SRI: Just the Beginning

SRI: Just the Beginning


Aug 16, 2024
Above: In the lab, Lauren Wigod, the author and member of SRI's inaugural cohort.

The Science Research Initiative celebrates the graduation of its first cohort.

April showers bring May flowers (and this year in Utah, snow), but more than just plants bloom each spring at the University of Utah. All over campus, students blossom into graduates after years of growth. Among the graduating class this year are many of the first cohort of students of the Science Research Initiative (SRI), marking the four-year anniversary of the program.

The SRI was created to involve undergraduate students in research from their very first day on campus. Former College of Science dean Henry White had the vision for this program and in 2019 passed the torch to Dean Peter Trapa at a critical time when there was a lot of investment. The main goal of the SRI is to facilitate relationships between faculty researchers and students. “We have a lot of great faculty researchers at the U, and there wasn’t a good mechanism to connect students with them, so the program helps eliminate those barriers,” says SRI Director Josh Steffen. The program puts students and faculty in contact and makes expectations of the partnership clear.

NAVIGATING THE PANDEMIC

During its inaugural year, the SRI was still able to engage with students despite the COVID-19 pandemic. Credit: Mathew Crawley

During its inaugural year, the SRI was still able to engage with students despite the COVID-19 pandemic that disrupted the majority of campus activities. For some first- and second-year students, the initial SRI cohort was their only connection with the College of Science during an extremely difficult time. “In the SRI, I felt so cared for and supported both during the pandemic and after," says senior Anika D’Souza. "The program really helped me feel like I can do science.”

“I feel lucky that I started with the SRI because we were taught the methods, and then we were given the opportunity to ask novel questions,” says senior Parker Guzman. With the motto “learn by doing” in mind, budding scientists in the SRI jumpstart their first fall semester at the U with an introductory class designed to teach them about how science happens, help them establish a community within the college, and discover where their research interests lie. The following spring semester, students are planted in a research stream that best fits their interests and begin their scientific journeys.

Current research streams span many scientific disciplines from mathematics to organic chemistry and to climate science. A sampling of projects include “Spintronics and Quantum Sensing,” “Pollination Biology” and “The Geochemistry of Noble Gases.” These streams aren’t just limited to the College either. Students can participate in cancer biology research with the Huntsman Cancer Institute, conservation projects with the Hogle Zoo or Red Butte Garden, or ecological inquiries with the Salt Lake City Mosquito Abatement District.

At its core, the SRI is a program designed to engage students in research, but its impact stretches much further. Early data indicate that SRI students are more likely to stay engaged in the College, maintain a higher GPA, earn other scholarships, and pursue additional research opportunities. Junior Chelsea Bordon says the SRI was a pivotal part of her first year at the U. “Getting into STEM can be really hard, but the SRI helped me meet so many people with different backgrounds that I probably wouldn’t have met otherwise which made that process easier.”

SRI Post-doctoral researcher Rodolfo Probst with undergraduates in Costa Rica.

IMPACTFUL EMPIRICAL RESULTS

While the student experience is at the heart of the SRI, the program engages with and enhances the scientific community beyond the U. Research projects facilitated by the program produce tangible and impactful empirical results that are shared in publications and presented at conferences. Members of the SRI get the opportunity to interact with the broader scientific community at gatherings on the local and national level. SRI students and postdoctoral researchers have presented at a number of conferences including the Ecological Society of America, American Chemical Society, Joint Math Meeting, Wildlife Society Meeting, Math for All, and Southwestern Social Science Association.

In addition to generating empirical evidence, the SRI contributes to the scientific community by creating space for scientists early in their professional academic careers. Postdocs were introduced to the program as stream leaders two years in. Not only do they help the program provide access to more undergraduates, but the postdocs themselves learn as well. Very few positions exist for postdocs to develop their skills after graduate school. As stream leaders for the SRI, they get the opportunity to mentor larger groups of students and run their own research groups. Out of the five post-doc researchers in the first cohort, three have already landed professorships at other research universities.

The SRI is unique from other undergraduate research programs because the experimentation extends beyond the physical laboratory. The program itself is an exploratory space where students can discover their passions — whether that’s in science or elsewhere. As the students are performing experiments, they’re also testing out the experience of being a researcher. The program invites curiosity and innovation with no one criterion of what success looks like.

“Coming into college, I had no idea what I wanted to do. The SRI helped me realize my love for biology and gave me skills as a researcher that will help me succeed in grad school,” says senior Sydney Larsen. Like Larsen, the rest of the first cohort of students graduating this year have their sights set high. Many are continuing their scientific careers in graduate programs, some are headed to medical school, and others have found their path outside of the sciences (one is the author of the article you’re reading right now).

STAYING ROOTED IN SRI’s VALUES

SRI students "learn by doing" beginning their first year at the U.

Just four years ago, the SRI was seeded with 27 students spread over seven research streams. This upcoming academic year, the program is aiming for 400 participants and 65 streams. The goal is that every College student who wants to be involved in research has the opportunity and resources to do so. In addition, SRI leaders want to bring on more postdocs and build the scientific community by engaging with other programs on campus and community partners to create more research projects.

In the next four years, the SRI is projected to continue growing, but leaders of the program hope that they can stay rooted in their values as the numbers of students multiply. “We want to make sure we have the resources we need to still offer quality experiences and support students financially as we grow,” says Associate Director Heather Briggs. The SRI will inevitably continue to yield publications, send students to conferences, and spur new scientific inquiries, but the most valuable aspect of the program by far is the depth of connection it fosters between students and their peers and mentors.

When the SRI was first launched, no one knew exactly how it would help promote the reputation of the U as a Tier-1 research university. It turns out that students shape the SRI just as much as they themselves are shaped by the program. With the inclusion of many student voices and perspectives, novel questions are asked and innovative approaches are taken. Now, with the graduation of the Science Research Initiative’s first cohort, it’s clear what the program’s legacy will be: a robust community of researchers informed by student inquiry; a community that holistically supports and celebrates graduates wherever their ambitions may take them.

By Lauren Wigod

Lauren Wigod HBS’24 enters a PhD program in philosophy of science this fall at the University of California, Irvine. She is a proud member of the first SRI cohort.

This story is featured in Synthesis, the College of Science's annual magazine.
You can read more SRI stories here.

Urban ‘Cool Zones’

Urban 'Cool Zones'


August 14, 2024
Above: A poster created by Salt Lake County to promote cool zones. Credit: KSLNewsRadio

Daniel Mendoza brings science (and change) to the people.

Daniel Mendoza

A research associate professor in the Department of Atmospheric Sciences at the University of Utah, Daniel Mendoza is not your typical academic scientist. With an impressive list of publications, averaging a new paper each month, academic scholarship is only one of his accomplishments. Mendoza has become an environmental social justice advocate, leveraging his research to get the attention of politicians and legislatures. The intersection between what’s happening in the atmosphere and what’s happening on the ground in people’s lives is where Mendoza readily enters.

This summer, Salt Lake has fallen victim to heat waves that mirror those throughout the United States. According to the CDC, extreme heat kills around a thousand people in the U.S. each year, more than any other natural-occurring factor. Effects from the heat are easily felt, but more insidious are the effects from increased concentrations of air pollutants, namely ozone. 

Mendoza explains in an interview with @theU’s Lisa Potter that “ozone is dangerous because it basically causes a sunburn in your lungs that impacts respiratory and cardiovascular health.”

In a recent study, Mendoza and his team asked the question, “can cool zones protect individuals from heat and poor air quality?” “Cool zones” are public buildings that serve as environmental refuges for vulnerable people during periods of extreme heat. Places like recreation centers or libraries are good examples of cool zones; Mendoza chose the Millcreek Library as the location for his case study. 

Obviously cool zones protect individuals from heat with the use of air conditioning, but the study found that the Millcreek Library also reduced exposure to atmospheric ozone by around 80%. 

Given their demonstrated efficacy, Mendoza is now critical of the current scope of cool zones. “We should be thinking about how to make these centers more accessible, for example, keeping them open for longer hours to protect people during the hottest parts of the day.” Many heat refuges close around 2-3 p.m. and aren’t open on weekends.

What people believe

Daniel Mendoza in the 2021 documentary "AWAiRE" that explores the impacts of air quality along the Wasatch Front. Credit: AWAIRE.

Mendoza understands that data alone is not convincing enough to enact change outside of the scientific community. “About 50% of people in the U.S. believe in climate change, but 100% believe in lung cancer, which is why I wanted to pivot from more climate drivers and greenhouse gas emissions and products towards more health criteria,” he says. Furthermore, he continues, “...150% of people believe in the dollar. I mean that’s ultimately what drives policy, what drives a lot of decision making.” 

It was during his Pulmonary and Critical Care Medicine Fellowship program at the U when Mendoza learned more about how to tie in the social and basic sciences with the health sciences. He finished the program in 2020 after completing a capstone project looking at the impact of air pollution on school absences. 

On “orange” or “red” air quality index (AQI) days, students are often still sent outside for recess, resulting in many children experiencing respiratory symptoms and needing to be sent home. Missing school every so often because the air quality is poor doesn’t sound like a huge issue, but it adds up to impact the student as well as the school, its district and the city where they live, he explains.

“When you have repeat absenteeism, then the potential to graduate is much lower, the potential to go to college is much lower, then your tax base is lower,” says Mendoza. Increased school absences cost the city around half a million dollars a year in terms of reduced workforce, education costs and healthcare costs. 

The solution to this pervasive issue of children being sent home because of the deleterious effects of bad air was surprisingly simple: emergency asthma inhalers in every classroom, right next to the Epinephrine Auto-Injectors branded “EpiPens” Says Mendoza, “I worked with Representative Mark Wheatley,” chair for the Utah Asthma Task Force, “and we passed a law…. Utah became the 14 (or 15th) state that has emergency asthma inhalers in every single school.” 

Now on bad air days, instead of sending a student home, students can use the rescue inhaler and remain at school, placing less of an economic burden on the city and giving themselves more time to learn. It’s a health-issue solution based on atmospheric data that changes policy and in turn saves taxpayer dollars. 

Empowering the Community 

Mendoza soon discovered what others had already discovered or at least suspected, that certain populations in the city were more endangered than others. What distinguished those populations was lower-income brackets and racial and ethnic inequities. When he first moved to Salt Lake City, Mendoza was excited about the buzz around air quality. “I thought, this is great. My research is going to be welcomed by the community,” he recalls. Instead, he discovered that these events were forgetting a key part of the problem: the people who are most impacted. 

Mendoza started attending community-based informational gatherings about climate change and the environment. “All of these events are held east of State Street. They were all in English. No one looked like me. Then at the end of the talk, the conclusion was ‘buy electric vehicles and solar panels and we’ll save the world together.’ Well that doesn’t work for everyone.” 

Not only is there a disparity in the communities affected by poor air quality, there is an inequality in accessible solutions to the problem. “For most of them, air quality is not a top priority… they don’t have the luxury of learning like we do,” says Mendoza of those who are most likely to be impacted by bad air quality. 

The first step in empowering the community and addressing this imbalance was to bring science to them. Mendoza began organizing outreach events, this time on the west side of State Street, held in both Spanish and English. 

“We provide them with actionable solutions. For example, we partnered with Utah Clean Energy, and we did an LED exchange where people bought in their normal light bulbs,” he says. Another switch he facilitated was to low-flow showerheads. 

And yet another initiative included furnace filter exchange with 100 homes in Salt Lake County. When indoor air was tested for 43 different potential problematic elements, researchers found elevated levels of uranium, lanthanides, arsenic and lead, “all the nasties.” 

Those “nasties” come from a variety of sources. “If you’re close to a highway, for example, you [breathe in] more of aluminum, associated with brake wear,” says Mendoza of the indoor air quality study, the first study of its kind. “When was the last time you sat outside for eight hours? You spend 90% of your time indoors and 60% of your time in your home, roughly speaking.” 

“The people that we really are very concerned about are, for example, the delivery drivers, who are constantly in that traffic, road construction workers as well. Those people are breathing [in] literally every single car’s tailpipe.” 

‘Run back inside’

Inequities in who breathes bad air requires that one looks closely at why and how bad air gets ingested. “Those with more and better resources can think about these issues involving bad air and what used to be only seasonal atmospheric inversions along the Wasatch Front, and then “just run back inside and we’re fine. But very few studies have been done on these concentrated pollution sources, again in conjunction with what they may be exposed to ‘naturally.’” 

From the 2021 documentary "AWAiRE." Credit: AWAIRE.

Those studies are being done by Mendoza and others and then made actionable on-the- ground initiatives involving switching out devices that are less effective and cost more money in populations who are most threatened by breathing bad air. 

These simple switches in affordable fixtures, for example, have tangible and meaningful impacts that inspire other actions, other policy decisions leading to better health outcomes. 

“Participants in these gatherings  soon became community leaders to help others improve their situation,” says Mendoza, another favorable result to his work. And then there is the financial incentive, that tongue-in-cheek statistic that 150% of people do in fact “believe in the dollar.” 

“These community members, they have to earn income to survive,” he reminds us. “They see their electric bills go down, they see their heating bills go down, they see their water bills go down, and they realize ‘Oh,okay, so it works. Let me tell all my friends about it.’”

Costs of inaction

Policy-makers and the public in general often look at the costs of solutions to problems that require action but sometimes they forget about the costs of inaction

Regardless of whether the focus of a study is cool zones, compounding wildfire emissions, or, most recently a recent study on the eBus project, a main tool for fine scale carbon emissions measurements in urban environements, Mendoza approaches each new inquiry with the same goal: “I want to make sure that my science gets understood by the general public. I want to write in as plain English as possible, because ultimately, I want to enact change, I want my work to do change.” 

Mendoza challenges the stereotypical ideal of a mad scientist locked away in a lab and detached from reality. Instead, he is present on campus, in the community, and at the state capitol building using science to advocate for justice.

Daniel Mendoza holds joint positions as research associate professor in atmospheric sciences; adjunct associate professor in internal medicine; and adjunct associate professor in City & Metropolitan Planning at the University of Utah.

by Lauren Wigod 

Read more on the 2021 documentary "AWAiRE," featuring Daniel Mendoza in @TheU

 

Those with the biggest biases choose first

How our biases are reflected in how fast we make decisions


August 13, 2024

Quick decisions more likely flow from biases, while people who take longer make better decisions, according to study led by Utah mathematicians.

Quick decisions are more likely influenced by initial biases, resulting in faulty conclusions, while decisions that take time are more likely the result in better information, according to new research led by applied mathematicians at the University of Utah.

A team that included Sean Lawley, an associate professor of mathematics, and three former or current Utah graduate students used the power of numbers to test a decision-making model long used in psychology.

They developed a framework to study the decision-making processes in groups of people holding various levels of bias.

“In large populations, what we see is that slow deciders are making more accurate decisions,” said lead author Samantha Linn, a graduate student in mathematics. “One way to explain that is that they’re taking more time to accumulate more evidence, and they’re getting a complete picture of everything they could possibly understand about the decision before they make it.”

The findings were reported this week in the journal Physical Review E.

The researchers explored how initial biases of individuals, or “agents,” in a group affect the order and accuracy of their choices. The goal was to determine whether a decision was driven mainly by an agent’s predisposition as opposed to accumulated evidence.

They found, in short, the faster the decision was made, the less informed it was and more likely to be wrong.

“Their decisions align with their initial bias, regardless of the underlying truth. In contrast, agents who decide last make decisions as if they were initially unbiased, and hence make better choices,” the study states. “Our analysis shows how bias, information quality, and decision order interact in non-trivial ways to determine the reliability of decisions in a group.”

Read the full story by Brian Maffly in @TheU.

Humans of the U: Nathan Patchen

Humans of The U: Nathan Patchen


August 12, 2024

“Initially, I chose to attend the University of Utah because I heard they had an excellent biology program and many opportunities for pre-medical students. I understood that the U was a top research school, and I knew I wanted to pursue a career in the biological sciences.

In my first year, however, I had some great experiences with the university’s chemistry department and fell in love with chemistry. Since then, I have decided to double major in biochemistry and biology. My goal is to pursue an MD-PhD, so I can do both research and work with patients.

I am passionate about improving the quality of life for patients, allowing them to lead healthier and hopefully more fulfilling lives. I hope to do this by working in the field of genetics/genomics and using gene editing techniques to find new tools to combat diseases that are otherwise untreatable. Additionally, I am interested in understanding why and how we age and improving patient outcomes through this process.

These interests are reflected in the research I have been a part of on campus as an undergraduate. The prestigious research that happens at the U is one of the reasons I was drawn to the school. Though research can be frustrating, time-consuming, and tedious, I have found it to be the most enriching part of my education. The incredible opportunity to participate in the forefront of science has drastically expanded my capabilities not only as a scientist but as a person.

Recently in my lab, the principal investigator (PI) assigned me to learn how to synthesize a compound we use for our experiments in an effort to bring our costs down. It was a difficult process to optimize the protocol for our lab, but through extensive troubleshooting and consulting with other labs, I became an expert on the topic.

After months of running the process over and over again without success, my PI and I discovered the error was occurring in a step I was not in control of. We were so excited to have found the solution After correcting the problem, I was able to successfully produce the desired product. Better yet, the new method dropped the cost of our experiments from $60 per experiment to less than a cent. It is exciting that I could play such a key role in helping my lab achieve a research goal that opens realms of possibility. It feels great to be able to contribute to something larger than myself.

I have recently been recognized as a Goldwater scholar which is exciting because it is a testament to my commitment to pursue science and my desire to make an impact on the world through discovery. To me, receiving this award is a great honor, it tells me that someone believes in me, and is willing to invest in my development. It is my goal to live up to that expectation, whether it be through science, medicine, or some other field, my goal is to serve and improve the lives of others.

—Nathan Patchen, a junior in the Honors College studying biochemistry and biology and a 2024 Goldwater Scholarship recipient 

This story originally appeared in @TheU.

Fueling Utah’s Booming BioTech Sector

Fueling Utah's Booming Biotech Sector


Aug 15, 2024

Over the last few years, opening a newspaper and seeing Utah at the top of the national economic rankings has become commonplace. 

In teaching labs through the Science Research Initiative (SRI) students learn by doing, starting their first year in the College of Science.

There has been a steady stream of articles about billion-dollar valuations for Utah startups and consistently low unemployment. Amid these headlines, there is growing recognition among analysts and policymakers in Utah that the biotechnology and life science sectors are playing a significant role in that growth. A recent report from the Kem C. Gardner Policy Institute found that the industries created $8 billion in GDP in 2022, part of a total statewide economic impact of $21.6 billion. Job growth in the sector has been particularly impressive; Utah’s 5.7% annual job growth rate significantly outpaces the national average of 3.2%. Due to these steady increases, Utah now has the highest share of statewide employment among all states nationally except Massachusetts. These jobs are also high-paying positions. Wages in the sectors average $96,000, which is 48% higher than the $65,000 average in other industries.

The University of Utah and the College of Science play an important role in this booming expansion, helping supply a sizable portion of talented employees and researchers. According to National Center for Education Statistics graduation data, the U awards roughly 37% of life science-related bachelor’s degrees and 95% of graduate degrees given by schools in the Utah System of Higher Education. Graduates from the College account for nearly two-thirds of those undergraduate degrees and over one-third of the PhDs. As they build their careers, alumni have the opportunity to take principles they learn by working with award-winning faculty and then applying them in professional settings.

“Innovation in biotechnology is touching on every aspect of our lives, from climate change and agriculture to health and wellness,” says Fred Adler, professor of mathematics and current director of the School of Biological Sciences (SBS), the largest academic unit in the College. “As discovery and innovation accelerate, so do the links between basic science and applications. In the SBS, faculty are making transformative contributions to drought-resistance crops based on fundamental discoveries in genetics, testing of drug safety based on research of animal behavior, and to neuroscience through new ways of imaging cells at the finest resolution.”

EXCELLENCE IN EDUCATION

In the School of Biological Sciences, faculty are making transformative contributions to drought-resistance crops based on fundamental discoveries in genetics. Credit: Mathew Crawley

The pipeline from the classroom, and the lab, to a successful career is most fruitful when exceptional instructors and researchers provide mentorship and guidance for students. College faculty have been recognized with a range of teaching and research awards, spanning honors like the National Medal of Science (given to three faculty members from the College of Science over the years) and MacArthur Genius Grants (four recipients) to the Rosenblatt Prize, the U’s highest honor for teaching and research (11 recipients). The College has also had 15 members elected to the National Academy of Sciences, 10 of whom are still actively teaching and pursuing research. These individual honors underscore the quality of the researchers’ academic units and are reflected in their national rankings: the SBS graduate program is ranked #13 and the Department of Chemistry comes in at #18 among public universities nationwide by U.S. News & World Report.

Chemistry and biological sciences, which educate a significant number of students that join the biotech and life science sectors, are the top-ranked programs in their fields in Utah and hold top-ten rankings among both public and private schools in the West. The two units also received over $28.4 million in external research funding during fiscal year 2023. These resources provide unique opportunities for students to learn relevant science in hands-on settings and engage in transferable research skills. Considering this impressive track record, it makes sense that life science and biotechnology-related faculty continue to garner recognitions in their fields.

Take, for example, Distinguished Professor and Thatcher President Endowed Chair of Chemistry Cynthia Burrows who won the prestigious Linus Pauling Medal Award. The Burrows Lab hosts organic, biological, analytical and inorganic chemists interested in nucleic acid chemistry, DNA sequencing technology and DNA damage. The team focuses on chemical processes that result in the formation of mutations which could lead to diseases such as cancer. Studying site-specifically modified DNA and RNA strands and DNA-protein cross-linking, Burrows and her group are widely known for expanding studies on nanopore technology to detect DNA damage. Burrows’ research in altering nucleic acid composition can provide valuable information in genetic diseases as well as manipulating the function of DNA and RNA in cells.

The Caron Lab studies the mushroom body of the Drosophila (fruit fly) to better understand how brains are developed to learn.

Another U chemist, Aaron Puri, has also drawn national attention as one of five recipients of the Simons Early Career Investigator Award in Aquatic Microbial Ecology and Evolution. The award will provide $810,000 to the Puri Lab over the next three years and, according to Puri, “will enable our research group to work at the interface of biology and chemistry to decipher the molecular details of interactions in methane-oxidizing bacterial communities.” His research looks at the molecular details of interactions in these communities, aiming to solve big problems with microscopic solutions. “These communities provide a biotic sink for the potent greenhouse gas methane,” he continues, “and are a useful system for understanding how bacteria interact with each other and their environment while performing critical ecosystem functions.”

Nearby, in the Skaggs Biology Building, is the lab of Ofer Rog, who recently won an Early Career Medal from the Genetics Society of America. Rog was recognized for work visualizing meiotic exchange between “sisters,” exploring synaptonemal complex proteins and tracking single molecules. Building on this work, the Rog Lab published a study in the Proceedings of the National Academy of Sciences in December that outlined a groundbreaking way to study the synaptonemal complex. Rog explains of the complex, “You can think of it like a zipper. The axes of the chromosomes are like the two sides of your shirt. The synaptonemal complex (SC) is kind of like the teeth of the zippers that lock onto each other and can pull and align the two sides of the shirt correctly.” Rog’s team was the first to pinpoint the exact position where the SC interacts with itself to facilitate genetic exchanges. Looking forward, unlocking the SC’s role in meiosis may lead to a stronger understanding of fertility in humans.

Another esteemed faculty member in biology is Sophie Caron, a U Presidential Scholar, who uses the Drosophila mushroom body — a computational center in the fruit fly brain — as a model system to understand how brains are developed to learn. With work described as “stunning” and “breathtaking,” Caron has built an interdisciplinary research program by drawing on computational models, species-comparative studies and various anatomical and behavioral techniques to elucidate the structural, functional and evolutionary pressures that shape the mushroom body’s learning function. In addition to her research, Caron — who was also awarded an outstanding teaching and mentorship award last year— designed and teaches an extremely popular neurobiology class (BIOL 3240), a course taken by hundreds of students.

FROM THE CLASSROOM TO THE BOARDROOM

Graduates from the College of Science also play crucial roles in Utah’s burgeoning biotechnology community. Equipped with cutting-edge knowledge learned in classrooms and research labs throughout campus, these alumni are at the forefront of research and development, contributing to significant advancements in life science fields. Their expertise not only drives the success of numerous biotech companies but also attracts substantial investment to the state. By bridging academic excellence with industry needs, alumni ensure a steady pipeline of talent that sustains the growth and dynamism of Utah’s biotechnology sector.

Tom Robbins and Amy Davis of bioMérieux.

There are many examples of these types of professional outcomes. Randy Rasmussen (PhD’98 biology) and Kirk Ririe (BS’05 chemistry) were two of three co-founders of BioFire Diagnostics. The company pioneered instruments that shortened DNA analysis techniques from hours to minutes. Using this technology, they created molecular diagnostics that now simultaneously test for multiple infectious agents, allowing healthcare professionals to get quick and accurate results from onsite instruments. In 2013 BioFire was purchased by bioMérieux, a French biotech firm, for over $450 million. The company is now one of Utah’s largest life sciences employers, with over 3,400 employees throughout its six sites. While Rasmussen and Ririe have since moved on to other projects, College of Science graduates like Amy Davis (PhD’03 biology), vice president of molecular biology, and Tom Robbins (PhD’04 mathematics), vice president of software development, continue to play significant roles in the company’s work.

Some College alumni have also found ways to share their experiences with a new generation of students. Ryan Watts (BS’00 biology) discovered a passion for research while an undergraduate. After he finished his degree, he earned a PhD from Stanford University and eventually co-founded the biotech startup Denali Therapeutics, focused on defeating neurodegeneration. The company went public in December 2017, breaking that year’s record for an initial market valuation of a biotech company. Today, Denali has over 400 employees and a market cap of over $3 billion, including a growing presence in Utah. Despite his busy schedule as CEO, Watts taught a winter semester course for five years at the U which tracked the biotechnology industry and introduced biology students to processes around drug discovery, business strategy, programming and portfolio decision-making.

Another alumnus, Berton Earnshaw (PhD’07 mathematics) used his academic experience to join the founding team of Red Brain Labs in 2012. When the machine learning-focused company was acquired by Savvysherpa in 2014, Earnshaw stayed on as a principal and senior scientist. Eventually, Earnshaw became director of data science research at Recursion Pharmaceuticals, a young clinical-stage biotech and drug discovery company based in Salt Lake City. In a succession of senior roles, Earnshaw has helped guide the company’s foundational machine learning and AI development, assisting in the company’s rapid growth to over 500 employees and an international expansion. Earnshaw started teaching courses at the U on machine learning and neural networks beginning in 2018. In 2024, he accepted a role as a senior fellow with the College of Science, in part to provide an industry perspective into the dynamic world of deep learning and AI.

LOOKING FORWARD

Berton Earnshaw, Recursion.

Unwilling to rest on its laurels, the College of Science is devoting significant resources to prepare graduates for what the Utah Department of Workforce Services deems accelerating growth in the rapidly changing fields of biotech and life sciences. The Department of Mathematics, School of Biological Sciences, and Kahlert School of Computing recently announced a new undergraduate degree in bioinformatics. New faculty hires throughout the College have included individuals with expertise in areas like data science, genomics, machine learning, gene editing and next-generation imaging techniques. More undergraduate students are participating in bioscience-related research than ever, either through the celebrated Science Research Initiative or direct placements in labs throughout campus. Together, these investments help ensure that future students will be well-prepared after they enter the workforce.

The notoriety of Utah’s burgeoning biotechnology and life sciences sectors continues to be indelibly linked to the College of Science in a feedback loop that benefits the economy, the community, and the University of Utah.

by Eliot Wilcox
Operating Manager, College of Science, University of Utah

This story is featured in Synthesis, the College of Science's annual magazine.

SRI Stories: Costa Rica Field Trip

SRI Stories: Finding the Right Path


July 29, 2024

“I absolutely loved this trip to Costa Rica. I learned things I could’ve only learned by experiencing them firsthand. We all got really close with one another. I think it’s an amazing opportunity. I’ve never seen anything like it. It’s probably one of the best highlights of [my experience at] University.”

This sentiment from Chloe Brackenbury is echoed by every student who shared her experience. Over the last two spring breaks, a handful of University of Utah students have had the opportunity to embark on a Science Research Initiative (SRI) trip across Costa Rica, affectionately referred to in Spanish as "Pura Vida" (or Pure Life). The trip was sponsored by the Wilkes Center for Climate Science and Policy.

Designed by SRI Postdoctoral Fellow Rodolfo Probst and with support from the Monteverde Institute (MVI), SRI students immersed themselves in a thriving environment for learning. There they interacted with local experts and community members and fostered new connections while tackling real-world climate issues and getting a first-hand sense of what long-term scientific endeavors look like.

Join us here for a virtual trip through the celebrated tropical clime of Costa Rica . . .

from the SRI student perspective!

On a research outing such as this, students could study the local wildlife up close while also assisting in rebuilding and enriching bird habitats. By catching and tracking different bird species (from tucanets to woodcreepers), students could confirm that birds were recolonizing areas recovered after deforestation. Ainsley Parkins, currently working under Rodolfo Probst’s SRI stream on identifying bird species using DNA tools, was overjoyed by the rich biodiversity surrounding her. In the accompanying video she delightedly shares just some of the fascinating lessons that would quite literally walk across the student’s path. No longer bound to the textbook to her, beautiful tropical birds could be freely observed in their natural habitats.

The many destinations of Costa Rica were also a wonderful source of learning. The MVI has been active in the country for decades, with a constant mission to integrate into the local culture. As such, students could see, via example, how scientific endeavors should actively strive to work with and assist local communities. That there are both benefits to and drawbacks of the growth of tourism, the importance of preserving the local culture as well as the local environment. An experience that made clear that conservation efforts are most effective when everyone is working together. I was lucky to speak with Jack Longino who views the institution as “One of the great success stories” of this kind. He sees a future where a constant cycle of undergraduate students could naturally slot into and assist these ongoing projects as part of their educational journey. To give them valuable firsthand experience in the field and show the importance of continually supporting scientific endeavors.

As exciting as these lessons can be, it's often the hard lessons that are the most valuable. Gabby Karakcheyeva (Photographer of the nature photos in the accompanying video!) describes how her experience helped tackle college burnout, clarify her future plans and discover that fieldwork was worth pursuing. Caden Collins realized the opposite: that while he enjoys fieldwork he'd “rather be the one the data is brought to.” A segment of the trip was led by bio-artist Rosemary Hall, whose focus on the soundscapes and exploration of natural spaces showcased the sheer variety of forms conservation efforts can take. And others still were caught off guard by the severe humidity and heat, or nocturnal creatures with no concept of personal space. One student in particular had a rude reality check as a scorpion dropped on their head. As amusingly put by Ainsley, “The outside doesn't like to stay outside!”

Regardless of the lesson learned, these experiences provide crucial context for students deciding their future careers. They’ve been devoting years of their lives to their studies, so to have avenues like this trip where they can clarify that the academic path they are walking is right for them is truly invaluable. And in this case, they got to do so while experiencing the beauty and culture of a new region and building strong friendships with their peers. The idea of going out into the world to make it a better place was an idea no longer. It was real, right in front of them, a beacon of hope that long-term conservation projects are thriving everywhere you look. With learning experiences like these and community partners eager to help, they know there’s a future where we join hands and walk down the path towards a better tomorrow.

Video and commentary by Michael Jacobsen

The students in this video story would like to thank post-doctoral researcher Rodolfo Probst, facilitator and director of the SRI field trip to Costa Rica. His expertise and generosity ensured students experienced an enjoyable, educational and safe experience in Central America. 

You can read more about Rodolfo’s research here.

Don’t Let This Blow You Away: Yellowstone’s Steam Threat

Don't Let This Blow You Away: Yellowstone's Steam Threat


July 29, 2024
Above: Yellowstone National Park officials survey damage near Biscuit Basin from a hydrothermal explosion that occurred Tuesday morning, July 23. Photo courtesy NPS/Jacob W. Frank

A hydrothermal explosion on July 23 at Yellowstone National Park sent visitors running for cover as steam shot into the air and rocks rained down on a popular viewing area.

The blast occurred about 10 a.m. local time near the Black Diamond Pool in Biscuit Basin, about two miles northwest of Old Faithful. No injuries were reported.

“Steam explosions like Tuesday’s incident have long been considered one of the most significant hazards posed to Yellowstone visitors,” says Tony Lowry, associate professor in Utah State University’s Department of Geosciences. “Biscuit Basin has had smaller, but still dangerous, events in the recent past.”

USU alum Jamie Farrell, research associate professor in the University of Utah’s Department of Geology and Geophysics and chief seismologist of the U.S. Geological Survey’s Yellowstone Volcano Observatory, says it was “very lucky” no one was hurt in today’s blast.

“Hydrothermal explosions happen quite frequently in the park, though they often occur in the uninhabited back country," says Farrell, who earned a bachelor’s degree in geology from Utah State in 2001. Farrell says the blasts aren’t volcanic eruptions and no magma is involved.“These incidents occur when very hot, mineral-laden water builds up and clogs the plumbing, so to speak; pressure builds up and is forced upward through pre-existing fractures to erupt at the surface,” he says.

Read the full article by Mary-Ann Muffoletto, Utah State University. 

Solving the Puzzle of Utah’s Summer Ozone

Solving the Puzzle of Utah's Summer Ozone


July 29, 2024
Above: A view of Salt Lake City shot from NOAA’s research aircraft. Credit: NOAA.

The Salt Lake Valley’s summertime ozone pollution is a complicated puzzle because so many different kinds of emissions contribute to the problem, which in turn is affected by the time of day or year, the weather and many other factors.

Without knowing which emissions are most culpable or understanding the role of the region’s topography, solutions to Utah’s ozone mess will remain elusive. In collaboration with University of Utah faculty and funding from the state, the National Oceanic and Atmospheric Administration (NOAA) is helping find answers.

A team of NOAA scientists is in Salt Lake City for the next few weeks gathering masses of air quality data that is expected to yield new insights that could help bring relief. Building on a long record of air quality data compiled by U scientists and the Utah Division of Air Quality (DAQ) over several years, this new snapshot data is hoped to illuminate what is driving elevated ozone levels along the Wasatch Front, according to Steven Brown, one of the NOAA research chemists leading the Utah Summer Ozone Study.

John Lin, professor of atmospheric sciences, on the roof of the Browning building where a phalanx of air quality monitoring instruments are stationed. Photo credit: Brian Maffly.

“Every city in the United States has an ozone problem, but every city is also different in terms of the sources that contribute to that ozone. And Salt Lake is no exception in that regard,” Brown said. “We’re certainly trying to understand the influence of wildfires. But then you’ve got this mix of industrial and urban sources in a valley with very unusual meteorology. We’re trying to characterize all those sources. What does that meteorology look like, and how do those things combine to produce the unique ozone problem that affects Salt Lake City?”

NOAA’s multi-platform study is being coordinated with the U’s Utah Atmospheric Trace Gas & Air Quality (UATAQ)) lab, headed by John Lin, a professor of atmospheric sciences. Also involved is Lin’s colleague Gannet Hallar, whose students are launching weather balloons and providing weather forecast briefings most days of the study to support NOAA’s regular overflights.While Utah has made strides reducing the severity of its particulate pollution-trapping winter inversions, summertime ozone has worsened to the point that Salt Lake City is out of attainment of the federal standard.

The primary ozone precursors are volatile organic compounds, or VOCs, which are emitted from countless sources—including oil refineries, gas stations, wildfire, paints, even personal care products, like deodorant—and nitrogen oxides, or NOx, a product of combustion.

Photons are needed to break up certain molecules, so the reactions typically will not happen without sunlight,” said John Lin, the associate director of the Wilkes Center for Climate Science & Policy. “It essentially chops up those chemical bonds. Then ozone reacts with other things and levels get lower at night.”

Read the full article by Brian Maffly in @TheU.

Satellite measurements of carbon emissions

Monitoring urban Carbon emissions at the global scale


July 30, 2024
Above: A map of the 77 cities at which the urban emissions monitoring framework was applied.

“We’re starting to see a globally consistent system to track [carbon] emission changes take shape,” says atmospheric scientist John Lin.

Faculty in the University of Utah's Department of Atmospheric Sciences, Lin is co-author of a paper in the journal Environmental Research Letters about a new satellite-based system for measuring CO2 emissions in support of global collective climate mitigation actions. As nations and cities continue to state their intentions to decarbonize for the purpose of becoming, in their activities, carbon-neutral, “we want to be able to see it happen from space.” 

Now we have a system to do so. 

That system is the culmination from standing on the shoulders of previous data scientists. It’s a story about how data is collected, interpreted and expanded through new technologies. It’s also about how this recursive process — now turbocharged with the advent of machine learning and AI — creates a space for potential application, innovation and policy that can change our world for the better, including mitigating carbon emissions that are warming our earth at a startling and deleterious rate.

But before any attempt can be made to save the planet, scientists have to secure a consistent measurement framework to better understand what’s happening as well as where it’s happening and how much.

The Backstory

John Lin

The backstory to this tale first begins in the Pacific Ocean. Tracking carbon emissions dates back decades to a single site in Hawai’i where, on a largely inactive volcano on the Big Island, instruments measured carbon dioxide in the atmosphere. At a high elevation, the site was very good at characterizing broad scale changes in carbon dioxide, globally, a “poster child for climate change because over time,” explains Lin who is also associate director of the Wilkes Center for Climate Science and Policy, “we know that from these Hawai’i  measurements, CO2 has this distinct cycle, seasonally, but then this upward trend due to all of us burning fossil fuels.”

Human-caused carbon emissions are not only leading to CO2 buildup everywhere in the atmosphere but the issue is widespread in public discourse. Whether it’s on the micro level of mitigating one’s personal “carbon footprint” by taking the bus, or on the meta level of international initiatives like the Kyoto Accords or the United Nations-brokered Paris Agreement, the effects of carbon emissions are on everyone’s mind. A cascade of cities and whole nations have established goals for mitigating emissions, but their estimates of carbon emissions have been relying on data that are inconsistent and sometimes missing altogether in parts of the world. 

That cities have singly established and even accelerated their carbon-neutral goals is a good thing, considering that over 70 percent of human-emitted CO2 into the atmosphere stems from cities around the globe.

Tracking progress toward city-scale emissions reduction targets is essential by providing “actionable information for policy makers,” the paper states. This while the authors acknowledge that earlier measurements and claims from municipal entities are based on “self-reported emissions inventories,” whose methodology and input data often differ from one another. These practices hamper “understanding of changes in both city-scale emissions and the global summation of urban emissions mitigation actions.”

Orbiting Carbon Observatory

This is where outer space in general comes into play and, in particular, the Orbiting Carbon Observatory (OCO). The NASA mission is designed to make space-based observations of carbon dioxide in Earth’s atmosphere to better understand the characteristics of climate change. After a literal “failure to launch” in 2009, NASA successfully placed a satellite (OCO2) in 2014 with equipment measuring CO2 emissions from space. Satellite-transmitted data promised to be an independent way to calculate, globally, emissions from cities. Not surprisingly, it has taken a while to learn how to use the data. In 2020 a graduate student in Lin’s research group, Dien Wu, developing early methods, did exactly that, looking comprehensively at a total of twenty cities around the world.

Based on essentially the same data set used by Lin and Wilmot in their current paper, but with fewer years, Wu was able to get estimates of the amounts of human emitted CO2 from OCO2 satellite transmissions. Separating out what carbon human activity is emitting to the atmosphere versus those from urban vegetation has now been determined through an expansion of the analyses over the additional years by Lin’s team of researchers, including a later graduate student by the name of Kai Wilmot, co-author of the current study.

In this round, four times as many urban areas as Wu studied and distributed over six continents, have now been assessed. This plant/human conundrum is further complicated by vegetation outside the city which has very different characteristics from vegetation inside the city. The difference creates patterns of CO2  that have to be taken out to distill the human component.

Strangely beautiful animations

Kai Wilmot

In short, Lin and company’s findings, published in Environmental Research Letters, represents a new capacity based on recent developments in modeling. And the animations of the assembled and interpreted satellite CO2 data delivered by the team are startling, even strangely beautiful. In one chart the left side displays latitude vs CO2. “This narrow swath,” explains Lin, indicates “each time … [the satellite] orbits. There's this narrow slice of data that becomes available.”

Using that data, he continues, “the NASA scientists can construct this nice animation of CO2 change in each latitude band over time.” Lin points to what he calls “ridges and valleys” on the the chart that represent the seasonal cycle, and he personifies the entire Earth as if it is “breathing in the carbon dioxide through photosynthesis during the summer growing season and then releasing it in the winter. They have these very sharp ridges — high CO2, low CO2, higher CO2 [the breaths] — but overall, the rug is going up, because we're emitting carbon dioxide into the atmosphere.”

Here, researchers are only looking at a small fraction of data points, the ones that intersect the targeted cities. They then do a more detailed look at whether they’re seeing a signal or not and whether they’re getting enough data.

“Personally,” says Wilmot, “I think the particularly neat aspect of this work is the capacity for global application. Leveraging satellite data and atmospheric modeling, we are able to gain some insight into urban emissions at cities around the world. We can see interactions between these emissions and socioeconomic factors, and we can identify large changes in emissions over time.”

 

The possibilities of creating more rigorous models, and more revealing data about how much cities emit carbon to the atmosphere are tantalizing. And so are the findings of the research. “This kind of information can be used by cities and the UN process,” Lin says. “But I’m pretty sure what they want is something more dynamic through time, how these emissions evolve. And also, probably more frequent updates.” As it was in this study, researchers had to aggregate multiple years of data to get enough points for each city. “So the challenge, I think, is to be able to track more dynamically these emissions over time.”

More to come

NASA’s next iteration of the Orbiting Carbon Observatory — OCO3 — has already been successfully docked on the International Space Station, although it was de-installed for a period of time recently to allow another instrument to carry out measurements. (It turns out that prime real estate on the crowded station is, well, at a premium.) But new data is forthcoming. 

Meantime, researchers have their work cut out for themselves in the data crunching/parsing/interpreting part of this saga. Scientists typically accrue data far faster than they are able to use and interpret them . . . and create cool animations for general consumption.

A log-log plot of the scaling relationship between direct emissions per capita and effective population density for all 77 cities.

“Naturally,” concludes Lin, “to bend the curve in terms of trying to reduce carbon emissions in cities is a primary focus. And there's a lot of excitement and social energy around reducing carbon emissions in cities, including here in Salt Lake. Many mayors have pledged carbon reduction plans, and the University of Utah has their own [pledge]. Lots of cities have very ambitious goals to reduce carbon.”

For Wilmot, this project will only add to the increased “social energy” around the issue of carbon emission mitigation. Satellite measuring will help identify a path toward monitoring urban emissions at the global scale in order to identify effective policy levers for emissions reductions. “Of course, realizing this monitoring ability is contingent on further development of the modeling, satellite observations, and a number of necessary input datasets,” he says. “So by no means am I saying that we are there already.” 

Clearly, this research has shown that the co-authors’ designed, multi-component satellite framework is capable of monitoring CO2 emissions across urban systems and identifying relevant driving factors. Their analysis not only pulled out data of the emissions from individual cities, but, because it is global, they could then do pattern analyses. In fact, the researchers, using an established relationship between emission-per-capita vs population density were able to plot from the data what happened, emissions-wise, during the COVID shutdown.

But, as co-author Kai Wilmot infers about work yet to be done, the ending to this story — from the Hawaiian Islands to outer space — is one of not-quite-yet “mission accomplished.”

“It’s more like mission half-accomplished,” John Lin concedes, “which is often the case in research.”

By David Pace

Read the complete paper in Environmental Research Letters.