Tag: Brain

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Scientists unveil complete cell atlas for mouse brain

Mandala combining visualizations of cell distribution in mouse brain
This mandala combines visualizations of cell types in the mouse brain. (Illustration via Allen Institute)

Neuroscientists have unveiled their most comprehensive and detailed map of cell types across the entire mouse brain, delivering the latest results of a six-year-long scientific effort in which Seattle’s Allen Institute has played a leading role.

Nine studies published today in the journal Nature document the identification of 5,322 different types of brain cells, and trace the similarities and differences found in a variety of mammalian species — including humans.

The work expands upon previous studies from the BRAIN Initiative Cell Census Network, including earlier surveys of cells in various regions of the mouse brain, as well as cross-species comparisons of cell functions. Researchers from the Allen Institute joined forces with colleagues from the Broad Institute, Harvard, the Salk Institute for Biological Studies, the University of California at San Diego, UC-Berkeley and other institutions to add to their “parts list” for the brain.

“Now we have the cell-type atlas of all the cells in the brain,” Hongkui Zeng, executive vice president and director of the Allen Institute for Brain Science, said in an explanatory video. “This is really a landmark achievement. … It marks the completion of a kind of work that strives for completeness. But it also marks the beginning of the next phase of the journey. It just opens up the door for the next generation of investigations.”

Zeng, who is the senior author of one of the papers in Nature and a co-author of five others, said the next step will be to figure out exactly what all those different cell types do, how their functions are affected by disease, and whether there might be yet-to-be-discovered ways to restore those proper functions.

“It’s not just about a catalog, a list of cell types and where they are — reference information which by itself is already important — but we begin to see how a brain is organized,” Zeng said.

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Fiction Science Club

How AI and quantum physics link up to consciousness

Illustration: Humanoid robot looking at screen covered with math formulas
Can AI help humans unravel the mysteries of consciousness and quantum physics? (Freshpixel Illustration via Bigstock)

Will artificial intelligence serve humanity — or will it spawn a new species of conscious digital beings with their own agenda?

It’s a question that has sparked scores of science-fiction plots, from “Colossus: The Forbin Project” in 1970, to “The Matrix” in 1999, to this year’s big-budget tale about AI vs. humans, “The Creator.”

The same question has also been lurking behind the OpenAI leadership struggle — in which CEO Sam Altman won out over the nonprofit board members who fired him a week earlier.

If you had to divide the AI community into go-fast and go-slow camps, those board members would be on the go-slow side, while Altman would favor going fast. And there have been rumblings about the possibility of a “breakthrough” at OpenAI that would set the field going very fast — potentially too fast for humanity’s good.

Is the prospect of AI becoming sentient and taking matters into its own hands something we should be worried about? That’s just one of the questions covered by veteran science writer George Musser in a newly published book titled “Putting Ourselves Back in the Equation.”

Musser interviewed AI researchers, neuroscientists, quantum physicists, neuroscientists and philosophers to get a reading on the quest to unravel one of life’s deepest mysteries: What is the nature of consciousness? And is it a uniquely human phenomenon?

His conclusion? There’s no reason why the right kind of AI couldn’t be as conscious as we are. “Almost everyone who thinks about this, in all these different fields, says if we were to replicate a neuron in silicon — if we were to create a neuromorphic computer that would have to be very, very true to the biology — yes, it would be conscious,” Musser says in the latest episode of the Fiction Science podcast.

But should we be worried about enabling the rise of future AI overlords? On that existential question, Musser’s view runs counter to the usual sci-fi script.

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Brain-cell atlases point to paths for future research

Brain graphic with magnifying glass
Researchers analyzed the cellular and genetic makeup of the brain. (BRAIN Initiative / HiClipArt Graphic)

In a tour de force for neuroscience, teams of researchers have published a voluminous set of brain-cell atlases for humans and other primates.

The atlases are detailed in 21 research papers appearing in Science, Science Advances and Science Translational Medicine — and could point scientists toward new strategies for addressing mental conditions ranging from Alzheimer’s disease and schizophrenia to epilepsy and ADHD.

“We need to understand the specifics of the human brain if we hope to understand human diseases,” Ed Lein, a senior investigator at Seattle’s Allen Institute, said in comments provided via video.

“Most of disease research tries to create a replicate or a model of a human disease in a species that doesn’t get that disease,” Lein explained. “But if we want to understand why we get it, and what the consequences are, and how one should treat it, we need to have a deep understanding of the human brain itself.”

The studies in the package released today are part of the National Institutes of Health’s BRAIN Initiative Cell Census Network, or BICCN, a program that was launched in 2017. The Allen Institute for Brain Science has played a major role in sharing data produced by the program.

One study analyzed more than a million cells taken from 42 regions of the brain. Another study drew high-quality samples from more than 100 brain regions. Yet another study focused on samples from prenatal brain tissue. The collective efforts of the research teams characterized more than 3,000 human brain cell types.

The researchers didn’t just examine the brain cells themselves. They also ran them through DNA analysis to learn which genes appeared to be linked to the cells’ functions and dysfunctions.

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Fiction Science Club

Scientist takes a trip to the frontiers of consciousness

Christof Koch on ferry
Neuroscientist Christof Koch rides on a Washington state ferry during a scene from "Aware: Glimpses of Consciousness." (Umbrella Films)

Could magic mushrooms hold the key that unlocks the secrets of consciousness?

Well, maybe not the only key. But Allen Institute neuroscientist Christof Koch says that hallucinogenic drugs such as psilocybin, the active ingredient found in special types of mushrooms, can contribute to clinical research into the roots of depression, ecstasy and what lies beneath our sense of self.

“What they can teach us about consciousness is that the self is just one aspect of consciousness,” Koch says in the latest episode of the Fiction Science podcast. “You’re still highly conscious, and very often this is associated with states of ecstasy, or states of fear or terror, or a combination of ecstasy and terror. … What’s remarkable is that in all of these states, the self is gone, and very often the external world is gone, yet you’re highly conscious.”

The quest to understand consciousness through detailed analysis of the brain’s structure and function, scientific studies of religious and traditional practices — and yes, research into the effects of psychedelic drugs — is the focus of a 102-minute documentary film titled “Aware: Glimpses of Consciousness.”

“Aware” has been on the film-festival circuit for weeks, and an online showing will be the centerpiece of a live-streaming event set for Nov. 10. The documentary will also air on PBS stations next April as part of public TV’s Independent Lens series.

Koch, who’s the chief scientist of the Seattle-based Allen Institute’s MindScope brain-mapping program, is one of the stars of the show.

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Scientists unveil ‘wiring diagram’ for a tiny bit of brain

Brain cell map
A color-coded 3-D reconstruction of cells from the MICrONS data set reveals complexity in a mouse brain. (MICrONS / Allen Institute)

Neuroscientists from Seattle’s Allen Institute and other research institutions have wrapped up a five-year, multimillion-dollar project with the release of a high-resolution 3-D map showing the connections between 200,000 cells in a clump of mouse brain about as big as a grain of sand.

The data collection, which is now publicly available online, was developed as part of the Machine Intelligence From Cortical Networks program, or MICrONS for short. MICrONS was funded in 2016 with $100 million in federal grants to the Allen Institute and its partners from the Intelligence Advanced Research Projects Activity, the U.S. intelligence community’s equivalent of the Pentagon’s DARPA think tank.

MICrONS is meant to clear the way for reverse-engineering the structure of the brain to help computer scientists develop more human-like machine learning systems, but the database is likely to benefit biomedical researchers as well.

“We’re basically treating the brain circuit as a computer, and we asked three questions: What does it do? How is it wired up? What is the program?” R. Clay Reid, senior investigator at the Allen Institute and one of MICrONS’ lead scientists, said today in a news release. “Experiments were done to literally see the neurons’ activity, to watch them compute.”

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Cosmic Science

Muon mystery, MindPong and a lost city revealed

Lost City of Aten
An ancient city once known as "The Rise of Aten" has been unearthed in Luxor. (Egyptian Ministry of Tourism and Antiquities)

Egyptian archaeologists unearth a 3,000-year-old lost city, magnetic readings from muons could lead to new physics, and Elon Musk’s Neuralink venture has monkeys playing video games with neural impulses. Get the details on the Web:

‘Lost Golden City’ found in Luxor

Egypt’s best-known archaeologist, Zahi Hawass, announced today that the long-lost ruins of a 3,000-year-old city have been found in Luxor. The sprawling settlement dates to the reign of Amenhotep III and his son, Akhenaten. Egypt’s Ministry of Tourism and Antiquities says it continued to be used by Tutankhamun and his successor, King Ay.

The city was at one time called “The Rise of Aten,” reflecting the religious shift brought about by Akhenaten. Today it’s being called the “Lost Golden City.” During the past seven months of excavation, several neighborhoods have been uncovered, but the administrative and residential district hasn’t yet been brought forth from the sands. “The discovery of this lost city is the second most important archaeological discovery since the tomb of Tutankhamun,” said Betsy Bryan, an Egyptologist at Johns Hopkins University.

Previously: ‘Lost cities’ teach lessons for future cities

Muon anomaly sparks deep questions

Anomalous results from a Fermilab experiment have added to the suspicion that scientists have finally found a flaw in one of their most successful theories, the Standard Model of particle physics. The anomalies have to do with the strength of the magnetic field for a weightier cousin of the electron, known as the muon. Data from Fermilab’s Muon g-2 experiment supported previous findings from Brookhaven National Laboratory that the muon’s magnetism is ever-so-slightly stronger than predicted by the Standard Model — just 2.5 parts per billion stronger.

If the results hold up, physicists might have to consider far-out explanations — for example, the existence of scads of particles that haven’t yet been detected, or a totally new take on the foundations of physics. But the findings will require further confirmation. Grand discoveries, like 2012’s detection of the Higgs boson, typically have to be confirmed to a confidence level of 5-sigma. Now the muon findings have hit 4.2-sigma — which doubters would say is still substandard.

Previously: Could the God Equation be our ultimate salvation?

Elon Musk touts mind control

Neuralink, the brain-implant venture funded by tech billionaire Elon Musk, is showing off an AI system that lets a macaque monkey play a game of Pong with its mind alone. Researchers monitored the monkey’s neural impulses as it operated a joystick to play the game, and then correlated the firing patterns of the neurons with the gameplay. Eventually, the brain-monitoring system eliminated the need for the monkey to use the joystick at all.

In a Twitter exchange, Musk said human trials of the mind-reading system would begin, “hopefully, later this year.” He said Neuralink’s first brain-implant product would enable someone with paralysis to use a smartphone with their mind faster than someone using thumbs. “Later versions will be able to shunt signals from Neuralinks in brain to Neuralinks in body motor/sensory neuron clusters, thus enabling, for example, paraplegics to walk again,” Musk tweeted.

Previously: ‘Three Little Pigs’ demonstrate Neuralink’s brain implant

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‘Three Little Pigs’ demonstrate Neuralink’s brain implant

Elon Musk with Neuralink brain implant
Neuralink co-founder Elon Musk holds a brain implant device between his fingers. (Neuralink via YouTube)

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.

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Scientists will map effects of Alzheimer’s disease

Healthy and Alzheimer's brains
This image shows a section of one hemisphere of a healthy brain from an older person at left,and a brain with advanced Alzheimer’s disease at right. (UW Medicine Photo)

A $40.5 million collaborative research center headquartered at Seattle’s Allen Institute aims to create high-resolution maps of brains ravaged by Alzheimer’s disease, to trace new paths to early diagnosis and treatment.

The center will draw upon expertise not only at the institute, but also at UW Medicine and Kaiser Permanente Washington Health Research Institute. Funding for the next five years comes from the National Institute on Aging, part of the National Institutes of Health.

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Study spotlights 3-D mouse brain atlas

The third time’s the charm for the Allen Institute for Brain Science’s 3-D atlas of the mouse brain.

Version 3 of the atlas, known as the Allen Mouse Brain Common Coordinate Framework or CCFv3, is the subject of a research paper published today in the journal Cell. It builds on a partial brain map that focused on the mouse cortex and was released in 2016.

Previous versions of the atlas were rendered with lower-resolution 3-D maps. The latest high-resolution maps are fine enough to pinpoint the locations of individual brain cells — which is crucial for interpreting datasets that contain thousands or millions of pieces of information.

“In the old days, people would define different regions of the brain by eye. As we get more and more data, that manual curation doesn’t scale anymore,” Lydia Ng, senior director of technology at the Seattle-based Allen Institute for Brain Science, explained in a news release. “Just as we have a reference genome sequence, you need a reference anatomy.”

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Allen Institute reorganizes brain science division

Allen Institute sculpture
A sculpture titled “MIRALL” stands sentry at the Allen Institute’s headquarters in Seattle’s South Lake Union district. (GeekWire Photo / Kurt Schlosser)

Seattle’s Allen Institute is heading into a new phase of research into neuroscience — a phase that includes reorganizing its current activities as well as adding new ones.

The Allen Institute for Brain Science, which is the largest division under the institute’s umbrella, was established by Microsoft co-founder Paul Allen in 2003 and has continued on its mission since Allen’s death in 2018. It’s grown to more than 300 scientists and staff members who work in two broad research areas.

One program, known as Cell Types, focuses on mapping out a “periodic table” of brain cells. The Allen Institute’s new 16-year plan calls for the Allen Institute for Brain Science to focus solely on studying brain cell types and neural connectivity.

The second program, known as MindScope, seeks to understand how the brain’s neural circuits produce the sense of vision. That field of study, along with the Allen Brain Observatory, will transition out of the Allen Institute for Brain Science to become a separate program at the Allen Institute.

A new division, due for launch in 2022, will focus on research related to neural computation and dynamics.

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