known to have an

impact in causing cancer, and found the mutation in the ion channel

involved in bile salt secretion. This mutation had possibly already

been connected to cancer in some way.”

In a series of life-saving steps, the surgeons at the Yale-New Haven

Children’s Hospital removed the tumor without harming the liver by

using her genomic data to identify malignant cell types. They then

created an exit pathway for the bile salt build-up, ensuring that it

would have no long-term consequences for Derin’s health. Derin

was monitored in case her cancer spread beyond the liver, but in the

meantime, her family was reassured that Derin was healthy and could

go home soon.

Derin’s treatment represents the beginning of a new approach to

fighting, and winning, the battle against cancer. In the past, scientists

have looked at cancers as diseases that attack each individual in the

same way. Now, researchers and surgeons are beginning to detect the

exact locations in the genome of each patient where carcinogenic

agents induce mutations, such as single nucleotide substitutions or

DNA damage, that can lead to tumor formation.

Genetic mapping provides a useful tool in diagnosing other

cancers as well. “Some cancers, such as those of the lung, experience

mutations in mostly the same areas, so there are already specific drugs

that can bind to the genes or their protein products and help regulate

them in all patients,” said Stern. “Yet, there is an overwhelming

number of mutations for which no drugs exist yet that can help.”

However, catalogues that contain tumor classifications through

genetic screening are becoming more commonplace. Based on these

genetic screens, drugs used to treat certain types of cancer could be

repurposed to treat other kinds as well.

Dr. Gunel’s work not only paves the way for further advances in

the field of cancer research, but also adds to the growing practice

of using personalized medicine as a more effective way of treating

patients. This focus on basing treatments on individual needs may be

the next step forward in cancer therapy.

8 Yale Scientific Magazine March 2014 www.yalescientific.org


Light and Truth:

Schoelkopf lab achieves photon control in quantum computing

BY GRACE PAN

Quantum computing is a dynamic field that combines theoretical

and experimental physics to develop novel methods of transporting

information. In the past decade, efforts to develop a working

quantum computer have garnered attention from government

leaders and research scientists alike. With ultra-fast computation,

quantum computers promise the ability to create complex simulations

and privacy systems outside our current reach. Physicists at Yale

University led by Sterling Professor of Applied Physics and Physics

Robert Schoelkopf recently achieved a breakthrough in quantum

computer development. They have devised a method to harness and

manipulate 100 light photons into a superposition of states known

as “Schrödinger cat states.” These cat states could serve as quantum

bits, or qubits, the basic unit of quantum information storage.

In classical computing, data is stored

in strings of binary units (bits), where

information is encoded in series of zeroes

and ones. While classical bits can only have

these two discrete values, qubits can have

values of zero, one, or a superposition of

zero and one.

However, harnessing these quantum

effects faces a difficult problem: error

correction. In classical computing,

error correction is simple — one can

run measurements, isolate the errors,

and fix them. But Michel Devoret,

Frederick William Beinecke Professor of

Applied Physics and Physics and a major

contributor to the project, explained

that quantum systems are different. “If

you make a measurement, you perturb

the system, so people initially thought

that quantum error correction would be

impossible,” says Devoret.

Over the past decade, quantum error

correction has been shown to be possible

but difficult. “Most of the research is

now aimed at solving the problem of

quantum error correction with minimum

hardware,” said Devoret, characterizing

the endeavor as “the next holy grail of

quantum computing research.”

Information in the quantum world exists in a specially designed

quantum state, or cat state. This condition is named after

Schrödinger’s classic thought experiment, in which a cat inside a

sealed box can be simultaneously dead and alive. Its condition, in

other words, is a superposition of the two states. Opening the box to

check on the cat destroys the superposition because the viewer learns

that the cat is either dead or alive; it can no longer exist in both states.

Similarly, directly measuring the state of a qubit will “open the box,”

undercutting the qubit’s ability to be two values at once.

The new advances in controlling photons suggest a poweraful

method to circumvent many of the difficulties in quantum error

correction. These photons are contained in a resonant cavity dubbed

a “photon box.” By measuring the parity, the even or odd-numbered

count, of photons in the cavity, scientists are able to detect an error

— a photon loss — without perturbing the encoded information.

Experimentally, the team employed a combination of microwave

engineering techniques to capture microwave photons inside their

cavities. The procedure was conducted at cryogenic temperatures

around 20 millikelvin to minimize disruption from dissipation and

thermal radiation. They created cat states comprising as many as 111

photons and manipulated the cat states to have up to four different

states in superposition.

Brian Vlastakis, a Yale graduate student

and the lead author of the Science

article published from the experiments,

adds that, aside from error correction,

scientists “can trap many photons all

at once in a single cavity, so everything

is much simpler on the hardware side.”

While current methods of creating qubits

from only superconducting junctions

offer some benefits, Vlastakis said that

“it is much easier to create many photons

and control them. This is a possible viable

source to create a quantum computer.”

This seminal work in photon

manipulation may be key in one day

creating manageable quantum computer

processors. As Vlastakis put it, “if you

built a processor that behaved quantum

mechanically, your processor can be

many processors simultaneously. This can

separate a problem into multiple smaller

problems, so you can solve your problem

much faster.”

Of course, the science itself is just as

charming. Studying quantum computing

helps define what exactly “information”

is in the physical world and is a prime

way to empirically observe non-intuitive

quantum-mechanical phenomena. “You get to play with very small,

very elementary kinds of systems,” said Vlastakis.

From the intrinsic science behind quantum systems arises yet

another perk. “The most wonderful aspect of quantum information,”

said Devoret, “is that it can be transferred but cannot be copied.” This

advantage would allow for heightened Internet privacy, protecting

credit card numbers, medical records, and other confidential

information. It would also give people greater control over their

information. The autonomy that quantum computing would give its

users is what Devoret brands as the “new paradigm of computing.”

IMAGE COURTESY OF BRIAN VLASTAKIS

Brian Vlastakis, a graduate student at Yale, was

the lead author of the November 2013 Science

article detailing the experiment’s findings.

physics

NEWS

www.yalescientific.org

March 2014

Yale Scientific Magazine

9


NEWS

chemical engineering

Form, Function, and Temperature

BY ZACHARY MILLER

All life exists on a knife’s edge, a delicate balance of the many

thousands of biochemical reactions that sustain it. At the cellular

level, life is nothing but the proper collection of such chemical

processes, all playing out in carefully choreographed sequence, like

a well-rehearsed ballet.

But every organism has one big problem: left to their own devices,

the chemical reactions necessary for life behave less like practiced

dancers and more like an unruly mob. Some reactions proceed with

reckless abandon, others unfold slowly, and still many more would

never occur at all in the span of human lifetime.

This is where enzymes step in. Enzymes are a class of proteins

— large, folded-up molecules — that work to accelerate specific

chemical interactions. Within the body, it is up to enzymes to make

the reactions run on time. In one extreme example, researchers

have determined that a kind of reaction involving molecules called

phosphate monoesters would take more than a trillion years to occur

on its own. But thanks to an enzyme, it happens in our cells almost

100 times every second.

The role of enzymes in reconciling disparate time scales in living

organisms makes them an important subject of scientific study.

Among those interested in the study of enzymes is Yale University’s

Corey Wilson, Assistant Professor of Chemical and Environmental

Engineering. Wilson’s research group has focused on exploring the

connections between how enzymes work and the temperatures at

which they function.

”Enzymes are very sensitive,” Wilson said. They are highly specific in

shape; enzymes match the molecules that they act upon just as a glove

fits a hand. However, they are not static. The microscopic workings

of enzymes involve minute changes of shape, called conformational

changes, and an enzyme’s ability to make these changes quickly is

essential to its ability to speed up a reaction. Enzymes must find

the proper balance between keeping their shape

and being able to make conformational changes.

Temperature control is the key. Keep an enzyme

too cold, and it will be stiff and unable to traverse

its proper range of motions. “Too hot,” Wilson

explained, “and they will deform.”

Wilson and his team have worked to understand

what determines this “Goldilocks” window for each

enzyme. So far, their research has allowed them to

successfully create designer proteins that function

best at a specific, pre-determined temperature.

Their work, published this year in the journal

Structure, introduces a new range of possibilities

for understanding and manipulating the so-called

“thermostability” of enzymes.

The team began by modeling protein structures

using pre-existing techniques, which do not take

temperature into account. They then compared the

results of these computer models with experimental

data. The gap between model and reality allowed

Wilson lab improves computer-aided enzyme design

them to elucidate the role played by temperature. Using this new

information about enzyme function at different temperatures, Wilson

and his team could “rationally design” enzymes that work optimally

at temperatures of their choosing.

To do so, they manipulated these protein structures to find more

or less stable configurations. “We ask, ‘What is our substrate?’ and

then we find another scaffold that will support the same activity,”

explained Wilson. The next step was to take these modeled

structures and express them as actual proteins in E. coli bacteria.

To demonstrate their control of thermostability, they designed and

tested 100 different variants of an enzyme called Bacillus subtilis

adenylate kinase (bsADK). Normally, bsADK has a very specific

thermal niche and “is enzymatically dead within a few degrees outside

this temperature,” according to Wilson’s paper. Their new enzymes,

however, “occup[ied] a broad distribution of thermostabilities.”

Wilson’s experiments offer scientists both the ability to design

enzymes optimized for a particular temperature and a better

understanding of enzyme function. The capacity to manufacture

custom-made enzymes for use at a specific range of temperatures

is exciting because enzymes have numerous applications in both

industry and medicine. Wilson sees the possibility of tailoring

enzymes to these specific uses. “One exciting example,” he said, “is

in biofuel production, where thermostable enzymes are needed to

convert cellulose into glucose.”

Wilson also hopes his work will lead to a new emphasis on the

importance of environmental conditions — factors like pH and, of

course, temperature — for enzyme function. Taking these factors

into account will lead to a clearer picture of the highly complex

relationship between the structure and function of enzymes. “After

all,” said Wilson, “the ultimate test of understanding a system is

being able to design it.”

PHOTO BY NICOLE TSAI

Corey Wilson’s research group focuses on exploring the connections between how

enzymes work and the temperatures at which they function. Temperatures that are too

low limit an enzyme’s motion, while temperatures that are too high cause deformation.

10 Yale Scientific Magazine March 2014 www.yalescientific.org


physics

NEWS

Overcoming Friction with Nanoparticles

BY AUDREY LUO

Imagine a miniature drone that fits on your fingertip, complete

with a built-in camera and microphone. The possibilities are endless:

it could serve the military for espionage or help Yalies scope out

potential screw dates. To power such a drone, researchers would need

to develop a micro-motor made of low-friction material capable

of running for extended periods of time. A recent collaboration

between Professor of Mechanical Engineering & Materials Science

Udo Schwarz and scientists at two German universities may help

boost development of such low-friction materials. They showed that

at an atomic scale, the principles of friction deviate from those at a

macroscopic scale.

On a macroscopic level, friction does not depend on surface area.

An organic chemistry textbook will slide the same distance whether

you push it flat or upright along on the table. The surface of the table

has tiny peaks that come in contact with those of the book surface.

In order for the book to keep sliding, the book’s surface has to

overcome these peaks on the table, which translates into lost energy,

or friction. The rougher the surface, the more friction is created.

At a microscopic scale, the same concept holds — atoms from one

surface obstruct atoms from the other surface, creating a potential

energy barrier, or peak, that must be overcome. The lower an atom

is nestled into a “valley,” the harder it is for it to come back up to

allow the surface to continue sliding. If, however, two surfaces have

different spacing between atoms, then the “hills and valleys” of

the two surfaces will not line up. Atoms from one surface will not

be caught in the valleys of the other surface, reducing friction in a

phenomenon called structural lubricity.

One of the key theories of structural lubricity is that there is an

unusual frictional dependence on surface area. Schwarz and his

collaborators showed that the friction force does, in fact, depend

on contact area at the atomic scale — an observation unique to the

microscopic level. They confirmed their predictions of the frictional

force by measuring the sliding resistance of crystalline gold and

amorphous antimony nanoparticles on crystalline graphite.

www.yalescientific.org

IMAGE COURTESY OF UDO SCHWARZ

Contact area on a macroscopic scale does not affect friction

because the contact area we perceive is much larger than the actual

contact area at a microscopic level.

Yale-led collaboration explores friction at the atomic level

“Nobody can predict how much [the friction] is by just looking

at the surface, but now we can predict it,” said Schwarz. “For tens

of thousands of atoms, you only need to tell me two things: what

material you have and what the diffusion barrier is for one atom. And

I can tell it to you.”

Schwarz used ultra-high vacuum conditions to create atomically

flat surfaces on crystalline graphite and deposited small “islands” of

gold and amorphous antimony on those surfaces. The surfaces were

designed to be very flat so that contamination and dirt would not

cause additional friction. The contact area, or size of the “islands,”

was measured against the frictional force. As the tip of an atomic

force microscope pushed the gold and antimony islands across the

crystalline graphite, the microscope measured the resulting friction

values.

Due to their different geometries and orientations, the gold and

antimony islands produced different friction values. Researchers also

observed a nearly linear relationship between frictional force and

contact area, which does not occur at the macroscopic level. The

measured friction force not only matched their predictions but was

also orders of magnitude lower in friction than what is normally seen.

Super-low friction surfaces can be used to run more efficient

motors. “Ideally, you can have a motor running on super-low friction

because then there would be less wear, and you can use less gas,” said

Schwarz.

In their study, Schwarz and his colleagues were able to create superlow

friction states for contact areas of up to 0.2 square micrometers.

They discovered a link between single atom diffusion — the pushing

around of a single atom — and macroscopic friction involving tens

of thousands of atoms, establishing a direction to engineer superlow

friction surfaces.

In the future, Schwarz hopes to apply their findings to constructing

practical devices. “Now the challenge is to make large enough

atomically flat surfaces that do not trap dirt inside to develop efficient

micro-motors,” he said.

March 2014

PHOTO BY APARNA NATHAN

Udo Schwarz, Professor of Mechanical Engineering and Materials

Science, elucidated properties of friction that may contribute to the

engineering of super low-friction surfaces in efficient micro-motors.

Yale Scientific Magazine

11


rewrite

the rewriting

the

genome

genome

BY BLAKE SMITH

ART BY NICOLE TSAI

By Blake Smith

Art by Nicole Tsai

Almost every day, scientists around

the world are discovering new life

forms. Archaeologists are digging

up past relatives, and evolutionary biologists

are adding new branches to the tree of life.

While millions of species are estimated to

have gone undiscovered to this day, scientists

at Yale and Harvard have created a new

organism that has wide-ranging applicability

in biomanufacturing for industry and

medicine alike.

Recoding the Genome

Currently, sequencing the human genome

– a process that used to take years – can

now be accomplished in ways that are rapid,

affordable, and informative. This “decoding”

of the DNA blueprint has led to our

understanding of specific genes, especially

in the context of disease. However, on the

opposite end of the spectrum, researchers

at Yale, under the direction of Farren Isaacs,

Assistant Professor of Molecular, Cellular,

and Developmental Biology, has successfully

“recoded” the genome of a strain of E. coli

bacteria.

Recoding the genome, in its most basic

sense, is introducing site-specific changes

across the genome in an effort to achieve

a phenotypic outcome, such as viral

resistance. “We wanted to ask, based on

our understanding of the genetic code and

certain important properties of the genetic

code, such as conservation and degeneracy,

could we change it?” said Isaacs. This

idea, conceived in 2005 when Isaacs was a

postdoctoral researcher in the lab of George

Church at Harvard Medical School, led to

one of his most recent of his publications

IMAGE COURTESY OF WIKIMEDIA COMMONS

Scanning electron micrograph image of a

lab-grown E. coli culture, magnified 10,000X.

in October 2013, entitled “Genomically

Recoded Organisms Expand Biological

Function” in the journal Science.

The work done by Isaacs and colleagues is

predicated on the translation machinery of

the cell. As the “central dogma of biology”

states, DNA is transcribed into RNA, and

RNA is translated into proteins. Isaacs’s

research focuses on the latter pathway:

translation. During translation, cellular

machinery reads the mRNA in threeletter

groupings, called codons, in order to

correctly add amino acid building blocks to a

growing protein chain.

In total, there are 64 codons. Sixty-one of

them code for the twenty functional amino

acids the cell uses to make proteins; the

remaining three codons code for a stop in

translation, a signal that the amino acid chain

is complete and should be released into

the cell to start its life as a protein. These

sequences are known as “stop codons,” and

are named by their specific base sequences:

UAG, UAA, and UGA.

Interestingly, the two proteins responsible

for the release of the protein into the body

at the end of translation, called “release

factors,” have some redundancy in function:

they both halt translation upon reaching

a UAA stop codon, the most abundant of

12 Yale Scientific Magazine March 2014 www.yalescientific.org


biotechnology

FOCUS

the stop codons in the E. coli strain that the

researchers used in their study. “The codons

are discriminated by the tRNA and release

factors. Not only do you have to think about

redundancy at the DNA level, but also how

that gets decoded at the translational level,”

said Isaacs.

Two release factors, called RF1 and

RF2, operate to release newlysynthesized

proteins from the

factories manufacturing them.

Each one of these factors goes

into action in response to two

of the three stop sequences

that are reached at the

end of translation. RF1

is responsible for both

UAG and UAA, whereas

RF2 is also responsible for

UAA and is additionally in

charge of the third stop

codon sequence, UGA.

This means that UAA has

the ability to prompt both of

the release factors to release

the translated protein. It also

means that if only two codon

stop sequences existed instead of

three, a single release factor could be

responsible for all of the protein release in

the organism.

Isaacs and his team decided to investigate

whether one of the stop sequences (UAG)

could be recoded – which would involve

changing one of the bases in its three-letter

sequence – to make it identical to another

one of the stop codons, creating an organism

with two instead of three stop codon

sequences. Decreasing the number of stop

codons from three to two would make one

release factor extraneous. Isaacs hoped to

create a system that simply had no need for

a release factor that is undeniably essential to

every life form.

CAGE and MAGE: Isaac’s Methods

Converting all of one type of stop codon

found in the specific strain of E. coli used in the

study to a different sequence simultaneously,

efficiently, and across the entire genome of a

single organism is quite difficult. Isaacs’ new

method, known as Multiplex Automated

Genome Engineering (MAGE), has allowed

his lab to do just that. MAGE employs the

use of single-stranded DNA fragments that

are ninety nucleotides long, eighty-nine of

which are complementary to a sequence

www.yalescientific.org

found in the genome, and one of which is

a “mismatch.”

In the context of this study, the researchers

inserted a single nucleotide change that

switches the

“G” in TAG

IMAGE COURTESY OF THE ISAACS LAB

Diagram depicting the recoded E. coli

genome. It is divided into 32 sections, each of

which corresponded to a single E. coli strain

that underwent MAGE from the outset.

to an “A” in TAA, effectively converting

all TAG’s in the E. coli genome to TAA

sequences. In MAGE, a wild-type population

of E. coli cells that all have an identical

genome is used at the outset. When ninety

nucleotide long fragments are introduced,

“site-directed” mutations are created in

the cell with efficiencies greater than 30%,

whereas conventional technologies operate

at an efficiency of, at best, less than one

percent. These mutations are engineered

to occur at a single, specific nucleotide in

the DNA of the E. coli genome. Even with

such high efficiency, however, the risk of

introducing deleterious mutations is quite

high. Because a high proportion of E. coli

DNA codes for genes, a single undesired

point mutation in the genome could result in

cell death. Successfully recoding the genome

with as few side effects as possible, therefore,

requires extremely careful work.

“Just like March Madness, we had 32 initial

strains, each of which had a different set of

codons recoded,” said Isaacs. Each strain was

targeted by Isaacs’ MAGE technology to a

different part of the circular E. coli genome,

like 32 slices of a pie. “Then the challenge

became,” said Isaacs, “‘how were we going to

get this into a single organism?’”

That is where a second technology

that Isaacs developed, known as

Conjugative Assembly Genome

Engineering (CAGE), is

useful. Isaacs used MAGE

to introduce site-directed

mutations to convert all

TAG sequences to TAA

sequences, on 32 separate

occasions. CAGE was

then used to “merge”

the 32 strains, over five

consecutive rounds, into

a single organism that

ultimately contained all 321

TAG mutations. After much

work, Isaacs’ team successfully

created a genomically recoded

organism. In the recoded E. coli

they created, the UAG stop codon

had been converted into the UAA

stop codon, deleting RF1 from the cell,

allowing for UAG to lose its ability to “stop”

translation. This rendered UAG a “blank

codon,” or a kind of canvas for future

experimentation.

A Canvas for Innovation

Astonished by the cell’s ability to grow

normally under a variety of conditions, Isaacs

and his team took the opportunity to use this

“blank codon” as an area for expanding the

genetic code. While the cell only uses the

same twenty standard amino acids, there are

several nonstandard amino acids (NSAAs)

that can be synthesized, each of which has

new chemical properties. Isaacs therefore

introduced a new tRNA that is specific for

UAG, but loaded with a novel NSAA, in an

effort to reassign UAG from a blank codon

to a “sense” codon, or one that is capable

of coding for an amino acid. Incredibly, the

scientists were able not only to recode the E.

coli by getting rid of a stop codon that the cell

naturally uses during protein synthesis, but

they were also able to convert an essential

protein, RF1, to a nonessential one, making

the UAG stop codon a blank template that

they then exploited to incorporate NSAAs.

March 2014

Yale Scientific Magazine

13


FOCUS

biotechnology

IMAGE COURTESY OF THE ISAACS LAB

Diagram depicting the recoded E. coli genome. It is divided into 32 sections, each of which corresponded to a single E. coli strain that

underwent MAGE from the outset.

Throughout this process, the researchers

found that not only were these E. coli recoded,

but also that, due to the newfound identity

of the UAG codon, they became resistant to

a bacteriophage, a virus that infects bacteria,

known as T7.

“By wiping out the function of an entire

codon and because the codon is conserved

across nearly every species, the hypothesis

was that we could possibly prevent the

proper expression of foreign genes that rely

on that codon,” Isaacs said. More specifically,

the T7 virus was unable to properly translate

its infectious proteins, as RF1 was lost in the

host cells.

By creating genomically recoded

organisms, the scientists successfully

produced a “genetic firewall” in which the

functional exchange of genetic material

between viruses in the environment and

the organism is hindered, due to the new

translation environment in the host cell.

Future Applications

Although this work has already

accomplished significant new feats, many

more applications may be possible. In the

past, the Isaacs lab has applied MAGE

commercially to mass-produce an anticancer

antioxidant at an unprecedented

speed in E. coli. When he was asked, Isaacs

affirmed the fact that there is much industrial

interest in his work and in the innovative

methodologies he has invented. With the

introduction of synthetic amino acids, these

genetically recoded E. coli have the potential

to produce new biomaterials that have uses

for entities like drug delivery vehicles and the

U.S. army.

The possibilities this research opens up are

tremendous. While some believe that this is

the start of a Frankenstein-esque, sci-fi future

of genetically recoded organisms, others, like

Isaacs himself, are enthusiastically optimistic.

“Biology is the most powerful technology

we have,” says Isaacs. Biology, unlike the

hardwired structures of computers, is

a dynamic, evolving system that is only

beginning to reveal its vast potential as a tool

for significant engineering innovation.

ABOUT THE AUTHOR

BLAKE SMITH

BLAKE SMITH is a sophomore in Jonathan Edwards College intending to major in

Molecular, Cellular, and Developmental Biology. He is an active member of YIRA,

and has worked in a glycobiology lab since freshman year.

THE AUTHOR WOULD LIKE TO THANK Professor Isaacs for his time and

willingness to explain his research in a patient, entertaining, and intelligible manner.

FURTHER READING

Lajoie MJ, et al. “Genomically recoded organisms expand biological functions.”

Science. 2013, 342: 357-360.

14 Yale Scientific Magazine March 2014 www.yalescientific.org



METAL FEVER

BY RENEE WU

ART BY JASON LIU

Silvery white and soft enough to cut

with a knife — at first glance, indium

is unremarkable, just another faintly

glittery mineral mined from the Earth.

In fact, indium quietly plays a central role

in modern society: It is the vital element used

to make smartphone screens touch-sensitive,

and it is used in the thin-film coatings of LCD

computer screens and solar cells. Yet, like

many of the specialty metals at the foundation

of modern electronics, understanding the

global supply of indium is not easy.

“What’s interesting about specialty metals

like indium is that they play such a crucial

role in modern technology,” said Dr. Barbara

Reck, a research scientist who studies the

ecology of metals at the Yale School of

Forestry and Environmental Studies’ Center

for Industrial Ecology (CIE). “Yet, most

people are completely unaware of their

importance.”

Reck and her colleagues at the Yale CIE

pioneer the emerging field of industrial

ecology, a field that investigates how factors

like economics and politics influence the use

of environmental resources. Their research is

at the forefront of answering one imperative

question on every national government and

smartphone-user’s mind: Do we have enough

metals to keep up with the technological

advances of society?

The “Omnivorous Diet Of Modern

Technology”

A generation ago, most products were

designed with fewer than a dozen different

materials. In contrast, today’s electronics

products use up to 60 elements, and a highperformance

wind turbine can use two

tons of one metal. This rapid expansion

was mainly driven by technology’s growing

appetite for specialty metals, particularly rare

earth metals like neodymium, lanthanum, and

yttrium. Characterized by tongue twister-like

names, the 17 rare earth elements comprise

a wide assortment of unique magnetic and

electrical qualities that medical diagnostic,

automobile, and many other industries heavily

rely on. Interestingly, rare earth elements

are somewhat plentiful in the Earth’s crust

despite their label as “rare.” However, they are

often not concentrated enough to make them

economically exploitable.

Although these metals themselves are not

new discoveries, many of their hallmark

properties are. In recent decades, the dawn

of a digital electronics age and the “green

energy” movement boosted specialty metals

into the spotlight, inspiring research to

divulge their other potentially useful qualities.

Simultaneously, materials scientists began

mixing these specialty metals with other

elements, creating new alloys with distinctive

and exploitable characteristics. As a result,

today’s devices are becoming sleeker, stronger,

and smarter at a swifter pace than ever before,

with progress seemingly limited only by the

imaginations of inventors.

A Sensitive Supply Chain

In reality, a very sharp, tangible limitation

to such progress exists: the supply of these

metals. On a basic level, metals are not equally

accessible in nature. Some mineral deposits,

such as copper, are found all over the world;

others, such as rare earths, are found in only

one or a few countries. Furthermore, the

majority of metals used today are mined as

“companion metals,” tiny elemental traces

that are extracted from the mine of another,

more abundant “host metal.” For one million

grams of zinc found in zinc mine, for example,

you might find a single gram of indium.

However, the more imminent limitation to

the supply of specialty metals is geopolitics.

The standard illustration of this delicate

balance is China, which supplies around 95

percent of the world economy’s rare earth

metals. Following a diplomatic row with Japan

in 2010, China restricted rare earth exports

to Japan, and these essential metals fuel its

electronics industry. Although the ban was

lifted, China did continue to cut back on rare

earth exports to the rest of the world.

The Yale CIE focuses on understanding

how situations like this one affect the global

supply and demand of metal. Established

in 1998 by current director Dr. Thomas

Graedel, the CIE laid the foundation for a

comprehensive understanding of the metal

cycle: where a metal comes from, how it is

used, and what happens when it is discarded.

While analysis of a metal’s life cycle is

useful for understanding the present state of

a metal, it cannot predict changes in supply

or demand. So, in 2006, the U.S. National

Research Council (NRC) started looking

into the concept of “criticality” for a metal,

a more comprehensive standard that is based

16 Yale Scientific Magazine March 2014 www.yalescientific.org


environmental science

FOCUS

on two variables: availability of the metal and

importance of use.

Reck cited copper as an example. “It would

matter a lot if you didn’t have copper, because

it’s hard to replace copper in electronics,” she

said. “On the other hand, its criticality is still

considered low, because there is a low supply

risk — you find a little bit of copper all over

the world.”

Since the NRC report was published in

2008, the CIE has focused on developing and

analyzing criticality assessments for all metals.

Graedel and his group also extended the

NRC definition to include a third dimension

in addition to supply risk and vulnerability

— environmental implications — to supply

restriction. Any metal element can now be

evaluated in this 3-D “criticality space.”

The CIE’s latest publication has elicited

the most buzz. In a comprehensive study,

Graedel, Reck, and colleagues evaluated how

replaceable each of the 62 metals is for its

major uses. According to their findings, not

a single metal currently has an exceptional

substitute. The best replacement for a metal

would need similar physical and chemical

properties to the metal, but such elements

would likely be found in the same ore deposits

in nature. Thus, the best alternative for a

scarce element would likely be scarce itself.

The Resource Economics Argument

www.yalescientific.org

IMAGE COURTESY OF BUSINESS INSIDER

Behind every smartphone is the dirty

process of mining for rare earth elements.

As a materials scientist with a lifetime of

semiconductor research and a number of

patents, Dr. Tso-Ping Ma is unfazed by this

finding.

“In my field [of microchips], we react

very sensitively to supply and demand,” said

Ma, a former scientist at IBM and now the

Raymond John Wean Professor of Electrical

Engineering and Physics at Yale. “If

something becomes very very rare, people

like us [materials scientists] will look for

something else as good or better.”

Resource economists argue that if

something becomes very scarce, its price

will skyrocket. That high price will then spur

development of substitutes for that material

before society ever grinds to a halt. Thus,

according to this argument, although indium

is rare, we are not in danger of running out

of smartphones or LCD screens, because

increasing costs of indium will force an

indium replacement to be found.

Their argument is not unfounded. A

recent example concerns IKEA, the popular

Swedish company known for its ready-toassemble

home appliances. Many of IKEA’s

kitchen and bathroom products are made of

a stainless steel alloy that, until 2003, included

nickel. However, China’s rapidly growing

appetite for nickel in the early 2000s led to

a spike in the price of the metal, motivating

some nickel users to look for alternatives.

Consequently, in mid-2003, IKEA opted to

completely eliminate nickel from its entire

repertoire of stainless steel products and

switch to ferritic stainless steel — not a

small shift, considering the company’s annual

consumption of stainless steel in 2007 was

around 60,000 tons.

In this age where virtually every element in

the periodic table is used, IKEA and other

forward-looking companies are focusing more

on element scarcity in addition to product

performance in their business decisions. “It’s

a materials gamble,” said Ma.

Seeking Sustainability

If the supply of materials were more

sustainable, this gamble could be less risky —

one reason why scientists strongly advocate

metal recycling. The goal is to achieve a

closed-loop system where all materials are

reused, thus creating zero waste. For example,

lead use in batteries is nearly a closed-loop

system; an estimated 90 to 95 percent of lead

is collected and pre-processed from batteries.

In contrast, only 5 to 10 percent of electronics’

platinum group metals are recycled.

Reck pinpointed two prime ways to improve

metal recycling. The first is simple: Improve

collection. This applies to metals that are

easy to identify and reprocess, like iron and

copper, as well as to specialty metals that are

used in tiny quantities in many consumer

goods. Improving collection of these metals

is especially important because many of them

are used in electronic devices with short

lifetimes and are currently not recycled at all.

The second challenge is to design products

with recycling in mind. Today’s products

are designed using diverse combinations of

metals that make them more functional than

ever before. However, this also means it is

a lot harder to separate these metals from a

mixture; rare earth elements are particularly

tricky because they share many similar

properties. Furthermore, some metals, if

not separated properly, can be disastrous

impurities — an expensive waste of both

scarce and common metals.

So are we actually running out of metals?

Experts at the Yale CIE cautiously say “not

exactly” while emphasizing the importance

of sustainability and offering a more nuanced

perspective as their answer.

“A more insightful question is to ask whether

supplies will be sufficiently constrained to

impede routine industrial use,” Graedel wrote

in a review for the MRS Bulletin. “There, our

conclusions are on shakier ground.”

ABOUT THE AUTHOR

RENEE WU

RENEE WU is a senior Molecular, Cellular, & Developmental Biology major in

Silliman College. She is the former Managing Editor and Features Editor for the

Yale Scientific and works in Dr. Eric Meffre’s lab studying B cell development in

humans.

THE AUTHOR WOULD LIKE TO THANK Dr. Reck and Professor Ma for their time

and enthusiasm.

FURTHER READING

Greenfield, A., & Graedel, T. E. (2013). The omnivorous diet of modern technology.

Resources, Conservation and Recycling, 74(0), 1-7.

March 2014

Yale Scientific Magazine

17


Tiny guts,

Big consequences.

Manipulating the

microbiome of the tick that

transmits Lyme disease

By Lorraine James

Art by Jeremy Puthumana

The blacklegged tick, Ixodes scapularis,

is about two millimeters long and

one millimeter wide in the nymphal

stage of its life. Unless it is moving around

on the skin, it can easily be mistaken as a

dark brown freckle or speck of dust, despite

its eight limbs. Many people never even see

the parasite as it feeds on them for at least

36 hours; at that point, the tick has already

transmitted the bacteria that cause Lyme

disease.

The gut of this arthropod, just like the

human gut, contains bacteria that benefit

from their host without harming or helping

it. These are known as “commensal bacteria.”

In contrast, some of the commensalism

in the human gut is actually mutualism, in

which both host and parasite benefit; for

example, E. coli bacteria in the gut help break

down materials that humans cannot digest

on their own, like cellulose.

A Tick’s Bacterial Life Cycle

Ixodes scapularis has roughly a two-year life

cycle, during which it progresses through

separate stages: larva, nymph, and adult.

Before molting and proceeding from one

stage to the next, the tick must feed on a host

to become engorged with blood. As it feeds,

compounds in its saliva prevent the host

from feeling the attached tick. Each of these

feeding events is an opportunity for the tick

to ingest bacteria from its host.

The bacterial inhabitant of the tick’s gut

directly responsible for the spread of Lyme

disease is a non-commensal spirochete

called Borrelia burgdorferi, named after Willy

Burgdorfer, who isolated and cultured the

bacteria from the midguts of Ixodes scapularis

ticks. Shaped like a helix, Borrelia is the

etiological agent of Lyme disease. During a

blood-meal, Borrelia travels from the blood

and colonizes the midgut. Then, it enters the

salivary glands where it can be secreted at a

subsequent feeding event.

Alexia Belperron is a researcher in the

Rheumatology Department at the Yale

School of Medicine. One of her projects

is studying Borrelia in infected mice using

optical tweezers, or lasers. She warned

that Borrelia is not to be underestimated,

especially when it comes to motility. “It has

to move within the [human] body and can

get to every tissue within the body,” she said.

“It moves into your bloodstream and then

moves into tissue.”

To travel to other parts of the human body,

Belperron said, Borrelia can “exert significant

forces” to return to the bloodstream. In

the tick, the bacteria has to travel in similar

ways, making its way from the midgut to the

hemolymph before positioning itself into

the salivary glands.

Amazingly, Belperron explained, Borrelia

knows where in the tick it is located and also

knows whether it is moving into or out of

the arthropod. This motility helps it avoid

the immune system and survive in animals’

blood and tissues.

Sukanya Narasimhan, a researcher in the

lab of Erol Fikrig in the Yale Department

of Internal Medicine, examines vector-host

interactions in the context of infectious

disease. She helped illuminate why Borrelia

prefers tissues to blood in both ticks and

humans. In some ways, it is a “bloodborne

pathogen that doesn’t particularly

like blood,” she said. In the short term,

blood exposure is tolerable for Borrelia while

long-term existence in the blood exposes

the spirochetes to “deleterious blood-meal

components.”

Changing A Tick’s Gut Bacteria

Narasimhan and colleagues from the

School of Epidemiology and Public Health

and the Center for Medical Informatics at the

Yale School of Medicine posed the following

question: How does altering the composition

of the tick’s existing gut microbiome, which

is comprised of the commensal bacteria,

affect the colonization ability of the diseasecausing

pathogen, Borrelia? To find out, the

researchers induced a state of dysbiosis in

18 Yale Scientific Magazine March 2014 www.yalescientific.org


microbiology

FOCUS

the ticks: By rearing and maintaining tick

larvae in sterile conditions, they altered the

composition of the microbial community

living in the arthropod’s gut.

They found that Borrelia colonizes

dysbiosed larvae less than it colonizes larvae

with unaltered microbe communities. In

addition, their results showed that dysbiosed

larvae had lower levels of the signaling protein

STAT, involved in arthropod gut immunity.

Interestingly, decreasing STAT expression

also decreased Borrelia colonization. The

observation was initially puzzling: The

immune system works to

shield an organism from

invading pathogens, so

why would a less active

immune system from

lower STAT levels result

in less colonization by

Borrelia?

According to

Narasimhan, researchers

had similar questions

until they figured out, in

this case, that STAT has a

more relevant role: tissue

repair and remodeling.

This became evident

when decreased STAT

expression compromised

the epithelium renewal

by thinning a specific

membrane that lined

the tick’s gut. Similarly, decreased STAT

expression resulted in decreased expression

levels of peritrophin-1, a protein important

for maintaining the integrity of this

membrane. The fact that Borrelia, though

blood-borne, prefers to reside in tissue

explains this phenomenon. Narasimhan and

colleagues wrote that if the membrane were

compromised, Borrelia “could risk exposure

to deleterious blood-meal components.”

These findings demonstrated how Borrelia

interacts with the tick’s microbiome, but there

is much left to be explored. Instead of just

perturbing the composition of commensals

in dysbiosis, researchers can try to increase

the percentage of a specific bacterial genus,

like Rickettsia, to see how this change affects

the colonization of Borrelia. The bacteria

could compete with each other for nutrients,

cooperate, or exchange DNA using

conjugation or other forms of horizontal

gene transfer. As the paper remarks, “such

an understanding might catalyze ways to

control vector-borne pathogens.”

The Challenges With Ticks

Despite this optimism, Giovanna Carpi,

a postdoctoral associate and resident expert

on tick microbiota in a vector ecology

laboratory at the Yale School of Public

Health, maintained that the field still faces

unique challenges. One significant challenge

of studying tick microbiota, she explained,

is “the preservation and isolation of high

quality genomic DNA and RNA from a tiny

arthropod or from its organs.” Similarly,

shallow sampling or sequencing methods

might detect an insufficient abundance of

bacterial taxa.

Belperron also teaches a class at Yale

College called “Malaria, Lyme, and Other

Vector-Borne Disease.” She noted that a

holistic explanation of Lyme disease can be

challenging because “you need a complete

understanding of the immune system,

microbiology, entomology, and ticks.”

“It’s impossible to be an expert on all those

things in… a semester,” Belperron said.

Those who study Lyme disease face

other, more philosophical challenges. In

an age where global health studies are

very prominent, Lyme disease is often

characterized as a first world illness,

considering that it primarily affects a

Northeastern population. “I

think it would be nice to

work on a disease that affects

a larger population,” said

Narasimhan. “But I think tickborne

diseases are also present

in the third world…When I do

Lyme, I’m not saying I’m only

looking at or understanding

Lyme; it’s a model. Some of

the lessons that you learn from

Lyme disease are transferable

to other disease like malaria.”

In fact, the initial inspiration

for this project was the vast

amount of insight required

to study the human and

PHOTO BY CHANTHIA MA

Tick larvae (above) pass the nymph stage before developing into mature

adults. Between stages, the tick must feed on blood from an animal host.

mammalian microbiome.

There remains much to be

explored on how a vector

encounters a pathogen and

becomes a vehicle for spreading disease.

Researchers hope that continuing to study

the metazoan gut will provide more answers

to the tick enigma.

ABOUT THE AUTHOR

LORRAINE JAMES

LORRAINE JAMES is a Trumbull junior majoring in both Molecular, Cellular, and

Developmental Biology and American Studies. She is a first time writer for Yale

Scientific Magazine and spent last summer assisting with research at the Diuk-

Wasser lab at the Yale School of Public Health.

THE AUTHOR WOULD LIKE TO THANK Dr. Narasimhan, Dr. Carpi, and Dr.

Belperron for their time, expertise, and affability. She would also like to thank

Professor Maria Diuk-Wasser and the researchers at the Diuk-Wasser laboratory

for teaching her about Lyme disease.

FURTHER READING

Gravitz, L. (2012). Microbiome: The critters within. Nature 485, S12–S13.

www.yalescientific.org

March 2014

Yale Scientific Magazine

19


Immortal Neurons

By Lisa Zheng

Art by Nicole Tsai

Most people know that neurons die

out with age, loosening our grip

on reality. Generally, people also

believe that neuron loss with age cannot be

prevented.

But what if neuron loss over time was not

an undeniable outcome of nature, and instead

something that we could treat? A new study

at the Yale School of Medicine by Professor

Marc Hammarlund and postdoctoral fellow

Alexandra Byrne suggests that neuron loss

may not be correlated with age, but that it

may be regulated by something else entirely.

Neurons, which transfer electrical signals

between the brain and the body, have spindly

projections called axons. Axons connect

neurons and pass along signals from one

nerve cell to another; thus, axon regeneration

is a process integral to proper brain function:

It allows the body to repair important

neuronal connections after injury. As most

organisms age, however, the potential for

axons to regenerate declines.

To investigate the regulators of neuron

loss, Hammarlund and Byrne examined

the ability of animals to regenerate injured

axons and how this ability declines with age.

“The goal of our study was to identify genes

that regulate this age-related decline in axon

regeneration,” Byrne said. “More specifically,

we wanted to characterize how these genes

were controlling whether or not an aged

axon could regenerate after injury.”

Instead of testing their hypothesis on

human subjects, Hammarlund and Byrne

used C. elegans, a one-millimeter-long

transparent worm that researchers often use

as a model organism due to its well-defined

nervous system and transparent nature.

Hammarlund had previously noted that

these worms’ motor neurons, like those in

humans, decline with aging. Because many

genes in C. elegans are conserved in mammals,

they function similarly to mammalian genes,

making them good models. In addition, the

worm’s nervous system is small and welldefined,

making it much easier to study than

that of a human.

As an adult animal ages, its neurons exhibit

several decreased functions: retraction,

growth response, and extension. Retraction,

also known as pruning, is an important

function of neurons that allows them to

recycle axonal contents to different parts of

the neuron. Growth response and extension

are key functions that allow a neuron to

respond to injury; when a break is detected,

they help initiate neuron growth and extend

the axon to bridge the gap of the break. Loss

of these functions severely limits the ability

of neurons to regenerate.

Hammarlund and Byrne investigated these

particular aspects of neuronal aging. They

began by researching the genetic relationship

between age and axon regeneration. To do

this, they injured neurons using a laser beam.

They then watched the neurons regenerate,

closely monitoring their progress to track

what percentage of the axons destroyed

by the laser beam ultimately regrew. This

process was carried out in both “young,”

one-day-old adult worms and “aged,” fiveday-old

adult worms to determine how much

age affects regeneration. In the young adults,

65% of axons regenerated in response to

injury, while in aged adults, only 28% of the

axons regrew.

This regeneration difference was mainly

due to the failure of growth cones, which

are the extensions at the ends of growing

axons that help determine the direction in

which to initiate growth. In the axons that

did begin regeneration, 31% in young adults

and 12% in aged adults made substantial

growth progress towards reconnecting with

the dorsal nerve cord, which is similar to the

spinal cord in mammals. With these results,

Byrne and Hammarlund showed that when

compared to those of younger adults, aged

adults’ brains are less able to initiate and

extend axon growth in response to injury.

After establishing that age was the

factor that prevented neuron growth and

regeneration, the researchers set out to find

some way to delay neural aging. Byrne and

Hammarlund hypothesized that certain

20 Yale Scientific Magazine March 2014 www.yalescientific.org


neuroscience

FOCUS

genetic pathways play a role in physical

aging and deterioration; manipulating these

pathways might suppress the decline in axon

regeneration. They tested several pathways to

find one that, when altered, would produce

aged adults that were physically as old as

the control, but able to regenerate axons as

quickly as young adults. In other words, the

scientists were looking for something quite

remarkable: a pathway they could manipulate

to create an old worm with the brain of a

young one.

The pathway they discovered, called

daf-2, is an insulin inhibiting pathway. Daf-2

is the only member of the insulin receptor

family that exists in C. elegans and is known

to regulate life span. When researchers

in the Byrne and Hammarlund groups

modified this pathway, ten-day-old adults

demonstrated neural regeneration ability that

far surpassed that of the control group.

These results imply that the daf-2 pathway

regulates age and neuron regeneration

separately. These two factors, contrary to

intuition and prior belief, are completely

independent: as the researchers showed, an

animal can age at a normal rate but still have

the neuron regeneration rate characteristic

of a younger animal.

The newfound effects of this pathway were

surprising. The daf-2 pathway was already

known to regulate life span, but that it also

regulates regeneration ability, independent

PHOTO BY CHANTHIA MA

Alexandra Byrne, a postdoctoral fellow in the Hammarlund lab, was the lead author of

the study. Professor Marc Hammarlund, Professor in the Department of Genetics, was the

principal investigator.

of life span, is a recent insight. With this

knowledge, Byrne and Hammarlund made

their most exciting discovery. “By activating

the insulin pathway specifically in neurons,”

they wrote, “we were able to create old worms

whose axons successfully regenerated despite

the worms’ normal life spans. We were also

able to do the opposite: create worms that

lived extended lives, yet had axons that did

not regenerate well.” They have shown that

the decrease in axonal regeneration ability

is not simply a consequence of old age, but

rather that the insulin pathway is responsible

for inhibiting regeneration with age. Their

research demonstrates that the neuronal

health span and life span can be uncoupled

with different pathway regulation.

While this study is still in its preliminary

phase, Hammarlund explained that its effects

are far-reaching. “The study has significant

implications for further research into how

the nervous system regulates its response to

time autonomously, and into the signaling

pathways identified,” he said. The fact that

the nervous system seems to be governed

by a different regulation system than its age

opens many doors. Researchers can further

explore pathways that prevent nervous

system deterioration as organisms get older.

The knowledge that insulin regulates motor

neuron regeneration furthers researchers’

understanding of regeneration response to

injury and suggests additional pathways that

can be explored.

Identifying genes that are involved in this

regulation in aged animals increases our

understanding of how the nervous system

ages. We can control neuronal health with

a mechanism separate from life span. The

creation of genetically modified worms that

regenerate neurons even at an older age

suggests that such a distinct separation of

age and neuron health may even be possible

for humans in the future. The discovery of

a similar neuron regeneration regulation

pathway in humans may hold medical

implications for Alzheimer’s disease or other

neuronal degenerative diseases. Regulating

the loss of neuron regeneration abilities

can potentially prevent or treat diseases like

these. Alzheimer’s affects 26.6 million people

worldwide, so such a remarkable discovery

would help improve many lives.

ABOUT THE AUTHOR

LISA ZHENG

LISA ZHENG is a sophomore Molecular, Cellular, Developmental Biology and

Economics major in Pierson College. She is a writer for the Yale Scientific Magazine

and is interested in studying the genetics of neurons.

THE AUTHOR WOULD LIKE TO THANK Professor Marc Hammarlund and

Alexandra Byrne for their time and enthusiasm and Julia Rothchild for her help.

FURTHER READING

Antebi, Adam. “Genetics Of Aging In Caenorhabditis Elegans.” PLoS Genetics 3,

no. 9 (2007): e129.

www.yalescientific.org

March 2014

Yale Scientific Magazine

21


Sustainability in Flight

by theresa steinmeyer art by audrey luo

When Gail Cameron of the Yale

Animal Resources Center heard

that there was a barred owl in a

tree outside of the Child Studies Center, she

rushed over to catch a glimpse. Although the

barred owl is not a rare bird, sighting one in

New Haven is unusual. Cameron checked on

the bird several times throughout the day,

pointing it out to visitors at the Child Study

Center. This sighting also attracted other

bird enthusiasts, who stopped by to snap

photos of the guest. Around four o’clock,

Cameron watched the bird fly away. “It was

just beautiful,” she recalled, beaming.

Cameron’s enthusiasm for wildlife is

exactly the spirit that the Yale Citizen Science

initiative aims to foster among New Haven

residents. Organized by the Yale Office of

Sustainability and the Peabody Museum

of Natural History, this project invites

participants to photograph and observe

various animal species on Yale’s campus.

The project hosts monthly guided walks so

that Yale staff, students, and New Haven

community members can explore the rich

biodiversity that the city has to offer. But

these participants — “citizen scientists,” as

they are often called — are not necessarily

experts, nor are they scientists by training.

In fact, many of them are identifying birds

for the first time, teaming up with more

experienced bird-watchers to observe and

record biodiversity in the Elm City.

Yale’s Citizen Science Program Takes

Flight

The Yale Citizen Science program was

inspired in part by the “BioBlitz,” a 24-hour

event in which biodiversity experts team up

to conduct an inventory of the biodiversity

in a given area. Yale launched its first BioBlitz

in 2007, partnering with the Beardsley Zoo

in Bridgeport. During the event, volunteers

and experts alike used motion-sensitive

camera filming, naked eye viewing, and

other observation techniques to identify 729

animal species in Stratford.

These data catalogued noteworthy outlier

sightings, including a spotted salamander, a

black amphibian characterized by its yellow

spots, and a purple gallinule, a bird with

bold green wings and long toes suitable for

navigating its native tropical wetlands.

Buoyed by the success of the BioBlitz, the

Yale Office of Sustainability and the Peabody

Museum launched their own Citizen Science

program in 2012. They hoped to engage

members of the Yale community — not

just scientists, but other citizens too — in

exploring the biodiversity within university

grounds.

Today, the Yale Citizen Science program

allows campus and community members

to gather information on New Haven’s

biodiversity, especially its plants, birds,

insects, and small animals. With a better

understanding of local species and their

needs, Yale can plan land usage around

buildings more effectively and ensure that its

landscaping projects are friendly to resident

species. However, the program seeks to do

more than gather information: it also seeks

to help its participants become more aware

of the wildlife thriving in their home city.

A Focus on Birds

Lauded for its biodiversity and named an

Urban Wildlife Refuge in 2013, New Haven is

home to a wide variety of plants and animals.

But, in order to launch a program suitable

for expert and novice citizen scientists alike,

the Office of Sustainability and the Peabody

began with a narrow focus: birds.

“We decided we wanted to start with

the low-hanging fruit,” explained David

Heiser, head of education and outreach for

the Peabody Museum. Birds draw a critical

mass of experienced birders to the program,

22 Yale Scientific Magazine March 2014 www.yalescientific.org


citizen science

FOCUS

but are also easily visible and identifiable to

inexperienced participants.

The program holds bird walks about once

a month in the morning or at mid-day. Before

heading outdoors, guides bring newcomers to

the Peabody Museum’s Hall of Birds, where

budding birders can familiarize themselves

with the sizes and colorings

of 40-50 taxidermied birds

that they can expect to see.

Armed with binoculars,

participants then depart

from the Peabody Museum

and follow a route up

Science Hill. Afterwards,

they can upload their

findings to Yale’s online

database, the YUBio Portal.

This database catalogs

birds by their scientific and

common names, along with

the times and dates of past

sightings.

For each species, the

resource also includes

images and interactive maps

of sightings throughout

New Haven. If citizen

scientists are uncertain

about their birds, they

can submit photos to the

Peabody Museum for

analysis.

Heiser insists on the

potential value of these

images. “The iPhone shot

of a bird out there in

the tree is rarely going to

produce something that

www.yalescientific.org

IMAGE COURTESY OF YALE OFFICE OF SUSTAINABILITY

Farnam Gardens, adjacent to the Yale Farm, provides a beautiful

location for observing New Haven’s biodiversity.

one of us can

identify, but you

never know,” he

said. “On occasion

it does, and there’s

a field mark on that

bird that you can

pick out from forty

feet away.”

Cameron, a

Sustainability

Leader who works

in the Animal

Resource Center

at the Medical

School, enjoys

watching for birds

on her daily walk

through Amistad

Park. Although

she often observes common birds such as

starlings, pigeons and sparrows, her favorites

are peregrine falcons. These tend to occupy

rocky cliff faces such as those of East Rock,

West Rock, and Sleeping Giant, but have also

been spotted on the Kline Biology Tower,

where Cameron hopes to increase interest in

campus bird watching.

Navigating Accuracy

As new birders become major contributors

to the biodiversity database, how can the

Peabody Museum maintain the quality of

this data? When citizen scientists register to

input data into the portal, they are prompted

to identify their birding experience level —

novice, intermediate, or expert.

“When members of the Yale community

are supplying data, if we recognize them as

experts, if they’ve been on our walks before

and we know who they are, we’re looking at

their observations and nodding our heads

and saying, ‘Yeah, that sounds right,’” Heiser

explained.

As the Peabody Museum checks over

uploaded information, it pays special

attention to sightings recorded by novice

birders. “On the rare occasion that a novice

was to report a bird that really stuck out like

a sore thumb, it would raise some flags,”

Heiser said. “If it seemed really far-fetched,

PHOTO BY NICOLE TSAI

David Heiser, head of Education and Outreach at the Peabody, displays one of the museum’s many owl

species, the Eastern Screech Owl.

March 2014

Yale Scientific Magazine

23


FOCUS

citizen science

IMAGES COURTESY OF YALE OFFICE OF SUSTAINABILITY

(left) Citizen scientists observing local vegetation on a plant walk on Sachem Street. (right) A flock of birds gathered in the Grove Street

Cemetary, a location frequented by avid birdwatchers.

we might be tempted to remove it from the

data, but that hasn’t happened yet. That’s a

good sign that people are taking it seriously;

they’re learning their birds.”

Researchers can also compare the data in

the YUBio Portal to other data nationwide.

For instance, the Cornell Lab of Ornithology

and the National Audubon Society maintain

a database called eBird. “There are enough

avid and active birders out there that if

something really weird pops up for a location

and it’s really there, you’ll have people driving

in from six states away to see it… The

community in a way polices itself,” Heiser

said.

Sprouting Initiatives

The bird walks are the first of many efforts

to allow citizen scientists to participate in

biodiversity research at Yale. “We wanted to

really capture more of the biodiversity than

just birds,” Heiser said when he reflected

on the decision to begin the program with

a focus on bird watching. “We knew that

plants were probably the next lowest hanging

[fruit], and then maybe insects.”

The program expanded to include plant

walks last fall and Heiser hopes that citizen

scientists will eventually be able to observe

insects, especially butterflies and dragonflies,

since these species are relatively easier to

identify.

Citizen scientists who want to make more

individualized contributions to the program

can now adopt trees throughout campus and

the city. Tree adopters begin recording the

development of their trees in early spring,

when flower buds and leaf buds first appear.

Throughout the year, these citizen scientists

note the dates of other benchmarks in a

tree’s life cycle, such as the bearing of fruit

or seeds, or the first appearance of fall color.

Since last fall, Cameron has documented a

sugar maple tree in Amistad Park, which she

greets every morning on her way to work.

Ultimately, the data that the program

collects on trees will help scientists to

understand how climate change is affecting

New Haven. “Because Yale is so old and we

do have photographs of certain trees; we

know how they looked at a certain time,” said

Virginia Chapman, Director of Yale’s Office

of Sustainability. “If they were flowering

during commencement, for example.” By

comparing data from the Citizen Scientists

program to existing records, climate

scientists may be able to draw conclusions

about the effects of changing climate on

species composition in New Haven.

Continuing to Climb

As it evolves, the Citizen Science program

finds that keeping its participants engaged

can be a challenge. While as many as eighty

participants may show up for a given bird

walk and collect valuable data, it is difficult

to find volunteers willing to contribute

regularly. “The data is needed long-term,”

Cameron said. “You might see a robin today,

but if you see robins every day of the year

for the next five years, that’s going to say

something about the birds that use this area.”

The program also encourages students

to get involved. Although most do not

live in New Haven year-round, they can

collect data on the biodiversity within their

college courtyards. “You don’t have to be

an expert,” Cameron said. “I think people

hesitate because they think, ‘I won’t be able

to contribute.’ But you really can.”

ABOUT THE AUTHOR

THERESA STEINMEYER

THERESA STEINMEYER is a sophomore English major in Trumbull College. In

addition to contributing to the Yale Scientific, she enjoys writing for the Yale Daily

News and playing her violin in the Berkeley College Orchestra.

THE AUTHOR WOULD LIKE TO THANK Gail Cameron, Virginia Chapman,

Amber Garrard, and David Heiser for generously sharing their time, knowledge,

and enthusiasm for sustainability at Yale.

FURTHER READING

Lundmark, Cathy. “BioBlitz: Getting Into Backyard Biodiversity.” BioScience 53,

no. 4 (2003): 329.

24 Yale Scientific Magazine March 2014 www.yalescientific.org


www.yalescientific.org

March 2014

cell biology

FEATURE

Glass-Like Properties of

Bacterial Cytoplasm Discovered

BY GEORGE MO

Small, prokaryotic organisms on the scale of micrometers, bacteria

have always been difficult to study. While most of the cellular

structures and functions have been discovered, the cytoplasm has

often been overlooked. A recent study from Yale University dove into

the mysterious nature of bacterial cytoplasm and how

its properties determine cellular behavior and

physiology. Dr. Christine Jacobs-Wagner,

Professor of Molecular, Cellular, and

Developmental Biology and of

Microbial Pathogenesis, led a

team that discovered unusual

glass-like properties of

bacterial cytoplasm.

Remarkably, these

properties seem to

depend on the activity

or dormancy of the

cell.

All living things

require some

mechanism for

transporting material

throught their cells.

While most eukaryotes

rely on active transport

involving cytoskeletal

filaments and motor

proteins, bacteria were

thought to rely mainly on

diffusion. However, diffusion of

bacterial cytoplasm is much more

complex than that of simple liquids

like water: Cytoplasmic contents span a

wide range of particle sizes, from just a few

nanometers to hundreds of micrometers.

The observation that metabolic activities

end up disrupting the equilibrium of the

cytoplasm intrigued Jacobs-Wagner and her

team. Thus, they set out to understand more

about the properties of bacterial cytoplasm and how it affects cellular

processes.

The scientists first noticed while studying the bacterial protein

crescentin that the protein in its native condition was bound to other

crescentin molecules and created a filamentous structure attached

to the membrane. Yet, when a bulky molecule was attached, the

crescentin strand detached from the membrane and moved randomly

in the cytoplasm. What was even more interesting was that when

the cells generating these proteins stopped growing, the crescentin

structures stopped moving. This led to an investigation of whether

IMAGE COURTESY OF NEXT NATURE

Once thought to not serve a crucial function

in diffusion, bacterial cytoplasm has now

been found to show glass-like tendencies

which depend on the activity of the cell.

metabolic activities play a role in the motion of diffusing cytoplasmic

components.

First, they tested whether this metabolism-dependent motion was

specific to the type of bacteria that produced crescentin. To do so, they

used standard E. coli with engineered DNA molecules

that were observed for movement through the

cytoplasm. These molecules exhibited the

same metabolism-dependent motion;

when the bacterial cells were

depleted of energy, the molecules

did not move very far. This

dependency was also

confirmed when a protein

probe that that did not

interact with bacterial

cytoplasm exhibited

the same movement

characteristics.

Wondering what

process drove this

movement, the

scientists investigated

multiple alternatives.

They found that it

was not driven by any

cytoskeletal “active

diffusion” or by any motorbased

actions of proteins.

Particle size, however, did have

an effect on this metabolismdependent

motion if the particles

were larger and the cells were depleted

of energy, then the particles would not

move as far. The movement of the particles

diffusing through the cytoplasm indicates

a possible glass-forming liquid system:

Larger particles “perceive” the cytoplasm

as glassy because it is difficult for them to

diffuse while smaller particles perceive the

same environment as liquid because it is easy for them to move

around. Scientists hypothesize that the bacterial cytoplasm exhibits

this property because of the high concentration of relatively big

molecules within the bacterium.

This study demonstrates that the cytoplasm has a greater role in the

diffusion of particles than researchers had initially thought. The idea

that metabolic activities can make the cytoplasm more fluid is very

novel, and Jacobs-Wagner and her team are further exploring these

properties by modeling the cytoplasm and predicting how molecules

of different sizes move.

Yale Scientific Magazine

25


FEATURE

medicine

BY TESSA ADLER

Jack Frost’s Invisible Hand

EXPLORING THE SURPRISING EFFECTS

OF COLD ON THE HUMAN BODY

This year, the cold has been much more than a mere nuisance,

given the early-January polar vortex that affected many Americans.

When temperatures drop, the shivers, the goosebumps, and the

numb fingers are all too apparent. But looking deeper, there are

many fascinating and unexpected ways that cold affects the internal

human body. Some of these lesser-known effects of cold include

rerouted blood flow and irrational undressing behaviors, along with

other forms of impaired decision-making.

In cold temperatures, the body’s primary goal is to keep its vital

organs warm. The region of the brain responsible for temperature

regulation, the hypothalamus, diverts the vast majority of blood flow

away from non-essential extremities in an effort to keep the critical

core functioning. This process is achieved through vasoconstriction,

in which veins constrict to prevent blood flow to the arms, legs,

nose, and ears. This shunting of blood away from the extremities

is what causes frostbite. The lack of warm circulating blood causes

tissues in the arms, legs, nose, and ears to freeze, rupture, and die.

An odd consequence of this vasoconstriction is that it causes

people to have to urinate more often. When the hypothalamus

reroutes blood towards the internal organs, the kidneys receive

greater blood flow. With more blood flowing through them, the

kidneys produce more urine than usual.

A more extreme outcome of cold temperatures is hypothermia,

which is especially dangerous because people are typically unaware

when it begins. Hypothermia occurs when the body’s core

temperature decreases to a point where metabolism slows down

and mental acuity and muscular functions are impaired. The body

functions optimally at 98.6 degrees Fahrenheit; even at 97 degrees,

survival instincts falter and judgment deteriorates. Interestingly, as

victims become more hypothermic, they become increasingly selfdestructive,

unable to help themselves.

Hypothermia also causes what rescuers call the “umbles.” First,

when the body reaches 96 degrees, the victim begins to stumble

and fumble as coordinated muscular activity begins to falter. By 95

degrees, the grumbles and the mumbles have set in due to decreased

brain activity. Amnesia eventually takes its toll as well, making it

more difficult for victims to get themselves to safety. Victims’

minds slow, and sleepiness and hallucination become common.

Bizarrely, when victims reach extremely low body temperatures,

they often begin taking off all of their clothing. This “paradoxical

undressing” is thought to cause the death of between 20 and

50 percent of hypothermia victims, and scientists have yet to

definitively determine why it happens.

One proposed theory is that the muscles that had been limiting

blood flow to the extremities become exhausted. This causes a

sudden influx of blood — and thus also heat — to the extremities.

Combined with their existing irrationality, victims feel panicked by

what they perceive as overheating, and thus start to remove their

clothes.

The risk of hypothermia varies greatly depending on the type

of activity that a person is doing. Runners, skiers, and bikers are

more at risk than walkers and hikers because their pace is faster

and they are thus exposed to greater wind chill. Athletes can also

experience a sharp decline of core temperature in the cold, because

they expend a lot of energy.

Alcohol consumption also poses an added danger in cold weather

in that it acts as a vasodilator. This means that it acts against

vasoconstriction and increases blood flow to the extremities, which

makes a person feel warmer even though they are losing heat more

quickly.

So, how cold is too cold? It is hard to say. Scientists cannot

experiment on people due to bioethics constraints, and results from

animal testing do not really translate to the human condition due

to varying metabolisms between species. Still, experts agree that a

wind chill below 50 degrees Fahrenheit, a temperature that many

Americans experienced during the polar vortex, can cause frostbite

in less than five minutes.

Experts warn that temperatures do not have to be extremely

cold for dangerous effects to occur. If the body is exposed for

long enough, dropping temperatures can cause physical and mental

disasters. The body has many coping mechanisms, but the best

way to avoid hypothermia is to stay in a group. It is difficult to

notice the progress of hypothermia when alone, but others can

easily observe the symptoms and prevent its occurrence. Only by

better understanding the impact of the cold on decision-making

will people really be protected against frigid winters.

14 Yale Scientific Magazine March 2014 www.yalescientific.org


ART BY CASEY MCLAUGHLIN


FEATURE

public health

Death by

Lightning

BY RAIN TSONG

to some countries, more than just a shock

Johannesburg, South Africa: lightning strikes a 9-year-old brother

and his sister who went out to play. The boy dies in transit to the

hospital; the toddler girl is blinded. The same storm destroyed six

houses and damaged another 36.

Johannesburg is a city self-proclaimed the “lightning capital of the

world.” This is more of a concern than a commendation; the city saw

13 schoolchildren struck by lightning over the course of two days last

February, and 14 miners struck last

November. According to the South

Africa Weather Service, these kinds

of lightning-related tragedies result

in a staggering 260 deaths a year.

This problem is not at all limited

to South Africa. In India, a single

lightning storm in October killed 32

people. In Nepal, the annual deathby-lightning

toll reached 130 in 2012.

Many other developing countries

have high rates of death and injury

by lightning; one estimate puts

the worldwide rate at up to 24,000

deaths per year. In stark contrast,

the United States recorded only 23

deaths by lightning in 2013. Why are

developing countries losing so many

more people to lightning?

Many of these countries have

both a hot, humid climate and an

agriculture-based economy, which

increase the risk of lightningrelated

tragedies. A more substantial

problem, however, is the lack of

lightning awareness across both the

scientific community and the general

public. Recently, researchers have

launched into studying how lightning

affects the body and how lightning deaths can be prevented. Of

course, many aspects of lightning safety have been established for

decades, and the greater challenge facing scientists now is how to

disseminate this information so people are more knowledgeable

about the risks associated with charged weather.

Many people are simply unaware of the existing scientific

literature. For a lightning strike, the worst-case scenario is a direct hit

to the head, which happens in open spaces. Most of these victims will

die instantly. However, if sheltered under a tree or similar structure,

a person may be hit by a side flash in which the lightning first strikes

the structure and then crosses over to the victim. These side flashes

are often, but not always fatal.

Expanding lightning research should increase awareness of the

dangers of lightning and reduce the lightning-related death toll. In

South Africa, people educated and uneducated alike believe that a

combination of natural and supernatural influences cause lightning

attacks; witch-caused lightning supposedly targets only sinful people.

Even among those who don’t believe in magic, similar superstition is

ingrained. Estelle Trengove of the University of Witwatersrand —

common known as Wits University —

reports a few rampant beliefs: “If you

are a boy, or you are wearing rubbersoled

shoes, or if you are already

wet, you will be safe.” Correcting

misconceptions by disseminating

long-established knowledge about the

dangers of lightning will hopefully

improve lightning safety in many

developing nations.

Finding a safe place to shelter

from lightning is another issue in

lower-income countries. Many deaths

in South Africa, for example, occur

in wide-open rural spaces with no

nearby shelter. Most shelters in the

poorer parts of South Africa and other

developing nations are made with

hastily constructed metal roofs or even

open-air designs. In the United States,

people stuck in a storm can find refuge

in their metal-framed cars; in most

developing countries, people don’t

have access to such vehicles.

ART BY DANIELLE CARROL

Expanding lightning research should increase

awareness of the dangers of lightning and reduce the

lightning-related death toll.

While safety rules will

circumstantially vary from place to

place, there are a few universals like

“never shelter under a tree” and

“shelter inside a sturdy building.” Many

countries are also taking their own steps toward educating the public.

In South Africa, the Wits University team created a simple children’s

videogame surrounding the topic of lightning safety. In Colombia,

the military recently hired lightning specialists to instruct farmers

on lightning safety in the field. Malaysia and other countries at high

lightning risk are taking similar steps.

While it may take some time for the results of these efforts to pan

out, Ken Nixon of Wits University believes that people are “really

starting to understand the risks associated with storms.” Further

research from Wits and other teams worldwide will hopefully improve

knowledge and safety regarding lightning attacks. In the meantime,

the best expert advice is to stay inside.

28 Yale Scientific Magazine March 2014 www.yalescientific.org


biology

FEATURE

Love at second sight:

sociality and mating behavior in fish

BY APARNA NATHAN

“Love at first sight” – it lies at the core of classic fairy tales,

but recent research into animal mating habits shows that this

phenomenon is likely just a fantasy. Scientists at the University of

Tokyo have published research that shows that the mating habits

of fish are heavily influenced by their familiarity with those around

them. In other words, fish are more likely to mate with a familiar

individual than with a stranger.

This research is shedding new light onto the factors that influence

social decision-making. Investigating the neural basis of this decisionmaking

allows us to extend applications of these aquatic experiments

to humans as well; through animal

studies, scientists are learning why

humans fall in love.

The University of Tokyo study,

published in early January, sprung

from a desire to investigate the

relationship between neural activity

and social decisions, especially in

the realm of familiarization. Social

familiarization, or becoming

familiar with another individual

through sensory contact, is a

common phenomenon in nature

that scientists have observed in

many animals. Previous studies

investigating mating preference

in guppies and voles have

demonstrated that familiarity

generally increases mating

preference.

Among humans, familiarity and

mating preference are certainly

linked, even though attraction as a whole is a complex psychological

and biological process. Still, research on love and attraction has

suggested that humans are more likely to fall in love with those

they spend the most time with. A 2011 study conducted at the

University of Rochester examined social familiarization in humans.

The experiment analyzed how the amount of interaction between

two people affected their mutual attraction. Results showed a positive

correlation between these two variables, and the University of Tokyo

experiment has yielded similar data from studies on fish.

The Tokyo lab chose to focus on medaka, colloquially known

as rice fish. This species was a suitable target for study because of

its well-understood sequential mating behavior. Mating in medaka

occurs in two steps: the male performs a courtship ritual, and then the

female either accepts or rejects him. This female’s decision-making

step was essential to the research, which investigates how social

familiarity influences how the female receives the male’s courtship.

The study consisted of various experimental groups. In some

groups, fish were familiarized with each other through transparent

walls. Meanwhile, in other groups, fish were kept apart. To collect

data, researchers combined male and female fish in a tank and timed

how long it took for a female to mate after the initial male courtship

display. The results of this study showed that the receptivity of the

female medaka was affected by how familiar she found her potential

mate. Groups in which the female was familiarized with her mate

displayed lower latency periods; when there was a lack of familiarity

between fish, latency periods were longer.

In order to better understand

the neural mechanisms

behind these observations, the

researchers next delved into the

medaka’s DNA. Two mating

mutants drew their attention.

These genetically-altered females

displayed increased receptivity

toward males regardless of

familiarity. Further genetic

investigation revealed that the

cause for irregular behavior

in both these mutants may lie

in the TN-GnRH3 neuron,

which is closely associated

with reproduction. Researchers

concluded that a protein

normally found in this neuron

may suppress female receptivity,

which explains why fish with a

mutant, altered protein are just

as receptive to courtship from

strangers as they are to courtship from familiar males.

Researchers around the world are now interested in the TN-

GnRH3 neuron and its role in social decision-making in all

vertebrates. These studies in the aquatic realm could uncover new

information relevant to human mating patterns, as TN-GnRH3

neurons also function in mammals.

Our own mating habits are still mysterious. Why are we attracted

to people? Is it just chance, or will we one day understand and be

able to control these instinctual emotions? TN-GnRH3 could be key

in answering these questions. Linking TN-GnRH3 to recognitionbased

mating preference will also allow scientists to explore how

this neuron type relates to recognizing kin, bonding with a mate,

and other aspects of social neuroscience. This field, located at the

intersection of biology and society, could provide us with the tools

needed to better understand the love-related mysteries within our

minds.

IMAGE COURTESY OF THE UNIVERSITY OF TOKYO; TOP RIGHT ART BY GRACE PAN

This study used medaka, a species of Japanese rice fish

considered to be a model organism for research on mating patterns.

www.yalescientific.org

March 2014

Yale Scientific Magazine

29


FEATURE

environmental science

Every Drop Counts

THE COLORADO RIVER, YOUR WATER FOOTPRINT, AND WHY IT MATTERS

BY TARYN LAUBENSTEIN

ART BY CHRISTINA ZHANG

The Colorado River was once a symbol of the majesty of the

American West. The brute force of its waters carved the Grand

Canyon, a national treasure that Theodore Roosevelt called “the

one great sight which every American should see.” Beginning in

the peaks of the Rocky Mountains, it wound its way southwest,

passing through seven states before entering Mexico and emptying

into the Gulf of California. In contrast to the arid lands of the

Southwest, its banks were verdant, an oasis for dozens of species

of birds and fish.

Today, however, the once-lush Colorado River Delta is now

barren and desiccated. For nearly a decade, the mighty river has

not reached the sea, petering out to a mere trickle and leaving

its marshlands dry. The culprit lies upstream, where 30 million

Americans have diverted and dammed the river for their own use.

The water is used not only to support the burgeoning populations

of cities like Los Angeles, Las Vegas, and Phoenix, but also to

provide irrigation for over 3.5 million acres of cropland. Without

intervention, it seems unlikely that the flow of the Colorado

River will return to its natural state anytime soon.

Unfortunately, the Colorado River is not the only body of

water suffering from a human population’s large water footprint.

Policymakers coined the term “water footprint” to capture the

total volume of freshwater used by individuals, communities, and

businesses. When people hear the term, most think of watering

their lawns, brushing their teeth, or washing their clothes. These

are all examples of direct uses of water, but they comprise only

one small part of a water footprint. The larger, unseen portion

of a water footprint is indirect use, which consists of all the water

used to produce the goods and services that an individual uses.

The full scope of indirect water use is difficult to grasp,

mostly because consumers never see the water used to make

their products. But groups like the GRACE Communications

30 Yale Scientific Magazine March 2014 www.yalescientific.org


environmental science

FEATURE

Foundation are working to expose the shockingly large water

footprints of some common goods. A single slice of pizza, for

example, requires 42 gallons of water. Surprised? Consider the

ingredients. Water is needed to grow the wheat that makes the

IMAGE COURTESY OF FRANS LANTING

The Colorado River, which stretches 1,450 miles over seven states,

was once a stunning picture of untamed natural beauty.

flour; water is needed to turn that flour into dough. There can

be no cheese without a cow, which of course requires drinking

water, and the tomatoes in the sauce would have withered without

regular watering. All of that water is hiding behind the production

of that one slice of pizza – and pizza is hardly the worst offender.

A dozen eggs require 636 gallons of water; a simple cotton

T-shirt uses up 700 gallons. Animal products are one of the most

egregious contributors to a person’s water footprint, with beef

clocking in at 8977 gallons of freshwater per pound.

These statistics can leave consumers feeling overwhelmed and

helpless – short of buying a chicken coop, how can they control the

water footprint of their breakfast omelet?

The key here is conscious consumption. By choosing to reduce

the amount of meat, eggs, and other animal products in their diets,

consumers can lower their indirect water footprints. In terms of

liquids, tea consumes 9 gallons of water to coffee’s 37 gallons,

making tea the caffeinated beverage of choice for a water-conscious

consumer. In choosing produce, consumers should pay attention to

season and source. A Connecticut native can enjoy local heirloom

tomatoes in late August at a relatively low water footprint, but

tomatoes in the dead of winter are likely coming from distant,

potentially water-threatened areas.

Professor Shimon Anisfeld of the Yale School of Forestry and

Environmental Sciences has witnessed firsthand the regional nature

of water use. Anisfeld, who studies human impacts on rivers in the

Connecticut area, noted that “many rivers in the state are depleted

relative to their natural flows,” not unlike the ailing Colorado River.

However, he continued, “in contrast to states like Colorado and

California where most water is used for irrigation of crops, in

Connecticut most water goes to household use.” For Connecticut

residents, then, reductions in individual use like shortening showers

and fixing leaky faucets are all the more important. “The population

www.yalescientific.org

of Connecticut certainly has the power to determine how much

water they use; it is the cumulative effect of individual actions that

will keep Connecticut’s streams flowing,” Anisfeld said.

The freshwater team at National Geographic thinks the same

principle of motivated individual action can restore the flow of

the Colorado River. Together with the Bonneville Environment

Foundation and Participant Media, National Geographic has

created the “Change the Course” campaign. On its website, people

can pledge to reduce their water footprints directly or indirectly.

Pledges include taking shorter showers, choosing vegetables over

meat once a week, and seeking locally-sourced meals. For every

pledge, corporate partners of the campaign will sponsor projects

that restore flow to the Colorado River on the scale of 1,000 gallons

of water per pledge. The benefits of a pledge are thus two-fold: on

the one hand, sponsors will target improved water conservation and

management strategies. On the other, individuals from Connecticut

to Colorado will reduce their water footprints, either directly to

ensure that their local rivers maintain a healthy flow, or indirectly to

decrease their global water impact.

Such efforts are especially important as climate change imposes its

own challenges to water conservation. A number of recent studies

show that climate change will likely decrease the Colorado River’s

flow by 5 to 35 percent; precipitation from the Rockies will lessen,

March 2014

IMAGE COURTESY OF PETER MCBRIDE

The Colorado River delta today is only a shell of its former glory:

dry, cracked, barren.

while rising temperatures will increase the rate of evaporation.

In the face of these worsening conditions, it is little surprise

that southwestern states are already experiencing unprecedented

droughts, forcing citizens, farmers, and policymakers to take a

critical look at their water consumption. Restoring the Colorado

River will not be easy, but it is important to remember that every

drop counts.

Want to restore 1,000 gallons of water to the Colorado River? Sign up at

www.changethecourse.us or text “River” to 77177 and make your

pledge to reduce your freshwater footprint.

Yale Scientific Magazine

31


FEATURE

undergraduate profile

Parker Liautaud (DC ’16)

BY MINA HIMWICH

the science behind his antarctic trek

In December, Geology & Geophysics major Parker Liautaud (DC

’16) set a world record by completing the fastest Antarctic coastto-pole

trek. In 18 days, he became the youngest man to trek to the

South Pole without assistance. And while his record transit time

attracts the most press, the focus of Liautaud’s journey was three

separate scientific projects that reflect his commitment to geoscience

and climate change issues.

Liautaud has been interested in climate science since he was young,

and has completed four polar expeditions since turning 15. Over

time, his trips have shifted to focus more heavily on science; In

this expedition, he was directly involved with an advisory board of

scientists and experts.

Liautaud began his December trek with a coast-pole-coast transit

of roughly 1,200 miles, and then completed a 350-mile race to the

pole. On the first crossing, Liautaud tested a new Antarctic weather

station and conducted isotope sampling in layers of Antarctic snow.

“We did the science first and the speed attempt afterwards,” Liautaud

said. “Doing them both at the same time would have compromised

one at the expense of the other.”

The first of Liautaud’s projects was testing a cheaper, lighter

Antarctic weather station that could be deployed in 15 minutes.

Antarctica’s existing weather stations are expensive and difficult to

maintain, and improving the precision of Antarctic meteorology

requires a cheaper, more fail-safe station network.

A second component of Liautaud’s expedition was a coast-polecoast

sampling survey of the stable isotope composition of Antarctic

snow. The isotope composition of at different depths provides

important information for reconstructing climate history.

Samples collected relatively close to the surface provide information

on a more recent timescale, and give a detailed picture of Antarctic

precipitation. Liautaud sampled shallow cores drilled two meters

deep, gathering information that can improve the understanding of

recent temperature and snow accumulation patterns.

IMAGE COURTESY OF PARKER LIAUTAUD

Liautaud’s team set up the ColdFacts-3000BX Weather Station in

Antarctica. It was tested over approximately 4-5 weeks.

IMAGE COURTESY OF PARKER LIAUTAUD

Liautaud finished the world’s fastest Antarctic coast-to-pole trek.

Liautaud’s third project involved the study of tritium, a radioactive

isotope of hydrogen with a half-life of 12.3 years. Tritium is produced

at an extremely low constant rate by the interaction of cosmic rays

with Earth’s atmosphere. It was released in disproportionately high

quantities during war-era nuclear bomb testing, but now its deposition

has returned to natural levels.

Tritium is useful for accurately dating snow samples across

Antarctica from the past 100 years. Understanding the factors

influencing natural tritium deposition could improve tritium dating

techniques. “With the tritium project, we were not using tritium

dating, but trying to refine its technique by learning about the

context of tritium deposition,” Liautaud explained. “Though it’s not

particularly glamorous, this project will generate new information to

make tritium even more useful in studying the Antarctic climate.”

Liautaud sampled tritium concentrations in order to study its

dependence on geographical conditions. The samples he obtained

will help reveal a trend in tritium variability that can be used to

solidify the usefulness of tritium dating in Antarctica. Liautaud will

participate via Skype in the analysis, which is being conducted in

New Zealand by the world’s most accurate tritium lab.

The combination of lab and field work is one of Liautaud’s

favorite aspects of geoscience. “Field work can take you anywhere,

and unexpected things happen all the time. It’s a constantly exciting

and challenging process,” Liautaud said. “There’s a flipside, of

course,” he added, citing the time Chilean customs confiscated an ice

auger. “But where there are new challenges to be addressed, there are

consistently new opportunities to be created.”

In the future, Liautaud plans to continue making scientific

expeditions and to attend graduate school. As a strong advocate for

improving climate and communication and policy, he has also worked

with the Yale Climate and Energy Institute. “Climate change needs

to be addressed, and public understanding is lacking,” Liautaud said,

While he appreciates President Obama’s recent climate initiatives,

Liautaud believes that we can and should do even more. “By the time

people realize the effects, it will be too late. We need to act now to

improve the way climate science is communicated.”

32 Yale Scientific Magazine March 2014 www.yalescientific.org


alumni profile

Robert Needlman (YC ’81, YSM ’85)

BY EMMY YANG

FEATURE

from english to pediatrics

In some ways, Robert Needlman (YC ’81, YSM ’85) is the modernday

Benjamin Spock. Both men studied English at Yale, and both

were interested in medicine alongside literature and language. As a

pediatrician at MetroHealth Medical Center and a professor at Case

Western Reserve University, Needlman is now tasked with updating

the classic parenting book trusted by expectant mothers and fathers

everywhere — “Dr. Spock’s Baby and Child Care.

Benjamin Spock was a famous 20th century pediatrician who first

published “Baby and Child Care” in 1946. It became the second

best-selling book in America after the Bible, and is currently in its

9th edition. Needlman is similarly talented. He has found a way to

combine his love of writing with his interest in science, primarily

pediatric medicine. From an English degree to an MD, Needlman has

demonstrated the value of a liberal arts background in the medical

profession.

Needlman first began to work on Spock’s legacy by writing for

drspock.com, a website that sparked his full-time commitment to

thinking about the kinds of issues Spock used to write about, such

as child developmental and behavioral disorders. Needlman went on

to revise the 8th and 9th editions of Spock’s famous book, which

contain updated sections on topics such as obesity and nutrition,

environmental health, and immunizations. Parenting, according to

Needlman, is a “moving target.” Thus, the book must be continually

updated as new research and information about parenting surfaces.

Though some consider English and medicine distinct fields,

Needlman sees an intuitive overlap. “What draws people to literature

is that it is a way of understanding human experience. Medicine is

also about appreciating and understanding the human experience,”

Needlman said. He supposed that Spock might have been interested

in development and child psychiatry for this same reason. “What was

www.yalescientific.org

IMAGE COURTESY OF GOODREADS

Like many current students, Needlman attended English lectures in

Linsly-Chittenden Hall. One of his favorite classes was Daily Themes.

Needlman works in Cleveland, teaches at Case Western Reserve

University, and gives talks about developmental-behavioral pediatrics.

interesting to me about English literature was the stuff that dealt

with how we got to be the way we are – how our experience shapes

who we are,” Needlman added.

At Yale, Needlman’s favorite classes included an English lecture

by Marie Borroff and Daily Themes with John Hollander. When

asked how he balanced his science and humanities classes at Yale,

Needlman laughed. “I have no idea. I haven’t been that efficient in

a long time,” he said. He added that his science classes provided an

enjoyable break from his English classes. Looking back, Needlman

felt that all the anxiety of writing English papers was worth it because

knowing how to write well “is a real plus as a doctor.”

After graduating from Yale College, Needlman decided to attend

the Yale School of Medicine. In his third year of medical school in

1984, he realized he wanted to be a pediatrician. Interacting with

parents and children felt like a good fit to him, and he became

emotionally invested in pediatric care. Though medical school was

filled with all-nighters, Needlman delighted in attending lectures and

learning about different parts of medicine. After his residency and

fellowship, Needlman began to work in developmental-behavioral

pediatrics, a relatively new subspecialty. As physical disorders became

less severe, doctors began to focus on more complex issues such

as obesity and behavioral disorders. In addition to his work at

MetroHealth and Case Western, Needlman recently gave workshops

at a Developmental-Behavioral Pediatrics Review in Atlanta.

Throughout his successful trajectory in the field of medicine,

Needlman continues to draw upon the lessons he learned at Yale,

whether it is in taking care of patients, teaching, or working with

colleagues. “The best of a Yale education, I’m convinced, is your

classmates,” Needlman reflected. He advises current students that

relationships with professors are important, but relationships with

peers are indispensable. “Delve wholeheartedly into your experience.

Going to a place like Yale is really a privilege. It is worth keeping

that in mind,” said Needlman. Living up to the privilege of a Yale

education is exactly what Robert Needlman has done for himself —

understanding humanity in the earliest stages of life.

March 2014

IMAGE COURTESY OF YOUTUBE

Yale Scientific Magazine

33


FEATURE

essay contest

Breaking Convention

by Amita Sastry

Winner of the 2013 Yale Scientific-Synapse High School Essay Contest

Congratulations to the winner of the second Yale Scientific-Synapse High School Essay Contest, Amita

Sastry, a student at Jonathan Law High School in Milford, CT. This year’s prompt required writers to discuss

how scientists have attained success by breaking convention. Additionally, writers were asked to propose

their own scientific innovation that encourages creativity in the face of opposition. In this essay, Sastry

comments on the historical hallmarks that have shaped modern science.

Many revolutionary scientific

discoveries initially received their

fair share of skepticism. When

looking at these discoveries, the results of

breaking conventions can be appreciated.

Daring to persevere in the face of opposition

has, in the past, redefined modern science,

and continues to encourage creativity and

improve upon existing standards.

Breaking with tradition can

often promote ingenuity; that

is, by challenging the nature of

existing things, scientists can add

By

a creative touch to an ordinary

item. Take, for instance, the

invention of the electric car.

At first glance, the thought of

a car that could be plugged in

and operated on battery power

seemed absurd, since people were

accustomed to filling up their

gas tanks frequently. However,

due to the commitment of

many scientists and engineers,

that vision is, today, a reality. According to

National Public Radio (NPR), electric cars

can be three times cheaper to fill up than gas

powered vehicles. Because people thought

beyond the ordinary, we now have cars that

decrease dependence on gas, an expensive

resource.

Other technological advances such as

the development of smart phones also

represent inventiveness. Previously, touchscreen

and Internet capable phones were

deemed ridiculous ideas. Nonetheless,

scientists developed this technology, which

allows for increased convenience in several

ways. According to CBS, 56% of American

adults own smart phones – a claim that

illustrates the overwhelming utility of these

phones. Thus, the progression from the

minimal design of the cell phone to the

initially disputed “smart” phone showed the

creativity that can arise out of departures

from convention.

Improvement upon existing standards

is also facilitated by the proposition of

novel ideas. The proposal of the vaccine

was originally thought to be an implausible

storing images seen

by the eyes ... eyewitnesses

can truly

become “eye”-witnesses

Amita Sastry

idea. People believed it was preposterous

to prevent illness by injecting a mild form

of the virus into the body. Consequently,

until the late 1700s, the standard and widely

used prevention method was to quarantine

people. It wasn’t until the 1790s and early

1800s that Louis Pasteur and Edward Jenner

produced the first vaccinations for chicken

cholera and smallpox, respectively. Critics

argued relentlessly that inoculation did not

adhere to the religious beliefs at the time, and

questioned the morality of the practice. The

issues regarding the effectiveness and safety

of vaccinations were also raised. In spite of

these protests, Pasteur and Jenner pursued

their ideas with relentless determination.

Today, thanks to Pasteur, Jenner, and other

scientists’ courage, it is possible to prevent

over two dozen deadly diseases. It is clear

that the development of the vaccine

greatly improved the previous standards

of preventive health, and modernized the

medical field.

A series of people who have dared to

be innovative in proposal of concepts

have shaped modern biology throughout

the years. Hooke, Leeuwonhoek,

Schwann, Schleiden, and Virchow,

among others, contributed to the cell

theory. Before this proposal, scientists

believed in spontaneous generation

of life. The development of the cell

theory redefined the fundamentals

of composition of organisms.

Decades later, Darwin found

himself in a similar situation, where

the predominant belief was single

ancestral sources, and Lamarck’s

theory of passing on acquired traits

to offspring. After suffering agony

from skepticism regarding his new

idea, Darwin finally proposed his theory of

evolution in which he stated that organisms

undergo gradual change over time through

natural selection. This proposition had a

monumental impact on evolutionary biology

and redefined the way scientists researched

the origin of species.

The impact of breaking conventions

is apparent in modern scientific settings

as well. One such example is the human

genome project. At first, people believed

that this project would be far too expensive

to be realistic, and would have no place in

modern medicine. In April 2003, however,

scientists were able to sequence the entire

genome, identify the location of genes, and

interpret this information to a certain extent.

34 Yale Scientific Magazine March 2014 www.yalescientific.org


ART BY CARRIE CAO

The human genome project will provide the

basis for gene therapy, and help geneticists

and doctors detect predisposition to disease.

The development of the cell theory and

evolutionary theory laid the groundwork

for an extensive amount of research of

the fundamentals of science. The human

genome project is evidence of how far the

research has come, and how much further it

can go.

While researching all of these innovations

in science, the spirit of curiosity inspired

me to offer the idea of storing images seen

with our eyes and the ability to transfer

them to a computer. This proposal is subject

to skepticism because it is a concept that

requires advanced technology that has not

yet been developed and it seems out of scope

with what is scientifically possible. While

www.yalescientific.org

this concept would require further research

to develop, this idea has several benefits in

various facets of society including criminal

justice and social media. By storing images

seen by the eyes, we can nearly eliminate the

process of court trials and uncertainty of

witness testimonies; eye-witnesses can truly

become “eye”-witnesses. That is, the images

they see in real time can later be stored and

used to convict criminals without ambiguity.

Moreover, society today is characterized

by the use of social networking websites like

Facebook, Twitter, and Instagram. Social

networks are used to capture photos of

memorable events and share them. Often,

the most memorable moments happen when

we are without cameras. Using our own

eyesight to take pictures without needing

to use a camera would make capturing

memories more natural and significantly

more convenient. People could then take

these pictures and share them on social

networks at their leisure, without the hassle

of connecting a camera to the computer to

import these pictures.

Promoting creativity, enhancing current

standards, and changing fundamentals

of science are just a few advantages of

breaking conventions. Challenging the norm

and expanding thought past the obvious

is extremely important to the future of

science. Many major discoveries in the past

have been a result of breaking conventions,

and the same will hold true for future

breakthroughs. Breaking conventions are an

important aspect of the scientific world, and

it is crucial that the scientists of tomorrow

be courageous enough to do so.

March 2014

Yale Scientific Magazine

35


FEATURE

neuroscience

Debunking Science

fmri: a not-so-reliable mind reader

BY SENZENI MPOFU

Imagine you had a superpower that enabled you to read people’s

minds.

Science has not yet advanced far enough to give anyone this ability,

but functional Magnetic Resonance Imaging (fMRI) is probably the

technology that comes closest. Over the past decade, use

of fMRI in neuroscience and psychology research

has greatly increased. While many features of

fMRI have helped these fields progress, there

have also been overly enthusiastic claims

about fMRI’s credibility in explaining

social science phenomena. There are

strict limitations to what fMRI can

confidently assert about people’s

thoughts; over-reliance on fMRI

scans has led to faulty research

claims and public misconceptions

about what this technology can

really do.

First, it is important to

understand how this technology

works. The procedure uses

magnetic fields and radio

waves to form images of

hemodynamic responses, or

changes in blood flow. Whenever

a particular brain area is active, it

consumes oxygen, which requires

increased blood flow to the region.

Performing even the most mundane

tasks, such as viewing a picture

of a political candidate or solving

a simple addition problem,

causes specific areas of the

brain to increase their oxygen

consumption. fMRI maps

these physiological changes

and creates images of the areas with elevated blood flow. These maps

can help researchers discern which areas of the brain are involved in

completing certain tasks.

One of fMRI’s most celebrated advantages is its ability to quantify

psychological processes that people are either unwilling or unable to

report honestly. For example, people might not be aware that they

respond emotionally to photos of loved ones, but fMRI can show

emotion centers in the brain demanding higher blood flow. Another

more controversial example is lie-detection. Deception activates the

prefrontal cortex; with this knowledge, fMRI can be used to indicate

whether or not an individual is lying.

However, that does not that mean scientists can divine someone’s

exact thoughts from what lights up in an fMRI brain scan. An

increasing number of cautionary voices have started to emphasize

IMAGE COURTESY OF THE BRAIN AND CREATIVITY INSTITUTE

Recent studies have claimed a correlation between regional

brain activity and political inclinations.

the limitations of fMRI. These experts’ concerns range from queries

on data collection methods to doubts surrounding the relationship

between fMRI and neuronal activity. Some are cautious; others are

cynical. Either way, scientists warn against overestimating the

current abilities of fMRI.

The problem with most fMRI psychology

studies is that they are based on the premise

that each cognitive task occurs due to the

activation of a particular area in the

brain. For example, the New York

Times article “This Is Your Brain

on Politics” explores the brains

of voters from the 2008 election.

The study claimed to predict

the political ideology and party

affiliation of potential voters

by simply tracking their brain

activity under fMRI while they

viewed pictures of the political

candidates. The study’s claims

were based on differences in

amygdala activation, which were

interpreted to indicate anxiety about

a particular candidate.

However, critics argue that it is

implausible to draw reliable conclusions

from mapping brain regions to mental states.

Given the complexity of the brain and the

interconnectedness of neural networks, such

a conclusion seems to be based on arbitrary

dismissal of other possible explanations for

these observations. Indeed, activation of

the amygdala can reflect “anxiety” about

a particular candidate, but amygdala

activation can also be caused by arousal

and positive emotions.

Some prominent neuroscientists have also questioned the validity

of generalizations about individual brains that are based on averaged

data. In a study by Harvard University professor David Cox, brain

activation varied from one individual to the next. The study, which

used a sample size of six, showed that different brains are activated

in different areas upon seeing the same object. At larger sample sizes,

such as those used in most fMRI studies, it becomes possible to

calculate a grand average of the data and thus provide an “average”

region of activation due to stimuli. Yet this average overrides the

uniqueness and individuality of each brain and therefore should not

be taken as a completely accurate representation of brain function.

These criticisms in fMRI’s applicability to mind-reading suggest

that the field of fMRI has not yet arrived at the stage where we can

confidently trust all of its results.

36 Yale Scientific Magazine March 2014 www.yalescientific.org


The Science of Identity

BY AMEY MAHAJAN

www.yalescientific.org

Unsolved Mysteries ?

The past century has seen marked improvements in

neuroscience. Scientists have discovered ways to observe

electrical currents that carry information around the nervous

system, employing techniques like electroencephalography

and transcranial magnetic stimulation. Doctors can now carry

out complex surgical operations to heal and restore the brain.

Social scientists can model individual behaviors based on

everyday psychological biases, such as the tendency to spread

gossip.

However, none of these fields have come close to a

complete definition of the mysterious concept of identity.

Key questions remain unanswered: how do we create a sense

of self? How do we identify and characterize people? Most

importantly, how do we characterize reality? Psychologists

argue about how identity develops, while neuroscientists

dispute where identity manifests itself in the human brain.

The main theories of identity formation come from two

psychologists, Erik Erikson and James Marcia. Erikson used

patient therapy, dream analysis and puppet plays with children

to develop his identity theory. Some psychologists questioned

his methods and his credibility (the highest academic degree

he earned was a high school diploma), but Erikson was

successful nonetheless in creating a widely accepted theory

for how identity develops in different life stages. Each stage

is characterized by a relevant crisis, such as “trust versus

mistrust” for a newborn, “competence versus inferiority” for

a young child and “generativity versus stagnation” for middleaged

adults.

The most important stage for identity formation according

to Erikson’s theory takes place from ages 12 to 18. The

crisis in this time period is “identity versus role confusion.”

Humans begin to ask, “Who am I?” Erikson postulates that

earlier conflicts must be resolved to conquer this critical stage,

termed the “identity crisis.” During this stage, Erikson claims

humans should begin to feel a deep-seated sense of trust in

others and a sense of independence and control over life. This

adolescence stage is crucial for forming a well-defined life, or,

at its worst, spiraling into a life of instability and confusion.

James Marcia, a Canadian neuropsychologist and professor,

added to Erikson’s groundbreaking work in identity theory.

Rather than adhering to Erikson’s dichotomy of identity

and confusion, Marcia proposed that identity arises from

the choices made about certain personal and social traits. To

clarify this decision-making process, Marcia described two

stages: crisis, in which previous life choices are re-examined,

and commitment, the outcome of crisis.

Individuals with a well-developed

identity, by Marcia’s theory, should

have a good sense of their

strengths and weaknesses and a

secure sense of self. Of course,

for many college students, it is

possible that Marcia’s model does

not hold much personal value.

College students often reach the age

of 20 before determining their majors, let

alone their career paths; in contrast, Marcia’s

model expects vocational decisions to be undertaken in

adolescence. Similarly, most college students have not yet

developed a complete sense of strength, weakness, and self

when they enter college at the age of 18. People in this age

group may thus face difficulty applying this model to their

own lives.

In addition to the ongoing debate surrounding identity

development, the cerebral location of an “identity region”

also has yet to be resolved. Scientists agree that several areas

of the brain work together to update the sense of identity, but

many experts have focused on the cortical midline structures.

This part of the brain is located near the center of the frontal

lobe. It communicates extensively with the medial temporal

lobes, which process memory and emotion.

In cases where the medial temporal lobes do not provide

complete or correct information to the cortical midline

structures, identity delusion can occur. For example, 23-yearold

Adam Lepak of Syracuse, New York sustained massive

brain injuries in a 2007 motorcycle accident. Now, he

frequently thinks his mother is part of an alternate, fabricated

universe, and he cannot maintain an up-to-date sense of who

he is because of lesions in his brain’s emotion and memory

centers. However, with extensive exercises, such as identifying

people in mirrors and doing physical therapy, some of the

brain functions Lepak lost are starting to reappear. His

story not only shows the progress of neuroscience but also

supports the theory that a combination of brain regions are

implicated in identity formation and maintenance.

The development of a large and capable brain explains

the intricate nature of human civilization today. However,

when it comes down to the deepest question regarding the

brain — “Who am I?” — scientists are confronted with an

unsolved mystery. Researchers can explore identity formation

through neuroscience and psychology, but this phenomenon

ultimately remains an incomplete puzzle.

March 2014

Yale Scientific Magazine

37


FEATURE

book review

SCIENCE IN THE

SPOTLIGHT

BOOK REVIEW : GULP

BY KEVIN WANG

We gulp dozens of times each day. We swallow our food and we

swallow our beverages, unaware of the evolutionary wonder that is

the alimentary canal.

Mary Roach, author of the best-seller Stiff, dives into the human

digestive tract in her new book Gulp. In her unapologetically blunt

style, Roach combines science and history, humor and sincerity to

take us from mouth to rectum and back up again. Although Roach’s

impressive compilation of historical anecdotes is indeed entertaining,

its effect is undermined by the forced nature of other topics in

the book.

The book’s main strength lies in Roach’s scientific run-down of

our bodies’ digestive processes and the ridiculous stories she tells

along the way. For instance, she dedicates a whole chapter to the

complex relationship between William Beaumont and Alexis St.

Martin. Beaumont was a surgeon who was fascinated by a gunshot

wound in St. Martin’s stomach. This wound created a hole through

which Beaumont could peek into the inner workings of St. Martin’s

stomach. Beaumont became obsessed with this stomach wound, and

was extremely reluctant to part ways with his patient.

From the mealworm’s ability to “eat out” of its host’s stomach to

the animal instinct of eating feces (autocoprophagia), Roach does not

shy away from any story about our digestive system, no matter how

revolting. Death and pain are rampant

throughout the book, and one grows

to see them in the humorous light she

does, especially when toxic flatulence

is involved.

But Gulp is far from all fun and

games. As much as Roach tries to

make us laugh, she also espouses the

nutritional value of including organs

in our diet, discusses the health

benefits of chewing, and questions

the modern state of health policy

in America. However, these brief

sparks of sincerity seem misplaced

and forced.

As smoothly as Roach’s stories flow from one to the next, some

are so brief and under-developed that it seems as if she is merely

crossing tasks off a checklist. Her day-to-day accounts add a personal

touch, but the book occasionally read too much like a diary.

Roach’s Gulp is certainly a delightful meal, but be prepared for

occasional stomach cramps along the way. Not to worry, though; they

will definitely not last long.

BOOK REVIEW : NEWTON’S FOOTBALL

BY ELENA MALLOY

Newton’s Football, the Science Behind America’s Game examines football

through the lens of physics and mathematics. Authors Allen

St. John and Ainissa Ramirez provide a unique view on the most

popular Sunday family-bonding event. Ramirez, a former Associate

Professor of Mechanical Engineering and Materials Science at Yale,

collaborates with best-selling author St. John to create an accessible

and enjoyable scientific novel. However, in their effort to increase

accessibility, the authors come dangerously close to oversimplifying

their explanations.

As the title suggests, Newton’s Football describes physics concepts

such as gravity and spin in order to explain ball movement and other

phenomena in football. St. John and Ramirez quickly and comfortably

dive into the hard science behind football. Each section of the book

alternates between an anecdote from the football field and a scientific

explanation for the phenomenon. This structure creates an easy-tofollow

and captivating novel for any football fan.

But those more interested in science than football might be

dissatisfied with the book’s easy pace. Chapter introductions

narrate the history of football in great detail; for example, St. John

and Ramirez discuss the creation of the actual ball from pigskin.

However, the accompanying scientific tidbits — that the making and

shape of the football relate to the direction of its movement, for

instance — seem mundane in comparison. Because of its simplicity,

the information presented in Newton’s

Football might seem like common

knowledge to the advanced scientist.

Most high school level physics

classes address the parabolic motion

of an object. However, St. John and

Ramirez do not wade deeper than this

high school explanation. In creating a

science novel for sports enthusiasts, the

authors unfortunately dilute most of

the science.

St. John and Ramirez have straddled

a difficult disciplinary line in their

book Newton’s Football, the Science Behind

America’s Game. They try to blend these two areas together, but

there are often jolting contrasts between sports slang and science

vocabulary. For example, the book refers to the football as a Wilson

“Duke” but also describes the ball’s shape as a “prolate spheroid.”

Of course, if given a chance, Newton’s Football can connect with

readers without a background in science or football. The novel

is worthwhile for any individual interested in sports and science,

although prospective readers should know beforehand that the

science is rather thin.

38 Yale Scientific Magazine March 2014 www.yalescientific.org


The Mistake

BY CELINA CHIODO and ANDREW SUNG

cartoon

FEATURE

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