Categories
Cosmic Science

Wonder and whimsy on the Web

Ever since Cosmic Log was founded, back in 2002, we’ve passed along links to tales that caught our eye elsewhere on the Web. With Twitter’s rise, there’s typically less need for that kind of aggregation — but just in case you’re not following me religiously at @b0yle, I’ll occasionally pass along a selection of the Web’s wonder and whimsy, like this one:

Categories
Cosmic Science

Antibody cocktail just might ward off COVID-19

An international research team led by University of Washington scientists has identified two kinds of “ultrapotent human antibodies” that could go into a drug cocktail for guarding against COVID-19.

  • UW’s David Veesler and Vir Biotechnology’s Katja Fink are the senior authors of the study published online today by the journal Science, which highlights two monoclonal antibodies known as S2E12 and S2M11. The antibodies were found to block SARS-CoV-2, the coronavirus that causes COVID-19, from latching onto molecular receptors on cells in hamsters.
  • An analysis of the antibodies’ molecular structure determined that they block the virus by gumming up its characteristic “spike” protein, which has been a target for many of the vaccines and therapies under development to fight COVID-19. Some of the researchers behind the newly published study, including Veesler, reported a similarly promising antibody called S309 in May.
  • Researchers say such antibodies could be combined in a drug cocktail to guard against the virus evolving to evade any single one of the ingredients. A drug that takes advantage of S309’s effect is already being tested in a phase 2/3 clinical trial launched by GlaxoSmithKline and Vir Biotechnology.

The principal authors of the Science study, “Ultrapotent Human Antibodies Protect Against SARS-CoV-2 Challenge Via Multiple Mechanisms,” are M. Alejandra Tortorici of the University of Washington and Martina Beltramello of France’s Pasteur Institute and CNRS. Other UW researchers among the 47 co-authors of the study include Ha Dang, Matthew McCallum and John Bowen.

This report was first published on GeekWire.

Categories
GeekWire

Premonition takes disease tracking to the next level

Five years after launching an experiment to see if advanced sensors and artificial intelligence could spot the signs of a disease outbreak before it happens, Microsoft says it’s ramping up Project Premonition to create an honest-to-goodness biothreat protection network.

The network will involve setting up about 100 sensor stations in Texas’ Harris County, to track swarms of mosquitoes that could transmit diseases ranging from malaria and dengue fever to Zika and West Nile viruses. AI algorithms will analyze that tracking data for the telltale signs of an epidemic in the making, just as weather forecasting programs look for the signs of a storm on the way.

“It will really be almost like a weather map, the likes of which has not really been seen before in the mosquito vector space,” Ethan Jackson, director of Microsoft Premonition, told me.

The expansion of the Premonition program was announced today in conjunction with this week’s annual Microsoft Ignite conference for software developers.

Get the full story on GeekWire.

Categories
Fiction Science Club

How the stars gave birth to the Human Cosmos

Once upon a time, the sky was filled with stories.

They might have been tales of migrating bulls, horses and antelopes, translated from the constellations into paintings in prehistoric caves. Or sagas about the cycles of life and death, commemorated in stone structures oriented to mark the seasons. Or legends about the Widower Sun and the Sky Coyote that dictated the timing of rains, ripenings and rituals for California’s Chumash culture.

Such stories helped ancient peoples get a grip on the workings of the natural world — and set the celestial stage for millennia of scientific advances. But ironically, those advances may be leading to the extinction of the stories, as well as the fading of the night sky.

“We understand so many wonders about the cosmos, but at the same time … we’ve never been so disconnected from the cosmos,” says Jo Marchant, the author of a new book titled “The Human Cosmos: Civilization and the Stars.”

In the latest episode of the Fiction Science podcast, Marchant and I delve into how our cosmic perspective has been simultaneously sharpened and dulled. Give a listen to the Q&A via your favorite podcast channel, whether that’s Anchor, Apple, Spotify, Google, Breaker, Overcast, Pocket Casts or RadioPublic.

As a species, Homo sapiens is exceptionally skilled at recognizing, replicating and creating patterns out of raw data. In her book, Marchant traces how ancient cultures connected the star patterns they saw in the sky with the natural cycles they had to deal with on Earth, and how those connections evolved in the ages that followed.

Our proclivity for finding patterns can sometimes get us into trouble, as illustrated by the attraction to the Face on Mars — or, more recently, QAnon conspiracy theories. But in the main, it’s a good thing: An argument could be made that the scientific method boils down to the ability to identify patterns that knit together data, and verify that those patterns apply to subsequent occurrences.

Jo Marchant
Jo Marchant (Photo by P. Marchant)

“I’m interested in how we built the scientific view, but I’m also interested in what have we lost,” Marchant said. “Does it matter that we no longer see the stars? We know from light pollution that most people in Europe and the U.S. can no longer see the Milky Way, for example. With artificial lighting and heating, and air travel, and our computers and phones, we’re living in a way that’s more disconnected from the cycles of the sun and moon than ever before.”

An overreliance on our devices, and on perspectives that are divorced from the natural world, could leave us unaware about emerging risks from climate change and viral spillovers. It could also rob us of the emotional response that pushed our ancestors toward discoveries: a sense of awe about the vastness and complexity of the cosmos.

“One of the most common ways that scientists use to trigger awe in studies is to show people pictures or videos of the starry sky, and they’re finding that when people feel awe, it makes them more curious, more creative, less stressed, happier, even weeks later,” Marchant said.

Exercising your sense of awe can also have a beneficial social effect. “People make more ethical decisions,” Marchant said. “They’re more likely to make sacrifices to help others. They care less about money. They care more about the planet. They feel more connected to other people and the Earth as a whole.”

Can we heal our social and political divisions and unite to solve environmental challenges just by looking at pictures from the Hubble Space Telescope? If only it were that easy. Marchant said we’re sorely lacking in the kinds of stories that knit together the human and the natural world.

“Now we have this view of a physical universe out there — the scientific universe, if you like, made of particles and forces, and we’re separate observers of that,” she said.

The Human Cosmos
“The Human Cosmos,” published by Penguin Random House

The closest things we have to the cosmic myths of ancient times are science-fiction tales such as George Lucas’ Star Wars saga or Isaac Asimov’s Foundation series. (The former took many of its themes from “The Hero With a Thousand Faces,”  Joseph Campbell’s distillation of mythic archetypes, while the latter was inspired by “The History of the Decline and Fall of the Roman Empire.”)

Even those sagas are more about all-too-human affairs rather than our connections with the heavens. The long-ago, faraway galaxy of Star Wars, for example, primarily serves as a new stage for war-movie drama, just as Lucian’s 1,850-year-old sci-fi novel served to satirize his own society.

When I asked what kind of sci-fi came closest to capturing the cosmic connection Marchant was looking for, she pointed to “Avatar,” James Cameron’s 2009 movie about the clash between naturalistic aliens and machinery-mad humans. (Due to coronavirus-related delays, the sequels are now scheduled for release between 2022 and 2028.)

But even before “Avatar 5” rolls out, another type of cosmic connection could well inspire a fresh wave of awe and innovation. Within the next decade, actual men and women could well be walking on the surface of the moon, and perhaps even on Mars.

“I think it makes a difference, having people up in space rather than just machines,” Marchant said. “It’s kind of going back to that ancient view of the heavens, of seeing these characters and people in the stars, in the skies. … There’s also that perspective of looking back down on Earth, which has been so influential — that view of Earth from space.”

Astronauts have long talked about the Overview Effect, a deep sense of oneness with the Earth that arises when seeing its full disk from space, paired with a heightened desire to protect the planet from harm.

Could a widening of the Overview Effect restore humanity’s cosmic balance? If so, it’d be a sky story worth retelling for ages to come.

Cosmic Log Used Book Club

After our podcast Q&A, I asked Marchant if she had any recommendations for science fiction worth reading or watching. On the streaming-video front, she talked up “Devs,” an FX/Hulu series that capitalizes on the many-worlds interpretation of quantum physics.

“What would the consequences of that be if you could have a computer that could literally predict everything that you were going to do in the future?” she asked. “How would that affect our sense of who we are, and our responsibilities?”

Deeplight cover
“Deeplight,” published by Pan Macmillan

On the book front, Marchant recommended Frances Hardinge’s “Deeplight,” a Lovecraftian fantasy tale that’s set in an underwater realm. “It’s a great adventure story, but also she’s looking into themes of power and the divine, and what happens when the gods are taken away,” she said.

Marchant said her favorite part of “Deeplight” was Hardinge’s disclaimer: “The laws of physics were harmed during the making of this book. In fact, I tortured them into horrific new shapes whilst cackling.”

Based on Marchant’s recommendation, I’m designating “Deeplight” as this month’s selection for the Cosmic Log Used Book Club, which spotlights books with cosmic themes that have been around long enough to pop up at used-book stores or your local library. For a list of previous CLUB Club selections going back to 2002, check out last month’s lineup.

UNESCO made Francesco Bandarin’s photo of the prehistoric auroch painted in the Lascaux Cave available under the terms of a Creative Commons Attribution-ShareAlike 3.0 IGO license. We’ve added a rendering of the constellation Taurus.

Use the form at the bottom of this post to subscribe to Cosmic Log, and stay tuned for future episodes of the Fiction Science podcast via Anchor, Apple, Google, Overcast, Spotify, Breaker, Pocket Casts and Radio Public.

Categories
GeekWire

Genetic sleuths flesh out pandemic’s origin story

Detailed genetic analyses of the strains of virus that cause COVID-19 suggest that the outbreak took hold in Washington state in late January or early February, but went undetected for weeks.

That’s the upshot of two studies published by the journal Science, based on separate efforts to trace the genetic fingerprints of the coronavirus known as SARS-CoV-2.

The studies draw upon analyses of more than 10,000 samples collected in the Puget Sound region as part of the Seattle Flu Study during the early weeks of the outbreak, plus thousands more samples from other areas of the world.

One of the studies was conducted by a team including Trevor Bedford, a biologist at Seattle’s Fred Hutchinson Cancer Research Center who has been issuing assessments of the virus and its spread since the earliest days of the outbreak. The first version of the team’s paper went online back in March and was revised in May, months in advance of today’s peer-reviewed publication.

The other study comes from researchers led by the University of Arizona’s Michael Worobey, who also published a preliminary version of their results in May.

Get the full story on GeekWire.

Categories
GeekWire

Scientists design proteins that confound coronavirus

Imagine being able to ward off COVID-19 just by spritzing a nasal spray into your nostrils. It may not be just your imagination: Researchers at the University of Washington have designed a batch of synthetic proteins that could conceivably block the coronavirus behind this year’s pandemic from gaining a foothold.

“Although extensive clinical testing is still needed, we believe the best of these computer-generated antivirals are quite promising,” Longxing Cao, a postdoctoral scholar at UW’s Institute for Protein Design, said in a news release.

Cao is the lead author of a study about the protein-building experiment, published today by the journal Science. It’s the latest innovation to come from the emerging field of protein engineering, and the technique could revolutionize how drugs are developed to counter future pandemics.

It may not be too late to counter COVID-19 as well. “We are working to get improved versions … deployed to fight the current pandemic,” senior study author David Baker, the director of the Institute for Protein Design, told GeekWire in an email.

The technique involves creating small-molecule proteins, or mini-binders, that are custom-designed to latch onto the spiky molecular structures that are scattered around the surface of SARS-CoV-2, the virus that causes COVID-19.

The spikes on the virus do their dirty work by fitting into molecular-scale receptors on the surfaces of cells, much like fitting a key into a lock to gain entry to someone’s house. Once the virus “unlocks” a receptor, it gains entry to the cell, hijacks its chemical machinery and churns out more virus particles to spread the infection.

Baker, Cao and their colleagues used high-powered computers to design more than 2 million candidate proteins that could conceivably gum up the works for the virus’ spike protein. More than 118,000 of the most promising candidates were synthesized and tested on lab-grown cells.

Get the full story on GeekWire.

Categories
Cosmic Science

Report lays out a road map for human gene editing

Experts on an international commission are saying it’s too early to tweak the human genome for future generations, but they’re also pointing to the first genetic targets to be tweaked.

The experts’ report, issued today, comes in response to the uproar that arose in 2018 over claims that Chinese researchers had edited the genomes of twin babies in an attempt to reduce their vulnerability to the HIV virus.

Those claims sparked a blizzard of questions about the ethics, legality and efficacy of the experiment. It also sparked efforts to lay down guidelines for the use of recently developed gene-editing tools such as CRISPR to make changes in the human genome that could be passed down to future generations.

In today’s report — prepared with the backing of the National Academy of Medicine, the National Academy of Sciences and Britain’s Royal Society — the 18-member commission says researchers will have to demonstrate that precise genomic changes can be made reliably without introducing unwanted changes. The commission also says no current technologies, including CRISPR, can satisfy that requirement.

Once the state of the art gets to that point, heritable human genome editing should initially be limited to the prevention of serious diseases that are caused by a single gene, the report says. Examples include cystic fibrosis, thalassemia, sickle cell anemia and Tay-Sachs disease.

Even in those cases, gene-editing therapy should be reserved for cases where parents who have a known risk for passing on such a disease have virtually no other options.

“Any initial uses of HHGE [heritable human genome editing] should proceed incrementally and cautiously, and provide the most favorable balance of potential benefits and harms,” Rockefeller University President Richard Lifton, the panel’s co-chair, said in a news release.

Today’s report will feed into the work of a different advisory panel at the World Health Organization, which is drawing up recommendations for governance mechanism that would apply to heritable as well as non-heritable genome editing research and clinical uses.

Those recommendations are due to be issued later this year. It’ll be up to individual countries to incorporate the guidelines as they draw up gene-editing regulations. Today’s report calls for the creation of an independent International Scientific Advisory Panel to track developments in the gene-editing field, as well as an international body to provide further guidance on regulating the field.

Francis Collins, the longtime director of the National Institutes of Health, gave the report his thumbs-up in a tweet:

Categories
GeekWire

‘Three Little Pigs’ demonstrate Neuralink’s brain implant

With grudging assistance from a trio of pigs, Neuralink co-founder Elon Musk showed off the startup’s state-of-the-art neuron-reading brain implant and announced that the system has received the Food and Drug Administration’s preliminary blessing as an experimental medical device.

During today’s demonstration at Neuralink’s headquarters in Fremont, Calif., it took a few minutes for wranglers to get the swine into their proper positions for what Musk called his “Three Little Pigs demonstration.”

One of the pigs was in her natural state, and roamed unremarkably around her straw-covered pen. Musk said the second pig had been given a brain implant that was later removed, showing that the operation could be reversed safely.

After some difficulty, a third pig named Gertrude was brought into her pen. As she rooted around in the straw, a sequence of jazzy electronic beeps played through the sound system. Musk said the tones were sounded whenever nerves in the pig’s snout triggered electrical impulses that were picked up by her brain implant.

“The beeps you’re hearing are real-time signals from the Neuralink in Gertrude’s head,” he said.

Eventually, Neuralink’s team plans to place the implants in people, initially to see if those who have become paralyzed due to spinal cord injuries can regain motor functions through thought alone.

Musk said the implant received a Breakthrough Device designation from the FDA last month. That doesn’t yet clear the way for human clinical trials, but it does put Neuralink on the fast track for consultation with the FDA’s experts during preparations for such trials.

Neuralink has received more than $150 million in funding, with roughly two-thirds of that support coming from Musk himself. Today he said the venture had about 100 employees. He expects that number to grow. “Over time, there might be 10,000 or more people at Neuralink,” he said.

Get the full story on GeekWire.

Categories
GeekWire

A new way to fight COVID-19 and other viral threats

A team including researchers from Seattle’s Benaroya Research Institute at Virginia Mason has identified a new pathway for protecting cells from deadly viruses — including the coronavirus that causes COVID-19 as well as the Ebola virus.

The technique, described in this week’s issue of the journal Science, takes advantage of a screening technique for seeking out new genes that can prevent infection.

In the newly published study, the research team pinpoints two genes that have already been the subject of biomedical studies. One gene is called the MHC class II transactivator, or CIITA. The second gene is known as CD74 — specifically, a variant known as p41.

Those genes have previously been thought to be involved in conventional immune responses involving T cells and B cells. The new findings, resulting from a screening technique called transposon-mediated gene activation, shed light on a different way in which the genes block infection.

The researchers found that CIITA can induce resistance in human cell lines by activating CD74 p41, which in turn disrupts the processing of proteins on the coat of the Ebola virus protein. That stops the virus from being able to infect its target cell. The same process blocks the entry pathway for an assortment of coronaviruses — including the SARS-CoV-2 virus that’s behind the current pandemic.

Get the full story on GeekWire.

Categories
GeekWire

Northwest researchers get in on a quantum leap

Microsoft, the Pacific Northwest National Laboratory and the University of Washington are playing supporting roles in the White House’s $1 billion effort to advance research into artificial intelligence and quantum information science.

Those three organizations have already been working together through the Northwest Quantum Nexus to develop the infrastructure for quantum computers, which promise to open up new possibilities in fields ranging from chemistry to systems optimization and financial modeling.

The initiatives announced today are likely to accelerate progress toward the development of commercial-scale quantum computers, Chetan Nayak, Microsoft’s general manager for quantum hardware, said in a blog posting.

“Today marks one of the U.S. government’s largest investments in the field,” he said. “It is also a noteworthy moment for Microsoft, which is providing scientific leadership in addition to expertise in workforce development and technology transfer.”

Get the full story on GeekWire.