Tag: University of Washington

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Nobel Prize in chemistry puts protein design in spotlight

Biochemist David Baker at home
Biochemist David Baker chats with a journalist online about his Nobel Prize. (Photo by Ian C Haydon / UW Medicine Institute for Protein Design)

University of Washington biochemist David Baker has won a share of this year’s Nobel Prize in chemistry for more than two decades of discoveries about the molecular structure of proteins — discoveries that have led to new medical therapies, new materials and new startups.

“I’m very, very excited about the future,” Baker, who is the director of the UW Medicine Institute for Protein Design, said today during a Seattle news briefing. “I think protein design has huge potential to make the world a better place, and I really do think we’re just at the very, very beginning.”

Baker shares the prize with Demis Hassabis and John Jumper of Google DeepMind, who have also pioneered computational techniques for predicting protein structure. They will be awarded their medals at a ceremony in Stockholm, Sweden, on Dec. 10.

In a news release, the Royal Swedish Academy of Sciences said Baker “has succeeded with the almost impossible feat of building entirely new kinds of proteins.”

“His research group has produced one imaginative protein creation after another, including proteins that can be used as pharmaceuticals, vaccines, nanomaterials and tiny sensors,” the academy said.

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Elon Musk’s views on artificial vision get a reality check

Cat images simulating artificial vision
Side-by-side images show a 45,000-pixel rendering of a cat image at left, and a simulation representing an image rendered by 45,000 electrodes in a brain implant at right. (Credit: Ione Fine / University of Washington)

If Elon Musk’s Neuralink brain-implant venture succeeds in its effort to create next-generation brain implants for artificial vision, the devices could bring about a breakthrough for those with impaired sight — but probably wouldn’t match Musk’s claim that they could provide “better than normal vision,” University of Washington researchers report.

In a study published today by the open-access science journal Scientific Reports, UW psychologists Ione Fine and Geoffrey Boynton point out that the brain’s vision system relies on complex interactions between neurons that don’t directly translate into a pixel-by-pixel picture.

“Engineers often think of electrodes as producing pixels, but that is simply not how biology works,” Fine said in a news release. “We hope that our simulations based on a simple model of the visual system can give insight into how these implants are going to perform. These simulations are very different from the intuition an engineer might have if they are thinking in terms of a pixels on a computer screen.”

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Scientists harness generative AI for cancer diagnosis

Illustration: Visualization of microchip with the look of a whole-slide image
Prov-GigaPath harnesses AI for digital pathology. (Ella Maru Studio via Providence / Microsoft)

Researchers at Microsoft, Providence Health System and the University of Washington say they’ve developed a new artificial intelligence model for diagnosing cancer, based on an analysis of more than a billion images of tissue samples from more than 30,000 patients.

The open-access model, known as Prov-GigaPath, is described in research published today by the journal Nature and is already being used in clinical applications.

“The rich data in pathology slides can, through AI tools like Prov-GigaPath, uncover novel relationships and insights that go beyond what the human eye can discern,” study co-author Carlo Bifulco, chief medical officer of Providence Genomics, said in a news release. “Recognizing the potential of this model to significantly advance cancer research and diagnostics, we felt strongly about making it widely available to benefit patients globally. It’s an honor to be part of this groundbreaking work.”

The effort to develop Prov-GigaPath used AI tools to identify patterns in 1.3 billion pathology image tiles obtained from 171,189 digital whole-slides provided by Providence. The researchers say this was the largest pre-training effort to date with whole-slide modeling — drawing upon a database five to 10 times larger than datasets such as the The Cancer Genome Atlas.

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NASA boosts four proposed climate science missions

Graphic charting extent of ozone hole on world map
A color-coded image based on satellite data shows the extent of the Antarctic ozone hole in September 2023. (ESA / DLR Graphic)

NASA has selected four proposals for climate science missions, including an effort led by a University of Washington researcher, to go forward for further study with millions of dollars in funding.

STRIVE, which has UW atmospheric scientist Lyatt Jaeglé as its principal investigator, would focus on interactions between the stratosphere and the troposphere.

“STRIVE would allow us to see the composition and temperature of the atmosphere with much finer detail than previously possible from space,” Jaeglé told me in an email. “It would enable us to observe how smoke from fires and volcanoes affect the ozone layer. It would give us needed information to understand how the troposphere and stratosphere interact, and how these interactions influence weather, climate and air quality.”

Jaeglé said “the entire STRIVE team is very excited at the prospect of moving forward in this next step to prepare the concept study.”

The three other studies winning support from NASA’s new Earth System Explorers Program are ODYSEA, EDGE and Carbon-I. Each of the science teams for the four selected proposals will receive $5 million to conduct a one-year concept study.

After the study period, NASA will choose two of the proposals to go forward to launch, with readiness dates expected in 2030 and 2032. For each chosen investigation, the mission cost will be capped at $310 million. That figure doesn’t include launch costs, which will be covered by NASA.

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Asteroid hunters make 27,500 new finds in old data

Asteroid orbital tracks
This visualization shows trajectories for scores of asteroids. (B612 Asteroid Institute / UW Dirac Institute / OpenSpace Project)

A team of asteroid hunters that includes researchers at the University of Washington says it has identified 27,500 new, high-confidence asteroid discovery candidates — not by making fresh observations of the night sky, but by sifting through archives of astronomical data.

The weeks-long database search was conducted by the Asteroid Institute, a program of the nonprofit B612 Foundation, in partnership with UW’s DiRAC Institute and Google Cloud.

The two institutes developed a program called THOR, which stands for “Tracklet-less Heliocentric Orbit Recovery.” THOR runs on a cloud-based, open-source platform known as ADAM (“Asteroid Discovery Analysis and Mapping”). The program can analyze the positions of millions of moving points of light observed in the sky over a given period of time, and link those points together in ways that are consistent with orbital paths.

Google Cloud’s Office of the CTO collaborated with the Asteroid Institute to fine-tune its algorithms for Google Cloud. The project analyzed 5.4 billion observations drawn from the NOIRLab Source Catalog Data Release 2.

“What is exciting is that we are using electrons in data centers, in addition to the usual photons in telescopes, to make astronomical discoveries,” Ed Lu, executive director of the Asteroid Institute, said in a news release.

Most of the 27,500 asteroid discovery candidates are in the main belt, between the orbits of Mars and Jupiter. But the candidates also include more than 100 apparent near-Earth asteroids.

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How to find signs of extraterrestrial life in a grain of ice

Illustration: Europa Clipper flying over Europa
An artist’s conception shows NASA’s Europa Clipper probe flying over Europa. (NASA / JPL-Caltech Illustration)

Scientists have verified that a method to look for cellular life on Europa, an ice-covered moon of Jupiter, just might work. The technique could be put to the test in the 2030s, when NASA’s Europa Clipper probe is due to make multiple flybys over the Jovian moon.

The technique involves analyzing grains of ice that scientists expect one of the instruments on Europa Clipper — known as the Surface Dust Analyzer, or SUDA — to pick up as it flies through plumes of frozen water rising up from Europa’s surface.

“It’s astonishing how the analysis of these tiny ice grains may tell us whether or not there is life on an icy moon. At least we now know that SUDA has these capabilities,” University of Washington planetary scientist Fabian Klenner told me in an email. Klenner is the lead author of a research paper about the process, published today in the open-access journal Science Advances.

SUDA will be capable of analyzing the chemical content of material that hits its detector, using a process called impact ionization mass spectrometry. The key feature of the process described by Klenner and his colleagues is that the analysis would be done on single ice grains, rather than on a blizzard of ice particles. That way, scientists can focus on individual grains that might hold a high concentration of the ingredients of a single cell.

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Scientists back AI principles for biomolecular design

Visualization of protein molecule
AI technologies now allow scientists to generate biomolecules unlike any seen in nature. (Illustration by Ian C. Haydon / UW IPD)

More than 90 researchers — including a Nobel laureate — have signed on to a call for the scientific community to follow a set of safety and security standards when using artificial intelligence to design synthetic proteins.

The community statement on the responsible development of AI for protein design is being unveiled today in Boston at Winter RosettaCon 2024, a conference focusing on biomolecular engineering. The statement follows up on an AI safety summit that was convened last October by the Institute for Protein Design at the University of Washington School of Medicine.

“I view this as a crucial step for the scientific community,” the institute’s director, David Baker, said in a news release. “The responsible use of AI for protein design will unlock new vaccines, medicines and sustainable materials that benefit the world. As scientists, we must ensure this happens while also minimizing the chance that our tools could ever be misused to cause harm.”

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Computer scientist goes from stunt flying to a startup

Cecilia Aragon
Computer scientist Cecilia Aragon tells her life story at the Women’s Leadership Conference. (GeekWire Photo / Alan Boyle)

BELLEVUE, Wash. — Three decades ago, Cecilia Aragon made aviation history as the first Latina to earn a place on the U.S. Unlimited Aerobatic Team.

She went on to write a book about it, titled “Flying Free.”

Today, she’s still flying free, as a professor and data scientist in the University of Washington — and as the co-founder of a Seattle startup that aims to commercialize her research.

Aragon recounted her personal journey today during a talk at the Women’s Leadership Conference, presented by the Bellevue Chamber. The conference brought nearly 400 attendees to Bellevue’s Meydenbauer Center to hear about topics ranging from financial literacy to sports management.

Aragon’s aerobatic days began in 1985, when she accepted an invitation from a co-worker to take a ride in his flying club’s Piper Cherokee airplane. “The first thing I thought was, ‘I’m the person who’s scared of climbing a stepladder. I’m scared of going in an elevator,’” she recalled.

But then she thought of her Chilean-born father. “I heard my father’s voice, saying, ‘What is stopping you from doing whatever you want?” she said. She swallowed her fears, climbed into the plane, and was instantly hooked.

“It’s so gorgeous to fly out into the water and see the sun glinting up on the water, like a million gold coins,” she said. “And when we got down to the ground, I said, ‘I want to take flying lessons. I want to be the pilot of my own life.’”

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Scientists take a freeze-frame look at excited electrons

Illustration: X-ray pulses blasting water molecules
Scientists used a pair of X-ray pulses (shown in pink and green) to study the energetic response of electrons (gold) in liquid water on attosecond time scales, while the hydrogen (white) and oxygen (red) atoms are ‘frozen’ in time. (Pacific Northwest National Laboratory / Nathan Johnson)

An international team of scientists has blazed a new trail for studying how atoms respond to radiation, by tracking the energetic movement of electrons when a sample of liquid water is blasted with X-rays.

The experiment, described in this week’s issue of the journal Science, required “freezing” the motion of the atoms with which the electrons were associated, on a scale of mere attoseconds. An attosecond is one-quintillionth of a second — or, expressed another way, a millionth of a trillionth of a second.

Attosecond-scale observations could provide scientists with new insights into how radiation exposure affects objects and people.

“What happens to an atom when it is struck by ionizing radiation, like an X-ray? Seeing the earliest stages of this process has long been a missing piece in understanding how radiation affects matter,” Xiaosong Li, a chemistry professor at the University of Washington and a laboratory fellow at the Pacific Northwest National Laboratory, said in a UW news release. “This new technique for the first time shows us that missing piece and opens the door to seeing the steps where so much complex — and interesting — chemistry occurs!”

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Scientists visit the kind of lake where life may have arisen

Scientists walking across Last Chance Lake
Researchers walk across Last Chance Lake’s crusty surface in September 2022. (UW Photo / Zack Cohen)

Several years ago, scientists at the University of Washington theorized that key ingredients for life could have built up billions of years ago in special kinds of environments known as soda lakes.

At the time, their hypothesis was based on previously published research, computer modeling and lab experiments. But now the same scientists say they’ve found a shallow lake that just might fit the requirements — and it happens to be just a few hundred miles north of their home base in Seattle.

Their findings, focusing on Last Chance Lake in British Columbia, were published this month in Communications Earth & Environment, an open-access, peer-reviewed scientific journal.

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