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Scientists study the brain cells that show us illusions

Jerome Lecoq points to diagram on computer screen
Neuroscientist Jerome Lecoq points to a diagram that was used to study how the brain interprets illusions. (Allen Institute Photo / Erik Dinnel)

Our brains are wired to fill in perceptual gaps in what we see, whether it’s a lion hiding in the trees or the shapes hidden in an optical illusion — but how does that wiring work? Neuroscientists are zeroing in on how special kinds of brain cells help us see things that aren’t actually there.

Researchers from Seattle’s Allen Institute for Brain Science and the University of California at Berkeley traced the role played by the cells, known as IC-encoder neurons, in a study published today by the journal Nature Neuroscience.

“The goal of this project was to understand the neural basis of pattern completion, or filling in when you are dealt ambiguous or missing data in your vision,” said senior study author Hillel Adesnik, a neuroscientist at Berkeley.

Such research could help scientists understand how our brains create a complete picture of the world around us from the data that our senses provide. It could also eventually reveal how hallucinations arise, or point the way to better computer vision systems.

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Cosmic Science

How an ancient eruption turned a victim’s brain into glass

Organic glass fragment from eruption victim's skull
This fragment of organic glass was found inside the skull of a victim of Mount Vesuvius' ancient eruption. (Credit: Pier Paolo Petrone)

Researchers say they’ve solved a nearly 2,000-year-old cold case, sparked by the catastrophic volcanic eruption that destroyed the ancient Roman cities of Pompeii and Herculaneum: What caused a victim’s brain to fuse into bits of glass?

The victim’s remains were unearthed in the 1960s, amid the ruins of a building in Herculaneum known as the Collegium Augustalium. In 2020, researchers announced that obsidian-like glass fragments found in the victim’s skull were actually vitrified bits of brain.

Archaeologists suspect that the victim was a guard who was caught up in the aftermath of Mount Vesuvius’ eruption in the year 79. The man died instantly, but how? For years, scientists have been debating the scenarios for vitrifying the brain in a way that’s never been seen elsewhere. Now an Italian-German research team has laid out a plausible explanation in research published by Scientific Reports.

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Cosmic Science

Scientists find links between whale songs and languages

Humpback whale breaching
A humpback whale breaches in waters near Maui. (Photo by Alan Boyle)

When whales sing, what do they sing about? Researchers haven’t yet cracked that code, but they say a statistical analysis shows that those songs reflect a structure that’s similar to human languages.

Two studies, published in the journal Science and in a sister publication called Science Advances, lay out evidence that the songs of humpback whales follow long-accepted rules of efficient communication at least as well as our own spoken languages do.

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Cosmic Science

Scientists map a fruit fly’s brain — and are thinking ahead

Fruit fly connectome
This image shows how a fruit fly's neurons are connected. (Credit: Amy Sterling and Julia Kuhl for FlyWire, Princeton University / Dorkenwald et al., Nature)

Researchers say they have created a complete map of an adult fruit fly, showing how almost 140,000 individual neurons are linked up to each other and turn sensory inputs into behavioral responses.

The connectome — basically, a wiring diagram that traces the connections between brain cells — is the subject of a flurry of research papers published today by the journal Nature.

It’s not the first such brain wiring diagram, or connectome, to be traced out: Previous projects have charted the brain of a roundworm (302 neurons), plus the brains of a larval sea squirt and a larval marine worm, as well as the brain of a larval fruit fly (3,016 neurons).

But the adult fruit fly connectome, encompassing 139,255 neurons and roughly 50 million connections — raises the bar considerably. And it’s getting scientists thinking about what it will take to achieve a similar feat focusing on the human brain.

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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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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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Synthetic peptide molecules open the way for new drugs

Peptides slipping through cell membrane
An illustration shows how peptide molecules can slip through a cell membrane. (Image by Ian C. Haydon / UW IPD)

Researchers at the University of Washington have discovered how to create peptide molecules that can slip through membranes to enter cells — and they’ve also created a company to take advantage of the discovery for drug development.

The findings, which were published today in the journal Cell, could eventually lead to new types of oral medications for health disorders ranging from COVID-19 to cancer.

“This new ability to design membrane-permeable peptides with high structural accuracy opens the door to a new class of medicines that combine the advantages of traditional small-molecule drugs and larger protein therapeutics,” senior study author David Baker, a biochemist at the University of Washington School of Medicine, said in a news release.

Small-molecule drugs — for example, aspirin — are small enough to slip through cell membranes to do their work. Protein therapeutics — for example, monoclonal antibodies — can target more complex ailments, but the protein molecules are typically too big to wedge their way through lipid-based cell walls.

Peptide drugs are made from the same building blocks as protein, and offer many of the advantages of protein-based drugs. They can bind protein targets in the body more precisely than small-molecule drugs, promising fewer side effects.

“We know that peptides can be excellent medicines, but a big problem is that they don’t get into cells,” said study lead author Gaurav Bhardwaj, an assistant professor of medicinal chemistry at the UW School of Pharmacy. “There are a lot of great drug targets inside our cells, and if we can get in there, that space opens up.”

The newly reported experiments used a couple of molecular design techniques to create types of peptide molecules that can get into cells more easily.

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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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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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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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