Faculty | College of Science

What do cycling and rocks have in common?

July 15, 2024

I’m not talking about the Olympics, but the Tour de France, which kicked off on June 29 in Florence, Italy and will finish July 21 in Nice, France. This is the first time the iconic bicycle race won’t finish in Paris, due to the city hosting the Summer Olympics.

The star they’re highlighting rises above the competition, literally. It’s also below and all around.

Peter Lippert and Sean Hutchings

The Geo Tour de France project (Geo TdF) is a blog exploring the geology of the various stages of the bike race. Lippert and Hutchings are two of the five North American contributors to the blog this year. They covered Stage 14, a 152-kilometer ride through the Pyrenees held Saturday and won Saturday by overall race leader Tadej Pogacar of Slovenia in just over four hours.

“The centerpiece of the stage is the Col du Tourmalet, a very famous fabled climb in the Tour de France that has lots of amazing history,” said Lippert, an associate professor in the Department of Geology & Geophysics and director of the Utah Paleomagnetic Center. “This is going to be one of the really decisive stages of the Tour this year.”

The entire race covers 3,500 kilometers (2,175 miles) in 21 stages.

“I’ve always loved this project, because it’s just such a fun way to share our science and share how we see the world with the public and particularly a public that’s probably not often thinking about the geology,” Lippert said.

For Lippert and Hutchings, as well as many of their peers across the world, geology and cycling go hand in hand.

“Riding a bike up and down a mountain gives you a lot of time to see how the mountains put together the rocks you’re riding over in the landscapes that you’re on,” Lippert said. “We’re both trained geologists for most of our lives so it’s hard not to always be thinking about [geology].”

Utah in particular boasts captivating and diverse geological features.

“It’s mountain biking Candyland around here,” said Hutchings, a graduate research assistant in the U of U Seismograph Stations. “It’s fun to be able to climb up to the top of the hill and it’s hard to not interact with rocks on the way as well.”

“You have this new identity with the landscape you’re on if you’re able to understand what’s going on beneath your feet and what made the landscape,” Lippert said. “I think cycling is a really great high impact sense of place type of experience. You’re going a little bit slower. You get to look around.”

Geo Tour de France project

This same sentiment was the original inspiration for Geo TdF project creator Douwe van Hinsbergen, professor of geology at the Netherlands’ Utrecht University.

“He wanted to explore a different way of sharing geology with the public,” Lippert said. “This is a total goldmine.’

Fans who watch the livestream of the race are inadvertently watching hours of spectacular geological features. The Geo TdF project enhances the viewing experience by telling geological stories that ground the competition in the larger history of the landscape.

Lippert first contributed to the blog two years ago, and this time around included Hutchings. The pair worked together during Hutchings’ bachelor’s degree at the U and often bike together.

“I know nothing about Pyrenean geology, so this was a great learning opportunity for me,” Hutchings said. “For graduate school, I’ve dipped more into the seismology realm, so getting back to my geology roots was a fun exercise.”

Col du Tourmalet. Photo credit: Gilles Guillamot, Wikimedia Commons

Tectonic training camp

Stage 14 passed through Pyrenees, the mountains on France’s border with Spain, with an average grade of 7.9%. That’s just under 95 miles at an average grade more than twice as steep as the incline from President’s Circle to the Natural History Museum of Utah.

“Let’s think big” is what Lippert and Hutchings thought when they were presented with the opportunity to cover this pivotal stage of the race.

“I mean the Tour de France is big, the Pyrenees are big, tectonics are big. Sean is more of a geophysicist working with earthquakes and things like that,” Lippert said. “My expertise is in collisional mountain builds, like what happens when oceans close and mountains form. So we thought let’s just go back to basics and keep it big.”

What could be bigger than beginning with the ancient supercontinent Pangea? For their portion of the project, Lippert and Hutchings focused on the creation of the Pyrenees mountain range which began with the separation of Pangea and subsequent plate collisions, a process they describe as a “tectonic training camp.”

A Wealth of information

Some readers might be wondering if these passionate geologists will eventually run out of topics to discuss, even though the Tour course changes each year. Lippert and Hutchings aren’t concerned about that at all.

“One nice thing about geology is that rocks usually stay put and you can go back to check them out year after year. So the rocks don’t change, but the way that we can talk about them does. The limit is our creativity now, what the rocks can provide, because they’re full of really good stories,” Lippert said. “There’s a wealth of information that a single rock can tell you. Where it came from, and the time it took to get there, and what it looked like at the time.”

A once-in-a-career discovery: the black hole at Omega Centauri’s core

July 11, 2024

Through a small telescope, it looks no different from other so-called globular clusters; a spherical stellar collection so dense towards the center that it becomes impossible to distinguish individual stars. But a new study, led by researchers from the University of Utah and the Max Planck Institute for Astronomy, confirms what astronomers had argued about for over a decade: Omega Centauri contains a central black hole.The black hole appears to be the missing link between its stellar and supermassive kin—stuck in an intermediate stage of evolution, it is considerably less massive than typical black holes in the centers of galaxies. Omega Centauri seems to be the core of a small, separate galaxy whose evolution was cut short when it was swallowed by the Milky Way.

“This is a once-in-a-career kind of finding. I’ve been excited about it for nine straight months. Every time I think about it, I have a hard time sleeping,” said Anil Seth, associate professor of astronomy at the U and co-principal investigator (PI) of the study. “I think that extraordinary claims require extraordinary evidence. This is really, truly extraordinary evidence.” A clear detection of this black hole had eluded astronomers until now. The overall motions of the stars in the cluster showed that there was likely some unseen mass near its center, but it was unclear if this was an intermediate-mass black hole or just a collection of the stellar black holes. Maybe there was no central black hole at all.

A medium Level panel zoom of the Omega Centauri star cluster’s intermediate black hole likely position. PHOTO CREDIT: ESA/HUBBLE & NASA, M. HÄBERLE (MPIA)

“Previous studies had prompted critical questions of ‘So where are the high-speed stars?’ We now have an answer to that, and the confirmation that Omega Centauri contains an intermediate-mass black hole. At about 18,000 light-years, this is the closest known example for a massive black hole,” said Nadine Neumayer, a group leader at the Max Planck Institute and PI of the study. For comparison, the supermassive black hole in the center of the Milky Way is about 27,000 light-years away.

A range of black hole masses

In astronomy, black holes come in different mass ranges. Stellar black holes, between one and a few dozen solar masses, are well known, as are the supermassive black holes with masses of millions or even billions of suns. Our current picture of galaxy evolution suggests that the earliest galaxies should have had intermediate-sized central black holes that would have grown over time, gobbling up smaller galaxies done or merging with larger galaxies.

Such medium-sized black holes are notoriously hard to find. Although there are promising candidates, there has been no definite detection of such an intermediate-mass black hole—until now.

“There are black holes a little heavier than our sun that are like ants or spiders—they’re hard to spot, but kind of everywhere throughout the universe. Then you’ve got supermassive black holes that are like Godzilla in the centers of galaxies tearing things up, and we can see them easily,” said Matthew Whittaker, an undergraduate student at the U and co-author of the study. “Then these intermediate-mass black holes are kind of on the level of Bigfoot. Spotting them is like finding the first evidence for Bigfoot—people are going to freak out.”

Neutrino Oscillation Research Advances

July 9, 2024

Neutrinos are also incredibly small and light. They have some mass, but not much and they rarely interact with other matter. They come in three types or "flavors": electron, muon, and tau.

Cosmic rays travel through space then crash into the earth's atmosphere and produce air showers that Include neutrinos and many other types of particles. When neutrinos are produced and start traveling, they can change from one flavor to another. The atmospheric neutrinos are then detected by DeepCore, a denser array of sensors in the center of the IceCube detector at the South Pole.This process is called neutrino oscillation and the IceCube Detector, a massive neutrino detector buried deep in the ice at the South Pole, has a special area called DeepCore that can detect lower-energy neutrinos.

Scientists at the IceCube Neutrino Observatory in Antarctica have made a breakthrough in measuring neutrinos. Using advanced computer techniques, they've achieved the most precise measurements to date of how these particles change as they travel through space, helping us understand fundamental properties of the universe that could lead to new discoveries in physics.

Shiqi Yu

Shiqi Yu, a research assistant professor in the Department of Physics & Astronomy at the University of Utah and others who published their findings recently in Physical Review Letters analyzed data from over 150,000 neutrino events collected over nine years (2012-2021). They used advanced computer programs called convolutional neural networks (CNNs) to process this data. The team made the most precise measurements ever of two important properties related to neutrino oscillation: Delta m²₃₂ and sin²(θ₂₃). These numbers help describe how neutrinos change as they travel.

“We also carefully studied the systematic uncertainties that arise from our imperfect knowledge of our models and chose some to use as free nuisance parameters that fit together with the physics parameters for our data,” says Yu.

Using CNNs, which use three-dimensional data for image classification, Yu and co-lead of the study Jessie Micallef first developed use cases for the CNNs to focus on the DeepCore region and trained them to reconstruct different properties of particle interactions in the detector. They then used the CNN reconstructions to select qualified neutrino interactions that happened in or near the DeepCore region to produce a neutrino-dominated dataset with well-reconstructed energies and zenith angles.

Jessie Micallef

Yu notes that the CNN-reconstructed analysis-level dataset is already being used for other neutrino oscillation analyses, such as determining the neutrino mass ordering and non-standard neutrino interactions and for atmospheric tau neutrino appearance analyses.

“The atmospheric neutrino dataset from DeepCore exhibits relatively high energies in the oscillation analyses, which is unique compared to existing accelerator-based experiments,” says Yu. “Given our dataset and independent analysis, it is interesting to see agreement and consistency in physics parameter measurements.”

This research helps confirm and refine our understanding of how neutrinos — fundamental particles that can tell us a lot about the universe — behave. The techniques developed here, animated by machine learning, can be used in future studies to learn even more about neutrinos and the universe. Those future studies will be informed by IceCube which is planning an upgrade in 2025-2026 that will allow for even more detailed measurements of neutrinos.

By studying neutrino detection and the phenomenon of neutrino oscillation, scientists like Shiqi Yu hope to answer big questions about the nature of matter, energy and the cosmos.

Journey to the Center of Biotech

July 8, 2024

Xie earned her PhD in biology from the University of Utah in 2004 and where she remained as a postdoc for several years. At the time, she never imagined herself working industry. Yet to her surprise, she amassed extensive experience in biotechnology. In her first foray from academia, she taught eighth-grade science and helped build the charter school’s AP biology program.

While she loved teaching, Xie always felt the urge to venture out and gain experience in molecular biology which she also enjoyed. As such, new technological developments in a local biotechnology startup, IDbyDNA, presented her call to action. She recalls “the startup company was pushing for a new technology that was obviously going to be the future. Now the question was, who was going to make it a reality? Why not us?”

To finally embrace the uncertainty of industry was scary, but Xie knew this was her time to act. “I can always go back to teach, but this leap of faith, if I didn’t take it, I may not have another opportunity,” she says. In fact, while learning new skills herself, she never stopped teaching and mentoring others.

Hypothesis-free Diagnostics

IDbyDNA is a local metagenomics company with an innovative algorithm that simultaneously profiles tens of thousands of microorganisms (or pathogens) in any sample by massive parallel sequencing, known as Next Generation Sequencing (NGS). Xie says this technology is fundamentally different from other available tests because it is hypothesis-free. “We’re not making any guesses, educated or not; we just treat everybody the same, and we sequence everything in there. And by analyzing the sequence in the sample, bioinformatics can tell you what it is. You don’t have to say ‘Tell me if it’s the flu.' It will tell you, ‘No, it’s not the flu, it’s something else.’”

By taking this approach to diagnosis, IDbyDNA circumvents two major problems. “The first issue is [the] diversity of the potential cause of the disease. The second issue is [one of timing as] some of the really dangerous pathogens that cause diseases such as tuberculosis, can take a long time to grow. By the time you can actually grow it and identify it, the patient's disease has progressed, and, [by then,] they might have been in the ICU for weeks.”

Hybrid Capture

Though these major concerns were sidestepped, other problems became apparent. “One problem we saw at IDbyDNA was when you get a patient sample and you start to sequence the DNA, the majority of the DNA is the host DNA because the human genome is orders of magnitude larger than the pathogen genome,” explains Xie. “Even a single human cell is going to give you much more sequencing information than the pathogen. So, you actually are not going to have the level of sensitivity you want for it to be clinically applicable.”

To bypass this problem, one can enrich the pathogen signal by selectively pulling the pathogen sequences (with complementary DNA) from the sample before analyzing. The challenge here is that the diversity of the pathogens would require extremely high complexity capturing, which means high-complexity DNA synthesis.

At IDbyDNA, Xie started as a research scientist, co-developing the Explify® clinical diagnostic platform and left as an associate director after six years. The company was eventually acquired by Illumina, a giant sequencing company.

Her next adventure in industry after IDbyDNA was as principal scientist at GenScript, a company that develops and manufactures gene synthesis products and services used by researchers in academia, pharmaceutics and biotech. Xie joined the Seattle campus because of the CustomArray technology that synthesizes millions of different DNA molecules on a semiconductor chip. This high-complexity, low-cost production of DNA became the natural extension of Xie’s earlier interest.

“When I went there [Genscript], this was pre-production, and I helped them evaluate and quantify how good they are and help them improve the product,” says Xie. Her work over nine months resulted in reduced costs and streamlined application of NGS technology in product development.

Precision Oncology

From GenScript, Xie took the position of senior director of pharma services at NeoGenomics Laboratory, a company dedicated to precision oncology. This newest endeavor is the perfect combination of her other experiences: a hypothesis-free approach applied with hybrid sequencing technology that can provide targeted therapies for cancer patients. At NeoGenomics, biopsies of tumors are sequenced and matched back to the mutation that caused them.

“Then, if the clinician needs to target the specific cancer, they can select suitable drugs that have been approved or are in clinical trials to [make a] recommendation to the patient based on the sequencing results.” This highly targeted therapy means that the patient doesn't have to suffer general chemo, Xie says. She and her team have launched several impactful tests since she joined NeoGenomics. More exciting tests are getting ready for the market.

Accelerating the pace

It took a while for Xie to leave academia, but she hasn’t looked back since. She has been dedicated to accelerating the pace in the biotech industry, making innovations at the top of the supply chain that impact research in industry and academia further down, or serving patients with state-of-the-art diagnostic technologies. While earning her PhD at the U, Xie never imagined the exciting career she would create for herself.

“[W]hat I absorbed in school was that there is no value outside academia because everything else is not as scientifically rigorous and not as innovative, not as cutting edge, not at the very boundary of human knowledge.”

But Heng Xie’s success at all levels of the biotech industry is living proof of the abundant exciting opportunities students have and a testament to the growth of science beyond academia. Her experiences showcase how rigorous research in academia impacts society through the commercialization of innovative technologies.

by Lauren Wigod

Delve into the puzzle of ice crystallization and uncover its secrets.

July 8, 2024

We learn in grade school that water freezes at zero degrees Celsius, but that’s seldom true. In clouds, scientists have found supercooled water droplets as chilly as minus 40 C, and in a lab in 2014, they cooled water to a staggering minus 46 C before it froze. You can supercool water at home: Throw a bottle of distilled water in your freezer, and it’s unlikely to crystallize until you shake it.

Freezing usually doesn’t happen right at zero degrees for much the same reason that backyard wood piles don’t spontaneously combust. To get started, fire needs a spark. And ice needs a nucleus — a seed of ice around which more and more water molecules arrange themselves into a crystal structure.

Valeria Molinero, a physical chemist at the University of Utah, builds computer simulations of water to study ice nucleation.

The formation of these seeds is called ice nucleation. Nucleation is so slow for pure water at zero degrees that it might as well not happen at all. But in nature, impurities provide surfaces for nucleation, and these impurities can drastically change how quickly and at what temperature ice forms.

For a process that’s anything but exotic, ice nucleation remains surprisingly mysterious. Chemists can’t reliably predict the effect of a given impurity or surface, let alone design one to hinder or promote ice formation. But they’re chipping away at the problem. They’re building computer models that can accurately simulate water’s behavior, and they’re looking to nature for clues — proteins made by bacteria and fungi are the best ice makers scientists know of.

Understanding how ice forms is more than an academic exercise. Motes of material create ice seeds in clouds, which lead to most of the precipitation that falls to Earth as snow and rain. Several dry Western states use ice-nucleating materials to promote precipitation, and U.S. government agencies including the National Oceanic and Atmospheric Administration and the Air Force have experimented with ice nucleation for drought relief or as a war tactic. (Perhaps snowstorms could waylay the enemy.) And in some countries, hail-fighting planes dust clouds with silver iodide, a substance that helps small droplets to freeze, hindering the growth of large hailstones.

But there’s still much to learn. “Everyone agrees that ice forms,” said Valeria Molinero, a physical chemist at the University of Utah who builds computer simulations of water. “After that, there are questions.”

You can read the full story in Quanta magazine. Read the published research @PNAS.

Meet Lokiceratops: Giant Blade-Wielding Dinosaur 

June 21, 2024

A remarkable, new species of horned, plant-eating dinosaur is being unveiled at the Natural History Museum of Utah. The dinosaur, excavated from the badlands of northern Montana just a few miles from the USA-Canada border, is among the largest and most ornate ever found, with two huge blade-like horns on the back of its frill. The distinctive horn pattern inspired its name, Lokiceratops rangiformis, meaning “Loki’s horned face that looks like a caribou.” The study included the most complete analysis of horned dinosaur evolution ever conducted, and the new species was announced today in the scientific journal PeerJ.

More than 78 million years ago, Lokiceratops inhabited the swamps and floodplains along the eastern shore of Laramidia. This island continent represents what is now the western part of North America created when a great seaway divided the continent around 100 million years ago. Mountain building and dramatic changes in climate and sea level have since altered the hothouse world of Laramidia where Lokiceratops and other dinosaurs thrived. The behemoth is a member of the horned dinosaurs called ceratopsids, a group that evolved around 92 million years ago during the Late Cretaceous, diversified into a myriad of fantastically ornamented species, and survived until the end of the time of dinosaurs. Lokiceratops (lo-Kee-sare-a-tops) rangiformis (ran-ɡi-FOHR-mees) possesses several unique features, among them: the absence of a nose horn, huge, curving blade-like horns on the back of the frill—the largest ever found on a horned dinosaur—and a distinct, asymmetric spike in the middle of the frill. Lokiceratops rangiformis appeared at least 12 million years earlier than its famous cousin Triceratops and was the largest horned dinosaur of its time. The name Lokiceratops translates as “Loki’s horned face” honoring the blade-wielding Norse god Loki. The second name, rangiformis, refers to the differing horn lengths on each side of the frill, similar to the asymmetric antlers of caribou and reindeer.

PHOTO CREDIT: MARK LOEWEN.
Completed reconstruction of Lokiceratops mounted for display. Study authors Brock Sisson (left) and Mark Loewen (right) peer through the frill fenestrae (windows) of Lokiceratops.

Lokiceratops rangiformis is the fourth centrosaurine, and fifth horned dinosaur overall, identified from this single assemblage. While ceratopsian ancestors were widespread across the northern hemisphere throughout the Cretaceous period, their isolation on Laramidia led to the evolution of huge body sizes, and most characteristically, distinctive patterns of horns above their eyes and noses, on their cheeks and along the edges of their elongated head frills. Fossils recovered from this region suggest horned dinosaurs were living and evolving in a small geographic area—a high level of endemism that implies dinosaur diversity is underestimated.

“Previously, paleontologists thought a maximum of two species of horned dinosaurs could coexist at the same place and time. Incredibly, we have identified five living together at the same time,” said co-lead author Mark Loewen, a paleontologist at the Natural History Museum of Utah and professor in the Department of Geology & Geophysics at the University of Utah. “The skull of Lokiceratops rangiformis is dramatically different from the other four animals it lived alongside.”

The fossil remains of Lokiceratops was discovered in 2019 and cleaned, restored and mounted by Brock Sisson, paleontologist and founder of Fossilogic, LLC in Pleasant Grove, Utah. “Reconstructing the skull of Lokiceratops from dozens of pieces was one of the most challenging projects my team and I have ever faced,” said Brock, “but the thrill of bringing a 78-million-year-old dinosaur to life for the first time was well worth the effort.”

Discover more about Lokiceratops by visiting the full article by Mark Loewen at @The U.
Read more about the story in Discover Magazine, ABC 4 News, KSL News, Science Daily, Science News.

Backtracking Core: Earth’s Inner Dynamics Unveiled

June 18, 2024

For the past two decades, the movement of this solid yet searing hot metal sphere, suspended in the liquid outer core, has been studied closely and debated by the scientific community. Past research has shown that the inner core has been rotating slightly faster than the planet’s surface.

But a different picture is emerging under a study led by the University of Southern California and published this week in Nature. The research team, which includes U geology professor Keith Koper, verified with new evidence—built on analyses of seismographic data—that the inner core’s rotation began to ease and synced with Earth’s spin about 14 years ago.

Keith Koper, University of Utah

The inner core is a solid sphere composed of iron and nickel, surrounded by the liquid iron outer core. Roughly the size of Pluto at 2,442 kilometers in diameter, it accounts for only 1% of Earth’s mass, yet it influences the magnetic field enveloping the planet and the length of the day. But the core’s location, more than 3,000 miles below Earth’s surface, presents a challenge to researchers since it can’t be visited or viewed.

Past research into the inner core’s movement has relied on data from repeating earthquakes, which occur in the same location to produce identical seismograms. Differences in the time it takes for the waves to pass through Earth indicate how the core’s position changed during the period between two repeater quakes.

In the latest study, researchers analyzed seismic data associated with 121 earthquakes that occurred in the South Atlantic between 1991 and 2023.

“The inner core is just sitting in this fluid outer core, so it’s decoupled a little bit from the rest of the planet. It’s rotating at a different rate,” Koper said. “The angular momentum has to be conserved, so if it’s rotating differently, then that could affect the rotation observed at Earth’s surface. One of the big ideas in this paper is we have basically a new model or new observations about how the inner core is rotating slightly differently than the rest of the planet.”

Bacteriophages: Nature’s bacterial killers

June 18, 2024

New research led by the University of Utah and University College London (UCL) has found that plant bacterial pathogens are able to repurpose elements of their own bacteriophages, or phages, to wipe out competing microbes. These surprise findings suggest such phage-derived elements could someday be harnessed as an alternative to antibiotics, according to Talia Karasov, an assistant professor in the U’s School of Biological Sciences.

This result was hardly what she expected to find when she embarked on this research with an international team of scientists. Microbial pathogens are all around, but only a fraction of the time do they sicken humans, other animals or plants, according to Karasov, whose primary research interest is in interactions between plants and microbial pathogens. The Karasov lab is seeking to understand the factors that lead to sickness and epidemics versus keeping the pathogens in check.

“We see that no single lineage of bacteria can dominate. We wondered whether the phages, the pathogens of our bacterial pathogens, could prevent single lineages from spreading – maybe phages were killing some strains and not others. That’s where our study started, but that’s not where it ended up,” Karasov said. “We looked in the genomes of plant bacterial pathogens to see which phages were infecting them. But it wasn’t the phage we found that was interesting. The bacteria had taken a phage and repurposed it for warfare with other bacteria, now using it to kill competing bacteria.”

A thale cress specimen collected in 1866 in Germany and preserved in a herbarium in Tubingen. Credit: Burbano lab, University College London.

Mining herbarium specimens for their microbial DNA

Burbano has pioneered the use of herbarium specimens to explore the evolution of plants and their microbial pathogens. His lab sequences the genomes of both host plants and those of the microbes associated with the plant at the time of collection more than a century ago.

For the phage research, Burbano analyzed historical specimens of Arabidopsis thaliana, a plant from the mustard family commonly called thale cress, collected in southwestern Germany, comparing them and the microbes they harbored to plants growing today in the same part of Germany. Lead author Talia Backman wonders if tailocins could help solve the impending crisis in antibiotic resistance seen in harmful bacteria that infect humans.

“We as a society are in dire need of new antibiotics, and tailocins have potential as new antimicrobial treatments,” said Backman, a graduate student in the Karasov lab. “While tailocins have been found previously in other bacterial genomes, and have been studied in lab settings, their impact and evolution in wild bacterial populations was not known. The fact that we found that these wild plant pathogens all have tailocins and these tailocins are evolving to kill neighboring bacteria shows how significant they may be in nature.”

Discover the full story behind bacteriophages and their antibiotic potential by Brian Maffly at @The U. More on this story at earth.com.