SRI Stories

SRI Stories: 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.

SRI Stories

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 Stories

SRI Stories: 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.


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.