YSM Issue 89.1


Yale Scientific

Established in 1894


DECEMBER 2015 VOL. 89 NO. 1



Live brain imaging helps patients

attack anxiety at the source

q a



How Is Dust Affecting the California Drought?

The future of the drought crisis in

California may depend on an unlikely factor

— dust.

The impact of dust on precipitation and

water retention in the ground is mixed,

which leaves scientists largely uncertain of

whether it will benefit or worsen conditions

in the torrid land. Unpacking the effects

of dust could prove vital as California

confronts its current drought conditions.

Some researchers fear that the state’s

accumulating dust will only escalate the

drought problem. Most of California’s

water supply begins as snow in the Sierra

Nevada Mountains before it melts and seeps

into reservoirs. As the state gets drier, dust

accumulates on the snow, darkening its

surface and accelerating the melting process

— dark surfaces more effectively capture

heat energy from the sun. By the estimates of

Thomas Painter, a NASA snow hydrologist,

this discoloration could cause the snow

to melt as many as 25 days earlier than it


►Discolored and darkened snow absorbs

thermal radiation more effectively than clean

snow, which causes faster melting. This is one

of many ways that dust factors into drought.

normally would. Instead of replenishing

California’s dwindling water supply in the

hot summer months, Painter has found

that this earlier snowmelt causes runoff to

occur in the spring, when the reservoirs are

already mostly full from winter rains.

Other scientists hope that the dust will

increase precipitation. Kim Prather, an

atmospheric climatologist at the University

of California, San Diego, has found that

dust induces water vapor to condense, form

clouds, and increase rainfall or snowfall.

This process, known as cloud seeding,

increases rain and snowfall by up to 40


Although it is not yet clear whether dust

is improving or devastating California’s

drought crisis, researchers know that the

situation is getting more urgent every day.

Understanding the dual effects of dust on

drought are important in working towards

these solutions to restore the parched and

drying land.


That late night coffee could be throwing

your circadian clock out of sync. A study

led by researchers from the University

of Colorado Boulder and Cambridge

University shows that caffeine in the

evening causes a delay in the human

biological clock — rhythms that coordinate

a healthy sleep-wake cycle. Scientists have

provided empirical evidence for the notion

that caffeine and sleep do not mix well.

Circadian rhythms are not trivial. They

respond to light and darkness in a 24-

hour cycle. They regulate hundreds of vital

physiological and biological processes.

And according to Yale School of Public

Health professor Yong Zhu, disruptions in

circadian rhythms can increase the risks of

depression and hormone-related cancers.

To determine how caffeine impacts circadian

rhythms, subjects in the present

study received one of three treatments:

How Does Caffeine Impact Your Internal Clock?


►A double espresso shot delays the human

biological clock by 40 minutes. Research on

caffeine and circadian rhythms could improve our

understanding of sleep disorders.

a caffeine dose equivalent to a double

espresso shot, a placebo pill, or exposure

to bright or dim light three hours before

bedtime. Caffeine delayed subjects’ circadian

clocks by an average of 40 minutes.

This was about half the shift induced by

bright light, a well-known time cue for our

natural circadian rhythms.

The researchers also discovered that

caffeine directly affects an intercellular

messenger molecule called cyclic AMP,

which plays a key role in maintaining

circadian rhythms. According to paper

author Kenneth Wright, the results of this

study suggest that caffeine may delay sleep

timing through circadian mechanisms.

Night owls and late risers can learn from

the study’s findings: To get out of bed

earlier in the morning, skip your evening

coffee. Your reset circadian clock will

thank you.

Yale Scientific

Established 1894




Battling OCD in

Real Time

Neuroscientists are using real time

fMRI to show people how to control

their own brain activity. Armed with

neurofeedback, OCD patients might

regain control of their anxiety.







Letter From the Editor

The Global Burden of Leptospirosis

Yale Radiobiologist Wins Nobel Prize

Dylan Gee Receives NIH Award

Linguists Illuminate Number Systems



Predator vs. Prey:

Who’s Changing Whom?

Predators may not deserve all the credit

for driving evolution. In isolated lakes,

fish prey have a profound impact on their

larger fish predators.



Ice in Action: Sea Ice

and Climate Change

Arctic sea ice is known to predict climate

change effects around the globe. A new

mathematical model makes sense of the







The Significance of Swine in Society

Textbook Explores Real World Math

Development and Bridges to Peace

HIV: Last Barrier to a Cure


Electrical Engineering

Portobello Mushrooms Power Batteries


Foresting from

20 the Ground Up

Private woodland owners in

Connecticut have found their

niche in modern forestry.

Environmental programs like

the Quiet Corner Initiative

offer resources and support,

but ultimately, it is up to

the individual landowner to

conserve and preserve the









Modeling Nanocrystals for Real World Use


Self-propelled Particles Halt Hemorrhage


You Have a Microbial Cloud!


Bugs and Bees: How Viruses Bridged the Gap

Materials Science

Magnetic Materials and Faster Computers

Debunking Science

The Martian

To Rebuild a Lung,

23 First Strip it Down


Science or Science Fiction?

Making Virtual Reality a Reality

Researchers are fine-tuning a

method of decellularizing pig

lungs to obtain an intact lung

scaffold. This scaffold could then

be populated by human stem cells.

The final product: a custom-made

lung, the dream for many who

wait on a long list for a viable lung






Undergraduate Profile:

Samantha Lichtin ES ‘16

Alumni Profile:

Richard Lethin YC ‘85

Science in the Spotlight

“The Infinite Monkey Cage”

“Science Vs”

More articles available online at www.yalescientific.org


December 2015

Yale Scientific Magazine







Science can be intimidating. It is fast-paced and unyielding. We are only

human. It’s natural to feel vulnerable to science when it takes the form of

a massive hurricane or appears as a microscopic virus hiding in your cells,

plotting to strike (pg. 11). But science can also give us agency, putting us back

in charge of our health and our planet. Our cover story for this issue of the Yale

Scientific (pg. 17) explores how developments in brain imaging technology

are allowing people to watch their minds at work. No longer are fMRI scans

only interpretable by doctors — with real time fMRI, OCD patients see their

own brains in action and can learn to regulate their own brain activity. With

science on their side, they regain control of neural networks that have been

hijacked by anxiety.

This is one of many stories you’ll read here that features people taking science

into their own hands. When two professors were unsatisfied by available

math textbooks, they published their own (pg. 9). Forest preservation in

Connecticut largely depends on individual woodland owners caring for their

property (pg. 20). Doctors are realizing the power of personalized medicine,

devising treatment strategies catered to the individual. In one step of this

movement, researchers in tissue engineering are working towards customized

lung transplants (pg. 23).

A couple years ago, this magazine released an issue themed “Science

and the Individual.” Remarkably, in less than 24 months time, we notice

tremendous progress in personalized medicine, citizen science, grassroots

campaigns for conservation and sustainability, and other scientific arenas

where individuals stand at the forefront. As science accelerates, we also see

new efforts to communicate it, to keep up. The pages that follow include the

Yale Scientific’s first ever reviews of science podcasts (pg. 38) and a debunking

of The Martian (pg. 34), a fictional film that still makes an effort to present

nuanced scientific insight.

Indeed, one of our goals as a publication is to adapt to the changing scene of

science and science journalism. To this end, in the past year we’ve established

a stronger online presence, launching a redesigned website, more social

media content, and a prolific science blog. Vol. 89, Issue No. 1 is the last

that we’ll publish as the 2015 masthead. We wish the best of luck to the new

editors of the magazine. We can’t wait to see what further change brings.

Yale Scientific

Established in 1894


DECEMBER 2015 VOL. 89 NO. 1




Live brain imaging helps patients

attack anxiety at the source


Payal Marathe


The cover, designed by arts editor Christina Zhang,

depicts how neurofeedback therapy can help patients

with OCD regulate their anxieties. In the foreground

is a rendering of a patient undergoing an fMRI

scan. The vividly illuminated regions of the brain

represent the real time fMRI signals that researchers

are using to correlate brain activity with strategies to

lower anxiety. The arrows in the background indicate

decreases in orbitofrontal cortex activity that occur

when patients are able to successfully control their

OCD-related fears.

Yale Scientific


Established in 1894

December 2015 VOL. 89 NO. 1


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in brief

Leptospirosis: An Unexpected Global Disease Burden

By Ruiyi Gao


►Albert Ko, professor of epidemiology

at the Yale School of Public Health, has

demonstrated that leptospirosis has a

higher disease burden than expected.

According to the research of Albert Ko at

the Yale School of Medicine, leptospirosis

makes a surprisingly high and previously unmeasured

contribution to the global burden

of disease. Ko’s team found that the tropical

disease results in more than 60,000 deaths per

year globally, and thus poses a burden comparable

to that of cholera.

Leptospirosis is a bacterial infection transmitted

from animals to humans via soil and

water. It often impacts subsistence farmers

and slums in countries such as Brazil and India.

Early symptoms of leptospirosis resemble

those of malaria or the flu, but further progression

often results in conditions such as

pulmonary hemorrhaging — bleeding from

the lung — which can be fatal. The exact

mechanism by which the bacteria cause disease

remains unknown.

In 1996, Ko began working in Brazilian

communities to prevent leptospirosis after a

large outbreak among urban slums. In 2010,

he was approached by the World Health Organization

to conduct a more formal study of

the disease burden. Ko’s group determined

the disease burden using hospital data to estimate

the morbidity and mortality of leptospirosis.

Despite Ko’s recent quantification of the

leptospirosis burden, future studies are still

needed for more precise approximations.

“Rapid urbanization and global expansion

of slum settlements, as well as future climate

change, will further increase disease transmission

and thus disease burden,” Ko said.

Ko emphasizes the importance of his team’s

estimates in working towards alleviating the

problem of leptospirosis in the developing

world. “Though these estimates are only the

first step in addressing the disease burden of

leptospirosis, they are critical for establishing

a baseline for future research and building

the investment case for public policy interventions,”

he said.

Former Yale Radiobiologist Co-awarded Nobel Prize

By Sarah Healy


►Aziz Sancar was awarded the

2015 Nobel Prize in chemistry for

elucidating a precise mechanism of

DNA repair.

Forty years after transitioning from

medical practice to biochemistry research,

Aziz Sancar has received the highest

honor in his field: the 2015 Nobel Prize in


Sancar shared this award with Tomas

Lindahl and Paul Modrich for their wideranging

“mechanistic studies of DNA

repair.” Specifically, Sancar was recognized

for his discovery of how multiple enzymes

work together during a process called

nucleotide excision repair to fix DNA

damaged by ultraviolet radiation in human

and bacteria cells.

From 1977 to 1982, Sancar worked as a

postdoctoral fellow in professor W. Dean

Rupp’s radiobiology lab at Yale. During

this period, the researchers studied UVsensitive

bacteria strains and discovered

that certain enzymes make two incisions

surrounding the UV-damaged region to

eventually release it. A previous model for

excision repair purported that only a single

cut was made.

“Up until that point, the method that

everyone believed was that [these enzymes]

only made a nick in the DNA, and then

other enzymes came along and removed

it,” Rupp said. Sancar’s revolutionary dual

incision discovery in bacteria allowed him

to later elucidate the more complex repair

mechanism in human DNA.

Regarding Sancar’s Nobel Prize, Rupp

explained that the primary significance

is the discovery of the bimodal incision,

which Sancar determined in Rupp’s lab.

Sancar’s findings expand upon the DNA

repair research that has been conducted

at Yale for decades. Now, he continues this

work as a professor at the University of

North Carolina.

Rupp described Sancar’s work ethic as

nothing short of outstanding: “He was a

combination of very bright, very original,

and very focused,” Rupp said. “He had

complete dedication.”

6 Yale Scientific Magazine December 2015 www.yalescientific.org

in brief


Professor Dylan Gee Receives NIH Research Award

By Cindy Yang

Dylan Gee, who will begin at Yale in July

2016 as an assistant professor in psychology, has

received an NIH Director’s Early Independence

Award. The award, which allows scientists to skip

postdoctoral training and move immediately

into independent research positions, supports

“exceptional students that have the intellect,

innovation, drive, and maturity to flourish

independently,” said NIH Director Francis


Gee’s research investigates the efficacy of

safety signal learning, a method to treat anxiety

disorders in children and adolescents. The

approach involves training individuals to identify

a safety cue to help reduce fear and anxiety.

Her research bridges neuroscience and clinical

approaches. Gee is interested in examining how

disruptions in the normal development of the

brain may contribute to anxiety disorders. She

also focuses on how safety signal learning might

help reduce anxiety during periods of increased

neuroplasticity early in life. The brain’s circuitry

is still forming in these early years, which makes

it more malleable.

“It is a tremendous honor to be selected, and

I think it really speaks to how excited people

are about the potential to target mental illness

through early identification and intervention,”

Gee said. With developmental neuroscience

looking at the brain as it grows, Gee believes researchers

can optimize mental health treatments

for children and adolescents.

Her decision to pursue this research was

influenced by her passion for neuroscience

and her experiences as an undergraduate at

Dartmouth College, where she mentored youth

who had experienced early adversity or trauma.

“I was inspired to help improve mental health

outcomes and to figure out how we can promote

resilience and enhance treatment,” Gee said.

The five-year grant from the NIH provides up

to $1.25 million for research, and affords Gee

the opportunity to launch immediately into her



►Professor Dylan Gee received the NIH

Director’s Early Independence Award

for research on anxiety disorders in

children and adolescents.

Linguists Illuminate Evolution of Number Systems

By Clio Byrne-Gudding

Associate professor of linguistics Claire

Bowern and Kevin Zhou YC’15 have published

a paper on the evolution of number systems

in Australian languages in Proceedings of

the Royal Society B. Studying the Pama-

Nyungan language family, Bowern and Zhou

used statistical methods to investigate how

the finite upper limits of those systems have

changed over the last 5,000 years.

The duo found that most numerical systems

in the Pama-Nyungan family are low-limit,

meaning their maximum values ranged

between three and five. An amount greater

than this, like six apples, would instead be

considered “many” apples. Bowern and

Zhou showed that these limits fluctuated

over evolutionary time, but when systems

reached numerals beyond five, they began to

grow rapidly, and would thus no longer be

categorized as low-limit. When examining

the numerals’ compositionality — how bigger

numerals are constructed from smaller

numerals — they also found that languages

tend to gain numerals primarily by building

them from existing numerals.

Bowern received a PhD in linguistics from

Harvard in 2004. She and Zhou, a biomedical

engineering major, made a unique team. “I just

approached her and explained my background

in statistics and we agreed that analyzing the

Australian numeral dataset using Bayesian

statistics would be interesting,” Zhou said.

Since joining Yale’s linguistics department

in 2008, Bowern has been running a project

on the history and structure of Australian

languages. This paper was a piece of that

overall project. While Bowern will not

continue numeral research, her work with

Zhou has shed much-needed light on lowlimit

numeral systems. “Previous work has

assumed that [low-limit numeral systems]

couldn’t be easily studied, or that they didn’t

change very much,” Bowern said. “We show

how diverse these systems are, even though

previous work had assumed that they are all

rather similar.”


►Women of the Warlpiri tribe in

Australia’s Northern Territory likely

speak a language evolved from the

Pama-Nyungan family.


December 2015

Yale Scientific Magazine





Yale conference examines pigs in human society


Mark Essig lights up when he tells the unlikely story of how

19th century hog drives in the Blue Ridge Mountains created a

complex infrastructure of taverns, roads, and pig statues across

North Carolina. This story fascinated Essig and led to his 2015

book Lesser Beasts: A Snout-to-Tail History of the Humble Pig,

an account of the changing human relationship with pigs over

time. It starts with humans raising hogs along the Nile, and takes

readers all the way up to the modern U.S. pork industry.

This past October, Essig was a speaker at the “Pig Out”

conference at Yale, where he and other porcine academics

gathered to discuss all things swine.

Fully titled “Pig Out: Hogs and Humans in Global and Historical

Context,” the conference drew academics from far-reaching fields

— from religious studies, to agriculture, to sociology, to genetic

engineering. These experts gathered in New Haven to discuss

how we can better understand human society — both today and

in historical context — by focusing on the pig.

Diverse issues are affected by the pig in a social, cultural, and

scientific context. Debates over vegetarianism and ethical animal

slaughter, for example, would benefit from an interdisciplinary

conversation, which is exactly what the Yale Pig Out conference

hoped to achieve.

One subject Essig touched upon was environmental issues, and

the fact that they cannot escape the porcine narrative, especially

as the industrial age has changed the role of pigs. Wooden fences

were replaced with concrete boxes that more effectively contain

hogs. The very definition of livestock as food was abstracted as

big agriculture herded animals into factories not unlike the car

factories that were springing up around the same time. The rise

of big agriculture had ramifications for our relationship with pigs

— generally speaking, we think of pigs today more as food and

less as sentient creatures. Essig argues that this mirrors our altered

interaction with the environment as a whole, which is one way

that the pig story sheds light on changes in human society.

“Culture plays a role in decisions about what to eat and the way

we use meat,” Essig said. “There are a lot of ways to get sustenance.

The particular decisions we make about the meats we eat say a lot

about how we organize ourselves as society.”

No aspect of modern American agriculture, which is

increasingly becoming industrialized, is “terribly pretty,” Essig

added. “Pork is the worst.”

Pigs are the smartest creatures that humans eat on a large scale.

They are unique livestock in several key ways — less mobile, yet

far more self-sufficient than any other livestock, and capable of

foraging and surviving on their own in almost any environment,

urban or rural. Understandably, humanitarian concerns have

been raised as companies capture pigs in tight cages and dose

them with antibiotics, effectively eliminating their self-sufficiency.

Furthermore, factory farming sometimes releases environmental

toxins. Methane from livestock is a major contributor to global

greenhouse gas emissions.

Essig describes the role of government regulation of the meat

industry as “a lack of regulation.” If anything, the U.S. government

has been a promoter of the meat industry, and authorities have

been known to turn a blind eye to environmental damage in

favor of higher profit, he said. In this way, the fate of the pig in the

industrial age reflects the key environmental and humanitarian

concerns of our time.

The pork industry through the ages is a case study of

industrialization and the environment. If these issues go

unaddressed, future consequences may be dire. The future of the

pig mirrors the future of our societal decision on how to interact

with our environment. As Essig put it, “food is about identity,”

and the human relationship with the pig shows how much that

identity has evolved.

The October conference looked to history as much as it

discussed modern day controversies related to the pig. “The

number of pig bones found at historical sites correlates with

political changes; there were more pig bones when the political

structure was weaker,” Essig said. Observations like this further

demonstrate how pigs might illuminate secrets of humans’

historical past. Pigs were a calculated choice by ancient social

systems, as they were animals that could be more easily organized

than other livestock, such as cattle, sheep, or goats. Subsistence

villages on the margins of empires benefited greatly from the pig.

Once again, pigs paint a picture of the political, economic, and

environmental climate at any given time.

Other key speakers at the Yale conference included renowned

food journalist Colman Andres, animal warfare advocate Bob

Comis, and Greger Larson, director of the paleogenomics

department at the Oxford School of Archaeology. The event was

sponsored by the Yale agrarian studies program.


►Mark Essig relaxes with a pig. Industrial pigs today can reach

a weight of more than 300 pounds in less than a year after birth,

due to modern methods of raising the livestock.

8 Yale Scientific Magazine December 2015 www.yalescientific.org




Textbook explores real world applications of math


Mathematics lies behind the circuitry of every computer,

the operation of every business, and even the composition of

every hit song. But millions of students struggle with math

every day, and many will never grasp the intricacies of algebra

and calculus. Indeed, mathematics is frequently pilloried

as tedious, convoluted, and ugly. In the hopes of making

math more widely accessible and enjoyable, two former Yale

University lecturers, Anna Lachowska and Apoorva Khare,

have authored a new textbook on mathematics that uses a

novel multidisciplinary approach to teaching the subject.

Lachowska and Khare, now at École Polytechnique Fédérale

de Lausanne and Stanford University, respectively, titled

their book Beautiful, Simple, Exact, Crazy and published it

with the Yale University Press. In the book, they showcase

the elegance and ubiquity of math. As its title suggests, the

textbook aims to convince its readers that mathematics is

worth learning — because it is a powerful tool, and because

it is beautiful.

The authors were inspired to write the book while teaching

a lecture course at Yale called “Mathematics in the Real

World.” When the two were selecting a textbook for their

class, they had trouble finding one that fit their needs.

“Despite the large number of entry-level math textbooks

available in print, we were unable to find a book that suited

our goals,” Lachowska said. “We wanted to have a concise

exposition of a wide range of accessible mathematical ideas

with the right level of rigor and a large variety of applications.”

The natural solution, of course, was to write this dream

book themselves.

And so Beautiful, Simple, Exact, Crazy was born. It is a

textbook intended for introductory college math courses

for non-majors. The book includes lessons, examples, and



►Anna Lachowska is a former Yale lecturer and coauthor of

Beautiful, Simple, Exact, Crazy. She now teaches at a university

in Switzerland.

practice problems, but Lachowska and Khare focused on

making it more readable and enjoyable than a standard

math instruction text. Where most textbooks highlight

specialized, technical applications of mathematics — largely

in the physical sciences such as engineering, physics, and

chemistry — Lachowska and Khare show math at work in

more diverse areas of the real world.

“‘Mathematics in the Real World’ was designed to be a new

entry-level math course for non-science oriented students

and would cover a wide range of topics without going into

the technicalities, but instead emphasizing practical or

amusing applications,” Lachowska said. She and Khare kept

this in mind when writing Beautiful, Simple, Exact, Crazy.

Non-science-oriented students often struggle the most

with mathematics, but as this book shows, no field can

entirely escape math. Lachowska and Khare chose examples

to illustrate this fact.

Unlike a traditional math textbook, Beautiful, Simple,

Exact, Crazy touches on subjects as diverse as art and music

theory. “We went out of our way to include amusing, artsy, and

philosophical topics,” Lachowska said. “Most importantly,

we tried to discuss how mathematics can be used and what

it means for the humanities — not in the obvious ways, as

statistical methods in social sciences, but in some surprising

and unexpected ways.”

For example, the textbook discusses the fundamental

connection between logarithms and the 12-tone equal

temperament tuning common in music. The book also looks

at applications of math in archeology and linguistics. It even

delves into an analysis of motion in a short story by the

Italian author Dino Buzzati.

While instructors have many textbooks to choose from

when teaching introductory mathematics, Lachowska and

Khare hope that theirs will have a special appeal. In addition

to its non-traditional content and focus, Beautiful, Simple,

Exact, Crazy also departs from most textbooks when it

comes to structure. “The sections of the book are only loosely

connected to allow the reader or the teacher to choose topics

they want to read about,” Lachowska said. And at 480 pages,

it is a slim volume compared to many mathematics texts.

“One of my main sources of inspiration was the interest

and curiosity about mathematics expressed by many of my

non-mathematical friends,” Lachowska said. “They wanted

to know what mathematics is, and how it is relevant to the

real world and to other domains of thought, and we hope our

book provides some of the answers.”

Beautiful, Simple, Exact, Crazy is currently in print. Its

authors hope that the book will accomplish their goal of

convincing readers why math matters.

December 2015

Yale Scientific Magazine





Interventions targeted to children show best results


To many, world peace might seem like a childlike concept

entrenched in innocence. But maybe a focus on childhood is

exactly what we need to work towards peace within communities.

Yale researchers have combined findings from multiple fields

— including psychology, neuroscience, and anthropology — to

champion early child development programs as pathways to

peace. The researchers focused specifically on the potentially

causal link between early childhood development and a culture

of peace within families, communities, or even nations. The team

found that providing group-based family support programs and

engaging with fathers are both effective strategies to promote a

peaceful disposition in children. But the positive impact of these

interventions goes beyond a single generation. Encouraging

peace during childhood could reduce violence and bring forth

peace for future generations as well.

“Child development is a huge and fascinating field of science,”

said Catherine Panter-Brick, Yale professor of anthropology,

health, and global affairs. “Another important and fascinating

field is peace-building. Usually, these two fields barely intersect.”

Panter-Brick and her team wanted to bridge this gap.

Over the past two years, both Panter-Brick and professor James

Leckman of the Yale Child Study Center, have participated in a

number of forums on promoting peace. These discussions and

conferences are a part of the United Nation’s Early Childhood

Peace Consortium, for which Panter-Brick and Leckman serve

as lead members.

In these forums, Panter-Brick and Leckman have discussed

the interventions that they believe will be most effective in

promoting peace. Some strategies target parenting behavior,

teaching parents skills on how to be sensitive towards their

children’s needs and how to raise them without a violent

disposition. Other initiatives harness the media and community

leadership, as was done in northern Ireland to help end many

decades of civil strife.

Panter-Brick emphasizes that the timing of interventions

matters. “Acting early in the child’s life to promote health,

competence, and empathy is far more effective than acting later

to persuade young adults to turn away from violence,” she said.

At other UN events, Leckman has highlighted the biology of

caregiving, pointing to the significance of hormonal changes as a

way to explain the efficacy of early nurture in reducing violence

over the course of a lifetime.

According to Leckman, epigenetics — the study of external

effects on gene transcription and expression — has been shown

to shape parental behavior in animals. Studies of Norwegian rats

show that the amount of pup grooming behavior from mother

rats corresponds to the amount of grooming they themselves

had received as pups. Researchers are now confirming that in

humans, a disposition to peace or to violence may also transcend


►Panter-Brick and Leckman found that including fathers

as well as mothers in intervention programs increased the

efficacy in terms of promoting peaceful dispositions.

across generations.

The team further highlights that group-based interventions are

preferable to family-based ones because they promote empathy

across ethnic, religious, and social divides. These strategies bring

together groups of parents in the same place and time, rather

than relying on solo families to access specific services.

One illustration of group-based parenting interventions is the

Mother Child Education Foundation, or AÇEV, an organization

based in Turkey that offers programs for early childhood

development. The programs were first designed for groups

of mothers, and then at the request of women, were designed

for groups of fathers and run as gender-specific Mother

Support and Father Support Programs. After participating in

the intervention, which aims to develop communication skills

and positive parenting behaviors, many of the fathers involved

became friends, despite coming from different religious

and socioeconomic backgrounds. These friendships led to

supportive communities that persisted to aid all parents with

their responsibilities.

“There’s something transformative about people coming

together to talk about their life experiences, sharing that

information with others, and going through a curriculum where

they report what they learned and how their interaction with

their children changed,” Leckman said.

Now that these results have been established, future steps

include translating these findings into effective programs in

different social, economic, and cultural contexts, and scaling

them up to reach more people. “The new message is that it takes

political leadership to reach peace, but it also requires good

science,” Panter-Brick said.

10 Yale Scientific Magazine December 2015 www.yalescientific.org




HIV researchers study reactivation of hidden viruses


In 1984, when human immunodeficiency virus (HIV) was

discovered as the cause of AIDS, researchers were optimistic

that a cure was on the horizon. Now, more than 30 years later, 35

million individuals around the world are infected with HIV. And

the cure is still elusive. Why has HIV proven so difficult to treat?

The answer lies partly in its ability to remain latent in the human

body, staying hidden until it unpredictably reactivates to become

deadly once again.

A team at the Yale School of Engineering and Applied Science,

led by professor Kathryn Miller-Jensen, is interested in the

reactivation of latent HIV. These hidden viruses pose a major

hurdle for HIV treatments — even the most potent drugs cannot

eliminate the virus until it resurfaces. Current treatments for the

disease involve a drug cocktail that patients must take for their

entire lives, since latent HIV could reactivate at any time. But

what if researchers found a way to force latent HIV back into

action in our immune system cells? By drawing these viruses

out of hiding, treatments could theoretically destroy nearly all

viruses in the body, effectively curing the patient. There is a long

road ahead in developing a cure, but projects at Miller-Jensen’s

lab might eliminate barriers by illuminating the details of HIV


The lab has several ongoing projects working to address the



►Kathryn Miller-Jensen and her team study the reactivation

of latent HIV at the Yale School of Engineering and Applied


mystery. The team is investigating, for example, how T-cells in

the human immune system respond to HIV infection. When

HIV invades a T-cell, it inserts its genome into the host genome.

Most of the time, the host cell transcribes the HIV genome, the

first step to gene expression that then produces more viruses.

However, in some cases, HIV instead enters a latent state where

it is hidden in the host genome until changes in the T-cells cause

reactivation. As such, the lethal virus remains tucked away in a

small percentage of the body’s cells.

What kinds of changes to host cells predict reactivation?

A component of Miller-Jensen’s research examines latencyreversing

agents (LRAs), or small proteins that stimulate HIV

back into action.

LRAs can be manufactured into small molecule drugs, which

could prove useful in HIV treatments — namely, in the “shock

and kill” method. This approach to combatting HIV forces

reactivation from the latent state, making all viruses in the body

vulnerable to drug action. Other medications then work to

eliminate infected cells.

“If we could get all the latent HIV to reactivate, that would allow

us to flush out the virus,” Miller-Jensen said. “Basically, there are

two parts to the method: First, LRAs are used to reactivate the

HIV, and then the immune system or the replicating virus kills

off the cells that are now producing HIV.”

Still, like so many promising solutions in science, the “shock and

kill” technique has its limitations. Sometimes, significant levels of

latent HIV remain in cells even after drugging with LRAs. One

possible reason for this is that fluctuations in the levels of gene

transcription between cells can cause some cells to respond less

strongly to the drugs. “Even if our cells are genetically identical,

they don’t always respond the same way,” Miller-Jensen said.

“That’s a very interesting question in the field of HIV.”

The group is further is interested in discovering the markers

that differentiate infected from uninfected T-cells, which would

facilitate identification of cells that are carrying latent HIV. Once

again, this could inform more successful therapies for the disease.

Is a cure for HIV a possibility in the near future, or are we still

as naïve as in 1984? Will an effective cure remain out of reach

despite our improved understanding of the disease? Miller-

Jensen is realistic. She does not claim that a cure will be developed

anytime soon. “It feels like we’re still pretty far from this goal,” she


However, she believes that researchers will continue to make

progress by collaborating across fields. “We’re much closer

than we were 10 years ago. With many researchers working on

different aspects of the problem — finding new LRAs, mobilizing

the immune system to kill reactivated T-cells, developing new

methods to track the size of the latent reservoir — we might get

some kind of combination that solves the problem,” she said.

December 2015

Yale Scientific Magazine







Who’s changing


by Sonia Wang

art by Ashlyn Oakes

Late October, twilight, Gorton Pond. The

water lies still, reflecting the pitch-black

night sky and the outlines of the fiery

orange autumnal trees bordering the shore.

The pond’s alewife juveniles are preparing for

their migration to sea as their six-month stay

in the freshwater pond comes to an end.

Four miles north of Gorton Pond, Pattagansett

Lake has a similar environment and

population of fishy residents, including alewife

and their predators, the chain pickerels.

But unlike Gorton Pond’s inhabitants, Pattagansett’s

cannot migrate; Pattagansett is a

landlocked lake.

These two bodies of water would have had

almost identical ecologies and fauna a few

hundred years ago. But European colonists in

southern Connecticut built permanent dams,

disconnecting lakes like Pattagansett from the

sea. Within these dammed lakes, landlocked

fish populations have since evolved in

ways that spark the interest of ecologists

and biologists alike. Among these curious

scientists is Yale’s David Post, a professor of

ecology and evolutionary biology.

Over the past decade, Post’s team of

researchers has studied the alewife and chain

pickerel populations in 12 lakes including

Gorton and Pattagansett. The group’s most

recent paper, published in the journal

Nature, showed that changes in the alewife

population can drive diversification and

adaptation in the pickerel population. This is

a departure from ecology’s traditional focus

on the trickle-down impact that predators

have on prey. Rapid predator evolution,

occurring over a short time span, can be

difficult to observe. But the Connecticut

lakes conveniently exhibit isolated predatorprey

systems, enabling the recent Post lab

study and others like it. Research on alewife

and pickerel fish is providing revolutionary

insight into the predator-prey relationship in


A split history

Post first began studying alewife in 2004

after he recognized that there are two forms of

alewife that are quite literally defined by their

ecologies: The anadromous form migrates

to the sea, and the landlocked form cannot

migrate and is restricted to its home lake.

The anadromous fish of Gorton Pond

and the landlocked fish of Pattagansett Lake

were at one point the same population of

migrating, anadromous alewife. Anadromous

fish are born in freshwater areas and migrate

to saltwater environments, returning to

freshwater lakes and rivers only later in life

to spawn a new cycle of migration. It was

not until after the construction of manmade

dams that alewife trapped inside Pattagansett

began to evolve in isolation while Gorton

Pond’s anadromous alewife continued to

migrate. The ecological isolation affected a

trend of increasing divergence between the

two populations. Distinctions between the

two types of fish would become apparent

across New England over the next 300 years.

One component of this divergence is

habitat. Any body of water — marine or fresh

— is divided into distinct regions such as the

littoral and pelagic zones, which differ in their

chemical makeup and species composition.

The near-shore littoral zone rings the lake and

contains many unique habitats because of its

numerous distinct species of rooted plants

and animals. Meanwhile, the pelagic zone

is what is considered open water, in which

structure is defined by the thermocline, or the

temperature gradient across varying depths.

Because temperature drastically affects the

amount of oxygen and nutrients dissolved

in the water, the thermocline can impact the

biology of the organisms living in the various

layers of a pelagic habitat.

In every lake observed by Post and his

colleagues, anadromous alewife lived in

both the littoral and pelagic zones during

their freshwater phase, whereas landlocked

alewife lived exclusively in the pelagic zone.

Although the reason for this choice of

12 Yale Scientific Magazine December 2015 www.yalescientific.org



habitat remains unknown, the effects of this

pelagic lifestyle are apparent in the alewife’s

physical characteristics. The landlocked fish

have comparatively smaller heads and more

fusiform body shapes, such that their bodies

are widest in the middle but taper off at the

ends. This streamlined, tuna-shaped body

allows them to swim faster in the pelagic

zone, where speedy hunting and escape skills

are necessary for survival.

Such landlocked populations are gold

mines for evolutionary biologists, since

isolation offers insight into a species’ rapid

evolution as well as the effect of this evolution

on other populations in the environment.

After showing that alewives drove evolution

in their prey, a plankton species, and in one

of their niche competitors, the bluegill, Post

decided to study the trickle-up impact of

these divergent fish populations on their

predator, the chain pickerel.

Nice to eat you

In the lakes that Post’s team was studying,

the chain pickerel is the native top predator,

or the keystone predator. Keystone predators

play a crucial role in the food chain and

ecology of their local habitat. In the lakes

examined, pickerel prey not only on alewife,

but also on yellow perch and sunfish — larger

fish native to the littoral habitat.

Traditionally, the chain pickerel stays in the

littoral habitat, where it hovers camouflaged

among the plants, waiting for the opportune

moment to lunge at its prey. Its body structure

is long and arrow-like, making it especially

advantageous for the pickerel to strike from

a hiding place, but not at all for it to swim at

length in open water.

It was thus surprising when the team found

pickerel in the pelagic zone of several lakes

home to landlocked alewives. Furthermore,

the pelagic pickerel ate pelagic alewife

almost exclusively, as discovered from stable

isotope signature studies. These studies

showed that the carbon isotope ratios in the

pelagic pickerels were far more similar to the

ratios found in pelagic alewife than those of

any other prey species, indicating that the

pickerel’s long-term diet had changed to

include a higher proportion of alewife.

On the other hand, in lakes with

anadromous alewife or no alewife, the team

found no pelagic pickerel. Since anadromous

alewife is only available a few months of the

year, it is not worth it for the pickerel in these

well-connected lakes to shift its habitat for


a few extra temporary alewife. However, in

lakes with a consistent landlocked alewife

population, the pickerel adapts to eat more

of the landlocked alewife. “They’ve made this

novel niche shift because there are alewife in

the middle of the lake, all the time,” Post said.

At an average of only 10 inches long, the

alewife is a much more appealing meal than

the jumbo-sized sunfish.

Keystone to success

Of course, it is not only the pickerel’s diet

that has changed. When Post’s researchers

studied the morphology of the species, they

found that pelagic pickerel had deeper, more

fusiform body shapes compared to their

littoral counterparts — the same adaptation

that they noticed in landlocked alewives,

which also adapted to open-water lifestyles.

Lipid composition, or fattiness, in fish

tissue also illustrated a striking difference

between littoral and pelagic pickerel. Openwater

pickerel had much higher lipid content

than did near-shore pickerel. Post offered

two reasons for this observation: First, the

alewife has higher lipid content relative to the

pickerel’s other prey. Eating more alewife thus

causes greater lipid content for pickerel as

well. Second, a landlocked alewife population

offers a much more stable source of food than

would a nomadic population of the same

species. As a result, the pelagic pickerel eats

more of its prey.

Lipid content is a significant measure

of evolutionary adaptation. A higher lipid

content can boost a fish’s health in several

ways. More lipids allow a fish to survive fasting

or invest more in growth and reproduction,

improving the evolutionary fitness of the

organism. Come wintertime when lakes

freeze, lipid reserves can substantially reduce

mortality by allowing fish to store energy and

brave the cold.

Feeding back to ecology

For the next 10 to 20 years, Post intends to

carry out a subsequent stage of the alewife

project: combining the landlocked and

anadromous alewife populations to see how

such a disruption affects the evolution of

the fish. In fact, the researchers have already

installed fish ladders on many dams, allowing

anadromous alewife to cross over into

landlocked lakes.

Post believes that his lab’s work demonstrates

the idea of feedback in evolution. “Our

work is suggesting that the way in which

organisms structure their environment

can create a feedback that then drives their

own evolution, which then changes the way

they structure their environments. We call

that an eco-evolutionary feedback between

ecology and evolution,” he said. “The pickerel

work, along with the work on bluegill and

[plankton], shows that this kind of feedback

can propagate throughout the food web.”

Notably, this study also provides insight

into rapid evolutionary relationships between

predator and prey. Classic rapid evolution

research claims that mortality is the driving

force of evolution: fishing and predatory

pressure are both methods of selection. But

the Post lab study is among the first to show

the powerful bottom-up influence that prey

species can have on keystone predators. Quite

literally, this work is upturning the way we

understand eco-evolutionary interactions

between predators and prey.



SONIA WANG is a sophomore molecular biophysics & biochemistry and

economics double major in Jonathan Edwards College. She is the advertising

manager for this magazine and spent her summer researching tsetse fly

olfaction in the John Carlson lab.

THE AUTHOR WOULD LIKE TO THANK David Post for taking the time to

talk about his research.


Brooks, J. L., and S. I. Dodson. “Predation, Body Size, and Composition of

Plankton.” Science 150.3692 (1965): 28-35. doi: 10.1126/science.150.3692.28

December 2015

Yale Scientific Magazine






by Zach Smithline

art by Ashlyn Oakes

Sea ice at the North

Pole has something to say

about climate change.

Talk of climate change in the news

is ubiquitous. Everywhere we look,

headlines are popping up, from deadly

record-breaking heat waves in Pakistan and

India to the notoriously cold and rainy

London reaching a record high of 98 degrees

Fahrenheit this past July. Earth’s climate

cycle is becoming increasingly erratic, which

has two conflicting effects — mapping these

patterns is simultaneously more important

than ever, and more difficult than ever.

In many ways, climate change is a complicated

beast. In a single season, we might see

intense spikes in temperature in one area of

the world and colder than normal weather

elsewhere. It is a problem fueled largely by

human activity, and so motivating environmentally

friendly behavior is important. But

change takes time: The climate concerns we

are experiencing now are the result of hundreds,

if not thousands, of years of change.

Similarly, the positive lifestyle choices we

might implement in service of our planet

will not fix climate disruption overnight.

These positive changes in human activity

are crucial, but the sobering truth is that

the planet does not respond immediately to


These complex issues are exacerbated by the

fact that measuring climate change is equally

complicated. Reliable, hard and fast data on

climate change patterns would perhaps be

universally convincing and motivating, but

is extremely hard to come by. Scientists use

diverse parameters in quantifying climate

change: They might measure sea surface

temperatures or precipitation. Maybe they

track volcanic eruptions. One method

stands out as particularly effective, and that

is measuring the thickness of Arctic sea ice.

The existing tactic to understand the

distribution of sea ice thickness up by the

North Pole is centered on a partial differential

equation. This formula depends on three

14 Yale Scientific Magazine December 2015



variables, one of which is particularly

problematic. A Yale duo has found a way

to circumvent this problem, updating

the partial differential equation so

that it can more accurately convey

information about Arctic sea ice, and

about global climate change.

The team consists of John Wettlaufer,

a professor of geophysics,

mathematics, and physics at Yale,

and Srikanth Toppaladoddi, a graduate

student. Their new model for

calculating Arctic sea ice thickness

could make a big splash in the field

of climate science.

All eyes on the Arctic

Wettlaufer and Toppaladoddi’s model

is significant not only because it is a more

accurate measure of sea ice thickness, but

because Arctic sea ice thickness is a highly

sensitive indicator of the Arctic climate

as a whole. And changes in Arctic climate

have long been understood as a harbinger

for what is to come farther south.

An important reflection of Earth’s

climate regulation is the hydrologic cycle,

more commonly known as the water

cycle — a staple of elementary school

education. At lower latitudes, this cycle is

regulated by the flux between evaporation

and precipitation. But in the polar regions,

the processes of freezing and melting

are extremely important, as they create

density differences that drive global water

circulation. Earth’s cryosphere — its frozen

water — has a global impact on climate,

and disruptions can cause temperatures to

plunge in some regions and skyrocket in


Not all Arctic ice is created equally. The

Greenland ice sheet sits three kilometers

thick upon a landmass and influences

global sea levels. This is one way to facilitate

the effects of global warming, namely a rise

in sea level. In contrast to Greenland, sea

ice is only a few meters thick and does not

alter sea level at all. Instead, sea ice affects

global climate because it rejects salt when

it forms, making it uniquely responsible

for patterns in global ocean circulation.

Large ocean currents, in turn, move warm

and cold water around the globe, and thus

impact weather events.

In addition, small changes in climate

at lower latitudes are amplified up in the

Arctic, a phenomenon known as polar

amplification. Thus, sea ice thickness

up north is a strong signal for the global

climate condition.

In 1969, Russian climatologist Mikhail

Budyko developed a simple energybalance

theory of climate that captured

a key feature of polar amplification. We

know from common experience that the

bright light reflected from a snow-covered

field in the winter is far more glaring than

that reflected from grass in the summer.

The reflectivity of a material, called albedo,

underlies Budyko’s theory of ice-albedo

feedback: Floating white ice has a much

higher albedo, or greater reflectivity, than

the adjacent blue ocean. Since the latter

absorbs more of the sun’s radiant energy

than does ice, the ocean warms and melts

the ice. This in turn exposes more ocean,

which absorbs more energy, which again

melts more ice. The cycle causes a runaway

effect, and the Arctic shoulders much of

the burden.

Budyko’s theory only emphasizes the

need for a reliable means of tracking

Arctic sea ice, which is likely to be in

flux as the planet warms. Prior methods

were insufficient. Enter Wettlaufer and

Toppaladoddi — and a new, tractable


The microscopic and the macroscopic

Geophysicists in 1975 developed a partial

differential equation that would in principle

allow for the calculation of the distribution

of Arctic ice thickness. The equation

has three terms that describe the dynamics

of sea ice. The terms that characterize

how wind and heat affect ice thickness

have a firm grounding. But the term that

describes the mechanical redistribution of

ice floes, or floating ice sheets, is difficult

to characterize mathematically. Without

a sound mathematical model, there is no

way to test the partial differential equation

observationally. Until recently, this intransigent

term has been a roadblock, getting

in the way of our complete understanding

of Arctic sea ice and global climate change


Yale’s Wettlaufer and Toppaladoddi

have devised a different approach to the

problem of Arctic ice thickness. The duo

December 2015

Yale Scientific Magazine




►Left: Sea ice in the Arctic is

not only picturesque. It also

holds the secrets of climate

change. A new study from

Yale scientists advances our

understanding of Arctic ice




►Right: Professor John

Wettlaufer (left) works in the

departments of geophysics,

mathematics, and physics at

Yale. Graduate student Srikanth

Toppaladoddi (right)

studies geology and geophysics

in the School of Arts & Sciences.

brought a new piece of information to the

table, and in doing so, made a fascinating

connection between the physics of the

microscopic and macroscopic worlds.

The concept the team evoked is known

as Brownian motion, first observed in

1827 by Scottish botanist Robert Brown

as he was watching the random motions

of pollen grains in water. When Brown

made his observations, atoms and molecules

were only abstract concepts. It was

not until 1905 that Brown’s observations

were quantified by Albert Einstein. A

synthesis of Brown’s and Einstein’s ideas

has led to a crucial conclusion: It was the

thermally induced motion of water molecules

colliding with Brown’s pollen grains

that produced an overall motion in the


Wettlaufer and Toppaladoddi used

the analogy of Brownian motion to deal

with the partial differential equation’s

40-year-old uncompromising term. They

recognized that mechanical events such

as ice rafting, or the movement of objects

via ice rafts, occur in seconds or less,

whereas a system of many rafts changes

ice thickness distribution only slowly. By

drawing from Einstein and Brown’s theory

of microscopic change and applying it to

a macroscopic environmental problem,

they were able to separate these two time

scales and convert the unsolvable partial

differential equation into a tractable one.

To test their modified equation, the

researchers used it to back predict ice

thickness between the years 2003 and

2010. They compared their theoretical

results to real Arctic data collected by

NASA’s Ice, Cloud, and Land Elevation

Satellite. Wettlaufer and Toppaladoddi

found that their solution curve accurately

predicted the observed distribution of

Arctic sea ice. With this verifying result in

hand, the two hope to soon extend their

equation to the task of predicting future

changes in ice thickness distribution.

The updated technique has huge

implications for understanding climate

dynamics, both in historical hindsight and

in preparation for the future. Eventually,

we may be able to track our own impact

on Earth’s climate using this revamped

equation. Such control over the future is

encouraging as we continue to change our

behaviors in small, positive ways while

recognizing that our planet’s response to

these changes will not be immediate. Over

time, the sum total of our positive actions

could amount to noticeable change for

the better. Wettlaufer and Toppaladoddi’s

method for studying Arctic sea ice and

climate dynamics may provide just the

tool for us to notice that change.

The team’s recent research was published

in the October edition of Physical Review

Letters. It quickly sparked conversation

among climate scientists everywhere, as

people search for better ways to predict

and understand our climate. Arguably,

this goal is now more important than

ever, as climate change becomes ever

more pressing.

Films like the 2004 hit The Day

After Tomorrow shock viewers with a

spine chilling — albeit unrealistic —

dramatization of extreme weather events

spurred by frightening climate change.

With any luck, researchers like Wettlaufer

and Toppaladoddi will prevent us from

reaching this point, by elucidating the

intricacies of climate and how it is

changing around the globe.



ZACH SMITHLINE is a member of the Saybrook College Class of 2018, and

is double majoring in molecular biophysics & biochemistry and the history of

art. In addition to working as a gallery guide at the Yale University Art Gallery,

he studies the structure and function of the ribosome in professor Thomas

Steitz’s lab.

THE AUTHOR WOULD LIKE TO THANK John Wettlaufer and Srikanth

Toppaladoddi for their helpful input, excitement, and stimulating discussions

about their work.


Letcher, Trevor M. Climate Change: Observed Impacts on Planet Earth. 1st

ed. Amsterdam: Elsevier, 2009.

16 Yale Scientific Magazine December 2015 www.yalescientific.org







Live brain

imaging helps

patients attack

anxiety at the source

by Marguerite Epstein-Martin

art by Stephanie Mao


December 2015

Yale Scientific Magazine




We all, occasionally,

feel anxious.

For most people, anxiety strikes at

specific moments — when turbulence

rocks the plane or when your

professor says, “we need to talk.” But imagine

if even in the most ordinary of moments,

every thought and experience you had was

challenged by crippling anxiety — anxiety

that has minimal basis in reality.

In fact, 3.3 million Americans suffer from

obsessive compulsive disorder, commonly

abbreviated as OCD. The disease is characterized

by unsubstantiated fear that leads

to time-consuming, distressing repeated

rituals. Someone with OCD might have to

wash her hands in a perfectly timed routine

for fear of her own death, or the death of a

loved one, or the destruction of her home

and possessions. Despite ongoing research

into the disorder, OCD continues to puzzle

psychiatrists and agonize patients.

But new treatments may be on the horizon,

thanks in part to a study by researchers at

Yale University. A collaboration between

the department of radiology and biomedical

imaging and the Yale OCD Research Clinic,

the study utilizes brain imaging to provide

neural feedback to OCD patients in real

time. The recently developed technology,

known as real time functional magnetic

imaging (rt-fMRI), presents an effective

therapy for OCD symptoms. In the new

era of personalized medicine, it seems the

answer to treating OCD is to show patients

their own brain.

Exposing true compulsion

The most recognizable symptom of OCD

is the obsessive conduct of apparently irrational

actions. This might include repetitive

hand washing (think Leonardo DiCaprio in

The Aviator) or hoarding (think the psychiatric

patient whose stash of chicken bones is

discovered by Angelina Jolie in Girl, Interrupted).

Many people experience so-called

“compulsive” behaviors. Without rhyme or

reason, we may prefer our books alphabetically

organized or our notes color-coded,

or we may have pre-game rituals that we

follow religiously in preparation for athletic

competitions, dates, or job interviews. But

quirky habits do not a disorder make.

Yes, OCD patients exhibit an unyielding

compulsion to move through specific

routines. But these rituals are prompted

by a relentless, obsessive, and irrational

internal message that terrible consequences

will follow unless certain behaviors are

performed in a precise sequence. A ritual

like hand washing can temporarily silence

the obsessive message, something along the

lines of “my grandmother will die unless

I wash my hands the proper way.” These

actions are not rational reactions to real fear,

but rather, are attempts to stave off an allconsuming

and often debilitating anxiety.

Surprisingly, individuals with OCD

can — when prompted — admit that such

beliefs are irrational. Yet they cannot help

but feel, often urgently, that their fears,

random rituals, and potential consequences

are all linked. The connection between

unrelated events is cemented in their brain

circuitry. Without targeted effort, the brain

is impossible to rewire.

A malleable brain

The good news: our brains are not actually

static. One of the key features of the human

brain is neuroplasticity: Our brains consist

of infinitely interconnected neurons that are

interwoven into an extraordinarily complex

system. But with each new experience, these

neural connections can be dissolved and

made anew.

This exciting premise of plasticity gives

hope to neurofeedback, or the idea that

people can learn by watching their brain

in action. The treatment tested by the

Yale team relies on real time fMRI, which

unlike traditional fMRI gives patients

on-line feedback regarding their neural

activity while they are in the scanner. With

this feedback information, patients can

potentially train their brains to correct

exaggerated and unfounded responses to

particular stimuli. The Yale researchers

were inspired by the possibility that rt-fMRI

could help the millions of people afflicted by


Anxiety-heavy disorders are particularly

well suited to treatment by neurofeedback.

“Anxiety is partly induced by environmental

experiences,” said Michelle Hampson,

assistant professor and director of rt-fMRI

at the Yale School of Medicine. “The brain is

obviously plastic in that circuitry can learn

to become more anxious or less anxious,”

she said.

In other words, if anxiety can be learned,

perhaps it can also be unlearned.

The power of real time feedback

OCD manifests in many ways, but the Yale

study led by Hampson focused on the type of

OCD that is characterized by contamination

anxiety, or a fear of coming into contact

with dirt or germs. This anxiety is linked to

a particular area of the brain known as the

orbitofrontal cortex (OFC) — hyperactivity

in this region is consistently correlated with

the severity of OCD symptoms.

Flashing certain images to subjects while

scanning their brains, the researchers were

able to locate a specific anxiety-related region

within the OFC, where activity levels

rose and fell in response to dirty and clean

images, respectively. Before treatment began,

subjects met with a clinical psychologist

who helped them create an individualized

strategy for controlling contamination

anxiety and activation of the OFC. Armed

with these mind control techniques, subjects

were then asked to mentally raise or

lower OFC activity depending on the image

shown. Because subjects were given fMRI

18 Yale Scientific Magazine December 2015 www.yalescientific.org



feedback while trying to regulate this brain

area, they were able to see the effect of their

intended anxiety control in real time.

Half of the subjects in this study underwent

neurofeedback treatment, while

the other half received a placebo, or sham

treatment. The sham biofeedback treatment

mimics neurofeedback in almost every way,

but instead of viewing their own OFC activity,

people were shown activity from another

subject of the same age and gender.

Before and approximately half a week after

their neurofeedback sessions, each subject’s

anxiety responses were assessed. The

neurofeedback group showed a lessening of

anxiety, but the sham group did not. Following

the treatment, neurofeedback subjects

also demonstrated an improved ability to

control their OFCs compared to the sham


These results are of course exciting,

but more work is needed to tell if anxiety

regulation and changes in brain circuitry

can be maintained over longer time spans.

In order for rt-fMRI to be a truly promising,

long-term treatment for OCD, patients

must be able to carry what they learn from

the lab into the real world.

Subjects in the Yale study also underwent

an assessment before and after training by

resting state, or rs-fMRI, which examines

brain connectivity by detecting areas of the

brain that activate synchronously. Connectivity,

which is exhibited even in a resting

brain, indicates that two brain areas have a

tendency to work in tandem. This phenomenon

is an active area of study for neurobiologists


Between the initial and final rs-fMRI tests,

researchers noted several startling changes in

their subjects’ brain connectivity. First, in all

subjects who underwent real neurofeedback

therapy, there was a significant decrease

in the connectivity of regions in the brain

associated with emotional generation and

processing, but an increase in connectivity

of regions in charge of the regulation and

control of emotion. These people, once

victims of exaggerated emotional reactivity,

were now better able to regulate their

emotions with the help of an experimental

neurofeedback intervention.

Secondly, subjects who saw a marked

decrease in anxiety symptoms also showed

a global decrease in connectivity between

the OFC and the rest of the brain. Strong

coupling between the OFC and other brain

regions has long been associated with OCD.

According to Hampson, perhaps too much

coupling causes overstimulation of the OFC,

increasing anxiety to unbearable heights.


►Michelle Hampson is the director of real

time fMRI at the Yale OCD Research Clinic.

“Anxiety levels could be higher because

you’re always tapping into this anxiety

circuitry, which is triggered by and linked

to a lot of different things,” Hampson said.

Neurofeedback treatment offers an escape

from this cycle, a way for patients to rewire

their own brain circuitry.

A less anxious future

Though strides have certainly been

made in understanding OCD, a complete

model of its causes and symptoms has

yet to be formalized. Without a strong

consensus from the medical and research

communities, effective treatments for

OCD will remain out of reach. Most

patients currently diagnosed with the

anxiety disorder rely on a system of trial

and error for treatment, experimenting

with psychiatric drugs and other therapies

that offer only limited relief for many

individuals. Many patients still await a

reliable treatment for their disorder. With

strong supporting results from the recent

Yale study, rt-fMRI neurofeedback may be

part of the long sought-after breakthrough

in combatting OCD.

Nevertheless, Hampson’s study is — more

than anything — a stepping off point. The

results show great promise for rt-fMRI neurofeedback

treatment, but further research

must be done on a larger subject pool with

a greater number of OCD patients before

any definitive conclusions are made.

Still, Hampson is hopeful that neurofeedback

will help sufferers of OCD, and that it

will perhaps help patients with other anxiety

disorders as well. She is collaborating

with researchers at the Veterans Administration

to investigate the application of

rt-fMRI feedback for treating post traumatic

stress disorder, or PTSD.

Neurofeedback is an exciting avenue

for personalized medicine — what better

way to take charge of your own treatment

than to peer into your own brain? The

intervention at the center of Hampson’s

study serves as a scaffold on which patients

can practice individualized strategies for

unlearning anxiety. The same plasticity that

allows for the onset of an anxiety disorder

may afford the perfect opportunity for a

lasting OCD treatment.



MARGUERITE EPSTEIN-MARTIN is a junior physics major in Saybrook


THE AUTHOR WOULD LIKE TO THANK professor Hampson for her time,

energy, and unabated enthusiasm throughout the writing process.


Hampson, Michelle, Teodora Stoica, John Saksa, Dustin Scheinost, Maolin

Qiu, Jitendra Bhawnani, Christopher Pittenger, Xenophon Papademetris, and

Todd Constable. “Real-time fMRI biofeedback targeting the orbitofrontal cortex

for contamination anxiety.” Journal of visualized experiments: JoVE 59 (2012).


December 2015

Yale Scientific Magazine



from the


art by Christina Zhang

UPby Rain Tsong

It is a late October day, and I am parked

in front of a house painted the color of

the woods. WIthin a few minutes, I hear

a friendly shout, and I turn to see two warm

faces — Guy Estell and his wife, owners of

the 90 acres of land that we are standing on

in northeastern Connecticut. They show

me around a small part of their property.

It is mostly wooded, and I cannot help but

notice how the two seem perfectly at home.

Guy inherited this property from his

parents. Ever since he was born down the

street, the woods have been an integral part

of his life. Formal forest management has

never been a top priority for him, but Guy

sees great value in the beauty and wildlife

habitats of his woodland.

Mary Tyrrell, the director of the Global

Institute of Sustainable Forestry, sees people

like Guy as the most important factor in

catalyzing change in service of the forests.

Guy and many others like him have a

strong stewardship ethic, even without an

active goal related to land management.

Environmental scientists must work with

woodland owners in confronting forest

preservation, and policies will only be

effective if they understand the motivations

of people like Guy, whose actions will

have the biggest impact on the health of

Connecticut forests.

The preservationist’s view

About 60 percent of Connecticut’s land

is covered by forest, according to 2006

data from the state’s Center for Land

Use Education and Research. Acreage of

core forest has been partly diminished

by ongoing development, leaving a

more fragmented forest across the state.

Fragmentation means smaller separated

blocks of forest, which threatens wildlife

habitats and water resource quality.

Preserving the essential ecological features

of the forest is possible, but challenging,

especially since many Connecticut

woodlands are privately owned. Forests extend

through private pieces of land, where

individual landowners have jurisdiction.

The land depends on landowners, and each

landowner’s decisions conversely affect the

forest as a whole.

In a recent report, Tyrrell found that 34




►Counting and measuring trees is a slow process. From left to right: Guy Estell, a private

woodland owner, and Bob Kuchta and Nicole Wooten, two spirited forestry students.

percent of Connecticut forest is spread out

among private family-owned properties

larger than 10 acres, most of which are upstate.

More than four-fifths of these larger

wooded properties are primary residences.

About a quarter have been passed down at

least one generation. The typical Connecticut

woodland owner is older than 50 and

has retired with a spouse. Typically, both

are highly educated. Tyrrell’s report emphasizes

the core values of these landowners

— scenery, privacy, and some concern

for woodland conservation. But in addressing

this last goal, few go looking for help

or even know where to start. Only a small

subset of woodland owners is aware of the

programs and organizations ready to aid in

forest preservation.

Part of the problem is a lack of sufficient

resources. The Connecticut Department

of Energy and Environmental Protection

provides free professional and technical

forestry planning services, as does Yale

University. Tyrrell sees a future in partnerships

between the government and other

organizations like Yale and the grassroots

Audubon Connecticut. She points out that

landowners sometimes take issue with direct

government involvement within the

bounds of their private property. “Once the

government finds something like a vernal

pool on your land,” Tyrell said, “they’ll tell

you what you can and can’t do.”

As a private institution, Yale does not

have to maintain the same rigid policies. Julius

Pasay is the manager for the Yale-Myers

Forest, an 8,000-acre expanse woodland.

Part of Pasay’s job is coordinating the Quiet

Corner Initiative (QCI), a 10 year-old program

that employs a variety of means to get

locals engaged in forestry. Named after the

conspicuous lack of urban disturbance and

development in northeastern Connecticut,

QCI encompasses both Guy’s woodland

and the Yale-Myers Forest. “Most people

[here] are interested in their forests for either

preservation or conservation,” Pasay

said. According to Pasay, the number of

people participating in the QCI has risen

from 30 to about 80 since its founding.

Most of these people, like Guy, own land


At the Yale Forest, Pasay tries to connect

these people with each other. Through the

QCI, he organizes workshops and speaker

events that vary in topic from shiitake

mushroom inoculation to animal-powered

logging. “People get together several times

a year for these events in the Forest, and

they see familiar faces,” Pasay said. “We’re

really trying to create a community of


But what does it mean to conserve a forest,

to keep a forest healthy? One mentality —

perhaps the obvious one — is to let nature

take its course. But sometimes well-calculated

human intervention can help us manage

our forests. A small amount of logging,

for example, is necessary for long-term

conservation. As old trees are cut down, new

ones grow, and the trees become diverse in

age. The importance of age diversity is clear.

After the 1850s, the forest began to recover

large swaths of abandoned agricultural land

across Connecticut. As a result, the state’s

entire forest with its many same-aged trees

was uniformly susceptible to a massive

hurricane in 1938. Most of Connecticut’s

woodlands were knocked down that year.

The memory of the hurricane’s destruction is

a reminder that we can engage in preemptive

and protective initiatives.

It is concepts like this that the Yale

School of Forestry and Environmental

Studies (F&ES) wants to bring to the

community. The F&ES course titled

“Management Plans for Protected Areas”

requires students to get involved in real

world forest management. Landowners

like Guy know the property and the forest,

though different landowners focus on

different issues — from fighting invasive

species, to bird-watching, to general

environmentalism. Students in forest

management work with these landowners

free of charge, brainstorming how to best

approach their forest related goals.


December 2015

Yale Scientific Magazine




The woodlander’s perspective

Guy can see the tree line of the Yale-

Myers Forest from his yard. He has been

going to workshops and seminars hosted

by the QCI ever since it began. Guy never

received formal forestry training, yet he is

familiar with these woods, having grown up

on this property. For a while he maintained

the forest by thinning the trees and selling

firewood, though ever since selling his saw

mill 30 years ago, he has not been able to put

as much time into the land. So when Pasay

reached out this past year about sending

some students to help Guy manage his forest,

he was happy to entertain the idea. “They

need to study the land, and I’ve got land for

them,” he said. “It works for both of us.”

We find the two forestry students, Bob

Kuchta and Nicole Wooten, counting and

measuring tree species just a quarter mile

north of us. Bob is an older Connecticut

local with a master’s degree in environmental

education. Nicole is a second-year F&ES

student who is working towards a master’s in

environmental management. Both of them

are here for the F&ES management plans

class. The two are energetic, knowledgeable,


Bob is the local inland wetlands officer and

tree warden in Madison, CT. This semester,

he is auditing the management plans class at

Yale to learn more about forest dynamics. In

Connecticut forests, there are a fair number

of wetlands, including where rivers trace

through the woods. “If you protect the

wetlands, you protect the water quality,” Bob

reminds us as he tallies some more trees.


►The Yale-Myers Forest (pale green) is surrounded by many smaller family-owned properties.

Taking a break from measuring, he picks up

a leaf from the ground. “It’s a Red Maple,”

he shows us, and adds a tally for the species

on his chart. “It’s got three main lobes, a red

stem, and red seeds too.” The Red Maple tree

is bare, but Bob can tell by the bark alone

if need be — he has been doing this for 40


In Bob’s town, he represents the local government.

About 60 percent of Connecticut

landowners prefer to receive information

from the local government. There is something

different about the people at this local

level — they seem to care. Bob is deeply

invested in the wetlands and forests of Connecticut.

For him, being on Guy’s property

is not about the class; his goal is to learn as

much as possible about how to approach environmental

management in his home state.

At some point, Bob points to a tree with

scaly bark. “Do you see this? It’s like burnt

potato chips. This is the bark of a black cherry.

Veneer wood, Guy!” He turns towards Guy

with a grin. “You’ll be able to really retire!”

Guy chuckles in return. “But I’ve got to

have something to do.”

Guy is not the type to sit still. For decades

he has been cutting down trees here and

there and selling firewood. In the early 1970s,

he built a new house, exterior and interior

both, all using wood from his property. After

Guy retired as a University of Connecticut

supervisor, he started working with a local

forest products company. “I ain’t quitting

work, not just yet. That’s when you get old

quick,” he said, and laughed.

Guy and his wife live off the land. During

the summers they plant a sizeable vegetable

garden and Guy does occasional hunting on

the property. The two of them are happy with

what they have. Forest management for Guy

and for many landowners is about a form of

practical environmentalism. His purpose is

not to save the world, one preserved forest

at a time, but to keep forests beautiful, and

to protect resources on the local scale. To

policymakers, it is important to save forests

as a whole. But they must realize that

landowners are not focused on the big, global

picture. For Guy, the woodlands are about the

individual and the family — a lifestyle that

revolves around simple self-sustainability.



RAIN TSONG is a senior at Yale studying geology and geophysics with a

deep interest in the environment. He is interested in how Yale engages with

the community and he volunteers through DEMOS. After he graduates, he

hopes to pursue geochemistry through teaching and research.

THE AUTHOR WOULD LIKE TO THANK Guy and Andrea Estell for their

warm welcome and support. He would also like to thank Mary Tyrrell, Julius

Pasay, and everyone else at Yale F&ES for helping to shape this article’s



Tyrrell, Mary L. 2015. Understanding Connecticut Woodland Owners: A

Report on the Attitudes, Values, and Challenges of Connecticut’s Family

Woodland Owners. Yale School of Forestry and Environmental Studies.

22 Yale Scientific Magazine December 2015 www.yalescientific.org


Strip a donor lung of its cells so only a translucent

white scaffold remains, lay on some of

your own stem cells, and watch a brand new

lung grow — a lung tailored just for you. This is

the dream for thousands who wait in line each

year for a lung transplant. More often than not,

these organ donations never come.

Researchers at the Niklason lab at Yale have

made progress in a crucial step towards improved

lung transplants — stripping donor lungs of their

cells without damaging the delicate scaffold below.

By using milder reagents and systematically honing

down the detergent requirement for donor

cell removal, scientists were able to dramatically

reduce the amount of scaffold loss even while

achieving better decellularization efficiencies than

previously reported. The result: a scaffold more

amenable to repopulation by lung cells and a step

towards successful regeneration of fully functional


The problem with lung transplants

By Lionel Jin

Art By Christina Zhang






Each year, more than 200,000 Americans die of

lung disease and more than 24 million show signs

of impaired lung function. Of these, a mere 2,000

get a fresh breath of life. Lung transplants are rare

because viable donor lungs are hard to come by.

Even those fortunate enough to receive

a lung transplant find the odds stacked

against them. They face a steep

post-transplantation mortality rate

— 53 percent die within 5 years.

“Lungs are fragile organs,”

the present study’s first author

Jenna Balestrini said. “They

often aren’t in as good a condition

as we would like by

the time we get them from

donor to recipient.”

Patients receiving a

new set of lungs are put

on immunosuppressants

so that their bodies do

not reject the transplant.

However, this treatment

makes patients vulnerable

to serious infections

because the weakened

immune system is no longer

able to launch a robust

attack against opportunistic


Patients receiving any kind of organ transplant

must confront this challenge, but the problem

is especially vexing in the world of lungs. With

each breath we take, we inhale millions of bacteria,

fungi, and viruses. Immune cells patrolling

the body typically keep these microscopic threats

under control, but a depressed immune system

may not be able to do the job. Hence, the staggering

mortality rate for lung transplant recipients.

“You are taking something that is not sterile to

begin with and putting it into the patient. And

what’s more, you need to tune down the patient’s

immune system,” Balestrini said. “All that doesn’t

make for a happy outcome.”

Betting on regenerative medicine

Perhaps a customized lung would lead to better

outcomes. This is the promise of regenerative

medicine, which creates lungs for patients using

their own cells.

One critical ingredient is the scaffold, an intricate

matrix of fibrous and elastic proteins on

which lung cells organize themselves. Scientists

are optimistic that they will eventually be able to

transform patient cells into stem cells that can be

coaxed to differentiate into each of the 50 or so

cell types that make up the lung. Such an organ

would not only be pathogen-free, but also rejection-free.

When the introduced cells are derived

from the patient’s own, the immune system is less

likely to reject them. Patients would be spared a

painful course of immunosuppressants and the

accompanying side effects such as cardiovascular


Looking for a source for these scaffolds, the Yale

team turned to pig lungs. The ready availability of

these organs made them a feasible research focus

— scientists could optimize a protocol on the

more plentiful pig lungs, and this protocol could

be subsequently applied to donated human lungs.

Moreover, because pig and human lungs are fairly

similar in size and composition, it may well

be possible to repopulate scaffolds derived from

porcine lungs with human cells. These newly built

organs would then be transplanted directly into


Of course, transplanting donor tissue derived

from another animal into a human recipient can

be tricky. The human body immediately recognizes

the animal tissue as foreign, said Stuart Campbell,

assistant professor at the Yale School of Medicine

and a co-author on Balestrini’s paper. Animal

lung scaffolds, however, are less likely to trigger an

immune response because they are composed of

a relatively limited assortment of proteins. Equally

important, pig lungs have dimensions generally

similar to that of human lungs, which makes

it possible to pick out a set of lungs that closely

matches the size of each patient’s own.

“You already see collagen implants from bovines

going into humans. Some are FDA-approved

and several show promising outcomes,”

Balestrini said. Pig lungs could be the next suc-


December 2015

Yale Scientific Magazine


cessful xenograft, or organ transplant coming

from a different species. According to Balestrini,

some companies are already exploring the


The extraordinary scaffold

Researchers walk a tightrope when pulling

cells off a donor lung. Apply conditions that are

too mild and DNA remnants cling to the scaffold,

inducing inflammation that renders the lung unusable.

Subject the lung to too harsh a treatment

and the scaffold is eroded.

Faced with this dilemma, researchers tend to

prioritize DNA removal at the risk of damaging

the scaffold. The Yale team found that one of the

most popular methods used to decellularize the

lung causes a major loss of matrix proteins, resulting

in a stiffer and more brittle structure that

no longer expands and contracts as effectively as

it did before.

Scientists are also beginning to realize that the

scaffold provides biological and mechanical cues

that play an essential role in helping cells organize

into the proper tissues. “We used to imagine the

scaffold as a biologically inert matrix that cells

simply sit on,” Balestrini said. “Now we are coming

to terms with how cells make use of the biological

code in this matrix to arrange themselves

in the right way.” The scaffold is no longer understood

as a mere platform, but as a dynamic system

that is essential in correctly organizing lung cells.

The Yale team’s goal was to develop a

protocol that minimizes matrix loss

even as it removes donor cells and

DNA from a pig lung scaffold.

Departing from existing methods

that involve incubating the

donor lungs under high pressure

in a mixture of harsh

detergents, the researchers

opted for milder reagents

at normal pressure. They

were also meticulous

in making volume and

weight measurements of

each lung and determining

the minimal amount

of detergent required. To

achieve efficient DNA removal,

the researchers set

up the lungs in bioreactors

so that a constant stream

of detergent solution flowed

through the chamber.

The protocol showed positive results,

besting existing protocols with its 96

percent DNA removal rate while also achieving

unprecedented levels of matrix retention and no

significant loss of key matrix proteins. “We weren’t

expecting this result, but it seems we really can

have the best of both worlds” Balestrini said.

The process also took less time — only 24

hours, whereas prior methods required two to

three days for decellularization. The integrity of

the scaffold translated into a structure that retained

better elasticity and was also more extensively

repopulated by introduced cells.

Campbell said the team’s improved protocol

harnesses one major advantage of decellularized

scaffolds: getting cells to organize into the right

tissues and ultimately into functional organs with

minimal researcher intervention.

The lung comprises dozens of different kinds

of cells, Campbell said, making it incredibly difficult

for researchers to induce each and every cell

to differentiate into the correct cell type and form

the appropriate connections with other cells. But

if the scaffold itself can direct the differentiation

process, researchers can theoretically sit back and

marvel as cells self-organize into the incredibly

intricate organ that is the lung.

An audacious effort

But Laura Niklason, professor of biomedical

engineering and senior author of the paper, is

quick to put the group’s achievement in perspective.

“Decellularization is really just an initial step

in the process. It will be decades before human

lungs are available for clinical testing,” she said.

An audacious effort indeed, taking an organ as

structurally complex as the lung and attempting

to strip it down and build it back up. Researchers

have pulled out every tool they have in their kit,

including using synthetic scaffolds and even trying

to adapt 3D printers to build complex organs.

Each of these methods encounters significant

challenges, but lung disease is such an important

problem right now that every approach is worth

pursuing, Campbell said.

“This is a field that needs the best and brightest

minds to get to the point where we can actually

create artificial lungs and hearts and organs,” he

said. “There’s still a lot to be done, but I’m optimistic

that we’ll get there.”

This lab work may still have a ways to go before

it reaches hospitals, but the team’s successful

decellularization of pig lungs is an exciting step

forward — for researchers, for doctors, and eventually,

for patients who find themselves on a lung

transplant list.



LIONEL JIN is a sophomore double majoring in biology and computer

science. He is operations manager for this magazine and spent the summer

engineering non-model organisms.

THE AUTHOR WOULD LIKE TO THANK Jenna Balestrini, Stuart Campbell,

and Laura Niklason for their enthusiasm in sharing their research.


Balestrini, Jenna. “Production of Decellularized Porcine Lung Scaffolds for

Use in Tissue Engineering.” Integr. Biol, 2015. doi:10.1039/C5IB00063G.

24 Yale Scientific Magazine December 2015 www.yalescientific.org

electrical engineering



Mushrooms make for environmentally friendly batteries



►The material of a portobello mushroom skin can be used

in battery anodes, yielding a more environmentally friendly

battery design.

It is no secret that manmade technology can cause

environmental harm. We see, for example, manufacturing

that leaches toxic waste into soil and water. Battery

production is no exception: To create the batteries used

in electronics and electric vehicles, companies use hard

chemicals that damage the environment. To respond to

this problem, researchers at the University of California

Riverside built a more environmentally friendly battery

using a surprising material — the portobello mushroom.

To build their battery, the researchers focused on the

anode, towards which negative charges flow. In order to

store energy, anodes need a sufficiently large surface area.

A standard lithium ion battery has a graphite anode —

the material is functional, but purifying and preparing it

requires hard chemicals that are both environmentally and

financially costly.

To lessen these costs, the researchers at UC Riverside

replaced the graphite anode with a low-cost, environmentally

friendly material from nature itself: the skin of a portobello

mushroom. Physically, the portobello version of a battery

looks just like a regular lithium ion one. However, the

mushroom material does not do the same environmental

damage, nor is it as expensive as graphite. The researchers

observed that the skin on the portobello’s cap contains

many pores in a ribbon-like structure that afford a vast

surface area. By heating the skin to temperatures as high as

1,100 degrees Celsius, they could dramatically increase the

amount of empty space, or porosity, in the structure. With

this, the energy capacity of the battery also grew.

And these bio-derived batteries do more than just

mitigate environmental and economic costs of production.

Compared to their graphite counterparts, they offer better

performances and longer lifetimes. Portobello mushrooms

contain high levels of potassium salt, which activates pores

and increases the structure’s surface area as the battery

repeatedly charges and discharges. As a result, run times

for devices running on portobello batteries may actually

increase with repeated use. In contrast, the run times for

devices reliant on graphite anode batteries decrease with


With these improvements, portobello batteries have

significant implications for the future, especially given

the increased prevalence of electronics and electric

vehicles. For example, cell phone batteries may be able to

better withstand frequent charging, according to Brennan

Campbell, a graduate student in the materials science

and engineering program at UC Riverside. “With battery

materials like this, future cell phones may see an increase in

run time after many uses, rather than a decrease,” Campbell

said to UCR Today.

Portobello batteries are also promising for the future of

electronic vehicles. By 2020, an estimated seven million

of these vehicles will be in operation in India alone. If

traditional graphite anode batteries were used for all of

these vehicles, the raw graphite needed would weigh around

one million metric tons, and would require a proportional

amount of hard chemicals. Utilizing portobello mushrooms

for the anode material could eliminate the use of these hard


Portobello batteries would decrease the risk of

environmental damage associated with improper disposal

of chemicals used in the manufacturing process. Chemicals

used to produce lithium ion batteries include hydrofluoric

acid, which can cause severe respiratory damage in

organisms, as well as sulfuric acid, which is toxic to

aquatic life and contributes to acid rain. Using batteries

that integrate mushroom material would mitigate much of

the damage caused when these chemicals are accidentally

released into ecological systems.

As researchers develop new battery technologies, it is

just as important to focus on quality as environmental

impact. Portobello batteries address both these goals

simultaneously. The technology still needs to be optimized,

but this new design for a battery presents an exciting

direction for future research and development. Batteries

have countless applications today, and the scale of their use

will only increase in the future. So, the next time you sit

down with portobello mushrooms in your salad, know that

you might be eating the anode of a future battery.


December 2015

Yale Scientific Magazine





Modeling cellulose nanocrystals for success in the real world


Nanoengineering is often limited by the divide that separates

concept from reality, with promising theoretical designs falling

short in application. However, a Northwestern University research

team led by Sinan Keten is working to bridge this gap as it

concerns one particular nanomaterial — cellulose nanocrystals,

often termed CNCs.

Capturing CNCs is not the problem. They are nothing new to

nature, found naturally within trees. CNCs currently on the market

— mostly for research purposes — are extracted directly from

wood pulp, a byproduct of the paper industry. They are accessible

and relatively easy to extract, nontoxic and biodegradable.

The challenge comes in what is lost in translation between the

nanoscale and the bulk scale — as these tiny components are

fabricated into macroscopic technology such as glass or body

armor, their properties might change. A recent paper describes the

modeling framework that the Keten lab has been developing. The

framework could allow us to design better functional materials

from cellulose nanocrystals, by predicting how physical and

chemical properties might change in the process.

A cellulose nanocrystal’s mechanical properties, including

strength and transparency, make it an ideal replacement for

synthetic products. As a promising alternative to the Kevlar used

in bulletproof glass and body armor, CNCs have already received

significant federal research funding. While CNCs can be used

alone as thin coatings and flexible films (in food packaging,

for instance), they really shine when they are integrated into

composite materials.

More broadly speaking, CNCs could be used in any product

employing polymer composites — materials made of multiple

chemical components with differing chemical or physical

properties, such as those used in car and airplane frames.

Unfortunately, CNC use up to this point has been limited to

academic research because accurately predicting the properties

of nanocomposite materials is challenging. While scientists are

currently capable of producing composites and materials that

show promising mechanical properties, research unraveling these

properties is scarce.

This is where Keten’s lab enters the scene. “The key bottleneck is

that the properties they’re exhibiting fall short of what we would

predict to be the optimal performance,” said Robert Sinko, a PhD

candidate in the Keten lab. “That’s where our research comes in.”

To better produce materials from CNCs, Keten, Sinko, and other

colleagues are developing frameworks to foreshadow a composite’s

properties at the bulk scale, factoring in the chemical and physical

characteristics that particles exhibit at the nanoscale. Thus far,

their model has made significant breakthroughs in accurately

predicting glass transition temperatures, where CNC materials

transition from a hard, glassy state to a rubbery, soft one.


The model has also helped determine the ideal molecule size for

CNC composites. In fact, when the researchers used the model to

predict the size at which cellulose nanocrystals best resist fracturing

under pressure, they found that the strongest CNCs were between

4.8 and 5.6 nanometers thick and between 6.2 and 7.3 nanometers

wide, the dimensions most commonly found in nature. In effect,

though the model was intended to improve CNC development for

industrial materials, it has also managed to explain why the crystals

naturally tend towards certain characteristic dimensions.

While the work of the Keten lab is exclusively computational,

partnerships with other research groups have enabled the lab

to test the model’s real world accuracy. “It’s really important to

connect with experimentalists that actually confirm some of our

hypotheses and help us design better tools,” Keten said. These

partnerships will help troubleshoot the model by establishing

where computed, theoretical outputs differ from characteristics of

real CNC materials.

The Keten lab plans to branch out from a specific focus

on a subset of CNC characteristics, namely glass transition

temperature, to a wider variety of properties. The team hopes to

overcome a challenge in describing the bulk mechanical behavior

of composite systems, especially fracture strength and toughness.

In addition, the group aims to better understand the relationship

between chemical and physical properties of the nanocomposite.

The recent study, published in Nano Letters, and the development

of a working model for nanocomposites has poised us to further

close the gap between theory and reality in engineering.

26 Yale Scientific Magazine December 2015 www.yalescientific.org





Self-propelled microparticles with healing potential

Hemorrhage describes the escape of blood from a ruptured

blood vessel. It is a life threatening condition, associated with

roughly 25 percent of worldwide maternal deaths from childbirth

complications. Recognizing the severity of hemorrhagic shock,

researchers at the University of British Columbia (UBC) have

developed an innovative mechanism to stop severe blood loss.

To prevent hemorrhaging at the site of injury, the team designed

self-propelled particles that travel through the bloodstream

to halt bleeding in hard-to-reach places. These particles are a

promising treatment for wounds that cannot be adequately

treated superficially or with injections — the common procedures

in use today. The team’s findings have immense implications not

only for medicine, but for global health, as these self-propelled

particles could be an effective treatment for bleeding in regions of

the world lacking sufficient surgeons and other trained medical


Only a couple of microns in size, the UBC particles propel

themselves through the bloodstream to injury sites, bearing

cargoes of blood-clotting agents called coagulants. In the study,

the microparticles carried thrombin, a coagulant that initiates

aggregation of platelets at the site of a wound to prevent blood loss.

In addition to encouraging platelets to clump together, thrombin

produces fibrin, a protein that forms a lattice to strengthen the

platelet clot.

While self-propelled particles could theoretically transport

various types of medications within the body, Christian Kastrup


— paper author and assistant professor at UBC — explained

that his research team is most excited about treating bleeding

specifically. “Hemorrhage is one of the leading killers of young

people worldwide, and it is particularly devastating in certain

types of bleeding, such as post-partum hemorrhage,” he said.

Uncontrolled blood loss, whether from internal complications

or external trauma, can have severe consequences. Extreme

bleeding eventually reduces blood pressure and hinders oxygen

transportation to the point where a patient experiences fatigue,

confusion, loss of consciousness, and even organ failure.

The newly designed microparticles are expected to be most

effective in situations where surgeons cannot access the blood

vessel directly. In these situations, which include injuries within

the sinus, uterus, and gastrointestinal tract, a piece of gauze with

coagulant is unable to stop blood loss. The superficial application

of coagulants is often unsuccessful in preventing bleeding from

severe wounds. In areas of the world where access to blood

transfusions is minimal, mortality rates due to hemorrhaging

are especially high. By providing new methods for delivering

coagulants, this recent research aims to treat a wider variety of

wounds and to increase treatment options available at locations

without adequate medical care.

According to Kastrup, self-propelling particles have been

extensively researched in the past, but prior studies failed to

identify a successful mechanism for propulsion within blood. His

team was the first to test microparticle transportation upstream

against blood flow. His engineered microparticles contain two

substances that react with each other to produce bubbles of

carbon dioxide. When the microparticles expel these bubbles,

they can push themselves through a solution. Thus, when used

in vivo, the microparticles can be transported against the flow of

blood and deeper into a wound.

Kastrup’s group showed the efficacy of coagulant-carrying selfpropelled

particles in animal models. The next step, not so far in

the future, is to test this technique on human wounds.

The transition from the discovery phase of research to the

clinical trial phase is often a challenge, but Kastrup is confident.

In fact, he believes that the timeline for preclinical experiments

of UBC’s self-propelled particles will be accelerated, since several

components of these microparticles are already in use within

clinics. For example, one ingredient of these particles is calcium

carbonate, which is also found in antacid tablets. Thrombin is

already used to prevent blood loss during surgery.

By reimagining the method of delivery for a known therapeutic

— the coagulant — these researchers present a thrilling new

treatment option. Hemorrhaging is a pressing medical concern

in all countries, and these self-propelled microparticles have

tremendous potential to advance trauma care around the globe.


December 2015

Yale Scientific Magazine






By Lakshmi Iyengar // Art by Marguerite Epstein-Martin

Forget your ID — there’s a

better way to show who

you are.



When a forensic analyst steps onto a crime scene, she scans the

ground for any biological evidence that can be used to identify

the culprit — a strand of hair, a pool of blood, a fingerprint. But

if these telling items are nowhere to be found, what is a detective

to do?

Thanks to a recent study conducted by a University of Oregon

team, our forensic analyst might simply sample the air. These

researchers found that the human microbiome emits trace

biological particles collectively comprising a microbial cloud.

The human microbiome is vast, consisting of microbes in

and on the human body. Each hour, it emits upwards of one

million biological particles through a variety of mechanisms:

direct contact with surfaces, aerosol emissions from the body,

and dust shed through skin cells and hair. These mechanisms

produce personal clouds of invisible bacteria that hover around


Although scientists have been studying human interaction with

airborne microbes for more than a century, most of the research

up until now has focused on disease causing microbes. Scientists

have only recently realized that interaction with other sorts

of airborne microbes is integral to our health. This discovery

prompted further research, which will have applications in

solving crimes through forensics and better understanding

human health through medical research.

The University of Oregon team set out to study microbial

clouds and the information they reveal. First, the researchers

placed volunteers in sterile climate chambers and sampled the air

inside, comparing the microbial makeup of an occupied chamber

to a sterile one.

Then, they performed a second experiment to explore

differences among the compositions of individual microbial

clouds. Using a set-up similar to that of their first experiment,

the scientists sequenced and compared microbial emissions from

eight volunteers. Analyzing the two experiments in conjunction,

the group determined that individuals shed detectable microbial

clouds that differ from person to person.

Microbial clouds offer a variety of possibilities for forensic and

medical research. Like fingerprints or leftover biological materials,

these clouds can be used to link people to geographic locations.



► Airborne microbes have traditionally been studied for their potential to

cause disease, but scientists are now interested in other possible values.

Since each individual sheds a distinct combination of microbes,

each microbial cloud is unique, with the potential to reveal a

person’s gender, age, and much more. A microbial cloud is also

much harder to hide than leftover biological materials — blood

can be cleaned up, fingerprints can be swiped. Understandably,

microbial clouds are incredibly exciting for forensic analysts.

The clouds could also prove useful to researchers studying

disease transmission through airborne pathogens, since they

offer clues as to how people emit bacteria into the air. Whether a

microbe is emitted via aerosols from the mouth or from the skin

can influence how epidemiologists attempt to manage the spread

of disease. Some outbreaks can be controlled by ensuring that the

infected wear surgical masks, while others require quarantine.

While the research done by the scientists at the University of

Oregon is promising, it is also preliminary. The composition

of an individual’s microbial cloud is variable — her emitted

bacteria may differ based on the time of day or changes in her

eating habits. Further research is necessary to unveil the intricate

correlations between the compositions of microbial clouds and

the characteristics they indicate, such as age and gender. We

know the microbial cloud can betray certain secrets, but our

scientific understanding of this link is still shaky, and definitely


Testing up until this point has been conducted in sterile

chambers, but normal air contains numerous microbes. Scientists

will thus have to learn to distinguish natural air microbes from

microbes emitted by humans. Finally, these clouds require a lot of

time, money, and effort to analyze. For microbial cloud testing to

be a feasible method in forensics and medical research, the DNA

sequencing machinery used to determine cloud compositions

will need to be made cheaper and more efficient.

Recent studies have shown that microbial clouds have a lot of

potential, but also that research has a long way to go. Perhaps,

sometime in the future, forensic analysts will be able to bring

decisive evidence to criminal court cases by taking quick and

easy samples of the air. In the meantime, scientists are left to

ponder the mysterious clues housed within our microbial clouds.

► Current forensic analysts rely on trace biological evidence such as

hair, fingerprints, and blood to relate suspects to crime scenes. The

microbial cloud is much harder to erase than these others clues, and

as such could improve forensic analysis.

December 2015


Yale Scientific Magazine




and the




art by

Stephanie Mao

How viruses bridged the gap

between wasps and butterflies

by Aviva Abusch

Getting scientists started on whether or not we should

genetically modify organisms is a bit like starting a discussion

with New Yorkers about the Mets and the Yankees: Both sides

are extremely opinionated, and everyone is quite certain they can

convince the other side to see things their way. GMO supporters

may not realize that they have a significant piece of evidence on

their side that could sway their rivals. The truth of the matter is

that GMOs are not exclusive to labs — rather, nature produces

them every day.

Recent research from a University of Valencia team explores

one example of a natural GMO, one that arises from the

relationship between wasps and caterpillars. Their insect orders,

Hymenoptera and Lepidoptera, have not shared a genome since

the pre-dinosaur days, 300 million years ago. That is, until now.

To explain the return of genetic overlap, and to clarify why

caterpillars worldwide are developing immunity to a deadly

virus, Laila Gasmi and her team of researchers uncovered a littleknown

evolutionary drama.

The wasp and the caterpillar have had a gory relationship

throughout evolutionary history. Usually, the caterpillar suffers

at the expense of the wasp’s reproductive success. When the

wasp is ready to lay its eggs, it injects the eggs along with a

malignant bracovirus into the body of a caterpillar host. The eggs

become larvae, which proceed to feast on the host’s inner fluids.

Meanwhile, the viral DNA from the wasp’s bracovirus inhibits

the caterpillar’s immune response, allowing the wasp larvae to

have free reign inside the host body. The larvae do take care to

avoid the vital organs so that the caterpillar will live — after all,

they need their host to stay alive until they are ready to hatch.

When the fateful day arrives, the larvae, which have by now

matured into pupae, use their razor-sharp teeth to burrow their

way out of the caterpillar’s thick skin. Up to 80 wasp pupae

emerge at once, timing their exits perfectly so that their final

molt happens on their way out. As they swarm through the holes

they drilled in the caterpillar’s skin, the pupae leave behind the

top layer of their exoskeleton — a slapdash surgery that keeps

the caterpillar alive just long enough for the pupae to manipulate

it into helping them build cocoons. In its final moments, the

caterpillar fights to defend its tiny trespassers before it eventually

dies of starvation.

This lovely mental picture is a testament to the extraordinary

effect that organisms can have on each other in an ecosystem, and

to the enormous power of the virus. When the small bracovirus

invades the caterpillar genome, it alters its gene expression, not

only by suppressing the caterpillar’s immune response but also by

rearranging its cytoskeleton, disrupting the structural integrity

of its cells. The bracovirus completely takes over the caterpillar’s

cell machinery, enslaving it to the will of the wasp larvae.

Still, the invasion of the wasp bracovirus is not a total loss for

the caterpillar. Instead, it is a perfect example of the multifaceted

nature of genes. While the bracovirus disrupts the caterpillar’s

immune system and cell physiology, it also provides the

caterpillar with immunity to another dangerous virus that affects

many types of bugs: the baculovirus.

If the bracovirus is ultimately going to assist in killing the

caterpillar, why does this secondary immunity benefit the ill-

30 Yale Scientific Magazine December 2015 www.yalescientific.org



fated insect? Imagine for a moment that a parasitized caterpillar

has just suffered through the evacuation of its wasp pupae. It

lies there as a mostly hollow shell, drained of its strength and

energy. However, since the wasp pupae have not touched a single

of the caterpillar’s vital organs, there is a slim chance that the

caterpillar could regain its strength and recover from the attack.

If it does make it through, it can go about its regular caterpillar

days, munching on leaves, turning into a moth or butterfly, and

hopefully avoiding future encounters with parasitoid wasps.

And the wasp bracovirus remains integrated into the heroic

caterpillar’s genome — the modification becomes a permanent

part of its genetic material. So, when it reaches adulthood and

has offspring of its own, it will pass some of its altered genes onto

its baby caterpillars. Over the course of future generations, the

evolutionarily useful trait from these viral genes — immunity

to the baculovirus — will spread across the caterpillar species,

converting the species into a population of natural GMOs.

When the University of Valencia team stumbled upon this

feat of natural genetic engineering in September, they realized

that this perseverant caterpillar’s life story could indeed be what

happened in the species’ evolutionary history. In their research,

the scientists found that pieces of the wasp bracovirus have been

incorporated into the caterpillar genome through a process called

horizontal gene transfer. Their observations spanned moth and

butterfly species around the world, from Canada to Australia, and

found widespread evidence of bracovirus insertion, suggesting

that elements of the virus are now fixed in the species.

While this finding is good news for caterpillars, it also gives

researchers a glimpse into just how much complexity there can

be in one species’ evolutionary history. These variations have

captivated scholars. According to Larry Gall, an entomology

specialist at Yale’s Peabody Museum of Natural History,

evolutionary history research has risen dramatically in recent

years. “What’s been happening in the last 15 to 20 years or

so, particularly in the last 10, is people have been grinding up

samples of anything they possibly can and subjecting them

to mitochondrial and nuclear DNA analysis,” Gall said. Using

modern DNA technology, researchers are looking to explore

genetic relationships like that between the wasp and the caterpillar

to resolve age-old questions about the evolution of species.

Natural history museums like the Peabody play no small

role in furthering this research. The Peabody’s entomology

department constantly sends out insect samples for analysis at

laboratories worldwide, as do its other departments for different

species. As Gall can attest, even a well-known species can hold

genetic surprises. Researchers may begin with preconceptions

about a species’ evolutionary past, only to find that its genetic

narrative reveals that there are actually two or three separate

species involved. “There are so many questions to ask, and the

techniques just keep getting better and better,” Gall said. “With

modern molecular technology, these collections have become a

genetic treasure trove.”

While manmade GMOs have been controversial since

their conception, this research on natural GMOs offers a new

perspective on the debate. Leaving evolution to its own devices

does not actually produce the unadulterated path one might

expect, and the results of natural genetic modification are often

no less twisted — or beneficial — than what humans engineer.

The tale of the wasp and the caterpillar finds that nature’s

evolutionary course may be more complex than it seems.


►Scientists at the University of Valencia looked at the genomes of several species, including the monarch butterfly. Their research reveals a

fascinating evolutionary relationship between wasps and caterpillars.


December 2015

Yale Scientific Magazine



materials science



Magnetic metamaterials could

lead to faster computers

By Chunyang Ding

Art by Marguerite Epstein-Martin

Steam, water, and ice are familiar to us — in the vapor rising

from a hot kettle, a healthy spring rainfall, and the smooth surface

of a skating rink. But to some materials scientists, these states

of matter are more than mere changes in physical properties.

They pave a path to new frontiers of computer science and data


Researchers at the Paul Scherrer Institute recently discovered a

method of organizing magnetic metamaterials so that they have

phase transitions — walking the line between solid and liquid.

This significant technological development, which draws on an

elementary understanding of solid, liquid, and gas, could lead to

better information storage.

The team, led by Laura Heyderman, examined phase shifts in

magnetic metamaterials — composite materials not found in

nature that can be created to interact with magnetic fields. In their

research, Heyderman and her colleagues tirelessly assembled

one billion tiny magnets to create a honeycomb structure only

five by five millimeters in size. This structure is unique in how

it transfers magnetic information across the entire honeycomb.

Then, the scientists subjected this layer of magnetic metamaterial

to different temperatures, observing how it reacted by arranging

its magnetic poles in different ways. As temperature decreased,

the poles adopted formations that were more efficient in moving

magnetic signals through the material. This phenomenon is not

so different from the way that water molecules bind more tightly

together when frozen into ice.

Phase shifting magnetic metamaterials like the ones produced

by Heyderman’s team are becoming more important as scientists

reach the limits of what conventional materials are able to

accomplish in electronics. Recently, metamaterials became a hot

topic in popular physics, when buzz surfaced over the creation

of “invisibility cloaks.” Of course, there is some discrepancy

between what is happening in the labs and what goes on at

Hogwarts. The real world invisibility cloak carefully manipulates

magnetic properties so that light can deflect around the hidden

object instead of reflecting back to the viewer. Metamaterials

have a variety of other potential applications, from photography

color filters that actually alter light wavelengths to more powerful


A huge potential market for metamaterials is nested in Silicon

Valley, where researchers at microprocessor corporations

are quickly running into difficulties as they try to build

smaller computers. In the 1970s, researchers predicted that

computational power would double every 18 months onward,

an observation known as Moore’s law. To achieve this progress,

the law actually anticipated that engineers would be able to

make computer components smaller by a factor of two every 18

months. If transistors, for example, could be built small enough

that twice as many would fit into the same computer, the machine

would run twice as fast. However, there is a practical limit to how

far scientists can shrink the size of computer pieces. As current

technology stands, within a few generations, Moore’s law could

32 Yale Scientific Magazine December 2015 www.yalescientific.org

materials science


be a dream from the past.

Magnetic metamaterials could help resolve the Moore’s

law dilemma, especially as these materials relate to engineers’

current efforts to store information using the spin of an electron

rather than its charge. This field of science is called spintronics.

Modern electronics rely on the movement of electrons to store

and retrieve information: As electrons move, their charges are

measured and translated into computer bits. Billions of these bits

are then used to load up websites and applications. Spintronics

takes a different approach, measuring the electron’s spin instead

of its charge. An electron’s spin, associated with magnetism,

takes only one of two directions — up or down. If scientists can

learn to manipulate electron spins, then this information could

be translated into a more efficient computer bit.

Heyderman’s research could help scientists master the art of

spintronics because it improves upon current understanding of

how electrons share magnetic information. Her team’s primary

discovery is that nanomagnets communicate more quickly with

one another at low temperatures than at higher temperatures.

To visualize nanomagnets’ increased efficiency at lower

temperatures, you can think of how much harder it is to push

liquid water than it is to push a block of ice. When you push

the ice, the entire block moves forward immediately. However,

when you try to push on a pool of water, it does not simply move

forward. Instead, you send ripples through the liquid, and it

takes a much longer time for your push to reach the other end

of the pool.

Magnetic metamaterials behave in a similar fashion, but

rely on a magnetic signal instead of a physical push. At higher

temperatures, the honeycomb of nanomagnets allows the signal

to slowly ripple through the entire grid. In contrast, at lower

temperatures, the magnetic metamaterials react more like ice,

and even nanomagnets far away from the signal’s initial push

respond almost instantaneously. If utilized in a computer chip,

these magnetic metamaterials and signals could speed up

information transmission.

Even with these accomplishments, Heyderman’s work is not

complete. Her group still needs to experiment with metamaterials

of different magnet arrangements and sizes, as small changes in

arrangement could have big influences on large-scale magnetic


►Left: Modern transistors are no larger than a few electrons, so

engineers are having trouble shrinking them even further. Without

smaller transistors, computers and smartphones will not be getting

any smaller or faster. Right: Trying to push water around is much

more difficult than pushing a solid block of ice. This principle applies

to nanomagnets, and to the design of efficient computers for the

modern age.

and spin effects. So far, the experimenters have tested the

effect with two different configurations of nanomagnets, each

with different magnetic properties. For the weakly interacting

sample of nanomagnets, the phase transition effect was almost

non-existent until temperatures reached approximately 10

Kelvin. However, for the strongly interacting sample, the first

signs of phase transition began at almost 145 Kelvin, a much

higher temperature. The group will continue to test different

arrangements of magnetic metamaterials, hoping to exercise

even greater control over these phase transitions.

It is likely that we will see improved spintronics in the

computer world within the next few decades, and consequently,

faster computers. And yet, magnetic metamaterials retain an

exciting similarity to nature’s own phase-changing products. The

ancient ideas of phase transitions, from simple ice, water, and

vapor, continue to spark scientists’ imaginations and promise

new technologies to enrich our world.

www.yalescientific.org December 2015 Yale Scientific Magazine








When astronaut Mark Watney is left for dead following a Red

Planet dust storm in The Martian, he struggles to survive, establish

communication with NASA, and get back home. The 2015 film,

based on Andy Weir’s book of the same title, draws on the 50 years

of research that have followed man’s first glimpse of the Martian

surface via the Mariner orbiter. Given the story’s engagement with

this scientific legacy, it is no surprise that despite a few glaring

errors, the film is mostly commendable in its accuracy.

As Watney puts it after he is abandoned on Mars, he intends

to “science the shit out of this place” — and it is easy to imagine

the film’s producers saying the same. To ensure that The Martian’s

science would be sound, filmmakers consulted with experts from

NASA and the European Space Agency. They confirmed details

from the burning of hydrazine fuel to the possibility of gardening

on Martian soil. Many of the technologies used in the movie

already exist or are in development, such as the computer Watney

uses to communicate while aboard the Mars Pathfinder spacecraft

and the chemical propulsion method that helps him travel safely

back to Earth.

While plotting his original novel, Weir enjoyed designing the

survival strategies and technologies that would later be imagined

on screen. “As the writer, I could always make sure he had whatever

was necessary to have a clever solution on tap,” Weir said.

Still, while technology can change, scientific laws cannot. The

film makes a few key scientific errors, most notably the dust storm

that strands Watney in the first place.

Since Mars’ atmosphere is only one percent the density of

Earth’s, storms on the Red Planet are far less intense. A storm that

would wreak havoc on Earth would not have the force to knock

Watney off his feet or to whip rocks and metal spikes through the

air. Weir admits that this sandstorm is the plot’s greatest scientific

inaccuracy. Given that wind force is a function of velocity and

atmospheric density, a 120 mile per hour Martian storm would

only have a dynamic force of approximately 12 miles per hour —

great for Martian kite-flying, but not much more than that.

Gravity, too, is an Achilles heel of the film’s scientific accuracy. In

The Martian, astronauts appear to exert themselves while walking

in their spacesuits, which in line with the filmmakers’ aesthetic

were built to the minimum girth at which they could support life.

Since Martian gravity is only about one-third of Earth’s, astronauts

would require spacesuits at least equal to their masses in order

to experience their Earth weights on Mars. With less gravity to

anchor them to the ground, their gaits would also be modified into

long, bouncing strides. None of this comes across on screen with

total accuracy.

The method of Watney’s rescue is also scientifically implausible.

To intercept the ship coming to rescue him, he cuts a hole in his

spacesuit so that the escaping pressure will propel him towards

the waiting crew. In reality, this maneuver could not possibly have

gone as shown. Instead, the vacuum of space would have pulled on

Watney’s hand to plug the hole. Or, as is likely, the suit would have

been so depressurized by the release of gas that Watney would have

been deprived of oxygen. Left to face the harsh vacuum, he would

have had only 10 seconds of consciousness and around a minute

left to live.

But Watney does not die. During his time unshielded —

plummeting through the thin Martian atmosphere and through

space, largely unprotected under the virtually non-existent

Martian geomagnetic field — Watney would have been exposed

to dangerous levels of radiation. As a result, he and his fellow

astronauts would be extremely susceptible to cancer. Nevertheless,

he survives his rescue, and the story flashes years forward to a

scene where he is teaching a future class of astronauts the hardknock

lessons that enabled his survival.

At the end of a film filled with so much strife, perhaps the plot

is best left on such a positive note. “I wanted to write a story

for people like me — people who know a fair amount about the

realities of space travel and still want to enjoy a good story that

doesn’t take too many liberties with reality,” Weir said. Mixing

solid science with a healthy dose of fiction, it seems that Weir and

The Martian have done just that.


► The Martian, starring Matt Damon, is a surprisingly accurate hypothetical

rendition of what would happen if a man were left on Mars. Of course, for

the sake of drama, Hollywood sensationalizes some of the science.

34 Yale Scientific Magazine December 2015 www.yalescientific.org

Science or Science Fiction?

Making Virtual Reality a Reality


How do you define reality? For Neo in The Matrix, this

is a hard question. Born into a virtual reality system so

realistic that robots use it to ensnare human society, Neo

struggles to come to terms with the fact that his world

is no more than a computer simulation. While Neo’s

virtual reality is fictional, similar realities do in fact exist

in our world — and they have a lot of potential for good.

Virtual realities, or virtual environments, are

simulated, 3D worlds that immerse users in sensory

experiences that mimic reality. In The Matrix and

other popular science fiction films, these realities are

controlled by a user’s brainwaves alone. Other films, like

Ender’s Game, feature virtual reality combat simulators,

in which actions in a virtual simulation translate to

real life actions. All of these fictional systems seem

relatively simple, appearing more like video games than

cumbersome programs.

Real world virtual reality systems are much more

interactive, relying on both software components to

simulate virtual realities as well as physical components

that users wear to enable simulations. Virtual reality

software is like that of a video game: each character

and environment correlates with a specific code that,

when processed, dictates how it interacts with other

characters and environments. To manipulate these

codes in a video game, users might press buttons on a

controller. Similarly, in virtual reality, users manipulate

environments and characters through input devices

in the physical gear that they wear or hold, such as

headgear, motion-tracking gloves, or joysticks. These

devices convert user movements into signals that can be

processed by the virtual reality software.

While the most obvious use for virtual environments

is in video gaming, this technology has a myriad of

other capabilities. First conceptualized for use in

military flight and combat simulations, virtual reality is

compelling enough that the military and NASA rely on

it for training exercises. Engineers and architects use the

technology to simulate safety tests for cars and buildings

as an alternative to constructing physical models.

Medicine is perhaps one of the most unique

applications for virtual environments. In these simulated

realities, doctors can conduct surgeries remotely by

manipulating robots. Virtual environments can also

be used in behavioral therapy to project various social


situations, opening up a whole new range of treatments

for cognitive and psychiatric disorders. So far, they have

been effective in treating anxiety disorders by exposing

patients to a series of virtual realities that simulate their

anxiety triggers.

In his research, Daniel Yang of the Yale Child Study

Center tests the efficacy of virtual reality treatment on

autism using neuroimaging. His findings show that

after virtual reality therapy, the brains of individuals

with autism conform more closely to neural images of

typical brain development. “Virtual reality therapy is

very flexible in simulating all kinds of social situations

and can overcome several barriers, including reducing

stress during face-to-face interaction, and increasing

motivation,” Yang said. “Based on my findings, I believe

it’s quite useful.”

Still, current virtual environment technologies have a

few kinks. Users may experience lag time between the

output and input of signals employed by their virtual

environment gear. In video games, this problem is only a

minor nuisance that delays characters’ actions on screen.

However, in virtual environments, this delay prevents

the brain from interacting with simulated settings as if

they were real, sometimes causing intense nausea.

Furthermore, researchers in a recent study conducted

at the University of California in Los Angeles discovered

that our brains are not as easily fooled by virtual realities

as The Matrix might lead you to believe. When exploring

a true landscape, the brain activates specific patterns

of neural pathways — but when the brain navigates a

virtual landscape, neurons fire off at random. Unlike

the high-level virtual realities of science fiction, current

virtual reality systems fall short of reality.

While virtual reality technology is still a work in

progress, the unveiling of one such technology in early

2016, Oculus Rift, demonstrates improvements in

real world virtual environments. The producers of the

commercial Oculus Rift expect to see it become a common

facet in many video games, a potential educational tool,

and a more accessible form of behavioral therapy.

Virtual reality has progressed a long way, from

a concept exclusive to science fiction to an actual

consumer product. Let us hope that — unlike the virtual

realities dramatized by Hollywood — ours will not lead

to the apocalypse.


December 2015

Yale Scientific Magazine






If you are looking for Samantha Lichtin at 2:00 AM on a Friday,

you may find her peering through a microscope at tiny, obscure

organisms as she works on a research project. When speaking about

science, her eyes light up and her voice crescendos. A double major

passionate about geology and evolutionary biology, Lichtin not

only craves learning and discovery, but also finds joy in sharing her

enthusiasm for science with others.

When Lichtin applied to college, she assumed she would study

environmental engineering and international relations. However,

by the spring of her senior year of high school, she realized that she

wanted more freedom to explore a variety of subjects. As a freshman

at Yale, Lichtin took a smattering of introductory science classes. One

stood out: “History of Life,” taught by professor Derek Briggs. This

introductory paleontology class focused mainly on morphological

diversity and evolution over the course of Earth’s history. The course

drew her to the idea that the world could be better understood

through the perspective of geology.

After receiving a Freshman Summer Research Fellowship from Yale,

Lichtin took part in a summer paleontology dig in northeast Arizona,

her first experience studying geology off campus. Lichtin and the Yale

Peabody Museum team collected fossils called archosaurs from the

Triassic period — 200 to 250 million years ago. The following summer,

Lichtin researched forams, tiny single-celled organisms with calcium

carbonate shells, at the University of Southampton in England. These

two adventures helped her make a final decision to major in geology

at Yale. “People in the [field] are pushing so many frontiers,” Lichtin


►Samantha Lichtin ‘16 is president of Yale’s Club Geo.

said. The constant sense of exploration and discovery she found in

geology and the field’s interdisciplinary nature were both powerful

incentives for Lichtin to forge ahead.

She has since delved deep into Yale’s geology scene. In her

sophomore year, she built herself a strong foundation by taking

classes in genetics, microbiology, and geology. As a junior, she

made the definitive decision to take on two majors — geology

and geophysics in addition to ecology and evolutionary biology.

Now a senior, Lichtin is head of Yale’s Club Geo, which provides a

support network for undergraduates studying geology, disseminates

information about geology related opportunities on and off campus,

and generally promotes interest in geoscience. This semester,

Lichtin is also conducting her senior thesis research, which involves

understanding the biological underpinnings behind ancient seasurface

temperatures. To this end, she is examining the biochemical

remains of unicellular microorganisms.

A variety of non-scientific extracurricular activities have enriched

Lichtin’s research life at Yale. As a freshman, she performed in the play

“Into the Woods.” Her love for playing the viola has been satisfied by

the Yale Symphony Orchestra and the Berkeley College Orchestra. In

addition, she regularly takes ballet classes and rock climbs, and she

has been a committed member of the Ezra Stiles College Council.

Since her freshman year, Lichtin has volunteered with VITA

(Volunteer Income Tax Association), a nationwide program that

provides free tax preparation to low-income taxpayers. “VITA

has been an amazing way to directly give back to the New Haven

community,” Lichtin said. Her desire and capacity to share knowledge

is reflected in her passion for teaching. Through VITA, she has led

courses on how to certify with the IRS.

Lichtin has also spent time tutoring general chemistry at Yale, and

she is the first to offer help to confused freshmen struggling with

biology homework in the library.

After graduation, Lichtin hopes to teach English in Argentina, a

country filled with fossils and frequented by geologists visiting its

important paleontological sites. To Lichtin, Argentina is a place

where she could expand her boundaries as both a scientist and

person. She hopes to become a better, more informed citizen of

the world through this next adventure abroad. Lichtin can also see

herself eventually working in a natural history museum or even in

the Department of Education.

Regardless of whether she travels across the world or stays right

here in New Haven, Lichtin will undoubtedly choose a path that

continues to spread her infectious sense of wonder.

36 Yale Scientific Magazine December 2015 www.yalescientific.org





A group of students listens intently as Yale professor Richard Lethin

gives a lecture on computer architecture. His course, which covers the

integration of software and hardware to produce computer systems,

intrigues students — just as similar lectures fascinated Lethin during his

undergraduate career at Yale.

By showing how far computer design has come — from simple

computer architectures of the past to artificially intelligent systems of

the present — Lethin inspires students to write the code for the next

chapter of computer science. As the current president of Reservoir

Labs, Lethin is helping to write the current chapter, by developing more

efficient computer systems and improved cyber security technologies.

His path from curious child to president of Reservoir Labs shows his

ever-expanding passion for computer science, regardless of the role he

plays — whether a student, an engineer, or a professor.

Long before Lethin was standing up at the front of a classroom,

encouraging students to pursue computer engineering, he was

motivated by his father’s work to study programming. His father —

also a Yale engineering graduate — helped design the radar used in

the Berlin airlifts, and often brought home early digital calculators that

captivated Lethin as a child. “[His] was a very glamorous job, and, as a

son, I admired him,” Lethin said. His fascination with engineering was

only heightened by the Apollo space program. The exciting environment

in which Lethin grew up, coupled with his early access to programming,

fueled his interest in engineering and computer science.

Lethin’s early passion for engineering pushed him to study the subject

at Yale. As an undergraduate, he not only dedicated himself to his

studies but also to extracurricular pursuits. He joined a number of Yale’s

music groups, and played the trombone in jazz band, concert band, and

marching band. Reflecting on his classes, he recalls his political science

and African art courses as fondly as his engineering ones. “I think Yale

engineering students have a unique advantage in their access to a broad

range of resources and courses,” Lethin said.

After four fulfilling years at Yale, Lethin — like many other engineers

— took time to work in the field before attending graduate school.

Between his time as a Yale undergraduate and his years in graduate

school at MIT, Lethin worked at Multiflow Computer, a company

founded by his computer architecture professor Josh Fisher. There,

Lethin got involved in a variety of tasks, from working on computer

circuitry and architecture to improving the efficiency of computer

systems. “I learned a lot about what it takes to build something real, and

that proved to be really useful in getting into graduate school,” he said.

Lethin added that his experience in research and development, when

he investigated the best ways to improve the speed and reliability of


►Lethin sits with the computer he was working on at the Yaliefounded

startup Multiflow Computer.

computer systems, further set him apart from those without research

experience when he applied to graduate school. When he arrived at

MIT, Lethin channeled his experience building special computers into

his work as a research assistant in the artificial intelligence lab.

Today, Lethin’s role as president of Reservoir Labs occupies most of

his time. The company works to develop security and communications

computer technologies for commercial and government customers.

When asked about the differences between being president — a

position he has held for more than 18 years — and being an engineer,

Lethin compared working at a company to eating from a plate of food.

Engineers with different specialties eat only one course, whereas the

president has some of everything, ensuring that the different dishes

complement each other.

Lethin can also provide an insider opinion about the current state

of progress in artificial intelligence and software engineering. Even

since he began teaching 15 years ago, Lethin has observed artificial

intelligence evolve from a topic viewed as a controversial subject to a

valuable, mainstream idea. Not only are companies now investing in the

development of artificial intelligence, but popular culture is capitalizing

on the public’s interest in intelligent machines. “I don’t really have an

opinion on transcendence or when it’s going to happen, but it sure is

interesting. Even if machines don’t achieve intelligence equal to humans

soon, they’re getting smarter every day,” Lethin said.

If an eager student in Lethin’s class were to ask him which of his roles

is his favorite, he might answer that his favorite is being a father. But if

you were to ask his favorite area within computer science, he would be

unable to choose. “There are so many interesting things going on right

now,” he said, “so there are just not enough hours in the day.”


December 2015

Yale Scientific Magazine



podcast reviews

“THE INFINITE MONKEY CAGE” Proves Delightful for a Wide Audience


“When is a strawberry dead?” This quirky question is one of many that

have sparked debates on BBC Radio 4’s science-meets-entertainment

podcast, “The Infinite Monkey Cage.” It is indicative of the show’s

character — nonsensical musings intertwined with surprising scientific


The infinite monkey theorem (supposedly the show’s namesake)

stipulates that a monkey sitting at a typewriter for an infinite amount

of time will eventually type any given literary text. In this case, merit

is just a matter of probability. The podcast has far less than an infinite

amount of time — episodes typically run for half an hour. Nevertheless,

the program leaves listeners with a practical level of understanding.

Since beginning in 2009, the program has produced 12 series, a U.S.

tour, and extended podcast versions of many episodes. The program

is led by University of Manchester particle physicist Brian Cox and

comedic writer Robin Ince. The seemingly mismatched pair bring a

certain whimsy to the podcast.

Each episode begins with a theme, such as forensic science, pandas,

death, or parallel universes. Cox and Ince are joined by a panel of three

guests — usually experts in the given field or entertainers. As the show

has garnered popularity, the guests have been more well known. Evolutionary

biologist Richard Dawkins, astrophysicist Neil deGrasse Tyson,

and a handful of famous British actors have all served on a Monkey

Cage panel. Questions like “when is a strawberry dead?” spur lively

“SCIENCE VS” Pits Fact Against Fiction with a Humorous Twist


Have you been told that the Paleo diet is the way to go if you want

to lose weight? Or that you can boost your happiness by keeping a

gratitude journal? These popular science sensations have proliferated

quickly, thanks to the internet and viral media. To find out whether

the latest craze is actually grounded in scientific evidence, look no

further than the new podcast “Science Vs.” Hosted by Australian

science journalist Wendy Zukerman, the program launches humorous,

informative, and sometimes snarky investigations into whether recent

trends are fabricated or factual.

Zukerman begins each podcast

by presenting a fad. Though she

has only recorded 10 installments

of her show to date, she has already

covered a wide range of topics, from

the differences between men’s and

women’s brain functions to the

efficacy of medical marijuana. After

a brief, often mocking overview of

the trend or belief and how it came


►“Science Vs” tackles fads

framed as scientific fact.

to be public knowledge, Zukerman

drops her trademark line — “There’s

YouTube,” she might say, “and then

there’s science.” Cue the angelic



discussion. Is a strawberry

still alive as photosynthesis

continues? How do we define

death? Is it dependent

on the definition of life?

The conversations progress

with an impressive and natural

flow, a credit to Cox,

Ince, and the show’s tone.

However, the podcast’s

effort to bring scientific inquiry

and humor together

is less smooth. Either the


►“The Infinite Monkey Cage” brings

science and entertainment together for

a fun listening experience.

humor is buried beneath data and concepts, or the science is oversimplified

for the sake of amusement and accessibility. Perhaps this is less the

podcast’s fault than it is the nature of its goal to make science humorous

and appealing to a general audience. Still, what the podcast lacks in

scientific detail, it makes up for in charm. Listeners will find episodes

amusing and thought-provoking, but they should not expect to become

experts on the scientific specifics.

So, when is a strawberry dead? There is no definite answer. But, with

some rumination (and jest), “The Infinite Monkey Cage” opens up a

new line of thought for its listeners.

sound effect.

Zukerman dissects trends with her own scientific knowledge and

the counsel of her many guest researchers, but she is also careful to

maintain a vocabulary that is accessible to non-scientists. Try not be

too embarrassed when you realize that you had also jumped on the

bandwagon before checking the facts — listening to “Science Vs” can

be humbling.

As a science enthusiast, Zukerman speaks with a bias for scientific

fact over popular fad. You can hear the smug satisfaction in her voice as

she debunks each myth. However, she does not hesitate to acknowledge

when scientists do not yet know enough to definitely disprove certain

widely-held beliefs. In one episode, when Zukerman tackles the belief

that pornography addiction negatively impacts our sexual behaviors,

she readily admits that scientific studies have neither sufficiently

affirmed nor disproved this idea. Although Zukerman seems to enjoy

subtly making fun of the more gullible among us, she never does so at

the expense of scientific integrity.

Despite its name, this podcast is not only for the scientificallyoriented.

“Science Vs” is a terrific choice for all who are curious about

the world and who would like to train their minds not to believe

everything they hear. Not to mention, it is perfect for anyone who

would now-and-again enjoy calling out their less-discerning friends for

confusing fact with fad.

38 Yale Scientific Magazine December 2015 www.yalescientific.org

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