Issue 98.1

Yale Scientific

THE NATION’S OLDEST COLLEGE SCIENCE PUBLICATION • ESTABLISHED IN 1894

MARCH 2025

VOL. 98 NO. 1 • $6.99

16

THE GRAND DESIGN

SMALL BUT MIGHTY 12

PHAGE SHIFT 14

MIND THE ELECTRON GAP 19

UPPER CRUST 22

TABLE OF

VOL. 98 ISSUE NO. 1

COVER

16

A R T

I C L E

The Grand DESIgn

Sophie Heitfield and Ellie Tillman-Schwartz

Dark energy may comprise up to seventy percent of the energy in our universe—so what is it?

The international, multidisciplinary DESI project has set out to measure the effect of dark energy

on the expansion of the universe. Its first survey has now mapped the universe to unprecedented

precision and laid the foundation for breakthroughs in our understanding of physics.

12 Small But Mighty

Makena Senzon

When a young software engineer named Monkol Lek developed a rare neuromuscular disease,

he struggled to find a doctor who could help him. Now, as a researcher and professor at the Yale

School of Medicine, Lek has dedicated his life to helping others like him. Last fall, he and his PhD

student Kaiyue Ma unveiled SMuRF, a quick, cheap, and scalable genetic assay that will prioritize

patients and help researchers investigate a vast array of diseases.

14 Phage Shift

Helen Shanefield

In every ecosystem, bacteria are under near-constant attack from bacteriophages—viruses that

target bacteria. A new method of microscopy has allowed researchers to view the interactions

of bacteriophages and their prey with unprecedented detail, paving the way for new discoveries

about the microbial interactions that shape so much of our world.

19 Mind the Electron Gap

Ximena Leyva Peralta

Superconductors could provide a solution for our ever-increasing energy demand, but the

mechanisms behind their behavior remain elusive. A Yale research team has provided the first

experimental evidence for a new driver of superconductivity: nematicity, a quantum phase that

breaks rotational symmetry.

22 Upper Crust

Daniel Havlat and Abigail Jolteus

Tectonic plates are constantly on the move, driving earthquakes, mountain formation, and

continental drift—but this was not always the case. New paleomagnetic research pushes back

the earliest verified tectonic plate movement to a distant 2.5 billion years ago, changing our

understanding of Earth’s geological history and the timeline for the development of life.

2 Yale Scientific Magazine March 2025 www.yalescientific.org

CONTENTS

More articles online at www.yalescientific.org & https://medium.com/the-scope-yale-scientific-magazines-online-blog

4

6

25

34

Q&A

NEWS

FEATURES

SPECIALS

What Is Used to Put Out Wildfires? • Joelle Kim

The H5N1 Bird Flu Outbreak in... Cows? • Toler Poole

Playing it Cool • Yuvan Chali

Understanding the Silent Struggle • Hien Tran

Healing Touch • Mia Cooper

Wired for Success • Sarah Heebe

Skin Deep Science • Gabriela Berger

They’re Watching Me, Aren’t They? • Genevieve Kim

Underground Guardians • Jake Robbins

Hair Today, Gone Tomorrow • Sammy Feingold

When Sulfide Binds, Memory Rewinds • Helen Zhang

Sorry Shakespeare • Aiden Zhou

Drugging The Undruggable • Crystal Liu

Stick and Switch • Estella Wittstruck and Lynn Dai

Illuminating the Past • Wyatt Aiken

Written in RNA • Risha Chakraborty and Megan Kernis

Undergraduate Profile: Angelin T. Mathew (YC '25) • Josefina De La Riva

Alumni Profile: John-Paul Menez (YC '07) • Neo Chen

Science in the Spotlight: Thinking 101 • Andrea Ortega

Science in the Spotlight: Shared Humanity • Kayla Sokunle

Rethinking Ultra-Processed Foods in the Obesity Debate • Isabel Matos

Science on Trial: Project 2025 and the Future of US Science Policy • Edis Mesic

www.yalescientific.org

March 2025 Yale Scientific Magazine 3

WHAT IS USED TO PUT

OUT WILDFIRES?

&

H5N1 BIRD FLU OUTBREAK

IN…COWS?

By Toler Poole

On March 25, 2024, the USDA, CDC, and FDA confirmed

that a new strain of avian influenza virus type A (H5N1)

had been found in dairy cows. While bird flu has long

circulated among poultry and occasionally infected mammals,

its emergence in dairy cattle marks a surprising shift—one with

potential economic and public health implications.

H5N1 is classified as highly pathogenic in poultry, meaning

it causes severe illness and high mortality in these domesticated

birds; the virus can wipe out entire flocks of chickens in a matter of

days, with a mortality rate of up to ninety percent. Cows and birds

often share close quarters, which cultivates an environment for the

disease to jump from species to species. Researchers suspect that

H5N1 is spreading through milk and milking processes, though

investigations, as of March 2025, are ongoing to determine the full

scope of transmission risks.

H5N1 is a zoonotic disease, meaning it can jump from animals to

humans through direct contact, inhalation, contaminated surfaces,

or insect vectors. While no cases of human-to-human transmission

have been reported, the CDC has documented sporadic infections

in people. Globally, nearly half of those who have been infected

have died. In response to the outbreak, federal and state agencies

have imposed restrictions and testing policies to limit the spread of

H5N1 and better understand its transmission dynamics to prevent

further infections. ■

By Joelle Kim

Amidst a fire-ravaged landscape, a bright pink substance

stands out: Phos-Chek WD-881. Typically dispensed

aerially, Phos-Chek slows combustion by altering plants’

carbon-containing molecules, making them non-flammable.

When every minute counts during wildfires, Phos-Chek

provides immediate relief and has thus been—and continues

to be—the default solution. Fire retardants like Phos-Chek are

more effective and longer-lasting than water, granting firefighters

valuable time to combat flames on the ground.

Despite its effectiveness, concerns have emerged over Phos-

Chek’s environmental impact. The chemical contains trace

metals, including cadmium and chromium, which pose risks to

ecosystems and aquatic life. Though some regulations prohibit

its use near bodies of water, runoff can still reach waterways,

disrupting ecosystems by causing nutrient imbalances and

harmful algae blooms. Additionally, exposure to airborne Phos-

Chek particles can irritate the human respiratory system, raising

health concerns for both firefighters and nearby residents.

In spite of these issues, Phos-Chek remains central to wildfire

management. Many alternatives, including controlled burns and

fire-resistant vegetation, focus on prevention rather than active

suppression, making Phos-Chek indispensable in emergencies.

Furthermore, firefighting infrastructure, including aircraft and

storage facilities, is built around chemical retardants such as

Phos-Chek. The main company that produces these retardants

lobbies extensively to influence wildfire policy, making a

transition away from Phos-Chek politically difficult.

Nevertheless, through careful application and stricter limitations

of use near water sources, Phos-Chek’s risks can be minimized

while maintaining its fire suppression benefits. As wildfires

become more frequent and intense, refining these strategies

will be critical to balancing environmental responsibility with

effective firefighting. ■


The Editor-in-Chief Speaks

AGAINST APATHY

Volume 98, Issue 1, of the Yale Scientific Magazine arrives at a time of

escalating attacks on science both in academia and in public life across the

United States. At the time of printing, thousands of scientists have been

forced out or fired from jobs at federal agencies, and billions of dollars in federal

science funding have been cut or frozen. The funding cuts, as well as proposed

restrictions on how universities can spend on overhead costs, threaten the ability of

institutions like Yale to provide the foundations necessary for all varieties of scientific

work. Meanwhile, attacks on diversity and freedom of expression at universities

imperil the intellectual landscape of higher education. To speak to this perilous time

in science, we are continuing the Yale Scientific Magazine’s longstanding tradition

centering the scientific process as the zenith of human curiosity. It is curiosity, after

all, that grants us sharp vision and the will to reach out to the world around us, even

in the face of obstacles.

In this issue, Yale physicists probe the nature of superconductivity, a Yale

psychologist questions the origins of cognitive biases, and multiple teams develop

new methods to glimpse inside the biochemical processes that animate the world’s

living systems. We profile the scholar of religions and medical anthropology Angelin

T. Mathew (p. 34), and we learn about new frontiers in a profile of the space startup

expert John-Paul Menez (p. 35). In the cover story, entitled “The Grand DESIgn,”

two Yale researchers construct imaging devices that help cosmologists build an

unprecedented map of the universe (p. 16). Stories of this nature are not new to the

pages of YSM. As ever, the broad coverage of diverse fields and the breaking-down of

technical explanations serve to make every field of science vivid and accessible. The

writers, artists, and designers behind the articles do the crucial work of translating

the scientific topics from the fresh pages of the world’s premier academic journals to

the timely magazine that our team hopes you will engage with today.

Moving into this new volume of YSM, I am grateful for the new and returning

members of the Masthead. As a result of conversations among members of the

Editorial Board, we are inaugurating a special series for this volume entitled “Science

on Trial” (p. 39). The new series, managed by the Special Sections Editor, focuses on

the complex interactions between the scientific process and the urgent realities of

the law and politics in the United States. We are also continuing to bolster efforts

within the magazine to highlight the contributions of historically underrepresented

groups in science and to expand the magazine’s multimedia presence online. We

look forward to a year of bold curiosity and bright science.

About the Art

William Archacki, Editor-in-Chief

How do we imagine the invisible?

How might we grasp something as

elusive and powerful as the dark

energy of the universe? In one of this

issue’s articles, scientists map dark

energy’s forces. This issue’s cover

features space, the vast blend of light

and matter which is propelled and

forever expanded by this dark energy.

Malina Reber, Cover Artist

MASTHEAD

March 2025 VOL. 98 NO. 1

EDITORIAL BOARD

Editor-in-Chief

Managing Editors

Full-Lengths Editor

Features Editor

Special Sections Editor

News Editor

Online Editors

Copy Editors

Scope Editors

Multimedia Manager

Archivist

PRODUCTION & DESIGN

Production Manager

Layout Editors

Arts Editor

Photography Editor

Cover Artist

BUSINESS

Publisher

Community Coordinator

Operations Managers

Subscriptions Manager

OUTREACH

Synapse Presidents

Synapse Vice President

Synapse Events Coordinators

Synapse Outreach Coordinator

WEB

Web Managers

Web Coordinator

Social Media Manager

Social Media Content Creator

STAFF

Luna Aguilar

Ebru Ayyorgun

Hannah Barsouk

Ryan Bose-Roy

Andre Botero

Sophia Burick

Risha Chakraborty

Yuvan Chali

Kelly Chen

Neo Chen

Yuanyu Chen

Kenny Cheng

Camille Chiu

Cara Chong

Rayyan Darji

Sara de Ángel

Josefina De La Riva

Pempem Dorji

David Gaetano

Ian Gill

Hannah Han

Daniel Havlat

Sarah Heebe

Sophie Heitfield

Molly Hill

Elisa Howard

Nusaiba Islam

Abigail Jolteus

Patricia Joseph

Genevieve Kim

Dahlia Kordit

Paul Alexander Lejas

Ximena Leyva Peralta

Crystal Liu

Samantha Liu

Rachel Mak

Nyla Marcott

Isabel Matos

Cullen Matthews

Blake Maulsby

Cindy Mei

Yossi Moff

Kenna Morgan

Lee Ngatia Muita

Diya Naik

Brandon Ngo

Kimberly Nguyen

Nicole Isabel Oo

Andrea Ortega

Lea Papa

Faith Pena

Toler Poole

Yusuf Rasheed

Jake Robbins

William Archacki

Mia Gawith

Evelyn Jiang

Max Watzky

Michael Sarullo

Asuka Koda

Sarah Li

Patrick Wahlig

Aiden Zhou

Makena Senzon

Michelle So

Brandon Quach

Jordan Thomas

Lawrence Zhao

Matthew Blair

Madeleine Popofsky

Lynn Dai

Melody Jiang

Ryder Lariviere

Alondra Moreno Santana

Emily Poag

Malina Reber

Matthew Blair

Claire Zhong

Nikolai Stephens-Zumbaum

Edis Mesic

Ethan Powell

Gabriela Berger

Mia Cooper

Mahitha Ramachandran

Joelle Kim

Wyatt Aiken

Megan Kernis

Sammy Feingold

Sunny Vuong

Claire Chang

Sophia Marie Rodriguez

Ignacio Ruiz-Sanchez

Agomoni Saha

Sharna Saha

Fareed Salmon

Jaime Seu

Helen Shanefield

Echo Simons

Kayla Sokunle

Nikolai Stephens-

Zumbaum

Kara Tao

Lynna Thai

Ellie Tillman-Schwartz

Melda Top

Hien Tran

Proud Ua-arak

Qinyi Wang

Elise Wilkins

Estella Wittstruck

Aiden Wright

Nathan Wu

Aaron Yu

Kayla Yup

Johnny Yue

Hanwen Zhang

Helen Zhang

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

Scientific Publications, Inc. Third class postage paid in New Haven, CT

06520. Non-profit postage permit number 01106 paid for May 19, 1927

under the act of August 1912. ISN:0091-287. We reserve the right to edit

any submissions, solicited or unsolicited, for publication. This magazine is

published by Yale College students, and Yale University is not responsible

for its contents. Perspectives expressed by authors do not necessarily reflect

the opinions of YSM. We retain the right to reprint contributions, both text

and graphics, in future issues as well as a non-exclusive right to reproduce

these in electronic form. The YSM welcomes comments and feedback. Letters

to the editor should be under two hundred words and should include the

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

before publication. Please send questions and comments to yalescientific@

yale.edu. Special thanks to Yale Student Technology Collaborative.

NEWS

Chemical Engineering / Medicine

PLAYING IT

COOL

THE HOT NEW DISCOVERY IN

MID-INFRARED DETECTION

BY YUVAN CHALI

UNDERSTANDING

THE SILENT

STRUGGLE

MOOD DISRUPTIONS IN

ENDOMETRIOSIS TREATMENT

BY HIEN TRAN

IMAGE COURTESY OF JÜRGEN VIA PIXABAY

IMAGE COURTESY OF WELLCOME COLLECTION

Mid-infrared (MIR) photodetectors have wide-ranging

applications, including medical imaging, security

surveillance, and pollution monitoring. However,

detecting MIR light has proven challenging because it has a

longer wavelength than visible light and therefore carries less

energy when it strikes a detector.

Existing methods of detecting MIR light typically require

cryogenic cooling or sophisticated device structures, which

are inefficient. To avoid these drawbacks, assistant professor of

chemical and environmental engineering Peijun Guo and his

group at Yale have developed an indirect, all-optical method to

detect MIR light.

The principle behind this detection method is that certain

materials have properties that change with temperature variation

due to the absorption of MIR light. One example of such a

material is two-dimensional metal halide perovskite (2D MHP),

a type of crystal in which changes in optical reflectance can be

measured upon irradiation with MIR light. This change in optical

reflectance is analogous to an object changing color upon heating.

This material was selected because it has low thermal

conductivity and temperature-dependent reflectance, and it can

be easily processed from a solution. Its low thermal conductivity

slows dissipation of absorbed heat, making it possible to detect

the absorption of MIR light as the change in optical reflectance

caused by the MIR-induced temperature rise can be measured.

Guo and his group have developed this technique to

precisely detect a wide range of MIR light, utilizing 2D MHPs

with a membrane structure and a complex photonic system.

In the future, they hope to integrate multiple detectors to

image an entire surface, enabling the capture of infrared

“images” of objects. ■

Alongside debilitating pains, heavy periods, and

increased risk of infertility, some women with

endometriosis are experiencing mood disruptions as

a side effect of their first-line treatment—oral contraceptives

(OCs). Endometriosis arises when tissue similar to the

endometrial lining grows on parts of the female reproductive

tract other than the uterus.

A study led by postdoctoral fellow Cansu Cevik at the Yale

School of Medicine found that endometriosis patients who

did not previously have depression and were prescribed OCs

reported new symptoms of depression, and those diagnosed

with depression showed worsening symptoms. The study

evaluated medical records of 5,392 hospital endometriosis

encounters at Yale New Haven Hospital over twelve years,

dating from September 2012 to September 2024.

OCs such as progestin are an accessible option that can

alleviate the painful symptoms of endometriosis. However,

because of potential mood disruptions, patients often

discontinue their treatments and end up suffering from

endometriosis symptoms. Because of the study’s findings,

the researchers are urging physicians to consider the mood

disruption effects of OCs and conduct deeper evaluations

with patients before prescribing OCs as a treatment option.

“Endometriosis often takes eight to ten years to diagnose, so

we should do our best to minimize the patients’ prolonged

struggles,” Cevik said.

One in three women with endometriosis do not respond to

the common OC progestin. Cevik’s current work has a focus

on identifying molecular markers for detecting progestin

resistance as it is crucial to optimizing the treatment pipeline

for endometriosis. ■


Materials Science / Biochemistry

NEWS

HEALING

TOUCH

SCIENTISTS CRAFT

THE PERFECT

CELLULAR CRADLE

BY MIA COOPER

WIRED

FOR

SUCCESS

ANCIENT BACTERIAL

ASSEMBLY LINE BUILDS

LIVING NANOWIRES

BY SARAH HEEBE

PHOTOGRAPHY BY MAKENA SENZON

IMAGE COURTESY OF SARAH HEEBE

Wound healing is a painful, yet normal, biological

process, and wounds repair themselves

routinely. However, some wounds deviate from

the norm. For example, people with diabetes often have

complications with the healing process, so their injuries

are more likely to progress to chronic wounds that may

have otherwise healed in a healthy person. A Yale-led

group synthesized a new composite material that adapts

to the wound’s environment and works to counteract

damage, potentially improving the wound healing process.

Three components make up this hydrogel material:

alginate, fibronectin, and collagen. Alginate is a

natural substance, originally derived from seaweed, and

frequently used as a base in wound dressings. However,

there are two key problems with alginate. First, it is not

the right viscosity to conform to the shapes of actual

wounds in patients. Second, alginate does not advance

the healing capacities of cells. Fibronectin and collagen

help to remedy both of these problems. Daqian Gao, a

postdoctoral associate in the Yale School of Medicine

Department of Surgery, worked with colleagues to

achieve a precise balance of all three substances to

produce a hydrogel that could be injected into wounds of

various depths and shapes. Their study also found that

fibronectin and collagen help recruit other cells needed

in the healing process.

Henry Hsia, a professor of surgery at Yale, highlighted

how important this hydrogel could be for future therapies

and further studies. “This offer[s] another way to better

understand, at a very molecular and cellular level, the

interactions that are important for healing,” Hsia said. ■

Finding a way to expel excess electrons isn’t exactly

what keeps most of us up at night. Thankfully, we

humans use oxygen to perform this vital function.

However, for many bacteria without access to oxygen, this

form of extracellular respiration is vital. Surprisingly,

certain bacteria can use nanowires made up of a chain

of heme molecules, just like hemoglobin in our blood, to

perform this function.

The nanowires’ ability to electrically connect the living

to the nonliving world, as well as their high degrees of

sensitivity, precision, and tunability, make them especially

useful for biomaterials, bioelectronics, and biofuels.

Already, these bacteria are being used to degrade toxic, even

nuclear, waste.

Now, Nikhil Malvankar, associate professor of molecular

biophysics and biochemistry, and his team at Yale have

found a way to manipulate these nanowires. Cong Shen, the

lead author of the team’s recent study, decoded the nanowire

machinery in Geobacter sulfurreducens. “For microbes in

the environment […] there is so much treasure—so much of

a goldmine there—and we can dig deeper,” Shen said.

Shen discovered the gene cluster responsible for the

creation of the Geobacter nanowires, but he didn’t

stop there. Accordingly, he kept digging until he could

determine how the proteins were assembled and could

thus be manipulated to control the growth of the cells.

With this information, the door is open for nanowires

to be engineered into bacteria important for our health

and environment. By delving further into this field, such

research may provide a key tool to mitigate pollution and

climate change, fuel a biomaterial revolution, or more. ■



FOCUS Cellular Biology

SKIN DEEP

SCIENCE

How Cells Dodge the

Mutation Bullet

BY GABRIELA BERGER

IMAGE COURTESY OF UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN

In the complex world of tissues, stem cells serve as the custodians of

the epithelial layer, the thin covering of cells that sits atop the surfaces

of organs and other structures in the human body. The stem cells

actively identify and eliminate cells that pose a threat to tissue integrity.

However, oncogenic mutations—genetic alterations that drive cancer

development—can disrupt this delicate balance. Surprisingly, even in

normal-looking tissues, these unfortunate mutations can be present

with frequencies similar to those found in cancerous tissues. In order

to understand how tissues stay healthy despite the many mutations,

and to explore possible advances in cancer treatment, researchers have

long sought to describe the biological processes that help cells dodge

the mutation bullet.

Researchers from the Howard Hughes Medical Institute and Yale, led

by Valentina Greco and Rachel Perry, investigated how metabolic states

might influence the outcomes of cell competition in the skin. Their aim

was to uncover the mechanisms that determine whether a mutated

cell survives, integrates into the surrounding tissue, or is eliminated.

“The body has mechanisms to deal with mutations, and our goal is to

understand how these mechanisms work to maintain tissue integrity and

eliminate potentially harmful cells,” Perry explained. The study focused

on two well-known mutations—β-catenin gain-of-function (βcatGOF)

and HrasG12V—that exhibit opposing behaviors in skin cells, making

them ideal for studying how mutant cells interact with normal cells.

Previous studies on mouse skin with a mixture of mutant and normal

cells have demonstrated that mutant cells employ various mechanisms to

correct tissue abnormalities and restore normal function. The βcatGOF

mutation, which activates a signaling pathway crucial for cell growth, leads

to the selective differentiation and elimination of mutant cells, positioning

them as “losers” in the competition for space within the tissue. In contrast,

the HrasG12V mutation, which involves a constantly active version of the

Hras gene (a key regulator of cell growth and survival), enables mutant cells

to outcompete and integrate into the surrounding tissue, “winning” the

battle. These opposing outcomes make skin an ideal model for studying

cell competition, as its accessibility and visibility allow researchers to

investigate how mutant cells outcompete or are eliminated by healthy cells.

The team tracked the fluorescence of certain molecules that reflect

cellular redox states (the balance between chemically oxidized and

reduced molecules) in normal and mutant skin stem cells in live mice.

Cellular redox states are often used to indicate the metabolic status of

cells. This technique, combined with techniques that track metabolic

pathways, enabled researchers to observe how oncogenic mutations

altered metabolic activity, influencing mutant cells’ energy production,

survival, and competitiveness.

The study revealed that both βcatGOF and HrasG12V mutations

caused a significant drop in the cellular redox ratio, indicating a

shift toward more oxidized redox states—a hallmark of oncogenic

transformation. However, the responses differed between the mutations:

while redox imbalance persisted in βcatGOF mutants, correlating with

their eventual elimination, HrasG12V cells quickly restored their redox

balance, allowing them to thrive and integrate into the tissue.

To explore the therapeutic potential of targeting these metabolic

changes, the team treated the mice with metformin, a drug often used

to treat high blood sugar levels that can adjust cellular redox states.

Remarkably, metformin reversed the usual cell competition outcomes

in both mutant models. In βcatGOF mutants, the treatment prevented

their elimination, allowing them to persist in the tissue. In HrasG12V

mutants, it decreased their speed in reproducing, inhibiting tissue

changes and preventing their competitive success.

These findings highlight the critical role of metabolic adaptation in

determining the fate of cancer-causing cells in epithelial tissues. The

ability of HrasG12V mutants to rapidly restore redox balance allows

them to overcome selective pressures imposed by normal cells, enabling

them to persist and expand. In contrast, βcatGOF mutants, unable to

adjust their redox status similarly, are ultimately eliminated. As it turns

out, some cancer cells proliferate by quickly balancing their internal

chemistry, while others that cannot do this are destroyed by the body.

Looking ahead, Perry emphasizes the potential for early cancer

intervention through metabolic pathway manipulation. “If we know

that someone is at risk for cancer because of a genetic mutation, could

we manipulate these metabolic pathways or the redox status of cells to

lower their risk?” Perry asked. While current strategies for intervening

in metabolism to prevent cancer are limited, Perry highlights the

importance of understanding the molecular connections between

cancer-driving mutations and potential interventions. Perry said, “In

the future, we would love to explore whether we can manipulate these

pathways metabolically to intervene.” ■


Psychiatry

FOCUS

PHOTOGRAPHY BY AGOMONI SAHA

Computer screen at the Belief Lab displaying the Animacy Detection Task created by

Ben van Buren and Brian Scholl.

“Is someone following me?”, “Is there someone behind me?”, or

even “Is there a monster in my closet?” are all familiar worries.

Yet, for some people, paranoid thoughts and tendencies take a

far larger role in life than a passing moment of anxiety. They can cause

lasting delusions and influence relationships, often pairing with other

symptoms within conditions like schizophrenia or bipolar disorder.

A new Yale study has even investigated paranoia’s ability to shape

something as basic as sensory perception.

Paranoia can be described as the incorrect belief that others

are intentionally attempting to cause you harm. In 2020, Santiago

Castiello, a PhD student focusing on schizophrenia at Oxford

University, became interested in paranoia within schizophrenia. He

reached out to Philip Corlett, an assistant professor of psychiatry at

the Yale School of Medicine, to see if they could work on a project

together. Simultaneously, Joan Ongchoco, a postdoctoral student

in Corlett’s lab, was studying a different phenomenon: teleological

thinking, which is when someone ascribes too much purpose to an

unintentional event. Common manifestations of teleological thinking

occur when people construct conspiracy theories or believe that their

own thoughts are being fed to them by outsiders. Little did Castiello,

Corlet, and Ongchoco know that their work would culminate in a

single surprising project.

Both paranoia and teleological thinking are associated with

delusions, but the mechanism for these thoughts is still not largely

understood. For example, delusions might stem from properly

perceiving the world around us but interpreting a collection of events

or details as harmful when someone with lower paranoia would not

interpret them as harmful. Alternatively, people with delusions may

experience changes in perception that subsequently alter information

about events and details, which are then interpreted the same way as

a non-paranoid person would. In other words, delusions may come

from altered interpretation of conventional information or altered

information interpreted in a conventional manner.

In December 2024, Castiello, working with Ongchoco, Corlett,

and other researchers, took one approach to understanding this

phenomenon by examining social hallucinations through a “sheep and

wolf” task. In the task, participants watched dots moving on a screen

THEY’RE

WATCHING ME,

AREN’T THEY?

How Paranoia Shapes

What We See

BY GENEVIEVE KIM

and had to decide whether one dot was chasing the other, and which

dot was the chaser “wolf” and which was the “sheep” being chased.

The researchers found that people with high paranoia and high

teleology perceive chasing when no chasing is actually occurring—

they consistently perceive agency when only random motion is

occurring. The researchers characterized this perceived chasing

when only random motion exists as a “social hallucination,”

reflecting a perception-based problem in daily life that may manifest

in the belief that one is being watched or controlled. These results

showed that paranoia and teleological thinking affect raw visual

perception, with deviations from normal thought being influenced

by this altered perception.

When the researchers looked more closely, they additionally found

that highly paranoid people were worse than others at identifying

the experiment’s sheep. Combined with the inability to differentiate

between random and chasing motion, the inability to identify who is

being chased could lead one with high paranoia to believe that others

are chasing a target and wrongly identifying that the target is oneself.

On the other hand, highly teleologically thinking people were worse

than normal at identifying the wolves. “Imagine believing that the CIA

is pursuing you, but you’re bad at detecting who the CIA officers are,”

Castiello said. Anybody you meet could be an agent.

Castiello’s results are promising for clinical diagnoses. Castiello is

hoping to determine the rate of false alarms with high confidence that

can accurately predict whether a patient has paranoid or teleological

thinking tendencies. Once this process is streamlined, you may be

able to play a game choosing sheep or wolves instead of a strenuous

psychological evaluation to be assessed for high paranoia and teleology.

Outside of the clinic, this work also has interesting implications in

faith. “It might be that the more spiritual events someone experiences,

the more agency they perceive in the world to increasing degrees. Or the

difference between someone spiritual and someone not spiritual may

cause a categorical difference in their teleological thinking,” Castiello

explained. His work raises questions of whether higher teleological

thinking can be induced through faith. Perhaps, if teleology can be

learned, it can be unlearned. This is a broad extrapolation from the

work that has thus far been done, but … do you follow? ■



FOCUS

Data Science

UNDERGROUND

GUARDIANS

How AI Helps Trap

Carbon’s Escape Act

BY JAKE ROBBINS

IMAGE COURTESY OF PEXELS

Since the industrial revolution, human civilization has

been adding more carbon dioxide to the atmosphere by

burning fossil fuels, supercharging global temperature

rise. This temperature change has resulted in food insecurity,

more severe storms, warming oceans, and much more. In an

effort to combat this, scientists have increasingly focused on

the study of carbon sequestration, where captured carbon

dioxide is collected from the atmosphere and put away in

permanent storage.

A promising approach for long-term storage involves

injecting carbon dioxide deep into the earth for permanent

geological containment. However, the way carbon dioxide

behaves when it is injected into the ground has long been poorly

understood. Researchers at Yale have worked to create a new

method that improves the simulations of underground carbon

dioxide using machine learning, combining neural networks

to efficiently handle the large and complex computational

challenge of modeling geological carbon sequestration. This

innovative approach is supported by a collaborative effort

from multiple scientific disciplines, pooling expertise to tackle

the complexities of carbon sequestration

Computer models can predict how the injected carbon

dioxide will move through pores in the rock underground

based on factors like pressure, temperature, and fluid

interactions. It is important for scientists to understand how

this carbon dioxide will move because they must ensure that

the carbon dioxide can be stored safely without leaking and

creating unwanted chemical reactions, which can weaken

the rock or cause further environmental damage. Traditional

models struggle to generalize the situations underground,

meaning if the conditions below the surface changed slightly,

the model would need to be retrained. Unfortunately, this has

made real-time simulation impractical and challenging.

The Nested Fourier-DeepONet (NFDN) method proposed

by Yale researchers improves older models by running these

simulations much faster and making them more adaptable

to new conditions. Machine learning models are programs

that take data and use it to learn and make predictions.

The NFDN model is a machine learning model designed to

address the problem of simulations of underground carbon

dioxide storage. This model uses a “nested” structure of neural

networks, incorporating variables such as movement over

an entire storage area and injection points at different scales

while it learns. Taking into account these varying conditions

allows the model to adapt to new and dynamic situations. “The

advantages of this architecture is that it can accurately predict

[...] the build-up of pressure and how saturated the gas is, but

the disadvantage is that we need a large amount of data, so

there is a trade-off,” said Jonathan Lee, a PhD student in the

Yale Department of Chemical and Environmental Engineering.

“Once we train the neural network, we can make predictions

within a fraction of seconds, so like for anything that requires

instant predictions, this deep network is more advantageous

over numerical simulations.” This serves to make geological

modeling of stored carbon dioxide more scalable and reliable,

which directly supports efforts to combat climate change.

One limitation of the model is that it can only make accurate

predictions for the training regime it has seen before. “We

can get some new data, like new cases, and do fine-tuning

with the new model, and the new model can make better

predictions for the cases. That’s the future area of research,

the fine-tuning part for samples it has not seen before,” said

Min Zhu, a PhD student in the Yale Department of Statistics

and Data Science.

This model can also equip scientists with the knowledge to

create more optimal carbon dioxide injection strategies for

safer long-term storage. These advancements also go beyond

carbon storage, opening the door to new possibilities in

energy, resource extraction, and sustainable technology. This

technology could be used in geothermal energy to model heat

flow dynamics, in oil recovery to predict fluid movement in oil

reservoirs while maximizing extraction efficiency, and to help

scientists find safe underground storage sites for hydrogen to

guide the future of clean energy solutions. ■


Biophysics

FOCUS

PHOTOGRAPHY BY ECHO SIMONS

Asheesh Momi discussing the intersection point of the graph to demonstrate the

balance between sensitivity to sound and system stability.

HAIR TODAY,

GONE

TOMORROW

The Delicate Balance of

Inner Ear Amplification

BY SAMMY FEINGOLD

Deep inside the ear is a strange place. Inward past

the eardrum are three small, intricately shaped,

interconnected bones called ossicles. The ossicles lead

deeper to the cochlea, a snail-shaped, fluid-filled structure

that ultimately supplies auditory information to the nervous

system. Sound waves hit the eardrum and make it vibrate in

waves that travel along the ossicles up to the cochlea, passing

through a membrane-covered opening called the oval window.

Struck by the vibrations of the ossicles, the cochlea’s inner fluid

moves in its own complex fluid waves. It is these fluid waves

that amazingly give rise to the nervous system’s perception of

sound. A hair-lined structure called the basilar membrane (BM)

spans the length of the cochlea and uses these waves to generate

electrical signals that are projected to the brain.

But this system isn’t perfect. Different segments of the BM

respond to specific resonant frequencies, which are the pitches

that cause the strongest vibrations. Each pitch has a “resonant

position” on a specific part of the BM. The problem is that there

is a certain amount of friction in the cochlea that removes energy

from the fluid waves traveling along the BM, potentially making

it harder to resolve quiet sounds. To overcome this, hair cells

work to counteract friction so the cochlea becomes sensitive

to faint sounds. However, the activity of hair cells runs the

risk of creating spontaneous, internally driven vibrations that

destabilize the BM. A study authored by Yale biophysics PhD

student Asheesh Momi and colleagues sought to figure out how

hair cells find the ideal operating region for their activity.

“If you had zero friction, if you ever stimulated something

at the resonant frequency, you would actually have infinite

vibrations,” Momi said. “Now this is, of course, impossible,

because there is never a system with zero friction.” The cochlea

thus faces an obvious dilemma: if too much friction is allowed,

our hearing would be impaired, but if there is too little, then our

ears would ring indefinitely.

Momi and his team proposed a mathematical model for BM

dynamics composed of passive and active components. The


passive model describes the general layout of the cochlea:

the fluid that undulates throughout it, the oval window by

which the ossicles’ mechanical motion “pushes” the fluid,

and the BM dividing the cochlea into two chambers. The

active part of their model takes into account how hair cells

detect BM movements and respond rapidly with active

processes. From this modeling, the researchers discovered

two types of modes of vibration that occur along the BM:

localized and extended modes.

“The localized modes are responsible for hearing a particular

frequency,” Momi said. “By contrast, the extended modes are

not really peaked at one position. They are very broad so they

have reasonable displacements across the entire cochlea.”

Because localized modes have specific BM resonant

positions, they are responsible for our ability to sense pitch.

Meanwhile, extended modes have not yet been shown to serve

a particular purpose in hearing. The localized modes are

tuned to the edge of instability via a process involving hair

cell activity strength and root mean square (RMS) height,

a parameter used to measure cochlear vibrational strength.

When hair cells experience RMS heights below a particular

threshold, they slowly increase their activity and are “tuned”

to reduce friction. This low-friction environment enables the

amplification of localized modes based on the active processes

of the hair cells at the given resonant position. Nonetheless,

the cochlea faces another obstacle: amplifying localized

modes’ signals can create instability among extended modes,

negatively impacting hearing.

“If one mode is unstable, the entire system is unstable,”

Momi explained. He and his team hope that their work

with modeling cochlear dynamics will segue into research

regarding the possible role of extended modes in hearing.

Inside that funny little snail in our heads, the feedback loop

established between modes of BM vibration and hair cell

activity is the root cause of our ability to perceive the plethora

of sounds that make up our world. ■


FOCUS

Genetics

SMALL

BUT

MIGHTY

BY MAKENA

SENZON

ART BY

ALONDRA

MORENO

SANTANA

SMuRF:

A GAME-

CHANGING

TEST FOR

RARE

DISEASES

Neither Kaiyue Ma GSAS ’23 nor

Monkol Lek ever imagined they

would work in genetics—Ma was an

aspiring evolutionary biologist and Lek was

an IBM engineer. But now as researchers at

the Yale School of Medicine, the duo recently

announced a new platform for genetic assays

with the potential to improve diagnoses for

those suffering from rare diseases.

The research has personal meaning for

Lek, who decades ago developed a

rare neuromuscular disease and

struggled to find a diagnosis.

From his insight into the

patient experience, he decided

to go back to school and

research diseases like his.

According to Ma and Lek,

rare disease research is not

profitable, and by definition, only

directly impacts a few people.

However, its effects ripple—

spreading hope through the lives of their

families, friends, and communities.

Last year, Ma, Lek, and their team

developed a framework for accessible, cheap,

and scalable genetic assays to investigate a

group of rare genetic diseases. They recently

published their work in Cell. Ma, the first

author of the study, wanted a catchy name

for this framework, something that he could

actually picture scientists remembering, so he

called it SMuRF, a name that encapsulates

its small but mighty characteristics.

SMuRF, which stands for “saturation

mutagenesis-reinforced assays,” was

developed as part of Ma’s PhD thesis.

Overcoming Obstacles

Current methods of rare disease

diagnosis are incredibly resourceintensive,

sapping patients’ time and

money during an already stressful period

in their lives. Ma explained that there are two

main obstacles for rare disease patients. The

first is to get an accurate diagnosis, which

itself could take years. The second obstacle

is to discover an effective treatment. SMuRF

targets the first obstacle, improving clinicians’

ability to connect variations in genes to

physical consequences in the body.

“We only know the genetic cause in about

fifty percent of the cases,” Ma said. “Why is

that? One of the reasons why is we haven’t

discovered all the genes associated with the

disease, and the other reason why is we don’t

understand the different kinds of variants

or DNA changes that we find in genes that

associate with disease.”

Thanks to years of advancements in the

field, geneticists can determine an individual’s

genetic makeup relatively easily. The challenge

is in interpreting the dizzying amount of data.

Sorting through every change in the genome

to deduce what makes patients sick or not


Left to right: Shushu Huang, Monkol Lek, and Kenneth Ng.

involves taxing experiments with specialized

reagents or even robotics. Previous methods

may also rely on large numbers of genomes,

which on the whole can take enormous

amounts of time and resources to sequence

and analyze. Instead, SMuRF employs a

technique called deep mutational scanning

(DMS) that can efficiently assess genetic

mutations at a large-scale. DMS

generates a collection of

mutants, individually tests

each variation, and compares

which variants affect protein

function.

The team chose to first

study dystroglycanopathies,

a group of disorders that

lead to muscular dystrophy,

or degeneration of the muscles.

Dystroglycanopathies are the

result of mutations in proteins

that serve like muscular glue,

binding muscle cells to a network

of proteins and other molecules

called the cytoskeleton. Without this

glue, the entire structure of muscular tissue

begins to fall apart. Since the proteins related

to dystroglycanopathies are known, the team

utilized DMS to analyze every possible singlenucleotide

variant of the two enzyme-coding

genes involved. By delivering the created

variants into the cells, they were able to analyze

how well the enzyme functioned.

Essentially, SMuRF allows scientists to

examine variants one by one, observing how

tiny individual tweaks can create downstream

consequences. Much like bricks in a game

of Jenga, some variants are unimportant,

while others are key to understanding the

foundations of diseases. Though the study

only tested SMuRF on

dystroglycanopathies,

the technique has the

potential applications

for other diseases

because it is flexible and

more cost-effective than

previous experiments.

Time is Money

is Muscle

Ma and Lek hope

that SMuRF can

be incorporated in

clinical research labs

across the globe,

helping to shorten

patient diagnosis time at a fraction

of the cost. As a patient himself, Lek

is very adamant that SMuRF and

other rare disease assays should be

affordable. He shared that when he first

moved to Sydney before his time at IBM,

he had nothing but the clothes on his

back, and struggled to pay for basic needs,

much less medical expenses. Because

of this experience, Lek viscerally

understands the need for affordable

healthcare options.

Additionally, Ma and Lek hope

that SMuRF will reduce the

loss of another resource for

patients: time. In the practice of

rare disease therapy, a common

saying is that “time is muscle.”

Many patients with dystrophic

muscular diseases are in a frantic

race against the clock, struggling

to find treatment before they lose

control of their bodies. In some

cases, the disease wins out before the

patient can even be diagnosed. Since

SMuRF is faster than other diagnosis tools,

PHOTOGRAPHY BY EMILY POAG

ABOUT THE AUTHOR

Ma and Lek hope that it will save time,

muscle, and lives.

From Testing to Therapy

Genetics

FOCUS

Though SMuRF might allow physicians to

identify the genetic origins of diseases, that is

only half of the battle. What is the importance

of a diagnosis if there is no treatment?

Lek explained that part of his motivation

to come to Yale was the dismay he felt when

he had to deliver unactionable bad news. “I

also wanted to work on therapy,” Lek said. “So

the impact I want to make there is to actually

create gene therapies that actually

go into clinics.”

Similar to Lek, Ma wants

to work to find treatment

options, and since his PhD,

Ma has transitioned into

the field of evolution. “For

those patients with advanced

conditions, even though you

can do gene therapies for them,

it can only stop the further

deterioration of the disease, it

cannot restore the muscle tissue. It

cannot repair the damage,” he explained. In

his future research in evolutionary medicine,

he strives to advance the technology of

muscle repair.

In the future, Lek and Ma hope that their

work will transition from labs to hospitals and

improve the lives of undiagnosed patients by

minimizing the length and financial strain of

the diagnosis period.

“We need to work with real patients and

patients’ families,” Ma said. Although they

took winding and unconventional paths to

genetic research, Ma and Lek’s problemsolving

approach now has the potential to

make incredible real-world impact, offering

hope to individuals and families who have

long been underserved in medicine. ■

MAKENA SENZON

MAKENA SENZON (PC ’28) is a chemical engineering major and is from Jupiter (not the planet),

Florida. When she is not writing or editing stories, she may be working at a garden, thinking

about her next adventure, or reading books across genres. Alongside YSM, Makena is involved

with Society of Women in Engineering, Yale Climbing Team, and Yale Taps.

THE AUTHOR WOULD LIKE TO THANK Dr. Kaiyue Ma and Dr. Monkol Lek for their time and

enthusiasm in discussing their research.

FURTHER VIEWING:

TEDx Talks (2019). Taking control of our genetic destiny | Monkol Lek | TEDxSydney [Video].

YouTube. https://youtu.be/Ad6a2Df-oiw?feature=shared



FOCUS

Microbiology

PHAGE SHIFT

PRECISION MEASUREMENTS UNLOCK VIRUS-

BACTERIA INTERACTIONS

BY HELEN SHANEFIELD

ART BY ALONDRA MORENO SANTANA

From ocean waters to soil, and from hot

springs to human microbiomes, tiny

battles between bacteria and viruses

are constantly unfolding. These battles start

when bacteriophages, the viruses that infect

bacteria, bind to receptors on a bacterial host

cell. In a process known as lytic replication, the

phage injects its genome into the bacterium,

using the host’s resources to create proteins

that are assembled into more phages. This

eventually causes the cell to rupture

and die, releasing the newly

created phages into the world.

In their simplest form, phages

consist of a viral genome encased

in a protein shell. Some types

of phages have spider-like

“legs” extending from their

main structure, giving

them an otherworldly

appearance reminiscent

of a robot or spaceship. These

microscopic oddities appear in

nearly every environment on Earth.

But phages are more than just a novelty.

Since they have spent billions of years

evolving to destroy bacteria, they could

be a potent weapon in the fight against

antibiotic-resistant germs. Scientists have

been studying phages for more than a

century, seeking to understand their attack

strategies. However, researchers have long

been limited by phages’ tiny size, which

are often orders of magnitude smaller

than the bacteria they target. In order to

understand phages, scientists have to see

them first.

In a recent study published in Proceedings

of the National Academy of Sciences,

researchers from the Yale Quantitative

Biology Institute—an inter-departmental

collaboration between biological and physical

scientists—described a new assay method for

dynamically visualizing these microscopic

interactions with improved resolution.

Seeing is Believing

The traditional method of visualizing

bacteria-phage interactions requires mixing

bacteria and phages together in a flask,

periodically taking small samples of the

mixture, and measuring how many phages

have not yet attached to bacteria at each

point in time. This process, known as a

classical adsorption assay, allows researchers

to calculate a phage adsorption rate—how

quickly phages attach to bacterial cells over

time. The downsides to this classic assay,

however, are that it is time-consuming,

labor-intensive, and only provides estimates

of the average adsorption rates across entire

populations of bacteria.

The team of Yale researchers developed

a Microscopic Phage Adsorption

(MPA) assay to quantify bacteriaphage

interactions at the level

of individual viruses. The first

step in the MPA assay is to label

phages using a fluorescent dye so

that they glow brightly under the

microscope. A carpet of nonmoving

bacterial cells is

prepared on a glass slide,

providing a stable

surface for phages

PHOTOGRAPHY BY MICHELLE SO

Jyot Antani observes cells in the laboratory.

to attach to. Then, the labeled phages are

introduced to the bacteria, and researchers

can visualize the sample using microscopes

that reveal the fluorescent labels. The phages

appear as bright spots against the background

of bacteria. Using this technique, researchers

can record videos of the phages and bacteria

in real time, documenting the dynamic

movements and individual attachments of

phages to bacteria.

“In the traditional approach, where you

mix viruses and bacteria together in a

flask, you are getting average readouts

from millions or billions of viruses

and bacteria,” said Jyot Antani, a

postdoctoral researcher and first author

of this study. “But here, you can actually

see what's going on at a single virus level.”

This level of detail is particularly

important because previous

methods of microscopy could not

account for possible variation

in dwell time—the length of


Microbiology

FOCUS

This shows that the MPA assay

method is an efficient, accurate

alternative to classical methods

of phage visualization.

Future Phage Technologies

time a phage

spends latched to a

singular bacterium—between

phages. Each type of phage can only attack

one specific bacterial species or strain, and

their attack strategies differ. Knowing the

differences in dwell time between different

phage types may help researchers better

understand the strategies that exist in phage

ecology and how these strategies influence

phage population dynamics.

A New Paradigm

Using mathematical software and the timelapse

videos taken of the phages, Antani and

the research team were able to chart the

trajectories of individual phages over time.

Some phages moved freely, appearing in

the microscope’s view for only a short time

before drifting away, while others remained

relatively fixed in place, staying attached

to the same bacteria for the duration of

the observation period. By analyzing these

movement patterns, the researchers could

distinguish between transient and stable

phage-bacteria interactions.

“In a biological population, there is always

heterogeneity, and this is a way to characterize

the heterogeneity in virus attachment to

bacteria,” Antani said. Observing the unique

behaviors of single viruses reveals variations

that ensemble-averaged measurements

might obscure, providing a more precise

and detailed understanding of virus-bacteria

interactions—much like how measuring an

individual person’s vital signs offers better

health insights than relying on population

averages. Antani explained that he performed

the phage trajectory analysis with seven

different strains of bacteria, whose phages

each have different dynamics of interaction.

The results of the MPA assay correlate with

the traditionally measured adsorption rate.


The targeted use of phages

in future technologies has

many important biological

implications. One of their

most emergent uses is in

phage therapy, a branch of

personalized medicine that

uses phages as drug candidates

to treat bacterial infections.

For instance, through phage therapy,

scientists could quickly sample a harmful

strain of bacteria in an infected patient and

determine the type of phage that would be

effective in treating their condition. This type

of phage treatment is currently undergoing

rigorous testing and clinical trials before

it can be used in humans on a wider scale.

In the future, as antibiotic-resistant strains

of bacteria become more prominent, phage

therapy might emerge as a potent alternative.

Another use of phages may be in

environmental engineering. Bacteria are

found in many natural ecosystems, but

they are especially prominent in water

systems such as oceans, lakes, and ponds.

When bacteria that are harmful to human

health end up in reservoirs, they can cause

widespread harm. Paul Turner, a professor of

ecology and evolutionary biology at Yale and

an author on this study, explained that MPA

assays could be used to quickly detect phages

in water samples. These phages, in turn,

indicate the presence of their bacterial hosts.

“If you can imagine this technology being

portable, you could go to a lake or reservoir

and use it to get a real-time readout of

ABOUT THE AUTHOR


Lab members wrestle a hoodie onto Bertha the inflatable dinosaur.

phages and bacteria of interest that might

be pathogens in some system,” Turner said.

Then, you could test for phages that may

destroy those particular pathogens and apply

them to the body of water in order to remove

harmful bacteria.

The diverse potential uses of phages make

them one of the most exciting new areas

to explore in biology. Thanks to the MPA

assay and its new method of visualizing the

microscopic behaviors of phages, researchers

can develop a better understanding of

the microbial interactions that shape

so much of our world. As

scientists continue to refine this

technology, the insights gained

could lead to both medical and

environmental applications,

harnessing the power of

phages to combat bacterial

infections and monitor

ecosystems. With

each advancement,

we move closer

to unleashing the full

potential of these ancient

microbial warriors. ■

HELEN SHANEFIELD

HELEN SHANEFIELD is a junior in Saybrook College studying Ecology and Evolutionary Biology. In

addition to writing for the YSM, she enjoys knitting, crocheting, and investigating the mysteries

of the fungal world.

THE AUTHOR WOULD LIKE TO THANK Jyot Antani and Paul Turner for their time and

willingness to share their insights.

FURTHER READING:

Antani, J.D., Ward, T., Emonet, T., & Turner, P.E. (2024). “Microscopic phage adsorption assay:

High-throughput quantification of virus particle attachment to host bacterial cells.” Proc. Natl.

Acad. Sci. U.S.A. 121 (52) e2410905121, https://doi.org/10.1073/pnas.2410905121.


FOCUS

Cosmology Computational Biology

The

Grand

DESIgn

Aphrodite's Skincare

How Mapping

the Universe Gives

Insights into Dark Energy

By Sophie Heitfield and Ellie Tillman-Schwartz

Art by Melody Jiang


Cosmology

FOCUS

The universe was born in a fiery

explosion, expanding outwards in

all directions. For billions of years

following the Big Bang, the tug of gravity

worked to slow its growth. But then, the

unexplainable happened—the universe

began to expand at an accelerating rate,

driven by an invisible force scientists have

termed “dark energy.” Determined to

explain this cosmic mystery, over nine

hundred researchers from around the world

joined forces to create the Dark Energy

Spectroscopic Instrument (DESI), the world’s

most powerful multi-object spectrograph.

Perched high in the mountains at Kitt Peak

National Observatory in Arizona, DESI is

now concluding a five-year survey with the

ambitious goal of mapping a third of the sky

and capturing data about the light spectra

emitted from thirty-five million galaxies. Its

unprecedented 3D cosmological map will

allow scientists to measure the influence of

dark energy on the universe’s expansion.

Two Yale researchers—Charles Baltay and

David Rabinowitz—have played a crucial

role in developing DESI’s key technologies,

from fiber-optic imaging to advanced data

analysis tools.

Baltay, Yale’s Eugene Higgins Professor

Emeritus of Physics, describes himself as an

experimentalist studying fundamental issues.

He began his career in the 1960s, studying

strongly decaying particle states, but has

more recently shifted towards astrophysics

and cosmology, researching dark energy

via the study of distant supernova explosion

events. “Just about one hundred years ago,

we thought we understood classical physics.

[...] Then along came atomic physics, and

atoms did not behave the way we predicted

[...], so we had to invent a whole new physics

called quantum mechanics and relativity,”

Baltay said. He suggests that we are at a

similar point now as the universe is not

doing what we predict it to do.

“We have to invent a whole new

physics, whether that’s dark

energy or a change in

general relativity, but

it’s a fundamental,

basic change in what

we understand.” As

DESI rapidly collects

data, scientists eagerly

await insights into the

creation and eventual

destiny of our universe.

Will the universe continue expanding? Or

is a more dramatic fate awaiting us—a

collapse as violent as the Big Bang?

Blasts from the Past

The fundamental issue

of dark energy lies in its intangibility.

Unlike ordinary matter and energy, dark

energy neither emits nor interacts with light,

making its direct observation impossible

with current telescopes and instruments.

Dark energy should not be confused with

dark matter; while both are cosmic and

invisible, dark matter pulls matter together,

while dark energy pushes it apart.

If dark energy cannot be touched or seen,

how do we know it exists? Well, dark energy

is our current term, coined by University of

Chicago astrophysicist Michael Turner in

1998, for some force pushing the universe

to expand faster than it should. Based on

our understanding of cosmology at the

time, scientists in the nineties expected the

expansion of the universe to be slowing

down over time as gravity pulled galaxies

together. However, this is not currently

the case. In fact, by observing supernovae

that exploded billions of years ago and

calculating the rate at which the galaxies

they are in are moving away, scientists have

been able to conclude the rate of expansion

of the universe is currently increasing. This

rate of expansion is now termed the “Hubble

constant,” after American astronomer

Edwin Hubble, who first discovered that the

universe was expanding decades prior.

These calculations have led to the

development of a mathematical model

for the Big Bang known as the Lambda-

CDM model. According to this model, the

universe’s expansion is shaped by two forces:

cold dark matter (CDM), which interacts

weakly with ordinary matter and slows

expansion through gravity, and dark energy

(Lambda), which drives the universe to

expand at an accelerating rate. The expansion

of the universe must have been slowing for a

time, as galaxies would not have been able

to clump together otherwise, but around

five billion years ago, dark energy’s repulsive

force must have overwhelmed the attractive

gravitational interactions between matter.

Using observations from supernovae

and light left over from the early years

of the universe after the Big Bang,

scientists have also been able to accurately

estimate the current quantity of dark energy,

estimating that it composes up to seventy

percent of the energy in the universe.

Attempting to reconcile this illusive energy,

an enormous part of our universe, with

our current cosmological understanding,

astrophysicists have developed three

primary theories of dark energy’s interaction

with classical physics.

The “cosmological constant” or “vacuum

energy” theory is the most widely accepted of

these conjectures. It argues that dark energy

is created by a vacuum of space, in turn

generating cosmic acceleration. In contrast,

the “evolving dark energy” theory proposes

the existence of an unknown universal field

that opposes the normal effects of matter

and energy, leading to varying quantities

of dark energy over eons. The final, aptly

titled “alternative gravity” theory suggests

that, perhaps, dark energy does not actually

exist—rather, Albert Einstein’s theory of

general relativity may be missing a piece,

causing miscalculations that incorrectly

imply the presence of dark energy.

DESI’s Galactic Census

All these differing theories on the nature of

dark energy raise the question—how do we

measure the invisible? Before DESI can track

cosmic expansion—which it accomplishes by

following galaxy movement—scientists must

first know the 3D distribution of galaxies in

space. To accomplish this, DESI measures

the influence of dark energy through baryon

acoustic oscillations (BAOs) and galaxy

redshift space distortions. BAOs arise out of

the composition of the primordial universe:

tiny fluctuations in ionized plasma sent

pressure waves rippling through a soup of

hydrogen and helium nuclei, regular matter.

As the universe expanded and cooled, the

waves froze in place, creating a characteristic

separation of galaxies that act as DESI’s

cosmic rulers.

In addition to BAOs, DESI tracks galaxy

position by measuring redshift. As light



FOCUS

Cosmology

PHOTOGRAPHY BY SARAH HEEBE

David Rabinowitz explains the design of a telescope

prototype.

travels from across the expanding universe,

its wavelength elongates, shifting towards

a lower energy form. For visible light, this

process transforms blue light into red. The

farther away a galaxy is, the more its light is

redshifted, providing a direct link between

distance and motion. While the light of

typical galaxies may eventually become too

faint to detect at extreme distances, DESI

looks at quasars, which are very bright

galactic cores with black holes at their

centers. As their light traverses intergalactic

gas clouds, the light spectra become

patterned with dark lines indicating various

redshifts depending on the clouds’ distances

from the quasar. This pattern of absorption

lines is known as the Lyman-alpha forest,

named such because it originates from the

Lyman-alpha transition that electrons can

make in hydrogen atoms. Using the distance

information encoded in the Lyman-alpha

forest, scientists can track BAO and redshift

measurements back eleven billion years.

To ensure the accuracy of these findings,

DESI is the first spectroscopic experiment to

perform a fully “blinded analysis,” in which

the data is concealed from the researchers

until the analysis is performed to limit

subconscious confirmation bias.

Collecting the precise galaxy positions

used in these measurements was made

possible by an extensive imaging survey

conducted before DESI began its

observations. Baltay’s team at Yale played

a critical role in this effort by rebuilding

and installing the Mosaic-3 Infrared CCD

Imager on the Kitt Peak telescope, allowing

for enhanced mapping of critical targeting

data. But finding these galaxies was just the

first step. Next, another Yale team, headed

by research scientist and imaging expert

David Rabinowitz, developed the Yale

FiberView Camera. The device enables the

efficiency of the DESI system by guiding

the robotic positioners, which ensure

each of its five thousand optical fibers is

aligned on its preselected target galaxy.

“It’s measuring spectra for five thousand

galaxies in a single exposure [...] and they

have to have a particular spectrum that

you know well enough in advance, so that

when it’s shifted because of its distance, you

know,” Rabinowitz said. Through this work,

the Yale team’s contributions have played

a crucial role in the success of the DESI

project, which has now collected data on

over thirty million galaxies.

In its first year of data collection, DESI

has already constructed the largest and

most precise 3D map of the universe,

offering a glimpse into whether our current

understanding of the cosmos—the Lambda-

CDM model—still holds true. DESI’s current

data supports the Lambda-CDM model and

the predictions of general relativity at cosmic

scales. Yet, DESI’s early findings also hint at

the fascinating possibility that dark energy

may not be a constant force, but evolving

over time. Therefore, DESI’s current results

still cannot rule out alternative theories of

modified gravity—hypotheses which suggest

ABOUT THE

AUTHORS

general relativity may not fully apply to vast

cosmic scales. Other important findings of

DESI’s measurements have included further

contributions to scientists’ calculations of

the Hubble constant and setting new upper

limits on the mass of neutrinos, the only

fundamental particles whose precise mass

remains unknown.

Expanding Horizons

As DESI continues its five-year mission,

each new data point will bring us closer to

answering these fundamental questions.

Will the Lambda-CDM model prevail,

or will new perspectives on dark energy’s

evolution spur an entirely new cosmological

understanding? DESI’s journey is only the

beginning; plans for DESI-II, an extension

set for 2029–2035, aim to continue this

research, while next-generation projects

like the Stage-5 Spectroscopic Experiment

promise to map multiple times as many

galaxies as DESI. ■

SOPHIE HEITFIELD is a first-year in Branford College majoring in Chemistry and Classics. Outside of

class, she enjoys playing violin in the Davenport Pops Orchestra, dancing ballroom and traditional

Chinese dance, and conducting alternative protein research at the Slavoff Lab.

ELLIE TILLMAN-SCHWARTZ is a first-year majoring in Biomedical Engineering, BS/MS. In addition

to writing for YSM, she competes on the Women’s Rugby team, plays cello in the Davenport Pops

Orchestra, and conducts medical device research at the Wiznia Lab.

THE AUTHORS WOULD LIKE TO THANK Charles Baltay and David Rabinowitz for their time and

insightful comments regarding their research.

FURTHER READING:

SOPHIE HEITFIELD

ELLIE TILLMAN-SCHWARTZ

Baltay, C., Rabinowitz, D., Besuner, R., Casetti, D., Emmet, W., Fagrelius, P., Girard, T., Heetderks,

H., Lampton, M., Lathem, A., Levi, M., Padmanabhan, N., & Silber, J. (2019). The Desi Fiber View

Camera System. Publications of the Astronomical Society of the Pacific, 131(1000). https://doi.

org/10.1088/1538-3873/ab15c2


Applied Physics

FOCUS

Mind the

Electron Gap

Quantum Asymmetries May Drive

Superconductivity


By Ximena Leyva Peralta

Art by Alondra Moreno Santana


FOCUS

Applied Physics

As energy demands soar and

environmental concerns grow, the

search for more efficient technologies

has never been more urgent. Superconductors—

materials that can conduct electricity with zero

resistance—offer an enticing solution. They

allow for continuous flow of energy without

loss. But there’s a catch: so far, superconductors

only work at extremely low temperatures.

Understanding the underlying mechanisms

behind superconductivity is essential to

improving their performance and making them

viable for widespread use.

A research group at Yale, led by assistant

professor of physics Eduardo H. da Silva

Neto, has uncovered a key piece of the

puzzle. Their new study, published in Nature

Physics, provides experimental evidence that

nematicity—an electronic phase that breaks

the rotational symmetry of electrons—plays a

crucial role in enabling superconductivity in

certain iron-based materials. “There’s a wide

range of [iron-based] materials which can

superconduct [...] and that have a nematic

phase,” said Pranab Kumar Nag, a postdoctoral

researcher in the da Silva Neto Lab and lead

author of the paper. Traditional models cannot

fully account for how superconductivity occurs

in some of these materials. Theorists have long

suspected that fluctuations associated with the

nematic phase could drive superconductivity.

Yet, concrete proof of this mechanism

remained elusive until now.

“This is the first time, as far as we know,

that nematic fluctuations have been found as

evidence for the driver of superconductivity,”

said Kirsty Scott GSAS ’26, a co-author on the

paper. By helping us understand the driving

mechanisms behind superconductivity, this

research brings us one step closer to achieving

the “holy grail” of materials

science: a superconductor that

works at room temperature.

Electrons That Attract

At its core, electricity is

simply the movement of

electrons. As these negatively

charged particles flow

through a material, they

transfer energy, powering

everything from light bulbs to

supercomputers. But there’s a

problem: electrons naturally

repel each other. As they

move, the constant jostling and

bumping leads to energy loss in the form of

heat. This loss is called electrical resistance. The

amount of resistance depends on the material—

metals like copper are excellent conductors with

relatively low resistance, while rubber, with its

high resistance, acts as an insulator.

Superconductivity flips this entire concept

on its head. Instead of repelling each other,

electrons in a superconductor form couples

called Cooper pairs that attract each other and

move effortlessly through the material with

zero resistance. “To create this attraction, you

need something to change the energy landscape

of your electrons and allow them to now be

attracted to each other,” Scott said.

But what allows for the creation of

Cooper pairs? The answer for classical

superconductors, discovered in 1911, lies in

lattice vibrations—tiny oscillations of atoms

within the material. As an electron moves, it

distorts these vibrations, creating a wave that

pulls a second electron along with it. This

pairing mechanism allows electrons to glide

together through the material unimpeded.

However, the mechanism only works at ultralow

temperatures, close to absolute zero. At

higher temperatures, the atoms oscillate more

rapidly, disrupting the Cooper pairs and

breaking the material’s superconductivity.

In the 1980s, scientists discovered a

new class of superconductors, known as

unconventional superconductors, that

function at much higher temperatures. Unlike

their classical counterparts, these materials

don’t rely on lattice vibrations to form Cooper

pairs, but the exact mechanism behind their

superconductivity is still unclear and may

differ between materials. Investigating

this mechanism is a key focus of the da

Silva Neto Lab at Yale.

A Sea of Spin

PHOTOGRAPH COURTESY OF PAUL-ALEXANDER LEJAS

Kirsty Scott (left) and Pranab Kumar Nag (right) operate laboratory

equipment to investigate the physical origins of superconductivity.

So how do these unconventional materials

form Cooper pairs at such high temperatures?

The key is understanding the “phases,” or

states, that electrons can inhabit. Just like how

compounds can exist in three different states

of matter—solid, liquid, or gas—electrons in

a material can also arrange themselves into

distinct quantum phases. Unlike conventional

phases, which are determined by temperature

and pressure, quantum phases arise from

the collective behavior of electrons and their

interactions. Observing and studying these

phases requires extremely low temperatures.

At higher temperatures, electrons and atoms

gain energy and move more freely, making it

difficult to distinguish the underlying quantum

effects. Lowering the temperature slows down

the motion, allowing quantum phases to emerge

more clearly and enabling precise measurements

of their properties.

One key example is the magnetic phase.

Electrons, being charged particles, generate

tiny magnetic fields due to an intrinsic property

called spin. In most materials, electron spins

point in random directions, canceling out

any large-scale magnetism. However, under

certain conditions, the spins can align in an

orderly pattern, forming a magnetic phase. For

example, in a ferromagnet like iron, all the spins

point in the same direction, creating a strong

magnetic field. In an antiferromagnetic phase,

neighboring spins alternate directions, canceling

out the net magnetization but still maintaining

an ordered magnetic structure.

But electron spins aren’t static; they fluctuate

and interact with each other constantly. This

dynamic behavior is known as spin fluctuations.

A helpful way to understand this is through


Applied Physics

FOCUS

phase transitions, like ice melting into water.

While to the human eye ice becomes liquid at

a well-defined temperature, on a microscopic

level, regions within the ice can behave like a

liquid even before the entire structure has melted.

Similarly, even outside a true magnetic phase,

spin fluctuations create local, short-lived regions

where magnetism begins to emerge.

In unconventional superconductors, these

fluctuations are extremely important. It is

commonly believed that in many such materials,

spin fluctuations can act as the glue that binds

pairs of electrons together. Imagine a sea of

electrons with their spins constantly fluctuating.

As the temperature decreases, neighboring

electrons can “feel” each other’s fluctuations. This

creates an effective attraction between electrons

with opposite spins, forming Cooper pairs.

Breaking Symmetry

Another type of quantum phase is the

nematic phase, or nematicity. In this phase,

electrons break rotational symmetry while

preserving translational symmetry. What’s the

difference? A circle, for example, has rotational

symmetry because it looks the same from

any angle. Meanwhile, a checkerboard has

translational symmetry, since shifting it by a

certain distance does not change its pattern.

In a nematic phase, electrons are arranged so

that translational symmetry remains intact,

but their behavior is no longer the same in all

directions. Like a crowd looking towards the

stage at a concert, the electrons all orient in

the same direction. This tendency for electrons

to favor a specific direction in nematic

phases is termed “anisotropy.”

Nematicity has drawn

much attention in

iron-based and hightemperature

superconductors.

In these systems, electronic

nematicity emerges when

the electronic structure

exhibits anisotropy, despite

the underlying atomic of

the material remaining

nearly symmetric. This

suggests that nematicity is

driven by electron interactions rather than by

distortions in the atomic arrangement—in other

words, it’s only the electrons at work. Similar to

spin fluctuations, nematic fluctuations can create

temporary, localized areas of nematicity that

break rotational symmetry but are neither stable

nor intrinsic to the material.


But does nematicity actually lead to

superconductivity? This is a hard question—

nematicity in iron-based superconductors was

observed for the first time less than a decade ago,

and researchers have faced major obstacles

in their efforts to investigate further. One

major challenge is that the nematic and

magnetic phases in these materials occur under

nearly the same thermodynamic conditions,

making it difficult to determine whether they

are interdependent or if nematicity can even

exist without magnetism. In theory, nematic

fluctuations could serve the same function as

spin fluctuations, allowing electrons to form

Cooper pairs by altering how they interact with

one another. While superconductivity mediated

by nematic fluctuations is well-supported in

theory, experimental confirmation has been

elusive due to this overlap.

Experimental Evidence

To investigate nematicity in superconductors,

the research team focused on one of the few

known families of materials where a true

nematic phase does not overlap with a magnetic

phase—sulfur-substituted iron selenium. These

materials are characterized by a basic structure

of alternating iron and selenium atoms, with

selenium occasionally replaced by sulfur. To

probe the electronic structure of these materials,

the team used scanning tunneling microscopy

and spectroscopy, a powerful technique capable

of imaging sample surfaces and their electronic

properties at the atomic level. “In our lab, we

have a very sophisticated experimental setup.

We do all of the experiments at a very low

temperature, [...] close to zero

Kelvin. At that temperature,

you can see all the quantum

effects,” Nag explained.

ABOUT THE

AUTHOR

Each measurement could

take several days to a week

and required a highly controlled, noise-free

environment to ensure high-quality data.

Careful analysis was essential, and the group

collaborated with international research

teams to strengthen their conclusions for

further verification.

The team’s findings show that at a certain

substitution threshold, nematic fluctuations

played a key role in driving superconductivity.

However, localized spin fluctuations are still

present and cannot be ruled out entirely. “We

found that nematic fluctuations have at least

taken over as the more prominent driver, but

[we can’t] go as far as to say that spin fluctuations

aren’t still important,” Scott explained.

Looking ahead, the da Silva Neto group

plans to continue studying this family

of iron-based materials, as well as other

unconventional superconductors. Their work

provides a fresh perspective on the potential

drivers of superconductivity, bringing us closer

to a more comprehensive understanding

of unconventional superconductors. This

knowledge could eventually enable scientists to

harness superconductivity for breakthroughs

that could revolutionize energy grids,

computing, and transportation. ■

XIMENA LEYVA PERALTA

XIMENA LEVYA PERALTA is a senior chemistry major in Jonathan Edwards College. In addition to

writing for YSM, they perform computational chemistry research in the Tianyu Zhu Lab and dance

with Ballet Folklórico Mexicano de Yale.

THE AUTHOR WOULD LIKE TO THANK Kirsty Scott and Pranab Nag for their time and wonderfully

clear explanations.

FURTHER READING

Nag, P. K., Scott, K., de Carvalho, V. S., Byland, J. K., Yang, X., Walker, M., Greenberg, A. G., Klavins, P.,

Miranda, E., Gozar, A., Taufour, V., Fernandes, R. M., & da Silva Neto, E. H. (2025). Highly anisotropic

superconducting gap near the nematic quantum critical point of FeSe1−xSx. Nature Physics, 21(1),

89–96.


FOCUS

Geology Computational Biology

Upper Crust

Geologists Narrow in on the Origins of

Plate Tectonics

By Daniel Havlat and Abigail Jolteus

Art by Alondra Moreno Santana


Geology

FOCUS

You may not feel it, but

the Earth is moving

underneath your feet.

Plate tectonics—the processes that

move the rigid, cohesive, rocky plates

of Earth’s crust—is something most of

us take for granted, despite its profound

effects on the state of the planet. How

long plate tectonics have been operating

on Earth has long been a subject of debate,

with implications for our understanding of

the evolution of the Earth’s early climate,

heat budget, and habitability.

A recent study published in Nature

Communications, co-authored by Yale

researchers, provides new evidence that

suggests Earth’s plate movements may go back

as far as 2.5 billion years to the Neoarchean

Era—pushing the onset of tectonic activity

further back than ever before.

A Lot on Our Plate

The question of when plate

tectonics first began is far from simple.

Some researchers argue that modern plate

tectonics goes back around seven hundred

million years, while others contend it emerged

nearly three billion years ago. This broad range

exists in part because modern plate tectonics

involves a suite of coupled processes beyond

just the movement of plates. Theories of

plate tectonics incorporate volcanic activity,

mountain building, and rock recycling via

plate subduction and ocean ridge spreading.

While geologists can find evidence of one or

more of these processes operating in the distant

past, that does not mean the whole system

functioned the way it does today.

Instead, researchers must look for clues as

to what processes were taking place at each

time, evaluating each of the criteria by their

own separate evidence. “There [are] ways to

do that, but one of them involves what my lab

does: the magnetism of rocks, which we call

paleomagnetism,” said David Evans, professor

of Earth and planetary sciences at Yale and

a senior author on the study. While other

methods may interrogate the rock record for

evidence of volcanic activity or remnants of

plate subduction, paleomagnetism looks at

the big picture: rocks moving around the

world in the

processes sometimes referred

to as plate mobilism.

Paleomagnetic analysis

leverages the fact that

crystalline minerals in

some rocks act like tiny

bar magnets, recording

a snapshot of the Earth’s

magnetic field at the

moment the rock was

formed. The analysis involves

carefully measuring the

magnetic orientations of

rock samples containing

these crystals, with the

knowledge that the rocks’

orientation may have been

tainted by intervening magnetic processes.

“You could have a magnetic mineral that

has the right size and chemistry to hold a

magnetic signal for billions of years, and it

still might be secondary,” Evans said. With

some trigonometry and good accounting for

any post-crystallization changes in magnetic

orientation, such as remagnetization by later

heating events or physical deformation,

geologists can estimate how far the rock was

from Earth’s magnetic poles when it was

formed. By carrying this analysis out for

many rocks of different ages, geologists can

reconstruct the motions of any tectonic plate

over long periods of time.

The smoking gun that geologists look for in

support of early plate mobilism is independent

movements of ancient crustal blocks. These

blocks are called cratons, which preserve some

of the oldest rocks on Earth and typically make

up the “cores” of modern continents. “One of

what we think are the necessary requirements

for plate tectonics is that you’ll have substantial

motion across the Earth’s surface—not just

motion of one piece of real estate across

the surface, but two pieces that are moving

independently of each other,” Evans said.

Previous paleomagnetic studies have shown

the apparent motion of one craton up to three

and a half billion years ago, but that data might

also be explained by a phenomenon called “true

polar wander.” True polar wander occurs when

the entire planet shifts relative to its spin axis,

settling into a new rotational equilibrium. This

global rebalancing usually results from slow

deformation of rocks within the Earth’s interior,

changing how mass is distributed. If more mass

shifts toward the planet’s axis, Earth rotates

slightly faster, whereas if mass moves

outward, the rotation slows

David Evans analyzes a rock sample.

down. These changes can subtly alter the length

of a day as well as the orientation of the planet’s

rotation. Because true polar wander involves

shifting the entire planet relative to

its spin axis, it can produce effects

that resemble the shifts observed in

tectonic plates within paleomagnetic

records. If geologists obtain data

from two cratons from the

same period, they can check

whether the plates are truly

moving relative to one

another or merely appearing

to move because of the true polar

wander phenomenon.

A Rift Between Geologists

PHOTOGRAPHY BY PAUL-ALEXANDER LEJAS

Scientists have debated for decades

the timing of the first movements

of the Earth’s crust that resemble

modern plate tectonics. The

Neoarchean period, which

spans from 2.8 to 2.5 billion

years ago, has been central to

this debate, as some models

suggest that early Earth’s crust

was largely immobile during

this time. In these models, the

idea goes that heat from deep

within the Earth generated slowmoving

currents that circulated

below the crust, somewhat like the firm

layer of cheese atop a bowl of hot French

onion soup. This would have kept the crust’s

plates from breaking up and moving around.

However, this study provides compelling

evidence to the contrary. “We think the

Neoarchean was not a stagnant lid because

our study illustrates that the plates were



FOCUS

Geology

moving,” said Jikai Ding, a former

postdoctoral researcher in the Evans

Lab and first author of the study.

This movement suggests that

continents were already shifting

in a way reminiscent of modern

plate tectonics, indicating that

large-scale mobility of Earth’s

crust and mantle began much

earlier than previously

confirmed. By establishing

a new minimum age

for this process, the

study provides a crucial

reference point for

refining models of early

Earth dynamics. “We

found strong evidence

of relative horizontal motion

between Wyoming and Superior cratons

before 2.5 billion years ago, which is critical for

understanding when and how Earth’s early

continents started behaving more like they do

today,” Ding said.

Today, the Wyoming and Superior cratons

make up much of the heart of the North

American continent. Based on paleomagnetic

data, however, we know they were separated by

a wide ocean 2.7 billion years ago. So, we know

they were once distant from one another, and

we know they eventually collided together to

move as one block. Relative plate motion must

have occurred in between these states.

Elucidating the intermediate steps was where

Ding, Evans, and their colleagues

stepped in. By analyzing the

paleomagnetic orientations of

rock samples from multiple

generations of mafic dikes—long,

narrow igneous formations that record ancient

magnetic orientations—the researchers built

a robust case for independent plate motion

PHOTOGRAPHY BY PAUL-ALEXANDER LEJAS

David Evans characterizes rock samples utilizing equipment in his lab.

from 2.7 to 2.5 billion years

ago. The study incorporated

additional geological

evidence, such as the timing

of craton assembly and

correlations in igneous

activity between Wyoming

and Superior, strengthening

the argument that large-scale

mobility was occurring.

However, while the

study supports ancient

plate mobility, it does not

necessarily confirm that

the full plate tectonic cycle

as we see it today was taking

place billions of years ago. A defining feature

of modern plate tectonics is subduction—

where one plate dives beneath another into the

mantle, recycling crustal material. No definitive

geological evidence of this process was found

from the Neoarchean period. “That’s why

we call it a ‘mobile lid’ rather than full plate

tectonics,” Ding explained. “Although calling it

plate tectonics might have been more exciting

and well-received, we have to respect the

evidence. Science requires precision.”

While the study stops short of confirming

modern-style plate tectonics in the Neoarchean,

it provides the clearest evidence yet that Earth’s

crust was already mobile by this time. This

discovery has far-reaching implications for our

understanding of Earth’s thermal evolution,

the formation of early continents, and even

the origins of life, which may have been

influenced by tectonically driven chemical

cycling. By refining our knowledge of when

ABOUT THE

AUTHORS

and how Earth's

dynamic crust began

shifting, researchers

are uncovering crucial

insights into the planet’s

earliest history.

Shifting Towards

the Future

As with any breakthrough,

this study raises new

questions. Researchers are now

looking to other ancient cratons

across different continents to see

if similar patterns of motion can

be detected. “Our work adds to the

growing debate on when modern

plate tectonics began. The next

step is to gather more data from

regions like India, Australia, and

South Africa to test whether other

ancient cratons also show signs of

early plate motion,” Ding said.

Future work will involve refining

paleomagnetic techniques to extract

more reliable data from ancient rocks,

as well as integrating geochemical and

geodynamic modeling approaches to better

understand how early Earth operated. The

ultimate goal is to determine when full plate

tectonics—including subduction—became a

dominant process on the planet.

As researchers continue to investigate, one

thing is clear: Earth’s early history was more

dynamic than we once thought, and the story of

our planet’s shifting crust is still being written. ■

DANIEL HAVLAT

ABIGAIL JOLTEUS

DANIEL HAVLAT is a senior in Trumbull College majoring in Earth & Planetary Sciences. He studies

oxygen isotope geochemistry in the Wostbrock lab. Beyond writing for YSM, he is an avid photographer

and rock climber.

ABIGAIL JOLTEUS is a senior in Berkeley College. Outside of YSM, she conducts mucosal immunology

research in the Konnikova Lab. She is also an avid runner, swimmer, and water skier.

THE AUTHORS WOULD LIKE TO THANK Jikai Ding and David Evans for their time and expertise.

FURTHER READING:

Tarduno, J. A., Cottrell, R. D., Bono, R. K., Rayner, N., Davis, W. J., Zhou, T., Nimmo, F., Hofmann, A., Jaganmoy

Jodder, Ibañez-Mejia, M., Watkeys, M. K., Oda, H., & Mitra, G. (2023). Hadaean to Palaeoarchaean stagnantlid

tectonics revealed by zircon magnetism. Nature, 618(7965), 531–536. https://doi.org/10.1038/s41586-

023-06024-5

Hawkesworth, C. J., Cawood, P. A., & Dhuime, B. (2020). The Evolution of the Continental Crust and the

Onset of Plate Tectonics. Frontiers in Earth Science, 8. https://doi.org/10.3389/feart.2020.00326


Neuroscience

FEATURE

WHEN SULFIDE BINDS,

MEMORY REWINDS

Hydrogen Sulfide Could Change Memory Degradation

in Alzheimer’s Disease

BY HELEN ZHANG

Memories make us who we are. Yet, memory loss is a strikingly

common phenomenon in our society, often manifesting in

people with neurological conditions such as Alzheimer’s

or Parkinson’s disease. In particular, patients with Alzheimer’s disease

(AD) often have difficulty storing memories long-term and associating

memories. While hydrogen sulfide has been previously considered

as a possible anti-inflammatory therapeutic for AD patients, its effect

on memory remained unclear. In a study published in the Journal of

Alzheimer’s Disease, PhD students Anoop Manakkadan and Dolly

Krishnan worked with Sreedharan Sajikumar, associate professor of

physiology at the National University of Singapore, to elucidate the

effect of hydrogen sulfide on synaptic plasticity: the ability of neurons to

modify the strength of their connections.

The researchers investigated this problem using a technique called in

vitro electrophysiology, which records the electrical activity of tissues.

Slices of the hippocampus, a key part of the brain involved in memory

formation, were taken from rats and electrically stimulated.

Their goal was to induce long-term potentiation

(LTP), a cellular phenomenon that strengthens

connections between neurons when they are

repeatedly activated together, aligning with

the principle that “neurons that fire together,

wire together.”

Depending on the type of stimulation,

LTP can be classified into different forms.

Early-LTP is induced by weak stimulation,

lasts only a few hours, and is associated with shortterm

memory. In contrast, late-LTP is induced by

repeated strong stimulation, lasts for many hours or

even days, and is associated with long-term memory.

In their study, the scientists simulated AD conditions

in the rat hippocampal slices and observed LTP

impairment. Saliently, when they added in a molecule that

donates hydrogen sulfide, LTP function was saved.

The researchers also wanted to test whether these

neuronal connections responsible for memory can

form associations with each other. To do so,

they relied on the framework of a fascinating

hypothesis: memory is largely associative and

involuntary. Our neural system conserves

energy by associating a strong memory with a

weak memory, transforming the latter into longterm

memory. “You might not remember what you

ART BY MADELEINE POPOFSKY

had for lunch last week, but if that lunch was part of a

special event—like your birthday—you’re more likely to

recall it,” Sajikumar said. The synaptic tagging and capture

(STC) hypothesis explains this process for converting

short-term memories to long-term memories at the cellular

level. According to the hypothesis, short-term memories leave

a “tag” at the synapses between neurons, making them temporarily

receptive to memory-related proteins. If, within a certain period, a

more impactful experience (like a birthday celebration) occurs, these

tagged synapses can “capture” memory proteins from the long-term

memory system. By doing so, they strengthen the weaker memory and

make it last longer. Even if what you had for lunch that day was seemingly

irrelevant, because it is linked to the salient memory of a birthday surprise,

the initial weak memory becomes reinforced as a long-term memory. AD

patients are hypothesized to have STC disruptions that prevent them from

associating and storing memories over time.

To test the STC hypothesis, early-LTP and late-LTP were electrically

induced in the rat hippocampal tissues. Late-LTP was induced in

one neuronal pathway, followed by early-LTP in a nearby pathway

thirty minutes later. While STC was disrupted in the AD-simulated

condition, early-LTP—due to its temporal proximity to a strongly

stimulated pathway undergoing late-LTP—was strengthened when

hydrogen sulfide was added. In other words, short-term memory was

strengthened when it was near neurons capturing long-term memories.

These findings highlight the importance of further study into the role

of hydrogen sulfide in rescuing memory function by strengthening

long-term memory storage and neural associations—

two processes that, when disrupted, are

hallmarks of AD. No side effects of

hydrogen sulfide were observed in

the preliminary study.

In the future, Sajikumar aims

to conduct behavioral

studies in AD mice

models, optimizing

dosage and method

of administration of

hydrogen sulfide. While

the road to curing

AD may be long,

hydrogen sulfide could

be a promising step

in the journey. ■



FEATURE

Mathematics

SORRY, SHAKESPEARE

WHY INFINITE MONKEYS WILL NOT WRITE HAMLET

BY AIDEN ZHOU

ART BY MELODY JIANG AND RYDER LARIVIERE

It’s a widely accepted idea that monkeys, given infinite time, can

type out the complete works of Shakespeare. And yet, it’s also

deceptive. Though the “infinite monkey theorem” holds in an

ideal universe—where monkeys never go extinct and the cosmos

subsists forever—modeling the situation in real life quickly goes

sideways. If we consider the finite lifespan of the universe, the

likelihood of Shakespeare’s folio—or even far shorter works—

being randomly generated falls to nearly zero.

Proving the “infinite monkey theorem,” in its traditional form, is

a straightforward exercise in probability. Let’s view Shakespeare’s

folio as a block of n letters and give a monkey a typewriter with

thirty keys. Then, the chance that the monkey does not succeed in

the first x blocks of n letters is

. At first, f(x) is nearly

identical to one; the monkey is almost certain to fail. But as x

approaches infinity, the value of f(x) converges to zero, shrinking

through repeated multiplication by a fraction of one. Thus,

Shakespeare’s works are guaranteed theoretically to appear

somewhere in the typewriter’s unimaginably, perhaps infinitely

long printout.

However, this approach does not work in a non-ideal universe.

Stephen Woodcock and Jay Falletta, researchers from the University

of Technology Sydney, put the finite monkey theorem to the test.

In their study, Falletta and Woodcock found that the success

rate of random generation was surprisingly low even for simple

phrases. A single chimpanzee only has a 0.05 probability of typing

“bananas” at any point throughout its thirty-year lifespan. For the

slightly longer sentence “I chimp, therefore I am,” this probability

becomes 10 -25 . “The chance of even a coherent sentence arising at

random is vanishingly, vanishingly small,” Woodcock said.

Next, the researchers calculated what would happen if the entire

chimpanzee population arbitrarily typed away until the heat death

of the universe: a period of 10 100 years. The results were shocking.

Woodcock and Falletta intuited that the decaying likelihood of

replicating text would be too rapid for generating any non-trivial

piece of literature. This prediction was correct, but not extreme

enough. Under the given conditions, the chance of replicating

Curious George—a children’s book shorter than most essays—

within the next 10 100 years is an astonishing 10 -15043 . This

probability was calculated using the equation

by

substituting appropriate values of n and x. That’s many, many

orders of magnitude smaller than the roughly 10 -80 chance of

picking a single atom at random out of all the matter in the entire

universe. “You very, very quickly go from ‘this will happen’ to ‘this

might have happened’ to ‘this almost certainly won’t happen’ to

‘the universe doesn’t have enough resources for this to happen,’”

Woodcock said.

In our day-to-day lives, it’s common to conflate enormous

numbers with infinity. For practical purposes, this rarely poses

an issue. However, applying this belief to mathematical questions

can lead to incorrect conclusions, and Woodcock and Falletta’s

efforts help to highlight the fallacy. “A lot of people think infinity

just means the biggest number that they can relate to, and it

doesn’t,” Woodcock said. Rather, infinity is not a number or a

concept that can be related to using any finite scale. Even the

universe’s lifespan, which appears endless, pales in comparison

to the sheer magnitude of the number needed to make the finite

monkey theorem feasible.

This discovery turns one of popular science’s favorite

hypotheses on its head, and in the process, it touches on a topic

that is particularly salient today. Although monkeys are not

able to recreate Shakespeare’s work, the idea of probabilistic

text generation has evolved and is the core of present-day AI

language models. ChatGPT, Claude, and other chatbots can write

works like Hamlet at the click of a button. “Purely random text

generation quickly kind of falls off the rails,” said Woodcock. But

modern AI is not guided purely by chance, giving it the capacity

to succeed where its predecessor fails. These models utilize a far

more sophisticated version of randomness, incorporating past and

present data into the probabilistic “decisions” they make.

This leaves us with a philosophical question to ponder: are

the results of artificial intelligence—a duplicate of Shakespeare’s

complete works, for instance—closer to the purely chance-driven

typing of monkeys or the cognition of human minds? And does it

matter, if the final product is identical? Thus, the old question and

new findings of the (in)finite monkey theorem remain relevant,

even in today’s age. ■


Pharmacology

FEATURE

DRUGGING THE UNDRUGGABLE

PEPPRCLIP’S PRESCRIPTION FOR PEPTIDE DESIGN SUCCESSCESS

BY CRYSTAL LIU ART BY DAHLIA KORDIT

Drug discovery is challenging. Drug-discovering

pharmacologists often start by examining a protein that

causes a disease. For the best insights, it’s often necessary

for scientists to arduously solve the protein’s structure, using the

predictable diffractions of light in a pure crystal of the protein

to calculate the positions of atoms. The process is laborious as

tens of conditions must be fine-tuned to grow a good crystal

of the pure protein. When all goes right, by observing the new

structure and drawing on chemical expertise, pharmacologists

design compounds that interact with and fit in the binding

pocket of the target protein.

Unfortunately, it is difficult to learn about some proteins

using this approach, as some proteins lack ordered, consistent

structures. The calculations start to break down, and a

three-dimensional structure solution gets messy. Many

pharmacologists abandon targets at this point and look instead

at upstream or downstream reactions. “Most diseases are caused

by disordered proteins—not something that a pharma company

would easily go after because they are large, disordered, and

have no binding pockets,” said Pranam Chatterjee, assistant

professor of biomedical engineering and computer science at

Duke University.

The Chatterjee Lab aims to tackle this problem with artificial

intelligence. In a study published in Science Advances, they

introduced a new drug discovery pipeline, Peptide Prioritization

via Contrastive Language-Image Pretraining (PepPrCLIP).

PepPrCLIP can take the amino acid sequence of any target

protein and predict what peptides, or short proteins, effectively

bind the target. Pharmacologists can then modify the peptide so

that it activates our innate targeted protein degradation pathway

once bound to the disease-causing protein.

How can peptides be designed given only a simple protein

sequence, without the key structural information telling

what parts of the protein are exposed and likely to bind these

peptides? The group came up with an idea: randomly generating

naturalistic peptide sequences and predicting how they would

interact with the target protein.

Kalyan Palepu, co-first author of the publication, started

from Meta’s protein language model, Evolutionary Scale

Modeling 2 (ESM-2), which can represent each peptide

with a vector, a group of numbers. The twenty canonical

amino acids—the building blocks of peptides—are more

likely to assemble in certain combinations due to their

specific chemical properties. Therefore, ESM-2 vectors

of natural peptides form clusters in probabilistic space.

Palepu proposed that adding random noise to these

vectors would generate a class of new, reasonably

stable peptides. This forms the library of possible

peptides for drug screening.


Suhaas Bhat, the other co-first author, modified OpenAI’s

Contrastive Language-Image Pretraining (CLIP) model to predict

protein-peptide interactions. CLIP trains on image-caption sets,

aligning an image and caption when they match up and contrasting

them when they do not. Using the same rationale, Bhat trained

the PepPrCLIP model on documented interactions between short

peptides and target proteins, so it can predict the binding likelihood

of a novel peptide to a protein from their sequences.

Researchers then applied the model to several target

proteins, from structured to disordered, and tested the

predictions in cell cultures. Among the top hits, they

found multiple peptides that effectively bound to

the protein and targeted it for degradation. One

example is SS18-SSX1, a disordered protein

that results from a fusion of chromosomes

18 and X and drives a cancer of the

connective tissue around joints called

synovial sarcoma (SS). “A lot of the

oncoproteins that we care about when

trying to target cancer are unstructured

and wiggly, so classical techniques aren’t

going to work,” Bhat said. Nevertheless,

the peptide generated from PepPrCLIP’s

fourth hit reduced SS18-SSX1 levels in cells

by over forty percent. This means that the new

peptide effectively tags the SS18-SSX1 protein for degradation.

Instead of designing millions of options and testing them in

the lab, PepPrCLIP allows researchers to assess most peptides

computationally and then experiment with the top ten or

twenty picks.

Members of the Chatterjee Lab also developed a protein

language model that incorporated protein post-translational

modifications (PTMs) called PTM-Mamba. PTMs are changes

to a protein done after it is synthesized in the body, and they are

important in physiological and disease pathways. For example,

many enzymes are modified by the addition of a phosphate

group. By replacing ESM-2 with PTM-Mamba, PepPrCLIP can

design peptides that might selectively target the modified

enzyme but not the unmodified version.

PepPrCLIP is now open-source to academics,

and the lab maintains a user-friendly web-based

code environment for public access. Since its

publishing, Chatterjee estimates, twenty

labs have reported success with this

model, and many more are learning

to utilize it. They hope that artificial

intelligence will help uncover many

drugs that were once off-limits for

biochemical discovery. ■


FEATURE

Chemistry

PHOTO-

SENSITIVE GLUES

TRANSFORM

PROTEIN

CONTROL

Since the famous publication of Robert

Hooke’s Micrographia in 1665, the

cell has captured the imagination

and fascination of innumerable scientists.

Although we now know about organelles

and their functions thanks to techniques

like CRISPR-Cas9 and single-interference

RNA, there is a barrier created by the

highly dynamic nature of the inside of

the cell. In other words, the cell’s inner

workings are so transient that it is difficult

for existing approaches to capture the full

picture—often only the beginning and the

end states of

ART BY DAHLIA KORDIT

BY LYNN DAI AND ESTELLA WITTSTRUCK

experiments are ascertained, not the inbetween.

The recent field of optogenetics is

one solution to this problem.

Optogenetics is a biological technique

where researchers shine light on cells to

activate and control their processes with

extraordinary precision. The speed and

reversibility of optogenetics allow it to

revolutionize the ways cell activity can be

switched on and off. Living systems, such

as cells, can adapt to short-term “genetic

perturbations,” alteration that involve

modifying genes to study their function,

such as with CRISPR-Cas9. By using

light to induce a change in gene function

faster than genetic perturbation, the living

system is given less time to adapt and can

give researchers a clearer view of actual

cellular processes. In particular, chemooptogenetics,

which combines genetic

engineering with synthetic chemistry, has

shown great promise for capturing rare

insights into otherwise hidden processes.

In Sweden at Umeå University, a team of

researchers led by Yaowen Wu is pioneering

a chemo-optogenetic technique that allows

them to control cell activity with light and

observe intracellular interactions working

quickly in real time. In this technique,

a so-called “molecular glue” utilizes light

to not only allow cells and substrates—the

molecules they act on—to bind together,

activate, and control their processes at a

highly precise level, but also to allow them

to do so reversibly.

Much like how we have photoreceptors

in our eyes, cells contain proteins called

opsins that detect light and function

as the “on” button for many necessary

internal processes. In the lab, these opsins

are repurposed to produce and study

new cellular interactions. However, these

natural opsins come with their own set

of challenges. The function of an opsin

relies on the specific structure within its

arrangement of the chromophore, the

key light-detecting compound within the

opsin. In turn, the opsins remain stable and

difficult to change: a double-edged sword

when it comes to experimenting with them.

“If you want to do more engineering, like

modifying or improving the [optogenetic]

system, it’s challenging,” Wu said. “If you

change one structure in the chromophores

or even the protein itself, then you might

lose this photoresponse, or you aren’t able

to control it.”

With synthetic chemistry, lightsensitive

molecules can be synthesized

and structurally changed, leading to


Chemistry

FEATURE

enhanced light response and control of cell

function. This eliminates the limitations of

regular optogenetics while also granting

an element of versatility and freedom to

modulate the system. Building off the

concepts behind chemo-optogenetics,

the Wu Lab developed photocleavable

molecular glues (photoMGs) to improve

the inner cell conditions that drive

protein reactions and functions. However,

these photoMGs only lasted one round

of light manipulation, making them

very short-lived and difficult to sustain

during experiments. In response to this

challenge, the more durable and versatile

modular photoswitchable chemically

induced dimerization (sCID) system was

born, thanks largely to the dedication

and innovation of Jun Zhang and Laura

Herzog, co-first-authors of the paper

published by the Wu Lab.

During key developmental phases of

the sCID system, Zhang said controlling

the light system was a big limitation and

thus a major focus of their research.

“In our earliest versions, we primarily

focused on blue light and found a couple

of drawbacks,” Herzog said. “Longer

exposure to blue light tends to be somewhat

cytotoxic and [involves] tissue penetration,

so other wavelengths would be required to

find different ways of delivering the light to

the affected tissues.”

One of the most substantial

breakthroughs with sCID is its ability to

perform multiple rounds of activation

and deactivation without degrading the

compound. “Whereas before we [had]

molecular glues that typically allowed a

single round of control […] here we can

switch the same compound back and

forth multiple rounds,” Herzog said. This

reversible capability is pivotal because

it permits repeated experiments using

the same cells and conditions, which

minimizes variability and maximizes

reliability in the data.

The research team achieved this through

innovative chemical design, particularly

by selecting the molecules azobenzene

and diazocine as photoswitch cores. They

can rapidly toggle between two states—

trans and cis—when exposed to different

wavelengths of light. Additionally, their

robust switching efficiency ensures precise

control over protein interactions.

Choosing the right linker was another

crucial aspect of the molecular glue’s

design. The linker bridges the photoswitch

core to the proteins being manipulated. If

the linker is too long, the proteins could

interact unintentionally, while if it’s too

short, the shape change induced by the

light-activated photoswitch would not

effectively control protein binding. “If

the linkers are incorrect, this small space

change will not affect the binding of the

two other proteins [the photoswitch

core and target protein],” Herzog said.

To overcome this, the team utilized

computer-aided rational design, known

as molecular dynamics simulation, and

experimented with multiple designs

before identifying the optimal linker

chemistry that consistently facilitated

protein binding in the trans state and

dissociation in the cis state.

The molecular glue system’s efficiency

was validated through rigorous in vitro

and cellular testing. In vitro, Herzog and

Zhang measured the photoswitch’s halflife,

thermal relaxation, and resistance

to reduction, ensuring the compound’s

stability before introducing it into

living cells. They also conducted several

rounds of activation and deactivation

to confirm the compound’s durability.

In cells, two key assays were used: a split

nano luciferase complementation assay

to track dimerization (a scientific test

utilizing special light-producing enzymes

to see if two proteins can “dimerize,” or

join together, in a cell), and subcellular

recruitment assays to observe protein

localization changes (where special

markers are used to track the motion of

proteins inside cells in real-time).

This modular sCID system’s versatility is

a game-changer for chemo-optogenetics.

It offers an unprecedented level of control

over space and time, allowing scientists

to manipulate

cellular processes

with precision. “We

illuminated parts

of cell populations and

upregulated a protein function

in one part, but not in the other

part of the population,” Zhang said,

illustrating the method’s capability to

target specific cellular regions.

The Wu Lab is eager to explore new

photoswitchable compounds and further

optimize the system for different cellular

contexts. The planned applications in

zebrafish and mouse models will enable

a deeper understanding of the system’s

efficacy and safety in organisms, paving

the way for studies that translate the

research into everyday life. Additionally,

expanding the use of this technology to

address challenges faced by conventional

optogenetic systems—such as light

penetration limitations and off-target

effects—could meaningfully enhance

its utility in complex tissues and whole

organisms. By exploring bistable

molecules, which can switch between

two states, and alternative protein

designs, their findings offer innovative

solutions for precision medicine and

synthetic biology. Their pioneering

work demonstrates how the

marriage of synthetic chemistry and

genetic engineering can overcome

the limitations of conventional

methods, opening new avenues for

biological research. ■



FEATURE

Anthropology

ILLUMINATING

THE PAST

BY WYATT AIKEN

ART BY LUNA

AGUILAR

LASER-

STIMULATED

FLUORESCENCE

UNVEILS

INTRICATE

MUMMY

TATTOOS


I

already know what you’re

thinking. Laser fluorescence?

Intricate mummy tattoos? This

sounds like an integral plot point in

Indiana Jones and the Temple of Doom.

You aren’t wrong, but stay with me here.

It turns out that many mummies have

tattoos. Across numerous cultures, tattooing

is and has been an important mode of

expression. The oldest identified mummy

tattoo dates back to ancient Egypt, circa 3100

BCE. Analyzing these tattoos gives us unique

insight into the culture from which they

came. They were important status symbols,

art forms, and even therapeutic practices. The

problem, though, is that as skin degrades, so

does the visual quality of the tattoos within.

Because of this, anthropologists run into a

host of problems when studying tattoos. In

the past, they generally used infrared and

white light imaging to examine tattoos on

preserved human remains. While better

than the naked eye, even the best imaging

left something to be desired. The images were

still blurry and lacked the fine detail of a fresh

tattoo on living skin, so anthropological

insights were slightly obscured.

This is where lasers come in. Laserstimulated

fluorescence (LSF) is a

non-destructive technique, most

commonly used by biologists,

that employs a high-power laser

to excite molecules, causing

them to emit light through the

phenomenon of fluorescence. A camera

records the fluorescent light to reveal hidden

details that evade typical imaging techniques.

The advantages of this technique have paved

the way for advances in other fields too. In

paleontology, it has been used to reveal

hidden muscle patterns and feather imprints

that provide valuable information about the

soft matter that does not usually reveal itself

in the fossil record. In medical research, the

technique has been used to

differentiate diseased cells

from healthy tissue. In

forensic sciences, it shows

traces of fluids and

bruises hidden to

the naked eye.

The list goes on—

long enough it even

includes mummies.

Michael Pittman, a

dinosaur paleobiologist

at the Chinese University of Hong

Kong, had been using this technique in his


research for years. In 2022, Pittman, among

other researchers, expanded the reach of

LSF imaging to examine ancient Roman

artifacts. In the study, they used LSF

imaging to reveal faded paintings

and fingerprints on preserved

pottery. They went on to speculate in

writing that this technique would be useful

in other archaeological studies.

“A Polish colleague, Judyta Bąk, saw my

paper and asked me the question: ‘Could

this technique work on mummified human

remains?’” Pittman said. “We hypothesized

that because human skin glows under laser

light, and anything on it that isn’t human

skin glows less, more, or not at all,

that would give us

a nice contrast to

develop an image.”

Bąk noted that the core

components of ancient tattoo ink supported

the base of her hypothesis. If this ancient

tattoo ink is composed primarily of carbon,

as most ink is, they would expect it to glow

less than mummified human skin. This gap

in fluorescence should allow them to create a

beautiful, clear image of details hidden from

the human eye, one clearer than those seen

with previous techniques. With these ideas

in mind, the researchers flew to Peru to test

their hypothesis.

The team obtained access to mummified

people from the Archaeological Museum

of the José Faustino Sánchez Carrión

National University of Huacho, Peru. These

mummies were from the pre-Columbian

Chancay culture, which developed along

what is now the central coast of Peru

between approximately 900 and 1533

CE. Much of what scholars know

about the Chancay people comes

from rich remnants of their

art through textiles, pottery, and

woodwork. Their textiles draw the most

attention, as many of them are painted with

complex figures and geometric patterns.

Scholars also know that tattooing was

common in Chancay culture, but ancient

tattoo specimens have degraded over time.

Because of this, it is difficult to learn

about the artistic qualities of the

tattoos or to ascertain how the

process through which they

were made.

The researchers performed

the standard white-light

and infrared imaging, and then they used

LSF imaging on the tattoos and compared

Anthropology

FEATURE

the results. The 0.1 to 0.2-millimeter detail

revealed by the LSF imaging showed that

each ink dot was placed by hand–a technique

that requires great skill and precision. With

this technique, the ancient artists produced

magnificent, complex, geometric, and

zoomorphic patterns. The imaging also

revealed that the object used was likely finer

than modern tattoo needles, likely a cactus

needle or sharpened animal bone. With

needles so fine, little pressure was needed to

apply the art to the skin.

This fine level of

detail revealed

by the LSF

imaging could

be crucial for

anthropologists looking to decipher

ancient tattoos and the methods used to

create them. In this instance, the detail and

complexity uncovered by Pittman and his

team seem to exceed that of other Chancay

cultural artifacts, including their pottery,

textiles, and rock art. This confirms

the centrality of tattoos in Chancay art,

although further research is needed to

place these empirical observations in a

social and historical context. Interestingly,

not all tattooed individuals showed signs

of the fine tattooing technique, possibly

indicating divisions in tattooing practices

among the population. Whatever the

case, the success of this team’s efforts

suggests that this technique could be

successfully applied to mummies

from other historical settings.

“In these Peruvian mummies,

because it’s on a coastal location

that’s very dry, even though it’s about

a thousand years old, it is still very wellpreserved,”

Pittman said. “Even if we found

a mummy that was ten thousand years old

that was beautifully preserved and dried up,

there's no reason to say that LSF wouldn't

work then.”

LSF imaging does have its limitations.

Even though it can uncover details past

what is visible, degraded tissue from

poorly preserved individuals is

less likely to present the same

image quality. Nonetheless,

Pittman and his team

are hopeful that the

technique will have

broad applications and

allow anthropologists to uncover even more

about ancient groups of people and their

cultures worldwide. ■


FEATURE

Biochemistry

WRITTEN IN RNA

CHILDHOOD TRAUMA'S LASTING

SIGNATURE IN SPERM

BY RISHA CHAKRABORTY AND MEGAN KERNIS


Traumatic events are often said to

leave invisible scars on a person.

Adverse childhood experiences

(ACEs), defined as traumatic events that

occur during childhood with lasting

negative impacts, leave these scars on

nearly two-thirds of all adults according

to the CDC’s Adverse Childhood

Experiences Study.. Developmental

researchers study ACEs because they

tend to confer an enhanced likelihood of

substance abuse, personality disorders,

and anxiety disorders. Such trauma

tends to manifest itself across several

generations, inspiring two primary

foci of research. One side delves into

sociological factors, including how

generational trauma is transmitted

by passing down learned behaviors,

disrupts healthy attachment patterns,

and inherits legacies of trauma within

socioeconomic groups. The other

side hones in on biological factors,

specifically exploring how ACEs

change gene expression in lasting ways

from parent to child.

Jetro Tuulari, principal investigator

of the FinnBrain Neuroimaging

Lab at the University of Turku in

Finland, is interested in the latter

avenue of exploration. He and his

team published a study in Molecular

Psychiatry investigating the impacts

of one type of ACE called childhood

maltreatment exposure (CME) on longterm

transmissible genetic expression,

or germline changes.

One key mechanism of transmission

involves modifications to DNA. The

epigenome consists of the collection of

these “epigenetic” DNA modifications,

which effectively control which genes are

expressed in humans. One such modification

is DNA methylation, where a small chemical

group called a methyl group attaches to the

building blocks of DNA. Depending on

the location, DNA methylation can have

variable impacts on the way the methylated

gene is read, increasing or decreasing the

gene’s expression.

Another mechanism that changes

how DNA is read uses a class of RNA

sequences called small non-coding RNAs

(sncRNAs). RNA is synthesized from

DNA and serves a variety of biological

functions. SncRNA is a catch-all term for

a group of regulatory RNAs transcribed

by our genetic code. These singlestranded

molecules contain codes that

alter DNA expression or the function

of other coding complexes in our cells.

One class of sncRNA is microRNAs

(miRNAs), which are involved in gene

regulation. Though every cell in the

body contains the entire genome,

miRNAs can change the way different

parts of the body express the genetic

information encoded within; this is

what differentiates cell types. Genes that

express eye color are transcribed in the

eyes but not in the brain. Likewise, genes

that are expressed exclusively in brain

cells are not transcribed in the eyes. To

do this, miRNAs make different parts of

the DNA difficult to access, inhibiting

their function and preventing them from

being processed into RNA and protein.

Modifying the genes encoding sncRNAs

changes the cellular profile of these

regulatory molecules.

Germline changes have previously

been shown to link parental cigarette

smoking, stress, and exposure to

environmental toxins to physiological

changes in the offspring. However,

there are no prior hypotheses involving

the strength or direction of association

between CME and sperm DNA

methylation and sncRNA profiles.

Hence, Tuulari’s goal was to explore

these novel associations.

From 2011 to 2015, data was collected

on the fathers of seventy-five families

who were evaluated eight months before

and nine years after their child’s birth. In

2024, the study remeasured the parents’

CME using an improved analysis: the

Trauma and Distress Scale (TADS)

questionnaire. This exam reviews the

amount of emotional neglect, emotional

abuse, physical neglect, physical abuse,

and sexual abuse that the parents were

exposed to by the time they were eighteen

years of age. A higher TAD score indicates

greater exposure at an early age. Their

sperm samples were also evaluated for

biomarkers of epigenetic change, including

changes in DNA methylation patterns and

expression of sncRNA sequences.

The sncRNA of sperm samples from

fathers with low versus high TADs

scores were sequenced using sncRNA-

Seq processing and compared, and

DNA methylation was analyzed using

Reduced Representation Bisulfite

Sequencing (RRBS). Both methods allow

for analyses across an entire genome,

or the set of genes in an organism, by

looking at the DNA’s building blocks.

The expression of sncRNA and DNA


Biochemistry

FEATURE

IDENTIFYING BIOLOGICAL MARKERS OF

TRAUMA OFFERS ANOTHER PERSPECTIVE

AND PROVIDES HOPE FOR A MEDICAL

SOLUTION TO PASSED-DOWN TRAUMA.

methylation can, in turn, change the

expression of the genome.

Tuulari and his collaborators found

differential expression of a particular

miRNA important for brain development

between the groups with different TAD

scores. This miRNA had lower expression

levels in the sperm samples of fathers

who experienced difficult childhoods.

Not only were they able to identify

this association in their study, but

they replicated the genetic inheritance

pattern caused by this miRNA in mice.

Replicable data is as good as gold in the

scientific community. Now, this miRNA

can be used as a biomarker in other

stress-related studies.

Tuulari suspects that there are also

other contributors at play. “I don’t

believe it’s [just] that one [miRNA], but

maybe something together with that in

humans,” Tuulari said. “We can use this

as an anchor molecule and look at what

happens around it.”

Tuulari also found significant decreases

in methylation in regions of three genes

in the high-TADS group, including

two genes that are necessary for brain

development. One of these regions was the

tail of the CREB-regulated Transcription

Coactivator 1 (CRTC1) gene, which,

among other roles, controls the formation

of the hippocampus, the region in the

brain responsible for capturing memory

and associations. This corroborates prior

work Tuulari’s group had performed

showing the correlation between CME

and differences in brain region structure

and size via magnetic resonance imaging

(MRI). Increased expression of CRTC1

has previously been implicated in moodrelated

disorders including depression.


Interestingly, decreased methylation of

this gene in the high-TADS group caused

increased CRTC1 expression, which

suggests germline epigenetic changes

in this gene may affect the likelihood

of parental-conferred mood disorders.

“[This work] is a very important stepping

stone for us, because this means we will

be able to base our future studies on

this,” Tuulari said.

Tuulari’s work has crucial implications

in the field of developmental epidemiology,

most importantly showing that early life

stress can cause distinct, stable epigenetic

signatures that can be passed down across

generations. His study identified novel

biomarkers of childhood CME, including

three methylated regions and a signature

sncRNA profile. His work has also shown

that human sncRNA profiles are similar to

that of rodent models, and this similarity

across species may suggest evolutionarily

significant signatures of stress. “There

must be something around this [miRNA]

molecule. We were able to replicate it

[in humans, which is] so rare,” Tuulari

said. Identifying individuals with such

epigenetic signatures might better

help target existing therapies for stress

management and trauma to individuals

who will most benefit from them.

Beyond simply identifying

biomarkers of CME, this work

opens the door to begin

imagining interventions

for intergenerational

adverse health

effects. After all,

CME is the single

most preventable

risk factor for

future mental

health in an individual’s life. Now, we

know that CME matters for the offspring

of these individuals as well. Sociological

researchers have long emphasized the

behavioral mechanisms by which parents

confer stressors to their children, often

placing blame on individuals’ actions

in perpetuating generational trauma.

Identifying biological markers of trauma

offers another perspective and provides

hope for a medical solution to passeddown

trauma.

Nonetheless, researchers must still be

conscious about the double-edged sword

of medicalizing mental health issues,

ensuring that identifying potential

molecular targets for intervention

doesn’t institutionalize such biological

endowments as out of a person’s control.

In fact, healthy lifestyle strategies, such

as exercise and a healthy diet, have been

shown to confer positive epigenetic

germline changes, highlighting how

a combination of controllable healthy

behavior and biological changes goes

against those resulting from CME.

“Maybe there could be a public health

policy recommendation to, let’s say,

exercise more before thinking about

getting children,” Tuulari said. This

perspective underscores a crucial shift:

rather than resigning to biological

determinism, we should empower

individuals with actionable steps—

emphasizing lifestyle choices as a firstline

defense in shaping not only their

own well-being but also the health of

future generations. ■


Profile

SHORT

ANGELIN T. MATHEW

THE JOURNEY OF BRIDGING MEDICINE AND RELIGION

Studying molecular biology and comparative theology,

2025 Rhodes Scholar Angelin T. Mathew ’25 is dedicated

to integrating medicine and spirituality in healthcare—

particularly in palliative care, which focuses on improving

quality of life for patients with serious illnesses. In a world often

defined by clear-cut career paths, Mathew’s journey is a powerful

testament to the unpredictability of life and interests.

At the age of sixteen, Mathew’s best friend, Sophia, was

diagnosed with terminal pancreatic cancer. As she supported her

friend through unimaginable pain, Mathew witnessed firsthand

how palliative care could ease suffering and provide comfort

beyond medical treatment. “Her palliative care became the most

important thing in her life,” Mathew said. “That’s when I first

heard about palliative care. It was the first time I truly understood

the power of faith in medicine, especially when a priest came to

visit her in the hospital and gave her strength in her final months.”

Sophia’s battle with cancer ignited in Mathew an interest in

humanizing healthcare. Angelin came to see that the best doctors

do not just cure—they listen, empathize, and contribute to a

holistic approach to healing that considers the patient’s emotional

and social well-being in addition to their physical health.

This realization became a catalyst, shifting her focus from

stem cell research to the humanities early on. “I was working in

a lab, but I felt I had to honor this new lesson I had learned from

Sophia,” Mathew said. “I transitioned into public health work and

started taking philosophy classes. I began analyzing data from

the CDC’s database, trying to understand the broader scope of


YC ’25

BY JOSEFINA DE LA RIVA


healthcare. It felt like the right move.” Mathew recalled attending

a lecture by Marci Shore, a historian of European intellectual

history, and feeling a complete change in her perspective on the

humanities. Philosophy, theology, and intellectual history could

eventually shape her vision for the future.

Mathew became a Global Health Scholar at Jackson School

of Global Affairs to study the connections between philosophy

and medicine, and she founded a startup that sells handmade lip

glosses to provide free lip gloss to pediatric cancer patients and

their caretakers—a small but meaningful philanthropic act. All

proceeds support girls with cancer.

Encouraged by her deepened interests, Mathew took a leap

of faith and applied for the Rhodes Scholarship, a prestigious

academic honor. Initially hesitant, she submitted her application

at the last moment. “It was a shot in the dark, but I submitted

it and left the rest to faith,” Mathew said. Her gamble paid off,

securing her a full scholarship to attend Oxford University this

fall to study theology and deepen her knowledge of palliative care.

Mathew plans to eventually attend medical school and

integrate these ideas into her work in healthcare. Her ultimate

goal is to raise awareness about palliative care and its vital role

in the American healthcare system. She believes that improving

the integration of palliative care into primary care starts by

having conversations with doctors, and encouraging them to

embrace this holistic approach.

Her journey serves as a reminder that life’s unexpected detours

can lead us to discover new passions and purpose. As Mathew

has learned, sometimes the most transformative experiences

come from honoring the lessons you learn and stepping outside

your comfort zones, following a new path that feels right in the

moment—no matter how uncertain it may seem. For Sophia. ■


SHORT

Profile

JOHN-PAUL MENEZ

COMMERCIALIZING SPACE

SOM ’07

The space industry, once dominated by government

agencies and aerospace giants, is undergoing a seismic

shift. With dramatic reductions in payload costs, influx

of private investment, and technological advancements, space

is becoming a flourishing marketplace for many entrepreneurs

and investors. According to John-Paul Menez SOM ’07, a

former naval intelligence officer who advises early-stage

commercial space companies, the space economy is estimated

to reach approximately one trillion dollars in value by 2030.

Investor interest in the space sector is soaring. In 2021, space

startups raised $15.4 billion in private financing, which is more

than double the amount invested in 2020 and ten times the

investment in 2014. Venture capital and private equity funds

are beginning to regard space as a promising, disruptive, fastgrowing

sector for investment.

Yet, many financial analysts lack a deep understanding of space

economics, creating a growing demand for specialized financial

services. Menez notes that while some space companies already

boast robust business models, the industry still faces hurdles in

financing, legal frameworks, and insurance before it can fully

mature into a stable market.

The commercialization of space extends far beyond satellites

and data services. Emerging technologies—such as nuclearpowered

propulsion, advanced mining systems for lunar rock

deposits, and next-generation mapping technologies like

synthetic aperture radar—promise to revolutionize both space

exploration and Earth observation.

Still, the promise of a new frontier for economic activity is

not without its obstacles, including one which could hinder

even the simplest of human activities in space. Orbital debris,

or space junk, threatens current and future missions beyond

Earth’s atmosphere by increasing the risk of collisions that

could damage spacecraft and satellites. A particularly grim

scenario involves a run-away chain reaction of collisions in

Earth’s orbit, resulting in an ever-growing debris field that

would further compound the problem. Menez describes one

idea for addressing this possible future: “Nuclear power is

extremely important because it could enable long-endurance

missions by autonomous spacecraft to clean up orbital debris

without refueling.”

Advancements in propulsion technology are equally critical.

Current chemical rockets and ion engines have limitations,

particularly for deep-space missions. Chemical rockets, while

powerful, require massive amounts of fuel, making long-duration

missions impractical without extensive refueling infrastructure.

Similarly, ion engines, though more efficient, generate low

thrust, which greatly extends travel time for missions beyond

our solar system. Continuous acceleration systems could enable


BY NEO CHEN

spacecraft to travel faster

and more efficiently,

reducing the time needed

for scientific probes to

reach distant planets or

manned missions to Mars.

“These systems offer much

more efficiency, with lower

thrust, but the ability to

accelerate continuously

for months,” Menez said.

One possible continuous

acceleration system involves

a mechanism at the front

of a spacecraft that collects

hydrogen from the sparse

interstellar medium for a

never-ending supply of

fuel that could be spent

through nuclear fusion.

IMAGE COURTESY OF JOHN-PAUL MENEZ

For entrepreneurs looking to enter the space industry, Menez

offers a simple yet powerful piece of advice: “Be true to yourself

as a space pioneer.” The space sector is not for the faint of

heart, as it requires the drive and willingness to take risks and

a passion for pushing the boundaries of what is possible. While

the commercial aspects, like securing funding, are critical, the

most successful space entrepreneurs are those driven by a desire

to make a lasting positive impact on humanity. There are easier

ways to make money than putting on thousands of tons of

explosives and igniting them. Innovation is crucial—in this

unique market, a conventional sense of entrepreneurship

and business strategy may lead a company to be a follower,

not a leader.

Menez also highlights the importance of collaboration.

Today’s space economy thrives on partnerships between

startups, established companies, and government agencies. For

those willing to embrace the challenges and opportunities of

this new frontier, the rewards are boundless.

The commercialization of space is sure to transform the future

of humanity beyond planet Earth. It may represent one of the most

exciting frontiers of the twenty-first century—a way in which

new ideas, technologies, and opportunities can flourish. Menez

expresses his excitement about the future of space exploration

and discovery. He also feels excitement as an entrepreneur:

“There’s not a better feeling an entrepreneur can feel than the

shaking of a successful rocket launch as their assets lift off on its

way to space,” he said. In this new era of space exploration, the

sky is no longer the limit—it’s just the beginning. ■


THINKING 101

HOW TO REASON BETTER TO LIVE BETTER

BY ANDREA ORTEGA

SCIENCE

I N

PHOTOGRAPHY BY RACHEL MAK

In Thinking 101: How to Reason Better to Live Better, Yale psychology

professor Woo-kyoung Ahn explores cognitive fallacies and biases that

shape and distort our decision-making. Ahn, who teaches one of Yale’s most

popular classes, “Thinking,” wrote the book in response to the overwhelming

demand and curiosity for its lessons on cognitive processes. She argues that

these thinking errors are not individual shortcomings but rather natural

byproducts of human biology. By framing these biases in the context of everyday

life, Thinking 101 offers guidance for her readers to take control of their minds

and decisions.

One of the most pervasive cognitive biases Ahn examines in the book

is confirmation bias, the tendency to seek information that confirms one’s

preexisting beliefs. This bias is more than just a misinterpretation—it can

actively shape behavior. For instance, Ahn presents the example of selfdiagnosing

social anxiety. If someone believes they are socially anxious, they

may selectively focus on moments of discomfort while discounting signs of

social competence. Over time, this self-reinforcing belief can lead to avoiding

social situations altogether, deepening the very anxiety that was the source of

fear. Since such cases of confirmation bias are so prevalent, we must remain

skeptical of our assumptions and consider alternative explanations, even when

they challenge our intuitions.

Another cognitive trap Ahn discusses is our tendency to be overly influenced

by vivid examples. People respond more strongly to specific emotionally

charged visuals than mere abstract ideas and definitions. Ahn discusses this

power in the context of donations, where people are more likely to donate

to charity when presented with a specific famine victim’s story rather than a

broad statistic regarding the food crisis. This phenomenon also takes shape in a

different way in many young people’s lives today. Adolescents scrolling through

Instagram, for instance, may be disproportionately affected by a carefully

curated, polished post, leading them to believe that others’ lives are far more

perfect than their own.

Recognizing cognitive biases is a necessary first step in addressing them, but

it is not enough on its own. We must continue to surveil our minds for flawed

assumptions and conclusions. “One must be prepared to be wrong,” Ahn writes.

Breaking out of familiar thinking patterns is not a passive process, as it requires

an uncomfortable consideration of alternatives. Ahn encourages her students

to choose small unconventional tasks as a way to practice stepping out of one’s

comfort zones. By cultivating awareness and embracing discomfort, individuals

can reclaim control over their reasoning and reshape the narratives that define

their lives. ■

Professor Ahn with her book, Thinking 101: How to Reason Better to

Live Better.


SHARED HUMANITY

"FIREARM INJURY, PUBLIC HEALTH, AND HOPE"

BY KAYLA SOKUNLE

What are the most pressing and controversial issues in the United States?

There are a lot of issues that come to mind with ease. But what issue

affects the country’s population most disproportionately? And what

has surged over the past two decades with minimal legislative intervention?

Did you think of gun violence?

The United States is a global force in economics, education, and

entrepreneurship—and yet, our firearm homicide rate is higher than the twentytwo

other most developed countries combined. For three years now, firearms

have been the number one cause of death among children and teens, surpassing

cancer and car crashes.

Health scholars increasingly recognize gun violence as a public health crisis,

advocating for strategies rooted in public health principles. This approach

involves defining and monitoring the problem, identifying risk and protective

factors, developing prevention strategies, and ensuring large-scale policy

implementation.

In Episode 8 of the Shared Humanity podcast, two passionate women sit

together and discuss the pressing firearm issue through a public health framework

and under a hopeful lens. This topic is deeply personal for host Nelba Marquez-

Greene, who lost her daughter in the Sandy Hook Elementary School shooting.

Drawing from personal experience and expertise in activism, she collaborates

with scholars and communities to address firearm violence. She is joined by

Megan Ranney, dean of the Yale School of Public Health and an emergency

physician who testified to Congress on gun violence as a public health issue.

Gun control has long been a contentious issue in the US. The Gun Control

Act of 1968 restricted convicted felons from purchasing guns, and mandated

gun sellers to keep customer records. However, legislative efforts have frequently

stalled, with resistance rooted in Second Amendment debates and cultural

attitudes toward gun ownership.

A public health approach can address the alarming rise in gun violence of recent

decades. “I partner for example with 4H, an incredible youth empowerment

THE

SPOTLIGHT

organization that helps proactively keep the youth safe,” Ranney said. By applying

public health principles at the community level, researchers and policymakers

can advance practical, data-driven solutions to curb firearm violence.

By identifying gun violence as a public health issue, evidence-based

interventions can be developed and scaled. In the podcast, Ranney highlights

early childhood education programs, targeted interventions for at-risk youth, and

environmental changes as powerful tools in reducing gun-related harm. These

strategies, grounded in rigorous research, are continuously refined to create

lasting, widespread impact. ■

IMAGE COURTESY OF LORIE SHAULL VIA FLICKR

An individual holds a poster for gun control at the 2021 National

Walkout Day at the Washington DC Capitol Building.



COUNTERPOINT

Rethinking Processed

Foods in the Obesity

DEBATE

By Isabel Matos

On February 13, 2025, the US Senate confirmed

Robert F. Kennedy Jr. as Secretary of Health and

Human Services in a 52–48 vote. Kennedy, one

of President Donald J. Trump’s earliest cabinet picks, was

a controversial choice, given his history of promoting

scientific misinformation. His role now puts him at the

helm of eighty thousand employees and over one hundred

programs, overseeing agencies like the CDC, NIH, and

FDA. Hours after his confirmation, Trump signed an

executive order establishing the Make America Healthy

Again Commission. With Kennedy as chair, he has

influence over federal health initiatives and allows him to

shape public health policies, regulatory frameworks, and

research priorities.

Through days of confirmation hearings, the Senate

questioned Kennedy about his views on various healthrelated

topics, including vaccines, HIV/AIDS, and ultraprocessed

foods. When it came to ultra-processed foods,

Kennedy did not mince his words. “Something is poisoning

the American people, and we know that the primary

culprits are our changing food supply—the switch to highly

chemical-intensive processed foods,” he said, responding to

Senator Roger Marshall of the Senate Finance Committee.

Kennedy linked processed foods to a slew of health issues

in the US, including autoimmune diseases, neurological

diseases, allergies, and obesity. While the connection

between processed foods and rising obesity rates in the US

may seem clear, Kennedy’s crusade against processed foods

steps into an ongoing debate among nutrition experts: Are

ultra-processed foods to blame for obesity?

As of now, the US government does not have a

formal definition that distinguishes processed and

unprocessed foods. Instead, agencies like the USDA make

recommendations against foods high in saturated fats and

added sugars, which tend to be more processed.

This issue becomes even more complex when considering

so-called “ultra-processed” foods, which are commercially

formulated products that often include artificial additives,

preservatives, refined fats, or refined sugars. These

ingredients have been linked to various health concerns,

including obesity, cardiovascular disease, and metabolic

disorders, raising further nutritional and public health

considerations. The difficulty is that nutrition experts still

IMAGE COURTESY OF VIRGINIA RETAIL VIA FLICKR

do not agree on what should be classified under the ultraprocessed

label.

Without a clear definition and consistent nutritional

standards within different categories, establishing a causal

relationship between processed foods and health outcomes

is difficult.

Compounding the issue, some foods widely considered

ultra-processed—such as yogurt and some cereals—are

associated with lower risks of cardiovascular disease and type

2 diabetes. Processed foods may also be more nutrient-dense

and come at a lower cost than alternatives. This paradox

highlights the challenge of categorizing all processed foods

as inherently unhealthy, as some may provide benefits that

are difficult to account for with rigid categorizations.

While Kennedy singled out processed foods as the most

important culprit behind the obesity epidemic, a 2024 report

from the CDC recognizes the complex roles of genetics,

stress, access to affordable food, and healthcare in driving

rates of obesity. Due to the lack of conclusive evidence, the 2025

Dietary Guidelines Advisory Committee, which is overseen

by the USDA and US Department of Health and Human

Services, declined to take a stance on ultra-processed foods.

Their October 2024 report serves as a precursor to the official

Dietary Guidelines for Americans, set to be released in late

2025—guidelines Kennedy may now attempt to influence.

Kennedy is not the only voice in the debate. The Guidelines

Advisory Committee has faced scrutiny for its financial ties

to food, pharmaceutical, and weight-loss companies, while

food and beverage industry lobbyists have spent millions of

dollars resisting restrictive guidelines.

If Kennedy moves forward with regulating processed

foods, the classification system must be carefully considered,

as it could affect the administration of the Supplemental

Nutrition Assistance Program (SNAP) also known as the

Food Stamp Program. Limits on food stamps based on a

hasty definition of processed foods could keep nutrientdense

foods out of the hands of already vulnerable

populations. A 2023 report from The Food Foundation

found that healthy foods are twice as expensive as unhealthy

foods. Without increased SNAP benefits, lower costs for

whole foods, and improved access to healthy groceries,

restrictions on ultra-processed foods could harm the very

populations they aim to help. ■


SCIENCE ON

TRIAL

AN ASSAULT ON SCIENCE

CONSEQUENCES OF PROJECT 2025

BY EDIS MESIC

In 2022, the Heritage Foundation launched Project 2025 in

anticipation of a second Trump presidency. Outlined in the

initiative’s policy guide, Mandate for Leadership: The Conservative

Promise, is a roadmap for reshaping federal agencies, with sweeping

changes that threaten to alter the scientific landscape for years to come.

The proposal directly challenges scientific consensus on gender identity,

climate change, and public health, framing these issues as ideological

rather than empirical.

A core focus of Project 2025 is combatting what its authors call “woke”

science. The document quotes Roger Severino, a key figure behind the

project, urging the next Secretary of Health and Human Services (HHS)

to dismantle transgender healthcare policies: “[HHS] must immediately

put an end to the department’s foray into woke transgender activism.”

While Project 2025 suggests a restrictive agenda on gender that frames

the idea of gender identity as an “ideology” rather than a scientific

reality, scientists have long agreed that sex and gender constitute

different yet equally valid aspects of identity. An article published in the

NIH’s National Library of Medicine stresses the importance of properly

distinguishing between sex and gender, defining sex “as a construct

based on genetics” and gender as “someone’s personal and deeply felt

internal sense of the self, which may or may not correspond with the

person’s physiology or designated sex at birth.” Project 2025’s rejection

of the lived realities of those who do not conform to conservative gender

expectations encourages a harmful new set of “biological realities” that

reduce gender identity to a symptom of “wokeness” and disregard the

longstanding opinions of scientists across the nation.

Beyond gender identity, the document

also targets gender diversity

in STEM, calling for the

NIH to end diversity quotas

for conference panelists

and for the CDC to stop

collecting gender identity data.

These policies contradict the

NIH’s stance, which stresses that

differentiating between sex and

gender is critical for addressing

health disparities.



Project 2025 also aims to reframe climate change as a political issue

instead of a scientific one by placing congressional regulations on the

EPA and abolishing the Office of Environmental Justice and External

Civil Rights. The proposed downsizing of the EPA favors economic

benefit in certain high-polluting sectors of the energy industry over

long-term environmental health, a common theme across Project 2025’s

policies that even extends to the repeal of spending bills that subsidize

renewable energy developers. Instead of focusing on sustainable

energy alternatives, Project 2025 proposes plans to increase fossil fuel

consumption by supporting the Willow pipeline project, an oil drilling

effort in Alaska that seeks to increase the number of drilling pads from

three to five. This operation will destroy natural habitats in the Arctic

National Wildlife Refuge, ignoring the science behind the importance

of climate-conscious energy resources.

The outlined politicization of climate change signifies a larger shift

of authority from scientists to policymakers. But policymakers are not

scientists, and this oppressive agenda plans to undo COVID-19 health

policies enacted under the Biden administration and disempower the

role of science in the response to future health crises. Project 2025 seeks

to end vaccine mandates for Medicaid- and Medicare–funded hospitals

and prohibit mask mandates in healthcare facilities, citing unnamed

randomized controlled trials that claim masks are ineffective. However,

organizations like the Mayo Clinic have consistently emphasized the

opposite: “Wearing a face mask slows how quickly the virus that causes

COVID-19 spreads.”

Perhaps most tellingly, the document asserts that “CDC guidance

must be prohibited from taking on a prescriptive character,” further

undermining the role of scientists in shaping public health policy.

This move suggests an effort not just to weaken scientific agencies

but to remove their role in governmental decision-making.

Project 2025 represents more than just a policy shift—it is a

systematic effort to erode the role of science in government. By

disregarding gender research, climate science, and public health

expertise, the initiative seeks to reshape federal agencies in ways

that could have lasting consequences for science, policy, and

society. If implemented, these proposals could fundamentally

alter how the US approaches scientific inquiry and evidencebased

policymaking for decades to come. ■


Interested in getting involved with

Yale Scientific

for writing, production, web,

business or outreach?

Learn more at

yalescientific.org/get-involved

Issue 98.1

Transform your PDFs into Flipbooks and boost your revenue!

Delete template?

Save as template ?