Tag: University of Washington

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Human genome sequencing rises to the next level

Human genome diversity
New reference genomes were based on an analysis of 32 samples from diverse populations. (UW Graphic / David Porubsky)

Twenty years after the first human genome sequence was published, an international research team has kicked the sequencing game to the next level with a set of 64 reference genomes that reflect much higher resolution and more genetic diversity.

Since the Human Genome Project completed the first draft of its reference genome in 2001, decoding the human genetic code has been transformed from a multibillion-dollar endeavor into a relatively inexpensive commercial service. However, commercial whole-genome sequencing, or WGS, often misses out on crucial variations that can make all the difference when it comes to an individual’s health.

“As a metric, 75% of structural variants that are present in that person’s genome are missed by WGS, but are captured by our long-read phased genome assembly,” University of Washington genome scientist Evan Eichler told me in an email. “Such variants are about three times more likely to cause disease.”

Eichler, who was a member of the original Human Genome Project, is one of the senior authors of a study laying out the new set of reference genomes, published today by the journal Science.

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Fossils flesh out the tale of the first primates

Purgatorius mckeeveri
Artwork shows the early primate species known as Purgatorius mckeeveri. (Andrey Atuchin Illustration via Burke Museum)

The shapes of fossilized teeth from 65.9 million-year-old, squirrel-like creatures suggest that the branch of the tree of life that gave rise to us humans and other primates flowered while dinosaurs still walked the earth. That’s the claim coming from a team of 10 researchers across the U.S., including biologists at Seattle’s Burke Museum and the University of Washington.

In a study published by Royal Society Open Science, the team lays out evidence that an ancient group of primates known as plesiadapiforms must have emerged before the mass-extinction event that killed off the dinosaurs. (Technically, modern-day birds are considered the descendants of dinosaurs, but that’s another story.)

The evidence comes from an analysis of tooth fossils that were unearthed in the Hell Creek area of northeastern Montana.

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How the pandemic changed the protocol for Mars

Mallory Lefland
First Mode's Mallory Lefland is part of the team for NASA’s Perseverance rover mission. (NASA Photo / Bobak Ferdowsi)

Veteran spacecraft engineer Chris Voorhees has witnessed six Mars landings in the course of his career, and he’s playing a role in the next one as president of a Seattle-based engineering firm called First Mode.

But even though First Mode has been helping NASA ensure that its Perseverance rover will get to the surface of Mars safely on Feb. 18, Voorhees will experience it in the same way millions of others around the world will: from home, watching a live stream via YouTube.

At least he’ll be munching on the traditional good-luck peanuts. “I feel weird if I don’t do it,” Voorhees said.

This Mars mission is already weird enough — and not just because it would be the first mission to store up samples for eventual return to Earth, and the first to try flying a mini-helicopter over Mars.

Because of the yearlong COVID-19 pandemic, the hundreds of scientists and engineers behind the Perseverance rover mission have had to work almost exclusively from home. On the big day, only a minimal crew of ground controllers will be on duty at NASA’s Jet Propulsion Laboratory in Pasadena, Calif.

Mallory Lefland, a JPL veteran who’s now a senior systems engineer at First Mode, will be there as part of the mission’s team for entry, descent and landing, or EDL.

“Most people won’t be on lab, working their shift, until 24 hours before landing,” she said last week during a mission preview hosted by Seattle’s Museum of Flight.

Whether they’re working at JPL or working from home, the people in charge of the $2.7 billion mission will serve mostly as spectators during the final minutes of the rover’s seven-month, 300 million-mile journey to Mars.

The capsule containing the rover will be on its own as it goes through a sequence known as the “seven minutes of terror.” Because of the finite speed of light, it takes more than 11 minutes for signals to travel from Mars to Earth. That means the rover will have finished its landing sequence before the team at JPL even knows it started.

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New study links sleep cycles to moon cycles

Full moon over Seattle
A full moon hangs over Seattle’s Lake Union on April 7, 2020. (GeekWire Photo / Kevin Lisota)

A newly published study adds to the long-debated evidence that humans are hard-wired to sleep less when the moon is full or the lights are on, probably due to the ancestral quirks of circadian rhythm.

The pattern has been documented in a variety of indigenous communities in Argentina — and at the University of Washington in Seattle, where bright lights and cloudy weather tend to dull even the full moon’s glare.

“We see a clear lunar modulation of sleep, with sleep decreasing and a later onset of sleep in the days preceding a full moon,” senior study author Horacio de la Iglesia, a UW biology professor, said in a news release. “And although the effect is more robust in communities without access to electricity, the effect is present in communities with electricity, including undergraduates at the University of Washington.”

The research was published today in the open-access journal Science Advances. It’s not the first study to report a correlation between lunar phases and sleep cycles. But it does make use of cutting-edge technology, in the form of wrist monitors, to track the sleep patterns of hundreds of experimental subjects reliably under natural conditions.

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Sex robots and seniors: A match made in AI heaven?

Robot and human hand
An ethicist says there shouldn't be any stigma about senior sex with robots. (Bigstock Photo / Digitalista)

Are sex robots just what the doctor ordered for the over-65 set?

In a newly published research paper, a bioethicist at the University of Washington argues that older people, particularly those who are disabled or socially isolated, are an overlooked market for intimate robotic companionship — and that there shouldn’t be any shame over seeking it out.

To argue otherwise would be a form of ageism, says Nancy Jecker, a professor of bioethics and humanities at the UW School of Medicine.

“Designing and marketing sex robots for older, disabled people would represent a sea change from current practice,” she said today in a news release. “The reason to do it is to support human dignity and to take seriously the claims of those whose sexuality is diminished by disability or isolation. Society needs to make reasonable efforts to help them.”

Jecker’s argument, laid out in the Journal of Medical Ethics, reawakens a debate that has raged at least since a bosomy robot made her debut in Fritz Lang’s 1927 film, “Metropolis.” In a 2007 book titled “Love and Sex With Robots,” computer chess pioneer David Levy argued that robot sex would become routine by 2050.

Over the past decade or so, the sex robot trade has advanced somewhat, with computerized dolls that would typically appeal to randy guys. At the same time, researchers have acknowledged that the world’s growing over-65 population may well need to turn to robotic caregivers and companions, due to demographic trends.

Jecker says sex should be part of the equation for those robots — especially when human-to-human sex is more difficult due to disabilities, or the mere fact that an older person’s parts don’t work as well as they once did. Manufacturers should think about tailoring robot partners for an older person’s tastes, she says.

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Moon rovers will get wireless charging systems

CubeRover
Astrobotic’s CubeRover prototype wheels over a simulated lunar surface. (Astrobotic via YouTube)

Seattle-based WiBotic says it’s working on a wireless charging system and energy management software for moon rovers, in partnership with Astrobotic, Bosch and the University of Washington.

The hardware and software for robotic lunar missions will build on the work that the UW spin-out has done on similar systems for applications here on Earth.

“We’ve conquered marine robotic systems, mobile terrestrial robots, aerial drones — and now, space,” WiBotic CEO and co-founder Ben Waters told GeekWire.

The team-up is supported by a $5.8 million NASA “Tipping Point” contract to overcome the power challenges that will face robots on the moon’s surface. One of the biggest challenges will be providing electric-powered rovers with enough juice to keep them active during the cold lunar night, which lasts two weeks.

Pittsburgh-based Astrobotic is the prime contractor. It aims to use WiBotic’s charging system on lunar rovers that will include its own CubeRover, a shoebox-sized, four-wheeled robot that would venture forth from a base station to take on exploration tasks.

“Bringing wireless power technology to the surface of the moon and beyond is a game-changer in the way space robotics systems have traditionally interacted,” Cedric Corpa de la Fuente, electrical engineer for planetary mobility at Astrobotic, said today in a news release.

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Industry alliance aims to advance DNA data storage

Image: DNA in test tube
Trillions of bytes of data could be stored in the pink smear of DNA at the end of the test tube at right. (Tara Brown Photography / UW)

Microsoft is teaming up with other companies to form an alliance to advance the field of DNA data storage, which promises to revolutionize the way vital records are kept for the long haul.

The founding members of the DNA Data Storage Alliance, unveiled today at the Flash Memory Summit, include Microsoft as well as Twist Bioscience, Illumina and Western Digital. Twist Bioscience has been partnering with Microsoft and the University of Washington for years on projects aimed at harnessing synthetic DNA for data storage.

Microsoft Research and UW’s Molecular Information Systems Lab have already demonstrated a fully automated DNA-based data storage and retrieval system — and in league with Twist, they’ve shown that their system can store a gigabyte of data in a DNA-based archive.

The UW lab is among 10 other organizations that have followed the founders’ lead and joined the alliance.

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New human cell atlases track how tissues develop

Cell atlas visualization
Human cell atlases are visualized here as the day and night sides of the globe. (Cognition Studio Inc. Illustration / Dani Bergey)

Two new human cell atlases have mapped the molecular machinery that builds tissue in the weeks after conception — and could eventually point the way to addressing developmental disorders.

The researchers behind the atlases say their method for single-cell analysis, detailed in a pair of studies published by the journal Science, could dramatically accelerate efforts to trace how individual cells develop from the embryo to adulthood.

“The key point is that the method scales exponentially,” said University of Washington geneticist Jay Shendure, a senior author for both studies. “When you think about the human body, there’s 37 trillion cells. To really get the kind of comprehensive atlases that we want, we want this kind of scalability.”

Study co-author Dan Doherty, a UW pediatrics professor, compared the procedure’s promise to the impact of the Hubble Space Telescope or the Human Genome Project. “Single-cell methods — it’s hard to overestimate their importance for understanding developmental biology,” he said. “They’re really giving us a picture that we’ve never seen before.”

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Satellite attacks could spark a new nightmare

Satellite constellation
Satellite constellations are becoming increasingly important for military communications. (DARPA Illustration)

In the years ahead, the long-running nightmare of the nuclear Cold War — mutually assured destruction — could return in a new context on the final frontier, a Pentagon adviser said today at a Seattle-based space policy conference.

Brad Townsend, a space strategy and policy adviser to the leadership of the Joint Chiefs of Staff, raised the alarm about anti-satellite weapons, or ASATs, during a virtual symposium sponsored by the University of Washington’s Space Policy and Research Center.

He noted that China and Russia are already experimenting with methods to disable other nations’ satellites in the event of a future conflict. But in the course of destroying an enemy satellite, attackers could set off a catastrophic chain reaction of out-of-control orbital debris.

Such a phenomenon, sometimes referred to as the Kessler syndrome, has fed into the plotlines for movies such as “Gravity” and novels such as “SevenEves.” But Townsend warned that the threat is more than just a science-fiction possibility.

“If nations start arming with ASATs as a way to deter other nations from attacking their orbital assets, they risk creating a new form of mutually assured destruction,” he said.

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Triumphs and tragedies in the vaccine quest

GeekWire Summit stage
GeekWire founders John Cook and Todd Bishop chat with a trio of vaccine experts. (GeekWire Photo)

The good news is that Operation Warp Speed, the multibillion-dollar effort to develop vaccines for COVID-19, is moving ahead at a pace that justifies its name.

The bad news is that despite all that effort, the coronavirus outbreak is still likely to be with us next year — and low- to medium-income countries such as India are likely to be hit particularly hard.

“We’re going to probably see a lot of deaths,” said Lynda Stuart, deputy director for vaccines and human immunobiology at the Bill & Melinda Gates Foundation. “It’s going to be a great inequity and tragedy that will unfold.”

Stuart and other experts involved in the vaccine quest laid out their assessment of the road ahead today during the first session of the 2020 GeekWire Summit.

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