Biology Highlights 2022, Harvey Mudd College

B I OLOGY HIGHLIGHTS 2022

Update from the Department Chair Dear Alumni, Parents and Friends of HMC Biology, We’ve reached the end of the 2021–2022 academic year, and I’m happy to update you with some news from our department. This year was definitely more normal for us than the previous two. We enjoyed having students back on campus and being able to return to the more usual patterns of classroom teaching, research and so on. The dining hall even opened part way through the year, which added a lot to the sense of community on campus.

Probably the biggest joy for biology faculty has been having students in-person for research. During the school year and this summer, we have had normal-size research programs (dozens of students during the year and dozens in the summer).

Seniors were able to do laboratory and field-based projects for thesis, and faculty have also been traveling for research and conferences.

Graduating seniors have once again found interesting destinations for themselves ranging from graduate programs to positions in companies and labs.

I also have several faculty-related notes. Danae Schulz received tenure this year.

And Dan Stoebel was promoted to full professor. Congratulations to both. I’ll also note that Steve Adolph is about to rotate back into the department chair position (I’ll be stepping down and going on sabbatical).

We hope to see you on campus sometime soon!

Eliot C. Bush Chair, Department of Biology bush@hmc.edu

HARVEY MUDD COLLEGE | BIOLOGY HIGHLIGHTS 2022

Schulz Receives NSF Early Career Grant, Joins Multidisciplinary Effort to Detect and Counteract Emerging Pathogens The Faculty Early Career Development (CAREER) Program supports early career faculty who have the potential to serve as academic role models in research and education and to lead advances in the mission of their department. Danae Schulz is the latest HMC faculty member to receive the award.

She received the CAREER grant from the National Science Foundation for her research “Characterizing molecular mechanisms that drive life cycle transitions in the African trypanosome.” The nearly $630,000 award covering a five-year period enables Schulz to pursue research questions in the lab using state-of-the-art technology, including highthroughput sequencing.

“The project’s purpose is to understand how parasites adapt to different environments as they move between organisms,” Schulz says.

“The African trypanosome is an example of one such parasite that moves between the blood of infected animals and the tsetse fly. When a tsetse fly bites a human or a hooved animal, parasites are transferred to the bloodstream and cause a fatal disease called African trypanosomiasis or sleeping sickness.”

Last fall, Schulz joined a multidisciplinary group of early career researchers to address the global threat to human health from animalborne infectious diseases. The Mitigating Zoonotic Threats conference—sponsored by the Research Corporation for Science Advancement and the U.S. Department of Agriculture—was the first meeting of a three-year initiative that tasks researchers with augmenting their understanding of

the interactions between animals, people, pathogens and their environments. During the meeting—a Scialog (short for science + dialog)—researchers developed new ways of rapidly detecting emerging pathogens then developing and deploying new countermeasures.

Schulz was one of 54 multidisciplinary early career researchers selected by RCSA for the Scialog. Guided by a group of senior facilitators, participants discussed challenges and gaps in current knowledge, built community around visionary goals and formed teams to propose cutting-edge, collaborative research projects. Schulz, who recently earned tenure and promotion to associate professor, submitted ideas related to her research on the African trypanosome.

How Human Networks Can Be Made Ant-like Ant behavior has been a source of inspiration since at least the time of Aesop, and 2,500 years later, it appears these insects still have a certain kind of wisdom to impart—perhaps to engineers building subways.

“Each individual ant doesn’t know much about the world beyond her own antennae,” says Professor Matina Donaldson-Matasci, “but they can collectively do really tricky things and find good solutions very efficiently—so much so that computer scientists have developed a whole subfield studying tough problems that can be solved by ‘ant colony optimization.’”

In a paper published in the Proceedings of the Royal Society B, Donaldson-Matasci, Harvey Mudd alumna Hannah Larson ’20 and collaborators at George Washington University and at the universities of York and Exeter in England used laboratory and field observation of ant behavior plus computer modeling to explore how ants build complex transport networks. Larson, a mathematical and computational biology graduate, spent summer 2019 working on the project at the University of York.

Researchers have long known that ants leave trails of pheromones, chemicals that induce other ants to follow those trails. The ant colony optimization algorithm was inspired by ants that, simply by laying pheromone HARVEY MUDD COLLEGE | BIOLOGY HIGHLIGHTS 2022

unconditionally wherever they go, find the shortest paths between locations.

While some ants tend to build networks including only the shortest paths and without any extra links, many seem to add strategically placed long-distance trails to their network as well. The newly published paper suggests that these long-distance trails are there because these ants selectively leave more pheromone on trails that lead to better food sources even if those sources are farther away. Those longer trails raise the cost (the distance traveled) but result in more efficient travel and alternative routes in case something goes wrong, Donaldson-Matasci says.

“The ants sometimes use faraway but super-awesome food resources,” DonaldsonMatasci says. “The resulting network costs a little more to build, but it’s also more efficient at transport, and it still functions when damaged.”

So how could this be applied to subway systems or, as another example, internet routing networks? The researchers used computer modeling to simulate networks based on the hypotheses they made about the rules of the ants’ behavior, finding that the networks they created corresponded closely to the actual observed transport systems of the ants.

“Our goal was just to figure out simple

rules to make networks that look ant-like,” says Donaldson-Matasci, who had another paper published on tree ant networks. “But different ant species make different kinds of networks: some tend to make low-cost networks with few and short connections, while others make efficient and robust networks with more connections. We hope that by studying the networks of different types of ants, we will inspire computer scientists to come up with more flexible algorithms, so we can build networks that balance cost, efficiency and robustness in different ways.”

Red wood ant nests (the mounds) with lines drawn in to represent pathways between the nests and to trees, where these ants harvest food from colonies of aphids living in the trees. [Credit: Valentin Lecheval]

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Faculty Promotion Promotions and tenure appointments for faculty were approved by the board of trustees at its May 2022 meeting.

Upon discussion and the recommendation of the Academic Affairs Committee, the board unanimously approved Daniel Stoebel’s promotion to full professor.

A biology faculty member since 2010, Stoebel studies the genetics and evolution of bacteria, and his teaching interests span molecular and evolutionary genetics, from first-year to senior courses, in lab, seminar and lecture settings. He also enjoys teaching statistics and courses at the interface of biology and the humanities. In 2017, he was awarded a National Science Foundation grant to further his research on the molecular

biology and evolution of bacterial regulatory networks. The grant also allows him to improve students’ experience in the lab and increase opportunities for those traditionally underrepresented in the sciences. He continues to collaborate with the College’s Upward Bound program, which works with local high school students who aspire to be the first generation in their families to attend college.

Interdisciplinary Class Explores Genetics and Race Professors Dan Stoebel (biology) and Vivien Hamilton (history of science) observed a desire among their students to talk about ways that current scientific work intersects with society.

These conversations would usually occur at the end of a class, when the technical or historical focus of the lesson was over, and the remaining time was limited. To create more space for these conversations, Hamilton and Stoebel created and co-taught the course Genetics and Race. An article about their experience teaching the course was included in Isis, a journal of the History of Science Society published by the University of Chicago Press.

“I had a sense that we needed to be having more conversations about race at Mudd because systemic racism is a fundamental challenge for our society,” says Stoebel, who studies the genetics and evolution of bacteria.

“Science has played a role in the creation of that oppression, and scientists have a role to play in creating a more equitable society,” he says.

A study of the history of genetics allowed the professors and their students to explore the relationships between ideas of race and the

science behind those ideas. “So many claims to the biological reality of race have appealed to genetics,” says Hamilton. “We often tell a comforting story about the second half of the 20th century, arguing that the biological reality of race was firmly rejected after WWII, as scientists repudiated the horrors of eugenics and the Holocaust. But scientific racism hasn’t ever really gone away.”

While biology content was not the focus of the course, Hamilton and Stoebel did use some primary sources by biologists, and Stoebel facilitated a deeper exploration of technical aspects of scientific debates. This approach allowed the class to comprehensively address the College’s mission—to educate engineers, scientists, and mathematicians well versed in all of these areas and in the humanities and the social sciences so that they may assume leadership in their fields with a clear understanding of the impact of their work on society.

Stoebel says that collaborating with Hamilton and teaching the course and has helped him see the College’s mission statement

in a different light. “An understanding of the history of genetics and race—or the history of most any other science, I suspect—shows that science and society impact each other reciprocally and in sometimes surprising ways.”

Art and Biology Students in Professor of Media Studies Rachel Mayeri’s Art and Biology course (fall 2021) presented Undesirable Pets, an exhibition “inspired by or created for reptiles, fish, bugs and other un(?) charismatic flora and fauna” during November 2021. Celine Wang ’21 (chemistry/biology), Risa Purow-Ruderman ’22 (biology) and Lian Morales ’22 (mathematics/computational biology) were among the artists who showed their work.

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2021 Goldwater Scholar Mathematics and computational biology major Tonatiuh Gonzalez ’22

Watson Fellow Studies Healthcare Equity Abel Sapirstein ’21 (mathematics and

computational biology) was awarded a prestigious 2021 Thomas J. Watson Fellowship to study alternate perspectives in healthcare equity while traveling to Bhutan, Chile and Japan.

Fellows receive a $36,000 stipend for 12 months of travel and college loan assistance as needed.

“I will be shadowing community physicians and interviewing community members to gain insight into how different nations have generated novel solutions to healthcare inequity,” says Sapirstein, whose winning project is titled, “Past, Present and Future Alternatives in Health Equity.” He has strategically selected locations where he can observe healthcare systems, culture and politics to gain insight that may lead to solutions related to healthcare equity.

Sapirstein will visit Chile to study the impact its history of centralized and decentralized healthcare has had on the country. While he considers Chile’s current healthcare system to be fairly equitable, Sapirstein is interested in interacting with people who have lived through the shifts in healthcare structure and gaining insight about the positives and negatives of this system.

He also intends to study in Bhutan, which has integrated traditional medicine and Western medicine into its healthcare system. He selected Japan due to its changing demographics and what other countries may learn from its people.

Growing up in Baltimore, Maryland, Sapirstein witnessed inequality and systemic racism and how this plays a role in life expectancy, job opportunities and health in the U.S. It inspired him to study inequity in healthcare on a global scale.

“I believe access to healthcare is a prerequisite for a just society,” Sapirstein says. He says data-driven policy and resource allocation could unlock solutions to healthcare inequity, especially in countries where fewer financial resources are available. Sapirstein notes that major corporations, when financially driven, can deliver rapid solutions to consumers, though this tactic is not as common in the healthcare industry.

Sapirstein deferred his Watson Fellowship for one year to enter a PhD program at Georgia Tech, studying operations research.

was among the four Mudders who received a 2021 Barry Goldwater Scholarship, the most prestigious national award for undergraduate STEM researchers.

Gonzalez conducted research with Professor Eliot Bush, who studies microbial genome evolution.

“Our research is about reconstructing the evolutionary history of bacteria and identifying events that may have given bacteria environmental or antibacterial resistance or increased virulence,” says Gonzalez, who intends to pursue either an M.D. or PhD in computational biology and conduct research in disease genomics. His career interests include cancer research and practicing medicine.

In 2020, Gonzalez was named an HMC Outstanding Emerging Leader for demonstrating collaboration, integrity, respect and support.

The 409 2021 Goldwater Scholars were selected on the basis of academic merit from a field of 1,256 natural science, engineering and mathematics students nominated by 438 academic institutions. All four of the HMC students who were nominated received a scholarship, which covers the cost of tuition, fees, books, and room and board up to $7,500 per year.

Outstanding Mudder Award Lian Morales ’22, a mathematics and

computational biology major, received the Outstanding Mudder Award, which recognizes students who contribute to the community and demonstrate creativity, leadership, teamwork, ethics, inclusion, community engagement, wellness and communication in curricular and co-curricular endeavors.

HARVEY MUDD COLLEGE | BIOLOGY HIGHLIGHTS 2022

A nominator wrote, “[Lian] is set apart by her artistic talents and her passion for biology that helps people. Within STEM, she is passionate about disease and cancer biology, with a special emphasis on HIV/AIDs.” The nominator continued, saying that Morales has shown leadership via her initiative to create an exhibition for art concerning social justice and making a space for LGBTQ+, people of color and other minority communities.

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PIC Scholars The College’s Postdoctoral Program in Interdisciplinary Computation (PIC) is now in its third year.

Two of the scholars have been working with biology faculty members, incorporating computational skills within their courses.

Morgan Carr-Markell, who earned a PhD in

entomology at the University of Minnesota, says, “I’ve really enjoyed finding ways to answer interesting basic questions about honey bees while providing useful information to beekeepers, farmers, land owners and conservationists about what habitats are likely to attract honey bee foragers and support colony health,” she says. “So, I have always enjoyed teaching and public outreach, and my ideal future job has always been to teach and do research at a liberal arts college.”

Carr-Markel says she received encouragement from her PhD advisor at

the University of Minnesota to pursue her interests in teaching and training other future scientists. “One thing that I realized as I finished my dissertation was how much research in biology now relies on computational tools and also how important it is to train future scientists to use and develop those tools,” she recalls.

“I felt that I could be a much more effective researcher and teacher if I knew more—then I saw a Tweet about the PIC program and read that Matina Donaldson-Matasci was one of the research mentors,” she says. “I had already been in contact with her years ago because of her fascinating work using machine learning to identify pollen grains collected by bees, so it just seemed like a perfect opportunity to get support from great mentors and gain exactly the skills that I wanted.”

Joe Wirth joined the program in 2020 after earning his PhD in microbiology from the University of Georgia. He says he was drawn to the PIC program because of its emphasis on training for a classroom setting in academia. “I realized that it’s a rare opportunity to learn CS and

computation techniques from people who actually know how to teach them, so caught my attention and convinced me that I should apply.”

Wirth says he received valuable insights and encouragement from Zachary Dodds, the College’s Leonhard-Johnson-Rae Professor of Computer Science. “He first convinced me that basic computation is going to be a key part of how other subjects are put forth now when it comes to teaching and learning STEM,” Wirth explains. “Currently, everyone needs to have a basic understanding of simple math in order to comprehend the things in their field, and it seems clear to me that computation is going to be like that for teaching other disciplines.”

As someone who is planning for a career in academia, Wirth says the PIC program has delivered on its promise over the past year. “The CS education part of this program is awesome, but the even bigger picture is the fact that the College is funding me and not just the usual postdoc approach of supporting me through my professor’s grant, and I view this as a much more meaningful and effective way to teach and train someone like me who had very little in the way of a formal computer science background.”

Mudd Talks: Mudders on Jeopardy!

Julia Lee ’14 and Natt Supab ’08 participated

in a Mudd Talks series event, joining other Mudders with whom they share something unusual in common: they each appeared on the popular TV gameshow Jeopardy! “Mudders on Jeopardy!” featured Mudders describing their experiences on the show and playing a friendly round of trivia.

Lee (chemistry/biology) appeared on Jeopardy! season 33 in 2016. After graduation, Lee spent two years working in vaccine development, then returned to school at University of California, San Francisco for her PharmD. She is a pharmacy resident at

the University of Utah Health, where she is pursuing specialized training in hematology/ oncology pharmacy. Before appearing on Jeopardy! she was an active member of The Claremont Colleges Quiz Bowl team.

Natt Supab ’08 (biology) is a cancer research coordinator, Southern California native, rock climber, potter and out-of-practice divemaster. She is a dabbler in many other hobbies and a lover of baked goods, sharks and bad puns.

Julia Lee ’14

Watch the full video: youtu.be/q4YIo0kq5yM Natt Supab ’08

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Biology Talks BioMakerspace Series The HMC BioMakerspace is a student-run biology laboratory and an HMC-chartered club funded by the Shanahan Grant, ASHMC and the Office of Community Engagement. It is also the host of the Biomakerspace Talk series, which hosts experts discussing their research.

Professor Matina Donaldson-Matasci and postdoctoral research scholar Morgan Carr-Markell presented “Social Insect Behavior,” a discussion about their research on social insects, in particular, honey bees and turtle ants. DonaldsonMatasci and Carr-Markell discussed the way that these social insects coordinate group behaviors, such as foraging for food and selecting new nests. Both scholars work in the HMC Bee Lab, an interdisciplinary lab where research is conducted on social insect behavior using computational, mathematical and biological methods.

Stephen Adolph, the Stuart Mudd Professor of Biology, presented “Ecology of Lizards in Southern California,” describing the ecology of some local lizard species (and a few snakes). He shared some of the research projects he’s conducted with his students, including studies of locomotion, habitat use, thermal biology and the effects of climate on population dynamics and geographic distributions.

Professor Stephen Adolph researches the ecology of Southern California lizards.

Summer Seminar The College hosted weekly seminars throughout summer 2021 during which scholars discussed their specific research interests and the scholarship they have produced. Catherine McFadden, Vivian and D. Kenneth Baker Professor of Biology, delivered the talk, “Hidden in plain sight? The cryptic biodiversity of coral reefs.”

“Coral reefs are the world’s most diverse marine habitats, often referred to as ‘the rainforests of the sea,’” McFadden says. “But how many species live on coral reefs? In truth, we simply don’t know. It’s estimated that as many as 90% of the species inhabiting our oceans are still ‘unknown to science.’

Most of these are small organisms that are difficult to detect and collect, but many of the largest, most conspicuous animals on shallow-water coral reefs—including the corals themselves—also remain undescribed and unnamed. My research focuses on ‘the species problem’ in corals.”

McFadden discussed what a species is, how we distinguish species from one another, why it’s a difficult problem in corals and why it matters. “By using the latest technologies in DNA sequencing and microscopy to distinguish species, we’re learning that corals and many of the other organisms that live with and depend on them are far more unique than previously realized.”

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2020–2021 Biology Department Awards W.A. Brandenburger Biology Prize

Biology Writing Fellows

Awarded annually to a senior biology major for outstanding performance and promise in the field of biology.

The department annually appoints students who have demonstrated great prowess in the field of scientific writing.

Gabby Teodoro ’21

Macallan Penberthy ’21, Emily Petroni ’21

William K. Purves Biology Prize

Best Senior Thesis

Awarded to a junior biology major who combines scholarship with some kind of breadth (intellectual, cultural, athletic or service).

Awarded annually to a senior or seniors with an outstanding research project during their capstone.

Roya Amini-Naieni ’22, Tonatiuh Gonzalez ’22

Fiona Callahan ’21

2020–2021 Thesis Projects Fiona M. Callahan ’21: Evolutionary Patterns in the PEVK Region of Titin in Marine and Subterranean Mammals

Gabby Teodoro ’21: Molecular Immunology Advisor: Danae Schulz, assistant professor of biology

Advisor: Findley Finseth, assistant professor of biology, WM Keck Science Department Yuanzhou Chen ’21: Investigating Potential Regulatory Roles of DNA Glycosylase OGG1 in Yeast Under Oxidative Stress, and Making Contents of Research Articles More Accessible

Advisor: Karl Haushalter, professor of chemistry and biology

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Alumni News Philip Cheung ’96: After 20 years in the

pharmaceutical industry, I’ve branched out and started my own bioinformatics/scientific software consulting firm, Refactor BioSciences.

For the last three years, we have been working closely with leading biotechs and Big Pharma to provide custom software solutions from machine learning algorithms for generating new compounds to building target knowledge base tools for better target selection.

Peter Jarrell ’94: Kat and I have been in Portland, Oregon, about eight years with our boy enjoying the PNW. Coming up on 18 years with Genentech.

Sarah (Moskowitz) Sagi ’94: I have been coaching an elementary school math team for several years. Recently, I began teaching classes and webinars for Math Kangaroo USA, an organization that teaches students to love math. They offer math contests for students in grades 1–12.

Chris Alef ’96: After a brief stint in HIV research at Fred Hutchinson Cancer Research Center in Seattle, I transitioned to high tech in 2000. By 2001, I started at Amazon where I joined an eclectic group of people that built an online bookstore into the behemoth that it is today. I had a couple of short breaks along the way to try out other things but kept going back to Amazon. In March 2020, I started my current sabbatical just as the COVID-19 pandemic picked up. Outside of work I have been running our local public school district bond and levy campaigns for eight years, and I serve as a city planning commissioner. I live in the Seattle suburb of Snoqualmie with my wife and two kids.

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Jeff King ’97: Greetings from the Arabian Peninsula. For the past nine years, my wife, Renee SCR ’97, daughter and I have been living in the United Arab Emirates. I’ve been providing patient care as a family medicine doctor, and for the past three years have been teaching students at the College of Medicine and Health Sciences at the United Arab Emirates University. We have loved Emirati hospitality and being a part of building national capacity to take care of their own citizens.

We’re headed home to the U.S. this summer so that our daughter can attend college. See you soon!

Alexander Bobbs ’03: After spending many years in the cancer research field, I’m now a professor at Ivy Tech Community College. I live in Kokomo, Indiana (north of Indianapolis), with my wife, Kathryn, and 2-year-old daughter, Zelda. I deliver lectures on COVID-19 immunology, make indie RPGs and occasionally appear in off-off-off-way-off Broadway productions.

Terence Wong ’09: I completed a PhD in biological and biomedical sciences at Harvard University in 2017 and worked in clinical diagnostics using whole genome sequencing to diagnose rare disease for a few years. In 2021, I transitioned into life science consulting at ZS Associates, where I deliver innovative solutions to biomedical research, clinical development and medical affairs challenges for clients in the biotech and pharma industry. During the pandemic, I completed an MBA with a concentration in healthcare administration at National University. In addition, I teach a genetics course at University of California, San Diego Extension and I volunteer as a mentor for the Promises2Kids Guardian Scholars Program, where I provide support and encouragement for former foster youth as they pursue higher education.

Daniel Garcia ’10: Since graduating from Mudd, I’ve been working toward my career goal of contributing to the discovery and development of new medicines for patients in need. After getting my PhD from University of California, San Diego, in biomedical sciences in 2018, I began working as a postdoc in industry at Ionis Pharmaceuticals. In 2021, I moved on to Arcturus Therapeutics, a local biotech focused on lipid nanoparticle-based delivery of mRNA therapy. As a scientist in the Drug Discovery Group, my role is to identify new disease targets, conduct preclinical studies and support the progression of drug candidates into clinical trials in humans. I hope my work will one day lead to an FDA approval of a medication for patients of diseases with unmet medical needs.

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Alumni News Jozi McKiernan ’16: I am thrilled to be working as a data specialist for Union Station Homeless Services in Pasadena, California. In my free time (among my too many hobbies), I’ve enjoyed tormenting my remote trivia group with biology-themed rounds and playing Writing Center consultant for my friends’ grad school applications.

Philip Woods ’17: I’m working on a PhD in geobiology at Caltech. I’m in the Orphan Lab studying the evolution of anaerobic methaneconsuming archaea that live on the sea floor.

Hopefully, I’ll have a paper about it submitted soon. Outside of academics, I’ve been participating in several small choral groups.

Your News Have you changed jobs?

Retired? Celebrated a milestone?

In addition to updates you submit, we compile information from a variety of sources: campus event notices, newspaper and magazine articles, press releases and Google alerts.

Please submit updates to alumni@hmc.edu.

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