homenews

Making Machine Learning Accessible to All

July 18, 2023

 MAKING MACHINE LEARNING ACCESSIBLE TO ALL

 

 

“Many call this the age of information” says Rajive Ganguli, the Malcolm McKinnon Professor of Mining Engineering at the University of Utah. “It is perhaps more accurate to call it the age of data since not everyone has the ability to truly gain from all the data they collect. Many are either lost in the data or misled by it. Yet, the promise of being informed by data remains.”

Ganguli who is also the College of Mines and Earth Science’s associate dean (assessment) is launching UteAnalytics, a new, free analytics software which makes artificial intelligence (AI) or machine learning (ML) accessible to all.

Founder of the ai.sys group at the U, Ganguli says that as long as a client knows their data (that is, is an expert in their domain), they can use UteAnalytics to understand  better the problems they are trying to solve. The research group’s mission is to seek insight from data, models systems and to develop computational tools for education and research.

One-to-one relationship between fields in air quality data. Credit: Rajive Ganguli

At various points in time, Ganguli has developed ML tools that his students could use in class. Years ago it occurred to him that more could benefit from ML if only his workflow and tools were more user-friendly. His vision was finally brought to fruition by graduate student Lewis Oduro MS’23 who leveraged the numerous public domain ML tools available to programmers and converted the concept into Windows-based software.

“The tool is problem agnostic,” Ganguli says. “Hence it can have a broad group of users. I have used it for a variety of projects I am involved in, including mining, atmospheric sciences/air quality and COVID/hospital admissions.”

He reports that tens of subject matter experts (SMEs) who are non-coders have already subscribed to receive the software in advance of its formal release. “Many are professionals across a broad spectrum of fields from social science to business,” along with scientists and engineers.

Master of a domain

Potential clients for UteAnalytics may be “master of their domain,” with large sums of data in various formats and curious about what insights they can gain with ML, but they know nothing about it and certainly not about how to code ML or even do basic data analysis.

Designed to empower the domain expert, UteAnalytics allows a client to clean their data (remove nulls, convert data type from string to numeric, etc.); apply filters, to consider data within specific magnitudes, among other functions; conduct exploratory data analysis on the data; and apply linear regression, random forests (regression and classification) and neural networks (regression and classification).

Lewis Oduro and Rajive Ganguli

The software also allows users to estimate effect of each feature (input) on the output as well as develop models in advance of predicting on a new dataset.

Daniel Mendoza, who holds faculty appointments in the Department of Atmospheric Sciences and elsewhere at the U, is an early adopter of the software. Through his work with air quality monitors on UTA trains and electric buses in Salt Lake Valley he and his team have successfully collected data for over 8 years for particulate matter and ozone data and now nitrogen oxides.

“When we look at neighborhood-specific data we can drill in and really see some social justice impacts,” Mendoza reported last year. Today, he is “using UteAnalytics to quickly and efficiently analyze the temperature data that we’ll be collecting in real-time from our mobile and stationary sensors. UA ,” he says, “gives researchers the power to look at data in a very streamlined way without endless hours of coding. The included tools facilitate a thorough interpretation of data and save time without compromising reliability.”

The difference that data — assisted by UteAnalytics tools — make in Mendoza’s work on air quality is most recently seen in the Urban Heat Watch campaign, involving citizen scientists who are helping collect data along the streets of Salt Lake Valley.  As one of the top three urban heat islands in the nation, the Salt Lake City metropolitan area features a groundbreaking monitoring program. In fact, no where else in the world is there an initiative that exists at this density and scale than in Utah’s capital city and environs. And now UteAnalytics is helping Utah’s clean air initiative as well.

An Auspicious Launch

UteAnalytics is just the latest deliverable for Ganguli who has led approximately $13M in projects as primary investigator. He is currently involved in several projects in five different countries — U.S., Denmark/Greenland, Mongolia, Saudi Arabia and Mexico — on topics ranging from ML to training. With the launch of UteAnalytics, it’s the fruition of a long-term ambition that, now available to the public, has an auspicious future ahead of it.

Meanwhile, Oduro, who defended his thesis this past spring, has since taken a job near Phoenix, Arizona as a mining engineer at Freeport-McMoRan, a leading international mining company. A native of Ghana, Oduro says of his mentor, “He gave me the chance to work under him and provided me with the kind of relationship only evident between a father and a son.” Under Ganguli’s tutelage and support, Oduro was the principal player in building UteAnalytics as desktop software used for data analytics and building predictive ML models.

“I will forever be indebted to him and to the entire faculty at the University of Utah’s Mining Engineering Department,” the young scientist says on his LinkedIN page.

By David Pace


SMEs who are curious about applying ML to their data sets
can now download UteAnalytics from the website.

How statistical physics illuminates sea ice

July 14, 2023

How statistical physics illuminates sea ice

Since he began studying polar sea ice at NASA in 1975, mathematician Ken Golden has helped document alarming changes in the seasonally shifting, thin veneers covering the Arctic and Antarctic oceans.

Ken Golden. Feature photo above: Arctic melt ponds. Credit: Donald Perovich

There’s now a lot less ice and the University of Utah scientist has since devoted much of his career to applying statistical mechanics—the physics of phase transitions and complex collective behavior in systems like gases and magnets—to better understand the role of climate change in the disappearance of our polar sea ice covers. The stakes couldn’t be higher as the impacts accelerate. In recent decades, according to Golden, the extent of Arctic sea ice has shrunk by about half.

“Not over the past million years, like on geophysical scales, not over a thousand years, but over the past 30 or 40 years. A couple of months ago, even in Antarctica, we just saw a new record low,” Golden said in his opening remarks at the May 17 Climate Summit hosted by the U College of Science’s Wilkes Center for Climate Science & Policy. “But just like throwing a rock into a pond, there are ripple effects, and the bigger the rock, the bigger the ripples and the further they go. The extent of sea ice we’ve lost in the Arctic is about two-thirds the area of the contiguous United States and is probably the largest change on Earth’s surface due to planetary warming. That’s a big rock.”

The part of Earth’s climate system featuring snow and ice, known as the cryosphere, is experiencing severe disruptions as the planet continues warming. Ice still covers 9% to 15% of Earth’s ocean surface, but the trends are ominous.

Read the full article by Brian Maffly in @TheU. 

Nalini Nadkarni: Bright Red Arrow

July 12, 2023

When the ‘Bright Red Arrow’ turns Earthward

 

“[P]retty much all my adult life I’ve been on what I think of as riding this bright red arrow that will take me higher and faster and better with more achievements and more accomplishments, so that people will think, Oh my God, she’s really hot, she’s really worthwhile.”

That’s how Nalini Nadkarni, professor emerita of biology at the University of Utah, describes what it was like before the 50-foot fall she took in Washington state seven years ago. The forest ecologist has been called the “Queen of the Forest Canopy” because of her foundational work in the ecosystems found in the tops of trees, whether in the Northwest or in the tropical clime of Costa Rica. But following her accident in which she was severely battered — including a broken pelvis, ribs and five vertebrae “exploded” — it was, needless to say, a seminal moment in her life.

“Over the weeks, my graduate students visited me,” she says of her stay in the hospital. “I had all kinds of friends who visited me, colleagues came, and I realized that one of the most critical things in recovery. Whether it’s an accident like mine was, or whether it’s the loss of your pet, or whether it’s a heart attack of your neighbor, or whether it’s a broken engagement, what matters most is the web of relationships that you have that carries you through.”

In a recent podcast, Nadkarni talks about her experience. “When I meet someone who’s had a disturbance of some kind, yes, you have to take in the hard parts of that, but there are some generative things about that, and you’re gonna be arriving not at the original state you were, and you’re not gonna be at the disturbed state that you were. You’re not gonna be crumpled on the forest floor, but you’re never gonna get back to that original state, and that’s OK.”

“I’m a better person because of it.,” she concludes. “So I have to, in some ways, thank that rope that failed, that brought me from the canopy to the forest floor. Now, I’m walking again in the new world that I find myself in.”

Listen to the podcast on the Daily Rally above, and read the transcript of the podcast, edited for length and clarity, in Outside magazine.

U seismologists probe Earth’s inner core

July 10, 2023

At the center of Earth is a solid metal ball, a kind of “planet within a planet,” whose existence makes life on the surface possible, at least as we know it.

Keith Koper. Banner Illustration above by Todd Anderson | College of Science

How Earth’s inner core formed, grew and evolved over time remains a mystery, one that a team of University of Utah-led researchers is seeking to plumb with the help of seismic waves from naturally occurring earthquakes. While this 2,442-kilometer-diameter sphere comprises less than 1% of  Earth’s total volume, its existence is responsible for the planet’s magnetic field, without which the planet would be a much different place.

But the inner core is not the homogenous mass that was once assumed by scientists, but rather it’s more like a tapestry of different “fabrics,” according to Guanning Pang, a former doctoral student in the U’s Department of Geology & Geophysics.

“For the first time we confirmed that this kind of inhomogeneity is everywhere inside the inner core,” Pang said. Now a post-doctoral researcher at Cornell University, Pang is the lead author of a new study, published July 5 in the journal Nature that opens a window into the deepest reaches of Earth. He conducted the study as part of his doctoral dissertation at Utah.

The other final frontier

“What our study was about was trying to look inside the inner core,” said U seismologist Keith Koper, who oversaw the study. “It’s like a frontier area. Anytime you want to image the interior of something, you have to strip away the shallow effects. So this is the hardest place to make images, the deepest part, and there are still things that are unknown about it.”

This research harnessed a special dataset generated by a global network of seismic arrays set up to detect nuclear blasts. In 1996, the United Nations established the Preparatory Commission for the Comprehensive Nuclear-Test-Ban Treaty Organization, CTBTO, to ensure compliance with the international treaty that bans such explosions.

 

Read the entire story by Brian Maffly in @theU.

Research ties worsening wildfires to bird mortalities

July 3, 2023

Research ties worsening wildfires to bird mortalities

 

 

Recent research from the University of Utah explores how wildfires affect migratory birds across the western United States. “We started to see these alarming signs with the migratory birds in the West,” biology graduate student Kyle Kittelberger said. “We got these huge mass mortality events, with the peak of the mortalities occurring in early to mid-September…these were largely occurring in New Mexico, but also throughout states in the southwest. So, Colorado, [and] here in Utah, we were having mortalities.”

Researchers collected over 10,000 dead birds from the 2020 mortality event. However, it’s probable that many birds were missed simply because they died in areas that weren’t easily accessible to humans.

“It’s likely that upwards of 100,000+ could have perished across the Southwest, just in regions where people were not out finding these dead birds,” Kittelberger said.

To Kittelberger, the timing between widespread bird deaths and the peak of the 2020 wildfire season seemed to be more than a coincidence.

Read the full story or listen to the full broadcast on Utah Public Radio.

Bringing Nature to Everyone

June 30, 2023

Bringing Nature To Everyone

A walk in the woods, in the desert, or even a city park can boost both your mood and your health — but access to nature isn’t always equal.

Above: Nalini Nadkarni. Banner Photo: Austin Green (right), SRI Post-doc and SBS graduate leads a group “into the woods” Credit: Myra Gerst

A group of scientists, healthcare researchers and community practitioners, including nearly a dozen representatives from the University of Utah, want to change that. In 2022, the group created the Nature and Health Alliance (NHA)—and their movement has support and financial backing from the REI Cooperative Action Fund.

The NHA convened for the first time in person in May for an interdisciplinary planning conference, bringing together some of the brightest minds in the burgeoning field of nature and human health from across the country. The two-day conference focused on creating a shared vision, goals, action items, and a leadership structure for the NHA to enhance understanding of and make more people aware of the health benefits of engaging with nature.

Nalini Nadkarni, PhD, professor emeritus in the University’s School of Biological Sciences, is one of the group’s leaders and facilitated hosting the conference in Salt Lake City.

“This is a group of people whose disciplines have few ‘crosspoints’ because of the siloed nature of academia and our society,” Nadkarni said. “We had hard-core medical researchers conversing with people who do hands-on community work with minority groups, with people who are thinking innovative ways to train the next generation of healthcare workers, and with those working out ways for insurance companies to pay for nature services. The emerging collaborations promise new ways of looking at both human and planetary health .”

Read the full article by Sarah Shebek on @TheU.

 

Here Comes Trouble Shooting

June 28, 2023

Here Comes Trouble Shooting

That portion of the foliage of trees forming the uppermost layer of a plant community is called the overstory. But just as critical to the health of that community is what’s called the understory: everything else in a tree down to its deepest roots.

As with trees, so with universities, in particular the School of Biological Sciences (SBS) at the University of Utah. There’s an overstory of students learning, teachers teaching and faculty doing research and publishing their results and making broad impacts everywhere — an overstory of laboratories and facilities continually being built and remodeled. But the understory of that enterprise is, well, its own story. And it’s made up of a fleet of skilled staff that makes the whole shootin’ match run smoothly.

SBS Administrative Coordinator Karen Zundel is the epitome of that understory. Winner of this year’s College of Science Outstanding Staff Award, the twenty-year veteran in what is now the School of Biological Sciences has pretty much seen it all. But to talk to her about her work, her contributions and her stamina is like pulling a sequoia out by the roots (not that anyone would dream of doing that these days).

“Everyone speaks very highly of you,” she is told. “I was excited to meet you.”

Zundel’s response: “Well, we have a really, really terrific faculty. You know, some of the intelligence just sometimes makes my jaw drop.”

It is true that SBS, one of the largest academic units on campus (47 tenure-line faculty with four more waiting in the immediate wings), is well-regarded, with a large footprint of scientific inquiry, from plant biology to mammals (including Right Whales off the coast of Patagonia); from cell and molecular biology to ecology; and from mitochondria to vast forests — data sets plotted for miles and years on both the x and the y axes.

It's also true that SBS is shot through with a high volume of grant money flooding in while sporting a strong claim to gender-equity, rare in any STEM discipline. The School also claims Utah’s only Nobel Prize winner, Mario Capecchi who did much of the research that led to his acclaim as a faculty member in what was then the Department of Biology.

But what about that understory? What pilings of support exist under all that canopy of excellence? No luck hearing about that here; for Zundel, faculty reigns supreme.

“Well, like I say about all of the faculty, I am always just awestruck by the kind of work they're doing. It's one of those things where some people that are not as intelligent as they think they are and are self-important that are kind of a pain to deal with. All of these people [in SBS] are extremely intelligent and genuine and just a joy to work with.”

It’s a generous sentiment by biology’s administrative coordinator and all-around shooter of troubles but one that others might find more nuanced. “The university is a series of individual entrepreneurs held together by a common grievance about parking,” Clark Kerr once said somewhat tongue-in-cheek. The first chancellor of the University of California, Berkeley and twelfth president of the University of California was never affiliated with the U, but he could have easily been talking about the wide swath of life science studies and its faculty at the School of Biological Sciences. And what Kerr never did say was who kept those perpetually unhappy-about-parking faculty happy and productive everywhere else.

Credit: 365 Seattle

Zundel isn’t about to give away the hows, whys and wherefores of what it’s like to be the kingpin of a celebrated understory as large as that of U Biology’s. How does she administer the labs and classrooms of as many as 16 faculty members at a time, faculty who earlier relied on her to manage and submit grant applications and then report on the use of those grants later? How do all of the other assistants whom she manages do the same for the remainder of the faculty pool? Ask her about what it’s like, who she is and how she does it, and she immediately detours to the overstory of amazing work being done by faculty.

“No, no, it's not me. It’s thanks to our faculty. It was a pleasure to help them with some of those [grant] submissions, because, you know, a lot of it is government paperwork. You know they're brilliant at the science and they go, ‘Oh, I really have to submit a form' [and I say,] 'I'll do that for you.' But it’s their science and research at the heart of the grant and we just helped with paperwork and forms. [We] made sure they were complying with all the government requirements, even when the instructions are contradictory.”

Perhaps it’s the nature of the job, like a stage manager in a theater, or a forest ranger taking care of hectares of Douglas Fir:  have your influence be immeasurably felt but don’t ever be heard or seen; you aren’t the one to take that bow.  And Zundel wouldn’t have it any other way. Fortunately, biology faculty at the U who nominated her for the College award are keen to acknowledge Karen’s work, not to mention why she’s so deserving of it.

“Every unit has one person who works behind the scenes and makes things come out right,” wrote SBS Director Fred Adler and David Goldenberg, professor and associate director of undergraduate programs. Karen Zundel “is that person for the School of Biological Sciences.” She is famous for being the go-to person to troubleshoot problems big and small. Additionally, her institutional memory is invaluable, everything from her recollection of fielding members of the public carrying specimens into the front office to find out what they've found to ruminating on the life and times of the late, celebrated plant biologist Robert Vickery, a WWII soldier who was witness to the raising of the American flag on the Japanese Island of Iwo Jima.

But beyond Zundel's being the in-house historian and trouble-shooter, biology professor Dale Clayton puts a finer, somewhat comical, point on it, referring to Zundel’s acumen managing faculty similar to “herding feral cats.” Tasks include travel arrangements for faculty

Sampling of denizens making up the SBS "Understory": Jason Socci, April Mills, Karen Zundel and Jeff Taylor.

and the “convoluted process of wrangling visas” for international faculty. She manages biology’s website updates as well as the messaging on TV monitors in the halls of biology. “Despite our interesting collection of personalities,” quips Clayton, she “has the power to embarrass anyone with a few strokes of the keyboard, “ … however, she has yet to humiliate anyone. It would be fascinating to know how often she has been tempted.”

That sort of hubris doesn't likely live in Zundel. She not only has high regard for faculty, but for staff — even as the stable of administrators has declined recently while faculty membership has grown. She mentions, in particular Ann Polidori, executive assistant to the director and others in the front office and on the front lines of the biology hustle.

“We have got really good staff, and most of them have been with us for a while,” Zundel explains. “On the administrative side, it's really fun to work in it, [making] the department run. And there's nobody that goes nuts, [or says] ‘that’s not my job.’ So they're just a fun group of people to work with.”

Outside of work, the Salt Lake City native loves to travel, especially to the Pacific Northwest and Southern Utah, singling out the viewing the trove of rock art in Nine-Mile Canyon north of Price. She also loves to read, in particular, “cozy mysteries.”

So it turns out the understory is the overstory and vice versa. Which suggests, in true biological form, that the total organism of SBS is like Pando—the stand of aspens spreading over 106 acres in central Utah with an interconnected root system that makes it the largest living organism on earth. And like Pando’s 47,000 genetically identical stems, the organism of School of Biological Sciences is a holistic one, interconnected but as resplendent in its totality as are the individual, reflective and tremulous leaves of a single quaking aspen.

An impressive story — but above and below —if there ever was one, and Karen Zundel is one of the reasons why.

By David Pace

 

 

What happened to Co2 emissions during pandemic lockdown?

June 28, 2023

Reduced traffic during the COVID-19 lockdown was likely the primary driver behind reduced CO2 emissions in Salt Lake City (SLC), according to a new study led by University of Utah professors Derek Mallia and John Lin, published in the Journal of Geophysical Research – Atmospheres.

Derek Mallia

High-density measurements of CO2 were combined with a statistical model to estimate reductions in greenhouse gas emissions across SLC during the lockdown.

The paper reports on evidence of an observable decrease in anthropogenic CO2 emissions. The analysis used measurements from the Salt Lake area’s two CO2 networks–Utah Urban Carbon Dioxide Network (UUCON) and a CO2 instrument installed on a light-rail train car (TRAX) that traverses the Salt Lake Valley. Together, the two networks estimated CO2 concentrations across SLC. The results suggest that high-density CO2 monitoring networks could be used to track the decarbonization of cities.

Of the paper, titled “Can we detect urban-scale CO2 emission changes within medium-sized cities?” Mallia said, “This work demonstrates that mobile-based carbon monitoring networks, like the one deployed on Salt Lake City’s TRAX train, will be critical tools for tracking decarbonization efforts for cities across the globe.”

Given that over half of anthropogenic CO2 is emitted from urban areas, cities will play a pivotal role in future decarbonization efforts, and quantifying CO2 emissions at the city-scale will be important for determining whether cities are meeting CO2 decarbonization targets.

The research was funded by the National Oceanic and Atmospheric Administration’s Climate Program Office (CPO) as part of an air quality research initiative to track impacts of COVID-19 lockdowns & recovery on urban atmospheric composition. The research showed that CO2 emissions across SLC relative to 2019 were reduced by ~20% during the first COVID-19 lockdown and that the largest reductions in CO2 were likely driven by reduced traffic, especially in downtown SLC on the northern end of the Salt Lake Valley.

Unlike other cities used to investigate emission reductions during the COVID-19 lockdown, SLC is a medium-sized metropolitan area with a population just over 1 million people and emits an order of magnitude less CO2 relative to larger cities like Los Angeles, San Francisco, and Washington DC/Baltimore. Determining whether CO2 emissions reductions are traceable for smaller cities and metropolitan areas has been an outstanding question which this paper now addresses. The study is the first to demonstrate that CO2 emissions in medium/small cities can be measured.

“While no one wishes for a repeat of the COVID shutdown, it does illustrate the large leverage a shift in societal behavior has on reducing greenhouse emissions, whether from reduced traffic or the transition to electric vehicles,” said Lin.

Ultimately, the analysis carried out here suggests that inverse models, combined with stationary and mobile CO2 observations, can track modest emission reductions in medium-sized cities, and to some degree, geographically identify emission adjustments at the city-scale. According to the researchers, novel urban CO2 observation networks, like the TRAX network, combined with new satellite-based measurements approaches, will also play a key role towards monitoring decarbonization efforts in cities.

Other contributors to the paper include Logan Mitchell, Andres Eduardo Gonzalez Vidal, Dien Wu, and Lewis Kunik.. Read the full paper here.

This research was tagged as a highlighted feature by Eos.org

By David Pace

Watch the cool video from Utah Educational Network about monitoring air quality in Salt Lake County along UTA TRAX lines below:  

Utah’s Environmental Challenges

June 27, 2023

“As bad as it is, I think there’s hope,” says John Lin, professor of atmospheric sciences in the College of Science at the University of Utah.

John Lin. Banner photo credit: Jim Steenburgh

Lin, who is also assistant director of the newly formed Wilkes Center for Climate Science & Policy, says the state’s desire to eventually host the Winter Olympics again has added some urgency to the matter of addressing Utah’s climate-related challenges, especially around air quality. He adds that the state’s response to such issues is often reflective of the “Utah way,” in which people with different beliefs talk to each other and work through problems.

The challenges are real, according to a story in U.S. News & World Report which often touts the Beehive State as “best” in many categories. The environment, including air quality, is not, however, one of them.

“With its five national parks, scenic mountain vistas and stunning red rock landscapes, environmental problems likely aren’t top of mind in most people’s perceptions of Utah,” the magazine reports.

“But the proof – and the pollution – is in the data.”

Utah ranks near the bottom in the natural environment category of the magazine’s recently released Best States rankings. “It’s a black mark on a largely sterling record for the No. 1-ranked state overall.”

 

Read the entire article by Elliot Davis Jr.

Gadusol: A More “E-fish-ent” Sunscreen

June 27, 2023

Gadusol: A More “E-fish-ent” Sunscreen

 

 

As temperatures rise, and outside activities become more popular, many people are thinking about protecting themselves from sunburns and melanomas, primarily using sunscreen.

Marlen Rice. Banner Image: Jamie Gagnon and Marlen Rice. Credit: Todd Anderson

 

However, humans aren’t the only species that have to worry about UV damage. Many species use sunscreen, but not the white lotions that humans are familiar with. Their sunscreens are coded in their DNA. The recently published paper: “Gadusol is a maternally provided sunscreen that protects fish embryos from DNA damage” is the culmination of years of research by University of Utah School of Biological Sciences graduate student Marlen Rice and Assistant Professor of Biology Jamie Gagnon. 

Gadusol is a chemical sunscreen that is found in the eggs of many fish species. The molecule was discovered in fish over 40 years ago, and was originally thought to come from dietary sources, but it has since been proven that gadusol is produced from a sugar intermediate in one of the metabolic pathways within the fish. The mother deposits the chemical into her eggs as she lays them to protect her babies from the sun. 

Rice grew up on a farm an hour south of Salt Lake, and attended Utah State University where he received a bachelor’s degree in molecular biology. He has always been interested in how animals develop in relation to the world around them. Rice says “The fun thing to me about biology is just the fact that [living] things are dynamic and they interact [with] their environment… I like thinking about animals in relation to ecology. I want to try to bridge those two gaps — the molecular field with ecology.” Rice’s lifelong passion for animals and his industry background inspired him to use laboratory tools to investigate ecological factors, starting with the sun.

 

UVR Exposure

Nearly all life on Earth has an important relationship with the sun, whether that be by using the energy from it to produce food, or consuming other organisms who do. This comes with the cost of extensive exposure to ultraviolet radiation (UVR). UVB rays are the specific wavelengths that are especially dangerous to living organisms. UVR damages proteins and DNA on a molecular level. This damage leads to mutations in DNA, and excessive levels of UVR exposure can even induce apoptosis or cell death, producing what we know as a sunburn. 

According to the paper, “[s]unscreens absorb UV photons before they penetrate vulnerable cells and dissipate this absorbed energy as less harmful heat.” Sunscreens act as physical shields over precious genetic material in cells, preventing damage and mutations. Even in the water, not all aquatic organisms are safe from UVR exposure because biologically harmful levels of UVB can penetrate over 10m deep in clear water. Organisms across many habitats have developed adaptations including nocturnal lifestyles and DNA repair mechanisms to help avoid and fix the problems associated with UV exposure. Furthermore, “since sunlit habitats can have significantly nutritive advantages over dark environments and because no repair pathway is completely efficient, many organisms employ sunscreens to avoid UVR damage from occurring in the first place.” 

Initially, Rice only looked at melanin as the primary sunscreen in aquatic life. In fish, melanin is produced in melanophores that migrate to cover aspects of the brain and body as the fish matures. What he found was that zebrafish embryos were dying from UVR exposure at the same rate, regardless of whether or not their genotype was altered to knockout the gene for melanin production. It became clear that there was something else protecting the embryos. 

Zebrafish

Two-day-old zebrafish. Credit: Marlen Rice

Rice created gadusol-deficient mutant zebrafish through CRISPR-Cas9 gene editing to test gadusol as a sunscreen. Zebrafish were chosen for these experiments because they naturally live in sunlit waters, produce gadusol and are amenable to genetic manipulation. He determined that gadusol is provided for zebrafish embryos by the mother, is the most effective sunscreen over other methods of protection and is lost evolutionarily in fish species when their embryos are not exposed to sunlight.

To show gadusol’s importance, Rice delivered precise doses of UVB to both the wildtype and mutant zebrafish embryos and measured the effect on swim bladder inflation. When exposed to the same dose of UVB, the gadusol-deficient mutant fish were all unable to inflate their swim bladders, indicating that the UV exposure had caused significant developmental defects. This experiment demonstrated that gadusol is critical for the survival of embryonic and larval zebrafish exposed to UVR. 

Fish have been benefiting from gadusol for eons, but in the future, humans could too. Gadusol Laboratories, started at Oregon State University, has been acquired by Boston-based beauty company Arcaea. Their research focuses on synthetically producing gadusol to create sunscreens that would be safer for both humans and the ocean. 

For fish, gadusol offers a tremendous advantage over other sunscreens due to its invisibility. “Transparency as camouflage,” they write, “is a common trait in aquatic animals, especially in the open ocean where there is nothing to hide behind.” This is one of the largest drawbacks for melanin: since it absorbs most wavelengths in the visible light spectrum as well as the UVB spectrum, it is detectable by predators. 

The Beauty of DNA

The sun is just one of the unique ecological challenges that aquatic ecosystems pose to their inhabitants. Gagnon says, “you sort of forget they actually evolve out in the world, [a] very challenging world full of pressures on their survival. …  The environment that they evolved in, which is filled with sunlight and viruses and predators and temperature switches and all this crazy stuff that doesn’t happen in our fish facility, and so if you can bring a little bit of that into our laboratory, now we can apply what’s cool to more questions.” 

These environmental factors will inspire their research with zebrafish moving forward. Rice is also curious about the evolutionary history of gadusol itself. He says, “I’d really like to fill out on the tree of life how widespread gadusol is. And another thing I’m really interested in thinking about is, it seems like at some point, land vertebrates stopped using gadusol. I think evolutionarily it’d be really interesting to think about that. At what point did they move away?”

The answers to these mysteries lie within — within DNA to be specific. Rice says “I really do love the idea of DNA. I think it’s a really beautiful thing … . The fact that it’s an unbroken chain of DNA replication and now lives inside of you.” It will be the combination of molecular biology tools and ecological inspiration that translates the evolutionary history written into the genetic code for all living organisms. 

By Lauren Wigod

Read a first-person account from a zebrafish in Animals of the U: Zippy the Zebrafish.