Biology Student Stories: Bailey Landis

Biology Student Stories: Bailey Landis


April 3, 2024

by Maisy Webb

From playing the clarinet and majoring in music to finding inspiration in deciphering the As, Ts, Gs, and Cs relevant to fruit fly evolution and genetics, Bailey Landis has many interests but has dedicated his educational pursuits to biology.

The “major” shift happened when Bailey took Genetics from Nitin Phadnis. That was the moment he realized he loved biology and wanted to give research a try.

Bailey asked Phadnis if he knew of any lab openings, and the very next day he entered the research world…in the Phadnis lab! “Even though research was new to me, I was given the opportunity to jump into cutting-edge science. I immediately began investigating the genetic basis of a hybrid incompatibility between two subspecies of Drosophila.” Bailey artfully explained that “When two populations of a species are isolated from each other, they rapidly evolve [and this can] lead to speciation.” Deciphering the molecular and genetic basis of this process is the focus of the Phadnis lab.

Bailey finds the lab environment “unequivocally amazing” and  “is inspired by the motivation and drive of his peers in the lab.” He says, “Whenever you are doing something, people want you to do well ... and are not hoping for your downfall. So I have gotten courage knowing when I am presenting or doing something scary that people are hoping to see me succeed.”

Bailey has gained an appreciation for the collaborative nature of science, receiving mentorship and mastering new techniques with support from two other biology professors, Kent Golic and Clayton Dale. As it goes in research, things often don’t work and you always have to be on the lookout for something unexpected, Bailey shared. “I became frustrated that my hard work had yielded no results and began doubting whether the X-ray machine was working correctly. I examined the neuroblasts of mutagenized males, looking for fragmented chromosomes to ensure that the genetic material was being irradiated. ... My irradiation approach was simple and reliable [yet] lacked efficiency, relying on randomly mutating a single gene out of over 13,000. I felt like I was waiting for an accident and wanted my approach to be more precise. I returned to the drawing board, searching for a more efficient way to identify this gene. I pivoted to a targeted deletion system using CRISPR/Cas-9.”

Bailey’s enthusiasm and dedication has led to an evolution in his knowledge, which will definitely give him a head start when he begins his PhD in biology, at the U, in the fall of 2024.

Bailey is from Chico, California. When he’s not in the lab, you can find Bailey indulging his many other interests from drawing and painting, fly fishing, working on his jiu jitsu, snowboarding, and cooking lots of different dishes!

 

This article originally appeared at the School of Biological Sciences

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Placing geology at the foundation of essential discoveries

Placing geology at foundation of essential discoveries


March 29, 2024 | Carleton College

by Daniel Myer 

Above: Professor Bereket Haileab leads a geology field trip in 2023.

Bereket Haileab, MS'88, PHD'95, chair and professor of geology at Carleton College, is a researcher and teacher animated by his passion for geology.

Bereket Haileab

Haileab has been a cornerstone of geology at Carleton College, a small, private liberal arts college in the historic river town of Northfield, Minnesota, since he joined the faculty in 1993. Through his research over the years, he has also helped rejuvenate the study of the guiding principles behind his discipline, and connected that work with the larger Northfield and Carleton communities. His experiences, ranging from studying Rice County’s hydrology to helping chart the founding story of the entire human species, have revealed the role geology plays in multiple major disciplines. Today, he teaches these lessons to new generations of students, and shows that the College’s geology department is a true testament to the quality of a Carleton education.

At first, Haileab’s work had a utilitarian angle. After his undergraduate education at the University of Addis Ababa in Ethiopia, he had the opportunity to study for his PhD with well-known geochemists at the University of Utah. “There,” Haileab said, “I got the skills to do chemical analysis, interpret the results, and write about it.”

These experiences solidified his background in geochemistry, petrology, and mineralogy, which Haileab used to become an exploration geologist with the Geological Survey of Ethiopia. In his role, Haileab surveyed regions of western Ethiopia to find new gold deposits. Although he found the chance to apply his skills in chemical analysis fulfilling, he was interested in getting more involved with the interdisciplinary field of paleoanthropology — the study of human evolution through fossils, cultural artifacts, and more — which his graduate school experiences had introduced him to.

“When I came to Utah, I went to the field every summer and met many [experts in paleoanthropology] there and in meetings,” Haileab said. “My research was used in every place.”

Those who study the origin of the human species, like paleoanthropologists, depend on extensive geological research. With a lot of their modern work based on the fossils of early people or closely related species, scholars and scientists also need those fossils’ detailed geological contexts, including the current state and geologic history of their dig sites. After all, Haileab said, “you don’t find fossils floating by themselves.”

In 1985, Haileab joined a University of Utah research group working in Kenya, where just one year prior, the “Turkana Boy,” a Homo ergaster, was discovered. Haileab’s group needed to map the surrounding Turkana Basin in order to refine the dating process that allowed geologists and paleoanthropologists to prove that the Turkana Boy was 1.6 million years old. Haileab’s research, however, expanded far beyond one basin.

“We found that the volcanic ash from Turkana, to the sediments of the Red Sea cores, to the sediments in the Gulf of Aden, all the way south to Lake Albert in Uganda, to Ethiopia… was all formed originally [in the Turkana Basin], which makes it the most important point,” Haileab said. “For most of the fossiliferous [fossil rich] sediments, we could correlate all of the sedimentary basins and all of the findings temporally.”

Read the entire article at Carleton News.

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Hunting an underground epidemic

Hunting an underground epidemic


April 3, 2024

Above: The research team outside Toquerville, UT. Left to right: Kimberly Hanson; Kevin Perry; Alyssa McCoy; Katrina Derieg; and Schuyler Liphardt.

In 2001, 10 archaeologists working at a dig site in northeastern Utah suddenly fell ill with a respiratory illness that sent eight of them to the hospital, coughing and feverish.

The symptoms resembled pneumonia, but their diagnosis was unexpected. It was Valley fever, a fungal infection that spreads to people through spores in the soil and dust—and it wasn’t supposed to be there. Valley fever is more common in hotter, drier states; previous predictions of where the fungus could survive in the soil barely extended into the southwest corner of Utah. The archaeologists’ dig site, in Dinosaur National Monument, was hundreds of miles outside the disease’s expected borders.

The truth is, nobody really knows which areas of the state harbor Valley fever. But the archaeologists’ plight shows that its fungal culprit could be far more widespread than anyone predicted. And as the climate changes, the fungus will likely spread further, explained Katharine Walter, assistant professor of epidemiology at the Spencer Fox Eccles School of Medicine at the University of Utah.

A person bends over samples in a shade tent.

PHOTO CREDIT: KATRINA DERIEG

Eric Rickart in the field outside Santa Clara, UT.

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“There have been incredibly intense recent changes in temperature as well as precipitation and drought here in the American West. These all impact the range of where the fungus can exist,” said Walter.

Walter is on a mission to map where in Utah the Valley fever fungus can survive and predict how it will move across the landscape as the climate changes. Walter and her collaborators—Katrina Derieg, vertebrate collections manager at the Natural History Museum of Utah; Eric Rickart, adjunct associate professor of biology at the U and curator of vertebrates at NHMU; and Kevin Perry, professor of atmospheric sciences in the U’s College of Mines and Earth Sciences—recently received a $375,000 Climate and Health Interdisciplinary Award through the Burroughs Wellcome Fund to power their fungus hunt and raise awareness of what to do for the people most at risk of infection.

Read the full story by University of Utah Health's Sophia Friesen in @TheU. You can read another article about this story at KSL.

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The Beauty of Mathematics

THe beauty of Mathematics


April 2, 2024


by Fred Adler

After listening to an egregiously (and quite uncharacteristically) dull math colloquium some years ago, I had a revelation that there are three good reasons to do mathematics:  it is important (solves an open problem), it is useful (cures cancer) and it is beautiful.

 

These good reasons are not mutually exclusive, and my own ideal, rarely achieved, is to combine all three. In case you are curious, the dull talk exemplified one of the bad reasons (it is hard), that I'll say no more about.

So what is this vaunted mathematical beauty? Is mathematical beauty the same as beauty in the arts and nature, or does it just happen to go by the same name?

Faced with a problem of this magnitude, poet and Distinguished Professor Katharine Coles and I decided to do what we do best. Talk about it. This year's Symposium on Science and Literature takes on the idea of beauty, bringing together poet Claudia Rankine, physicist Brian Greene, and neuroscientist/artist Bevil Conway for three days of discussion. As part of the preparation, we are jointly teaching a course this semester on the theme of Beauty to a small class of remarkable students, half from math, half from English. The English students are facing the trauma of making sense of math and physics and attempting to see the beauty therein. The Math students are facing the terror of making sense of complex poetry and attempting to see its beauty. And we are all taking on the collective challenge of reading philosophy to peek behind the curtain to ask what beauty is.

At the atomic scale, when one sheet of atoms arranged in a lattice is slightly offset from another sheet, moiré patterns can create some exciting and important physics with interesting and unusual electronic properties. (Image courtesy of Ken Golden)

Before revealing the answer, I'll share some of the mathematical ideas we have discussed, largely following the charming “The Joy of x by Stephen Strogatz, inspired by his popular series for the New York Times online called "The Elements of Math.” Given the mixed group, the mathematics, in the spirit of Strogatz's book, is fundamental and not technical.

We began with an age-old question: What does the golden ratio have to do with rabbits? The golden ratio appears in geometry, describing the shape of a rectangle that is supposedly the most appealing to the eye, and appearing in the elegant logarithmic spiral. But this number also shows up as the limit of the ratio of the consecutive values of the Fibonacci sequence (1,1,2,3,5,8,13,21...). Each number is the sum of the previous two numbers, and the sequence can be generated by counting the population of immortal and fecund rabbits who produce babies every month and take just two months to mature. The beauty, we decided, lies in the unexpected connection of geometry and arithmetic.

The most elegant and venerable link between geometry and numbers is the Pythagorean theorem, that the sum of the squares of the sides of right triangle is equal to the square of the hypotenuse. Where do those squares come from anyway? I know three broad classes of proof. The first is rather pretty, involving drawing squares on the sides and hypotenuse and cleverly chopping them to get them to match. The second, which I came up with when I couldn't figure out how to do the first, is rather ugly, involving drawing lines, taking ratios, and doing a bunch of nasty algebra. The best proof, which I had not seen before, was attributed to the teenage Einstein in one of the books we read for the class ``A Beautiful Question" by Nobel-prize winning physicist Frank Wilczek. It is based on what we mean by area. If you take any shape and make it twice as big by stretching equally in all directions, the area gets bigger by a factor of 4. That's where the squares come from if you made the shape 3 times as big, the area would be 3^2=9 times bigger. Rather than building on tricky drawing or algebra, this proof requires adding just one line to the picture, and then thinking. In mathematics, beauty lies in deep simplicity. And, as in music and the arts, that kind of simplicity has to be earned.

Fred Adler writes equations inside his office at the University of Utah in Salt Lake City on Sept. 5, 2023. (Photo by Marco Lozzi | The Daily Utah Chronicle)

I became interested in mathematics because of the magic of numbers. And large numbers have an allure all their own. The Fibonacci series, like rabbit populations, grows rather fast. But what if you want to write down really huge numbers? We can use the way that mathematical ideas build on themselves, recalling the progression of arithmetic in elementary school. Addition is repeated counting (6+7=13 means counting to six and then counting to seven). Multiplication is repeated addition (6*7=42 means adding up seven 6's). Exponentiation is repeated multiplication (6^7=279936 means 6*6*6*6*6*6*6, multiplying together seven 6's). The numbers are starting to get pretty big. But to really turbocharge, let's try repeated exponentiation. Donald Knuth invented "arrow notation" to handle this question. ­6­­↑↑7 is 6 raised to the 6th power seven times, or 6^6^6^6^6^6^6. There's really no way to say how big this number is. Even 6­­↑↑3 has 36,305 digits written in decimal notation. But no matter how absurdly large these numbers become, they are still nothing compared with infinity. The beautiful has the sense of the inexhaustible, the beauty of a poem, the face of one you love.

We have touched on many other mathematical questions. Is the quadratic formula ugly, or does it have "inner beauty"? Is there a beautiful poetry behind the existential angst of probabilities? Will I ever get over my prejudice against fractals?

Along the way, we've learned a few things. Good things happen when geometry and algebra get together. Beauty has an element of surprise, evoked by connections between apparently different things. Beauty arises when complexity meets simplicity and when simplicity meets complexity. Einstein was a beautiful and deep thinker. Keats was a great poet who evoked deep thoughts with beautiful words.

There is a toast attributed variously to G.H. Hardy and other famous mathematicians: “Here’s to pure mathematics. May it never be useful for anything!” The Enlightenment philosopher Immanuel Kant argues that beauty indeed must lie outside anything useful, attractive or even morally good. But mathematics has the remarkable power to surprise us with beauty when it seeks to be useful, and with usefulness when it seeks beauty.

Fred Adler is Professor of Mathematics and Director of the School of Biological Sciences at the University of Utah.

The 2024 Science and Literature Symposium takes place April 10-12. This year's topic arises from reexaminations of beauty that are occurring broadly not only in the arts and across such disciplines as ethnic and disability studies, but also in biology, where dominant theories about the possible evolutionary purposes of beauty are being questioned. 

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The future of physics education

The Future of Physics Education


April 1, 2024

Above: Ricardo Gonzalez, REFUGES Afterschool Program Coordinator in class. Credit: Todd Anderson

The March issue of Nature Physics, a premier academic publication, was all about education. Physics Education Research (PER) is a scientific field of study in which researchers collect and analyze data related to the learning environment.

Ramón Barthelemy

“Physics curricula and education systems have remained largely unchanged for decades, and much can be done to improve them,” reads the issue’s editorial. “Nature Physics provides an overview of the current state of physics education research and offers recommendations on how to make learning environments more equitable and inclusive, diversify graduates’ skillsets and enable them to tackle important societal issues and challenges.”

The editors hand-picked contributors who focus on PER from varying perspectives. Ramón Barthelemy, assistant professor in the U’s Department of Physics & Astronomy and founder of the PERU Group, was co-author of a comment titled “Racial equity in physics education research.” AtTheU spoke with Barthelemy about his contribution to the landmark issue.

Nature Physics doesn’t typically focus on education. Was this issue a big deal?

Yes, it is! The editors reached out to my wonderful colleague, Dr. Geraldine Cochran at Ohio State, who brought in a bunch of folks from the U.S. and Brazil. I was excited to hear that Nature Physics chose to include a racial equity perspective in their journal, and I was excited that Dr. Cochran invited me to participate.

How did you and your co-authors decide which aspects of racial equity in PER to include?

Dr. Cochran made the overall framework, and within that, each one of us brought our unique perspective. For me, it was really important that we at least mention LGBTQ+ communities, for example. We are very intersectional in the work that we’re doing. The main focus is race, but you can’t talk about race and ignore the sociocultural, sociohistorical, sociopolitical differences that really impact people.

A big focus of all physics education research is identity—how can we get all students to see themselves as physicists? When we talk about one identity category, we have to think about it in terms of other categories as well—gender identity, sexual identity, income level, whether your parents went to college or not, and so on. I was just happy to work with a group of people that recognize that it’s not just the one thing that affects us, it’s all things that affect our success in physics.

Why is identity an important aspect to the physics education research field?

Physics historically has had one of the biggest challenges in terms of not only diversifying representation in the field, but also diversifying the experience of being a physicist. When we look across the physics literature, we’re not seeing gains in the experiences of women, People of Color and LGBTQ+ folks that we’d like to see. The same issues that people talked about in the seventies and the nineties are the same issues that people are talking about when I and my colleagues interview them today in our own research. So, we have to keep this at the forefront of the broader physics education conversation, because physics just isn’t seeing the kind of change that we are seeing in other fields, unfortunately.

Read the entire interview conducted by Science Writer Lisa Potter in @TheU

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Why does ice form at a range of temperatures?

Why does ice form at a range of temperatures?


April 1, 2024
Above: Chemistry professor Valeria Molinero. Credit: Brian Maffly

From abstract-looking cloud formations to roars of snow machines on ski slopes, the transformation of liquid water into solid ice touches many facets of life. Water’s freezing point is generally accepted to be 32 degrees Fahrenheit.

But that is due to ice nucleation—impurities in everyday water raise its freezing point to this temperature. Now, researchers at the University of Utah have unveiled a theoretical model that shows how specific structural details on surfaces can influence water’s freezing point.

A team led by chemistry professor Valeria Molinero presented its results at the spring meeting of the American Chemical Society (ACS). Held virtually and in person in New Orleans, March 17-21, the spring conference featured nearly 12,000 presentations on a range of science topics. Molinero’s study was just one of a handful the society highlighted.

“Ice nucleation is one of the most common phenomena in the atmosphere,” said Molinero, who investigates physical and materials chemistry. “In the 1950s and 1960s, there was a surge of interest in ice nucleation to control weather through cloud seeding and for other military goals. Some studies addressed how small shapes promote ice nucleation, but the theory was undeveloped, and no one has done anything quantitative.”

Read the full article in @TheU.

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