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Scientists simulate the brain on a supercomputer

Visuaization of mouse cortex
This color-coded representation of a mouse cortex simulates the activity of brain cells. (Video via Allen Institute)

Creating a virtual brain may sound like a science-fiction nightmare, but for neuroscientists in Japan and at Seattle’s Allen Institute, it’s a big step toward a long-held dream.

They say their mouse-cortex simulation, run on one of the world’s fastest supercomputers, could eventually open the way to understanding the mechanisms behind maladies such as Alzheimer’s disease and epilepsy — and perhaps unraveling the mysteries of consciousness.

“This shows the door is open,” Allen Institute investigator Anton Arkhipov said today in a news release. “It’s a technical milestone giving us confidence that much larger models are not only possible, but achievable with precision and scale.”

Arkhipov and his colleagues describe the project in a research paper being presented this week in St. Louis during the SC25 conference on high-performance computing. The simulation models the activity of a whole mouse cortex, encompassing nearly 10 million neurons connected by 26 billion synapses.

To create the simulation, researchers fed data from the Allen Cell Types Database and the Allen Connectivity Atlas into Supercomputer Fugaku, a computing cluster developed by Fujitsu and Japan’s RIKEN Center for Computational Science. Fugaku is capable of executing more than 400 quadrillion operations per second, or 400 petaflops.

The massive data set was translated into a 3-D model using the Allen Institute’s Brain Modeling ToolKit. A simulation program called Neulite brought the data to life as virtual neurons that interact with each other like living brain cells.

Scientists ran the program in different scenarios, including an experiment that used the full-scale Fugaku configuration to model the entire mouse cortex.

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Scientists enlist AI to map regions of the brain in detail

Illustration: Color-coded cutaway view of mouse brain
An AI-produced rendering shows a map of mouse brain regions, overlaid with network motifs. (UCSF Illustration)

Scientists say an artificial intelligence program that they compare to ChatGPT has helped them create one of the most detailed maps of the mouse brain to date, with 1,300 regions and subregions marked on the map.

Some of those subregions have never been charted before — and the researchers say there’s more to come. “I think there are already indications that we can go beyond what we see now,” said Bosiljka Tasic, director of molecular genetics at Seattle’s Allen Institute for Brain Science.

The mapping effort, led by researchers at the University of California at San Francisco and the Allen Institute, is detailed in a study published today in the journal Nature Communications.

“Our model is built on the same powerful technology as AI tools like ChatGPT,” senior author Reza Abbasi-Asl, a neuroscientist at UCSF, said in a news release. “Both are built on a ‘transformer’ network which excels at understanding context.”

That context could be important for treating neurological ailments, Tasic told me. “Location is everything in the brain,” she said. “Defining the geography of the brain, and then defining all these regions and their functions, not only leads to better understanding, but also better ability to treat.”

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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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Scientists create new toolkit to fight brain diseases

Color-coded images of mouse brain cell populations
This graphic shows different populations of mouse brain cells, each one targeted by a tool in a new genetic toolkit. (Allen Institute Graphic)

Scientists say they’ve put together a new kind of molecular toolkit that could eventually be used to treat a variety of brain diseases, possibly including epilepsy, sleep disorders and Huntington’s disease.

The kit currently contains more than 1,000 tools of a type known as enhancer AAV vectors, with AAV standing for “adeno-associated virus.” A consortium that included researchers from Seattle’s Allen Institute for Brain Science and the University of Washington combined harmless adeno-associated viruses with snippets of engineered DNA to create a gene-therapy package that could target specific neurons in the brain while having no effect on other cells.

Researchers laid out their findings in a set of eight studies published today in the Cell Press family of journals. The work is part of a project called the Armamentarium for Precision Brain Cell Access, funded through the National Institutes of Health’s BRAIN Initiative.

“Honing in on the right cells — in the right way and at the right time — is the future of precision brain medicine,” John Ngai, director of the BRAIN Initiative, said in a news release. “These tools move us closer to that future, while also expanding what we know about the brain’s cells and circuits today.”

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New clues in the search for the roots of consciousness

Map of the brain, plus charts of brain activity
This map of the human brain highlights areas in the prefrontal cortex (green) and the visual cortex (blue) that are thought to be associated with consciousness. The graphs track readings of brain activity. (Adapted from Cogitate Consortium Graphic / Melloni et al. / Nature)

Seven years after they started, neuroscientists have published the results of a landmark study that was designed to determine which theory of human consciousness came closest to the mark — and those results are decidedly mixed.

The bad news is that neither of the leading theories held a clear advantage in explaining how consciousness arises. The good news is that researchers picked up new clues about where to look.

One of the leaders of the effort — Christof Koch, a meritorious investigator at the Seattle-based Allen Institute — said he was heartened by the state of the debate.

“Adversarial collaboration fits within the Allen Institute’s mission of team science, open science and big science, in service of one of the biggest, and most long-standing, intellectual challenges of humanity: the Mind-Body Problem,” Koch said in a news release. “Unraveling this mystery is the passion of my entire life.”

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New ‘wiring diagram’ traces millions of brain connections

Allen Institute researchers Leila Elabbady and Clay Reid look at a computer screen displaying brain cells
Allen Institute researchers Leila Elabbady and Clay Reid examine brain mapping data from the MICrONS project. (Allen Institute Photo)

Researchers say they’ve accomplished a feat that was said to be impossible 46 years ago: mapping the cells in a cubic millimeter of brain tissue and tracing their activity.

The achievement, documented today in a set of research papers published by the Nature family of journals, is being compared to the Apollo moon shots that were launched more than 50 years ago, and to drafts of the human genome that were released more than 20 years ago.

Scientists from Seattle’s Allen Institute played a key role in the $100 million effort known as the Machine Intelligence from Cortical Networks program, or MICrONS. More than 150 researchers worked together through MICrONS to create a detailed 3D map of a cubic millimeter taken from a mouse’s brain — and figure out how the 200,000 brain cells in a speck the size of a grain of sand work together.

“It really has been one of the holy grails of the field from the beginning,” Clay Reid, a senior investigator at the Allen Institute, told me. “There are many thousands of neuroscientists who study the cerebral cortex, and pretty much everyone who studies the cerebral cortex would like to be able to know what are the sources of inputs to any given cell within the cortex, and what are the outputs of that cell. That’s what such a complete data set allows one to study.”

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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 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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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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Fiction Science Club

How a brainstorm could unlock mysteries of the mind

Jerome Lecoq in Allen Brain Observatory's lab
Allen Institute researcher Jerome Lecoq sets up a microscope in the Allen Brain Observatory. (Allen Institute Photo)

The Allen Institute’s OpenScope program lets scientists study the weird workings of the brain — for instance, how magic mushrooms work their psychedelic magic on neurons, how memories of the past influence perceptions of the present, and how the brain’s visual system interprets motion and texture.

But one of the program’s leaders, neuroscientist Jerome Lecoq, says he’s really excited about an experiment that hasn’t yet been fully defined. It’s a study that could support a theory about the mechanism by which sensory data is fed into our consciousness — to modify our view of the world, and perhaps to modify our behavior as well.

The experiment is being fine-tuned online by an international community of researchers, through an open-source process that the Seattle-based Allen Institute fittingly calls a “brainstorm.”

“You can just go and follow us on Twitter and visit the Google Doc,” Lecoq says in the latest episode of the Fiction Science podcast. “We’re going to meet in two weeks and a half in Boston at a conference and discuss this experiment. The document is very open. If you have a good idea, please chime in.”

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