SRI Stories: Lorelei Sole

SRI Stories

 

Hello, or as Lorelei Sole might say, Servus!

Sole served a volunteer church mission in Germany, Austria, and Switzerland before pursuing a biochemistry degree in the College of Science. Her path at the University of Utah has been shaped largely by her experience with the Science Research Initiative. 

Sole was personally motivated to join the SRI upon returning to the states and starting her degree at the U. “I’ve always been interested in health and science, and after losing my grandfather to cancer, I decided I wanted to learn more about the mechanisms of cancer and contribute to the field of oncology research.” says Sole. She found her home in Dr. Sheri Holmen’s oncology stream. 

After a semester as an SRI student, Sole was hired to work as a researcher in Holmen’s lab at the Huntsman Cancer Institute. “I’m studying the role of concurrent NF1, BRAF, and NRAS mutations in melanoma and how they drive tumorigenesis.” Sole says. “The NF1 gene was successfully cloned first by the University of Utah back in 1990. It’s really cool to now continue the research initially made possible by the University of Utah.” 

Her two years of research that began with the SRI stream (and a discovery at the U almost 4 decades ago) culminated in Sole being accepted to present at a handful of undergraduate research conferences. The most recent was Research on Capitol Hill where students are selected to showcase their posters to Utah State legislators. Sole is also slated to present at UCUR and NCUR later this semester. 

Sole’s experience with the SRI didn’t end after becoming a researcher. She has worked as a TA in Dr. Gennie Parkman’s SRI stream for the past year. Sole says that Parkman is one of her biggest role models. “I admire her for many reasons, one of which is how successful she is as a woman in STEM. She has one of the busiest schedules of anyone I know, yet still puts her family first and makes time for others.” 

Outside of the lab, Sole is a member of the Freeskier society and enjoys running, hiking, and yoga. After graduating from the U this spring, Sole aspires to attend medical school and continue her work in the field of oncology, in the spirit of her grandfather. 

 

By Lauren Wigod

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

SRI Stories: Irvane Nelson

SRI Stories

 

“At a young age, I witnessed the effects diabetes had on the lifestyle of my grandparents and extended family members,” says Irvane Nelson, a Sophomore at the U and a participant in the Science Research Initiative (SRI).

“As a result, I sought to gain a better understanding of the disease through research to aid in the efforts against diabetes.” 

Before getting involved in SRI, Irvane had the unique experience of conducting research in a lab starting in high school. Working in Dr. Owen Chan’s lab in the Division of Endocrinology, Metabolism, and Diabetes, Irvane was able to foster his interest in diabetes research, and names Dr. Chan his hero and biggest supporter in all his research and pre-med endeavors. 

Reflecting on this early exposure to diabetes research, Irvane notes, “Because of my background in sugar metabolism, I ended up working in a public health research lab to help develop ATSB sugar toxic baits.” His pivot to a different subject model as an SRI student was striking. Under the mentorship of Chris Bibbs, he is currently researching toxicology on mosquitoes, with a primary focus on creating less harmful insecticides. 

But his interest in diabetes continues in his SRI stream, reminding us all that there’s more than one path, ultimately, to find healthcare solutions through pure science. His current projects include studying how the brain responds to low blood sugar levels and investigating the toxicity of a substance called erythritol on Aedes Aegypti mosquitoes. Both projects involve aspects of sugar mechanisms, with the former analyzing the neural side of diabetes’ counter-regulation.

Irvane’s diverse research background, spanning academic research and public health issues, has helped set him up for success in his future plans. Looking ahead, Irvane has set ambitious goals for himself. Post-graduation, he plans to attend medical school and continue his efforts toward advancing diabetes treatment.

In the meantime, he is preparing to travel to Bangladesh this summer to shadow medical practices and gain insights into their treatments. Currently majoring in biology with a focus on cellular and molecular studies with a minor in chemistry, Irvane has found SRI to be a unique opportunity to learn and gain practical experience in his multiple fields of study. Outside of the lab, Irvane is an enthusiastic outdoor lover, and whether it's fly fishing in the picturesque Uintas or supervising swim lessons as a lifeguard, he makes sure to find time to enjoy all that Utah’s nature has to offer . . . while avoiding mosquito bites. 

 

By Julia St. Andre

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

M.A.D. about Skeeters

SRI Stories

 

Mosquitoes, those pesky little aviators we spend a lot of time swatting at, are pesky for two reasons: they carry diseases, like malaria–true–but they are also guilty of harassment.

Chris Bibbs, Great Salt Lake

Yes. Harassment, regardless of how you pronounce the word, will get you in trouble by your local mosquito abatement district (appropriately acronym-ed as “MAD”). It turns out that the pest in “pesky” can actually have a deleterious effect on lifestyle, kids walking to and from school, vacationers and can even, eventually, impact the local economy.

Whether it’s dodging dengue or out-maneuvering the little dogfighting Red Barons as you try to conduct business, Salt Lake Valley has one of the first MADs in the country, predating the Center for Disease Control and Prevention known for its recent flurry of COVID-19 mandates by more than twenty years.

And Salt Lake City MAD (SLCMAD), located north of the airport down on the floodplain by the Great Salt Lake, is also the catalyst for one of the Science Research Initiative’s (SRI’s) celebrated research streams that science students can participate in.

Ready to get bitten by the bug of composite biology research? You’ll be in good hands. Toxicologist and behavioralist Christopher Bibbs, SLCMAD’s laboratory director, and SRI stream leader with his colleague Nate Byers and others can take you the distance into the fascinating world of mosquitos as they interface with public health and environmental concerns.

“Although our job is to deal with the mosquitoes, we coexist with this entire system,” says Chris, meaning that scientists don't just survey only those of us with a blood-flush target on us. “We look at non-targets; we look at migratory bird pathways; we look at invasives; we look at general composite biology.” To work in abatement doesn’t just mean you’re a mosquito murderer–fly swatter in hand or the wielder of broad-spectrum pesticides, which do not discriminate what they kill; you have to be concerned about the types of interventions you experiment with.

“If you introduce this into the system, does it cause harm?” Chris is quick to ask. “If we use a pesticide? Does it create a pollution build–up? If we use a trap, does this give a reasonable inference on what's going on in the area? We do all these types of exploratory projects, because again, the goal is to help track and control mosquitoes. So, any discipline that we can use, whether that's biochemistry, bioinformatics, spatial modeling, whatever — engineering — it's a tool for us.”

Under the direction of molecular biologist Nate who sets up the traps — 60 at a time — team members do viral surveillance looking for viruses in field-caught mosquitoes. This is followed by collating and analyzing data. Research at SLCMAD presents a field as well as a lab component to the experience. And the work is not only ultimately a public service but the process sets up an exploratory site emblematic of the kind of pure science inquiries that undergraduates are asked (and encouraged) to do at the University of Utah.

Indubitably, sheer curiosity drives the research.

Past students during the spring semester (2023) stream were not just dodging bites by female mosquitoes (the ones who need a blood meal to produce eggs). No, these SRI students were asking questions and setting up experiments that helped vector the SLCMAD team in different but productive research directions, something SLCMAD is eternally grateful for.

“The stuff that we're doing isn't just some fundamentalisms about the fields,” says Chris, who has a lot to say about his work as SRI stream leader and preceptor with the U students and other interns. “It's stuff that can actually help people, maybe change a process, maybe improve the way you look at data. Maybe it's just a new method of doing something, designing equipment, new traps, or something like that. So, this is the kind of stuff that's actually very easy to get out there. Because it's tangible and useful to people. So that's something I can pretty reliably offer.”

Chris and his team are relatively regimented in their mentoring. “I try to figure out what you like,” says Chris, referring to his mentees. “It's not even what you've been trained in. What do you like, right now? What are you interested in? What do you want to do? And I try to take those interests and piece them together with stuff that we have already talked about that we would like to do.” This is followed by a review of the research literature and then, says Chris, “I kind of turn you loose.”

The result has been gratifying. Students have come to him with ideas–sometimes that make him raise an eyebrow–but that ends up productive, like looking at how common synthetic sugar additives trigger forceful hypoglycemic reactions that are toxic to mosquitoes. Or, like the freshman student who kept bringing up the component of vision in the animal which is typically thought to be olfactory driven. “He was absolutely right,” says Chris, of the student whose findings from bio assays were eventually paired with research being done by biology professor Neil Vickers who is on the SLCMAD board.

“On top of that,” continues Chris, “for us as a district, you know, [this student’s work] pertained to a mosquito that actively harasses people all year long.” Now, the District is planning on using this information to attempt better surveillance on the species which, if left unchecked, can cause heart-worm disease in domestic animals like cats and dogs.

But wait. There’s more!

Both of these research questions led to experiments, data, conclusions and eventually a paper–more than one. (Not a bad thing to publish papers as an undergraduate.)

“I'm super proud of the SRI involvement with this, because I kind of went into this not knowing what to expect, but I feel like with their unique creativity, and how they look at stuff, they really contributed a lot to this whole equation. It's kind of funny [the process], but it's like now … you were on the money!”

There’s something infectious, no pun intended, about Chris and Nate’s animated descriptions of what might appear as an unlikely marriage of an entity whose main goal is public health with an auxiliary function of research with an SRI teaching lab at the U. Part of that elevated feeling is likely that, to do their mission-driven job, MAD deploys every aspect of biology, ecology, chemistry, physics, and “every nuance and subdiscipline” to get the job of mosquito abatement done.

It’s a model for targeted, real-work experience connected with academics and research, and — except for the mosquitoes — everyone, especially SRI students, seem to benefit.

By David Pace

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

From the Lab to Costa Rica

From the lab to Costa Rica

 

Despite being over three thousand miles away from her lab back in Salt Lake City, Sylvia Lee was still able to sequence the DNA of the species she is studying.

While doing field work in Costa Rica, Sylvia continued her research by using Oxford Nanopore’s MinION, a portable technology that allows for DNA and RNA sequencing wherever you are.

Sylvia works in an SRI research stream that focuses on using Next Generation Sequencing (NGS) technologies to barcode and sequence DNA. This allows her lab to uncover new species and their phylogenetics. NGS allows in-house sequencing within the lab, rather than having to send it off to a company or lab. Or with the portable MinIOn, on a Costa Rican beach.

Sylvia’s main project is focused on ant-plant symbioses. She works to identify a third party within that symbiosis which is a crucial piece of the mutualistic interactions between ants and plants. The ants can’t get certain nutrients from their host plant, so the third party, mealybugs, are essential for this mutualistic relationship. She’s identifying the species of mealybugs involved, and after that, will look more closely at the nitrogen-fixing microbiome surrounding this entire process.

Sylvia is planning to go to graduate school, pursuing research in the biotech field. She’s a Social Justice Advocate, connecting U housing residents to resources and creating safe communities where they feel like they belong. She’s also part of the U’s undergraduate chapter of SACNAS, designed to support Chicano, Hispanic and Native American STEM students. 

“My parents are my heroes,” she said. “I look up to them because I have seen how much they’ve gone through, raising two children in a foreign country, far away from what’s familiar and far from where they called home. They did all of this just to make sure their kids would have a good life and a good future.”

Sylvia was born in Cheongju, South Korea, but at a young age moved overseas with her family. She traveled many places, but spent a lot of time in Mexico, and came to the U as an international student. Sequencing DNA has not only proven “portable” for Sylvia Lee; when she graduates with BS in biology and minor in chemistry, they’ll be infinitely “portable” as well. 

By CJ Siebeneck

SRI Story: Gap-Year Buzz

Gap-Year Buzz

 

“I joined the beekeepers club my first semester of college,” says Claudia Wiese, a recent graduate from the U and an alum of the Science Research Initiative (SRI). She became very interested in bees — both honeybees and native bees. “So when an opportunity arose to do research on bees, I was very excited.”

Not as excited, perhaps, as bees get when they’re being looked at and managed by an eager student researcher. Little do they know, they are in good (and ambitious) hands. The Missoula, Montana native graduated with no fewer than three degrees: two BS honors degrees, one in biology and the other in Environmental and Sustainability Studies as well as a BA in Latin American Studies.

But wait. There’s more. She also graduated with Honors Ecology and Legacy Integrated Minor which offers students a guided pathway through Honors, one where they can dive into environmental and ecological thinking in an interdisciplinary manner.

Busy as a bee, it would appear.

SRI experience

No wonder today, Claudia is taking a gap-year break before she heads back to academia for a graduate degree. In the meantime, she spends “a lot of time outside and work[ing] as a ski instructor and river guide. It’s also a priority of mine to be active in local organizations that work on protecting public lands.”

Bzzzzz . . .

“Honeybees,” she reminds us, “are only about eight species of 20,000+ bee species in the world! In other words, the vast majority of bees on earth do not make honey.” This isn’t your average backyard beekeeper. In her research, she explains, “I sequence the DNA of pollen from honeybees to understand what plants they are visiting. Specifically, I am using this approach to understand the effect of a mite treatment that is commonly used. Do bees visit different flowers due to the treatment?,” she asks.

Her SRI experience in the program's Pollen Metagenomics research stream was a definite introduction and asset to her field of study. And gap-year or not, she regularly leaves Snowbird during the winter where she works as a ski instructor to continue working in her SRI stream “with the goal to finalize my research and mentor other students.”

“I am very thankful for the opportunities that SRI has provided me,” says Claudia Wiese, the recent graduate, poised to take on the next hive of scientific inquiry. “They have been an incredible launchpad to culture my passion for research and [to demonstrate how to balance it with my other interests.”

 

By David Pace

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

SRI Story: Little Things Matter

little things matter

 

Ali Bouck (they/them) has always found enjoyment in the little things in life. Really little things. A scientist from a young age, Ali has been fascinated by what made seemingly simple processes work on a molecular level. 

Ali naturally gravitated towards chemistry classes in high school. Upon the recommendation of an influential teacher, Ali became more inspired by a future in chemistry and completed a pharmacy technician certification program to gain real-world experience in the field. Working as a pharmacy tech proved valuable for Ali; however, they craved work that was more “behind the scenes” of pharmacological development. This epiphany led Ali to recognize that research was their long-term career goal.

But what does a research-based academic and career trajectory look like? For Ali, and many other students like them, those opportunities are mysterious or unknown. This is where the Science Research Initiative (SRI) comes in.

During their second year at the U, Ali came across the new SRI program in the College of Science. Its mission: to place first and second-year science students in discovery-based research, thereby providing the skills and experience to prepare them for academic and professional success.

Ali immediately applied, though didn’t expect to be admitted. “I worried it was an exclusive program that was difficult to get into,” Ali says. So when Director Josh Steffen contacted Ali several weeks later to personally welcome them to the Science Research Initiative, they were “shocked.” That small but personal connection made a big difference to Ali, and demonstrated to them the accessibility of the SRI. 

After taking a one-credit course on research methods, Ali joined an SRI research stream, a specific area of study with a cohort of students, led by a faculty member. More specifically for Ali, it was Ryan Stolley’s Underexplored Molecular Architectures stream, which explores the behavior of atoms, the principles of organic chemistry and chemical experimentation. This was a natural fit for Ali’s interests in the infinitesimal. The stream also exposed them to methods of analysis, project management and practical lab experience. But for Ali, it was much more than that.

“I learned how to read scientific papers and [developed] my leadership and science communications skills,” says Ali. These skills helped them ascend to other research opportunities, scholarships and recognitions, which culminated in graduation with a bachelor’s degree in chemistry, along with several emphases.

Now in their first year as a bioscience PhD student, Ali reflects on their SRI experience with gratitude. “I received individualized support that helped me with my goals and authentically supported my wellbeing,” says Ali. Additionally, the tangible skills and knowledge they gained, is allowing them to study the development of novel organic and biosynthetic products as a graduate student. “As I learned different techniques in the lab. I found a love for organic synthesis, but having worked as a pharmacy technician throughout my undergraduate career, I want to expand to work on molecules that have relevance in that field.” Ali is poised for a career in industry research after their graduation. 

Several years after their SRI experience, Ali still sees their mentors and colleagues around campus and in the Crocker Science Center. “Josh [Steffen] says ‘hi’ every time he sees me and asks how I am doing,” they say. Whether it be science on a smaller scale, or the personal connections formed during one’s formative years, the little things truly matter.

When asked if they’d do it again, Ali Bouck says, “SRI set me on my academic and career path. Joining the program was the best decision I ever made.”

 

By Bianca Lyon

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

SRI Story: Signaling (career) pathways

Signaling (career) pathways

 

When students first met post-doctoral stream leader Gennie “Gen” Parkman in the Science Research Initiative (SRI), they likely did not know the backstory to that auspicious moment.

Gennie "Gen" Parkman. Banner Photo above: Parkman with student in the lab. ©Brett Wilhelm. Strada Education Network.

Auspicious not only because by design the celebrated SRI places first-year students in real science research, but because they were in the lab with someone who knows what it means to persist against tough odds before finding yourself in your career “happy place.”

Now an assistant professor at Weber State University with her own lab, Gen journeyed from her home state of Missouri where she was in a pre-admit program with Saint Louis University School of Medicine to the University of Utah and not entirely sure if a physician’s life was in her future or if there was something else rising above the jagged skyline of the Wasatch Mountains.

That was when, due to severe injuries, she had to face down the human body in medical terms: her own body.

What started as a dicey, harrowing experience with Gen’s health turned out to be a portal for her to that something else. “I knew I loved the human body, but I was also interested in understanding the deeper cellular and molecular processes,” she says. At the U she started as a technician for Jeffrey Weiss’ lab in the Musculoskeletal Research Laboratories as well as for Mahesh Chandrasekharan at Huntsman Cancer Institute (HCI). In 2015 she was technician in Sheri Holmen’s lab where she “absolutely fell in love with cancer biology,” and soon embarked on a PhD program at the U’s HCI in oncological sciences.

Last spring (2023) she transitioned from a post-doctoral researcher in the Holmen lab to a post-doc in the SRI where she led her own research stream titled “Functional Validation of Potential Cancer Targets” filled with those lucky students who didn’t know yet that they were witnesses of (and participants in) an extraordinary encounter.

“For many, many years,” Gen recalls about her arduous journey back into health, “I didn’t know if I ever would be able to complete school and make an impact with my career. It was during that time that I knew I wanted to teach in some capacity and mentor students through the ups and downs of life to reach their dreams.”

Part of that mentoring in the SRI stream she conducted was research that is vividly relevant. “Utah,” she reminds us, “has the nation’s highest melanoma rate, and it is the third most common diagnosed cancer in our state (preceded only by prostate and breast cancer). It is so important to study this disease to improve the health of our community!” That she was able to include first-year undergraduate students at the bench in her lab proved not only transformative for her students but astounding to Gen. (More on that later.)

Utilizing in vitro models, Gen’s research is focused on understanding more about the genetic alterations associated with a heterogeneous disease like melanoma. Those alterations involve the BRAF gene which provides instructions for making a protein that helps transmit chemical signals from outside the cell to the cell's nucleus. (This protein is part of a signaling pathway known as the RAS/MAPK pathway, which controls several important cell functions.) In BRAF mutant melanoma, alterations can be downgraded or upgraded and effect proliferation, invasion, and migration of cancer cells.

In her new lab at Weber State this research to evaluate tumor initiation and progression in mouse models continues.

Fresh out of SRI, Gen Parkman now recalls fondly her time in the College of Science and has this to say to an eager set of budding scientists: “If you continue to push and work hard, there are opportunities everywhere to be sought, and I am beyond grateful for the opportunities that I have been granted, such as by mentors and in the Science Research Initiative with such a supportive and encouraging team, to make it to this point in my career.”

“My students continue to blow me away with their passion and perseverance.”

By David Pace

SRI Stories is a series by the College of Science, intended to share transformative experiences from students, alums, postdocs and faculty of the Science Research Initiative. To read more stories, visit the SRI Stories page.

Information Engines Pay the Piper

Physicists sometimes get a bad rap. Theoretical physicists even more so. Consider Sheldon Cooper in the TV sit-com The Big Bang Theory:


Sheldon
: I’m a physicist. I have a working knowledge of the entire universe and everything it contains.
Penny: Who’s Radiohead?
Sheldon: (after several seconds of twitching) I have a working knowledge of the important things in the universe.

Mikhael Semaan

But a working knowledge of anything is always informed and arguably improved — even transformed — by robust and analytical “thought experiments.” In fact, theoretical physics is key to advancing our understanding of the universe, from the cosmological to the particle scale, through mathematical models.

That is why Mikhael Semaan, Ph.D. and others like him spend their time in the abstract, standing on the figurative shoulders of past giants and figuring out what could happen . . . theoretically. That Semaan is also one of the celebrated postdoctoral researchers/mentors in the Science Research Initiative (SRI), is a coup for undergraduates at the University of Utah who “learn by doing” in a variety of labs and field sites.

“The SRI is awesome,” Semaan says. It’s “a dream job where I can continue advancing my own research while ‘bridging the gap’ in early undergraduate research experiences, giving them access to participation in the cutting edge alongside personalized mentoring.”

Want to learn how to bake something? Hire a baker. Better still, watch the baker bake (and maybe even lick the bowl when allowed). And now that Semaan’s second first-author paper — done with senior investigator Jim Crutchfield of UC Davis, his former PhD advisor — has just “dropped,” students get to witness in real time how things get done, incrementally adding to the trove of scientific knowledge that from past experience, we know, can change the world.

Theory’s abstraction lets us examine certain essential features of the subjects and models we study, which in Semaan and Crutchfield’s case concern the first and second laws of thermodynamics. Is it possible to run a car from the hard drive of a computer? In the parlance of this brand of physics, the short answer is, “Yes, theoretically.”

Thermodynamics of Information Processing

From that question as a jumping off point, Semaan explains further. “The primary impact of our contribution is, for now, mostly to other theorists working out the thermodynamics of information processing. … [W]e suggest a change in viewpoint that simplifies and unifies various preceding lines of inquiry, by combining familiar tools to uncover new results.”

The physicist and writer C.P. Snow said that the first three laws of thermodynamics can be pithily summarized with, “You can’t win. You can’t even break even. You can’t stay out of the game.” Semaan elaborates on the second law, “the universe must increase its entropy — its degree of ‘disorder’ — on average…[b]esides offering an excuse for a messy room, this statement has far-reaching implications and places strict limits on the efficiency of converting one form of energy to another … .”

These limits are obeyed by everything from the molecular motors in our bodies to the increasingly sophisticated computers in our pockets to the impacts of global industry on the Earth’s climate and beyond. Yet in the second law’s case, there’s a catch: it turns out that information in the abstract is itself a form of entropy. This insight is key to the much-celebrated “Landauer bound:” stated simply, learning about a system — going from uncertainty to certainty — fundamentally costs energy.

But what about the converse situation? If it costs energy to “reduce” uncertainty, can we extract energy by “gaining” it — for example, by scrambling a hard drive? If so, how much?

Ratchet Information

To answer this question, previous researchers, including Crutchfield, imagine a “ratchet” which moves in one direction along an “information tape,” interacting with one “bit” at a time. As it does so, the ratchet modifies the tape’s statistical properties. That “tape” could be the hard drive in your computer or could be a sequence of base pairs in a strand of DNA.

“In this situation, by scrambling an initially ordered tape, yes: we can actually extract heat from the environment, but only by increasing randomness on the tape.” While the second law still holds, it is modified. “The randomness of the information in the tape is itself a form of entropy,” explains Semaan further, “and we can reduce the entropy in our thermal environment as long as we sufficiently increase it in the tape.”

In the literature, the laws bounding this behavior are termed “information processing second laws,” in reference to their explicit accounting for information processing (via modifying the tape) in the second law of thermodynamics. In this new paper, Semaan and Crutchfield uncover an “information processing first law,” a similar modification to the first law of thermodynamics, which unifies and strengthens various second laws in the literature. It appears to do more, too: it also offers a way to tighten those second laws — to place stricter limits on the allowed behavior — for systems which have “nonequilibrium steady states.”

Non-equilibrium steady state systems — our bodies, the global climate, and our computers are all examples — need to constantly absorb and dissipate energy, and so stay out of equilibrium, even in “steady” conditions (contrast a cup of coffee left out: its “steady” state is complete equilibrium with the room).

“It turns out,” says Semaan, “that in this case we must ‘pay the piper’:  we can still scramble the tape to extract heat, but only if we do so fast enough to keep up with the non-equilibrium steady states.” To demonstrate their new bound, the authors cooked up a simple, tunable model to visualize how much tighter the new results are with concrete, if idealized, examples. “This sort of idealization is a powerful tool,” says Semaan, “because with it we can ‘zoom in’ on only those features we want to highlight and understand, in this case what having nonequilibrium steady states changes about previous results.”

This uni-directional “ratcheting” mechanism may, in fact, someday lead to engineering a device that harnesses energy from scrambling a hard drive. But first, beyond engineering difficulties, there is much left to understand about the mathematical, idealized limits of this behavior. In other words, we still have a ways to go, even “in theory.” There are plenty of remaining questions to address, the fodder for any theoretical physicist worth their salt.

Complex Systems

However, far from being “only” a theoretical exercise, says Semaan, “these continued extensions, reformulations, and corrections are necessary for us to be able to understand how real-world, highly interconnected, complex systems,” like the human body, forest ecosystems, the planetary climate, etc., “exploit (or don’t) the dynamical interplay between energy and information to function. Since so many of the intricate systems we see in nature (including ourselves) exhibit non-equilibrium steady states,” he continues, “this is a [required] step to understanding how they [do this].”

Information ratchet system: At each time step, the ratchet moves one step to the right along the tape, and interacts with one symbol at a time. As it does so, it exchanges energy in various forms with its environment — signified by the T, aux, and λ bubbles in the picture. After running for a long time, the “output tape” generated by the interactions with the ratchet has different statistical properties compared to the “input tape” it receives. The information processing first and second laws are statements about the fundamental relationship between the energy exchanged with the environment and the information processing in the tape. Credit: Semaan and Crutchfield.

This is heady stuff, and the Southern California native is positively thrilled to be sharing it with young, eager undergraduates at the U through the SRI. Semaan is keenly aware of how critical the undergraduate experience in research needs to be to turn out future physicists. A son of Lebanese immigrants who both attended college in the U.S., neither were research scientists and no one he knew had studied physics. At California State University, Long Beach, where Semaan first declared electrical engineering as his major, he was “seduced into physics” through a series of exceptional and inspirational mentors. In the SRI, he hopes to carry this experience forward, and open new doors for undergraduate students.

It was the Complexity Sciences Center at UC Davis, when he applied to graduate school, that caught his attention because of its interdisciplinary nature and concern with systems in which “the whole appears to be greater than the sum of its parts.” The study of emerging systemic behaviors, helmed by Crutchfield, the Center’s Director, ultimately inspired both his PhD and his decision to join the SRI, working with students across the entire College of Science.

Following the third law of thermodynamics, Mikhael Semaan clearly “can’t stay out of the game” (nor would he want to), but one could argue he’s more than breaking even at it.

The release of this paper, titled “First and second laws of information processing by nonequilibrium dynamical states” in the journal Physical Review E is proof of that.


by David Pace

SRI Research: Smoke Plumes

Smoke Plumes


Western wildfire smoke plumes are getting taller.

In recent years, the plumes of smoke crawling upward from Western wildfires have trended taller, with more smoke and aerosols lofted up where they can spread farther and impact air quality over a wider area. The likely cause is climate change, with decreased precipitation and increased aridity in the Western U.S. that intensifies wildfire activity.

“Should these trends persist into the future,” says Kai Wilmot, a postdoctoral researcher in the College of Science's Science Research Initiative and in the Department of Atmospheric Sciences at the University of Utah, “it would suggest that enhanced Western U.S. wildfire activity will likely correspond to increasingly frequent degradation of air quality at local to continental scales.”

The study is published in Scientific Reports and supported by the iNterdisciplinary EXchange for Utah Science, or NEXUS, at the University of Utah.

 

“Given climate-driven trends towards increasing atmospheric aridity, declining snowpack, hotter temperatures, etc. We’re seeing larger and more intense wildfires throughout the Western U.S., and this is giving us larger burn areas and more intense fires.”

 

Smoke height

To assess trends in smoke plume height, Wilmot and U colleagues Derek Mallia, Gannet Hallar and John Lin modeled plume activity for around 4.6 million smoke plumes within the Western U.S. and Canada between 2003 and 2020. Dividing the plume data according to EPA ecoregions (areas where ecosystems are similar, like the Great Basin, Colorado Plateau, and Wasatch and Uinta Mountains in Utah) the researchers looked for trends in the maximum smoke plume height measured during August and September in each region in each year.

In the Sierra Nevada ecoregion of California, the team found that the maximum plume height increased, on average, by 750 ft (230 m) per year. In four regions, maximum plume heights increased by an average of 320 ft (100 m) per year.

Why? Wilmot says that plume heights are a complex interaction between atmospheric conditions, fire size and the heat released by the fire.

“Given climate-driven trends towards increasing atmospheric aridity, declining snowpack, hotter temperatures, etc., we’re seeing larger and more intense wildfires throughout the Western U.S.,” he says. “And this is giving us larger burn areas and more intense fires.”

The researchers also employed a smoke plume simulation model to estimate the mass of the plumes and approximate the trends in the amount of aerosols being thrown into the atmosphere by wildfires . . . which are also increasing.

The smoke simulation model also estimated the occurrence of pyrocumulonimbus clouds—a phenomenon where smoke plumes start creating thunderstorms and their own weather systems. Between 2017 and 2020, six ecoregions experienced their first known pyrocumulonimbus clouds and the trend suggests increasingly frequent pyrocumulonimbus activity on the Colorado Plateau.

Taller plumes send more smoke up into higher elevations where it can spread farther, says John Lin, professor of atmospheric sciences.

“When smoke is lofted to higher altitudes, it has the potential to be transported over longer distances, degrading air quality over a wider region,” he says. “So wildfire smoke can go from a more localized issue to a regional to even continental problem.”

Are the trends accelerating?

Some of the most extreme fire seasons have occurred in recent years. So does that mean that the pace of the worsening fire trend is accelerating? It’s too early to tell, Wilmot says. Additional years of data will be needed to tell if something significant has changed.

“Many of the most extreme data points fall within the years 2017 -2020, with some of the 2020 values absolutely towering over the rest of the time series,” he says. “Further, given what we know of the 2021 fire season, it appears likely that analysis of 2021 data would further support this finding.”

In Utah’s Wasatch and Uinta Mountains ecoregion, trends of plume height and aerosol amounts are rising but the trends are not as strong as those in Colorado or California. Smoke from neighboring states, however, often spills into Utah’s mountain basins.

“In terms of the plume trends themselves, it does not appear that Utah is the epicenter of this issue,” Wilmot says. “However, given our position as generally downwind of California, trends in plume top heights and wildfire emissions in California suggest a growing risk to Utah air quality as a result of wildfire activity in the West.”

Wilmot says that while there are some things that people can do to help the situation, like preventing human-caused wildfires, climate change is a much bigger and stronger force driving the trends of less precipitation, higher aridity and riper fire conditions across the West.

“The reality is that some of these [climate change] impacts are already baked in, even if we cut emissions right now,” Wilmot adds. “It seems like largely we’re along for the ride at the moment.”

Find the full study at Nature.com.

 

by Paul Gabrielsen, first published in @theU.