Showing posts with label nature. Show all posts
Showing posts with label nature. Show all posts

Inside interoception: The hidden sense of how you feel inside

Mike's Notes

I discovered this article in MIT Technology Review by reading a recent note about AI by John F. Sowa on the Ontolog Forum.

"The guys from Anthropic have ZERO understanding of the complexity and power of the human brain-body system.   For a better perspective, I recommend a recent article from MIT Technology Review.  It shows that our conscious information is a tiny fraction of the immense amount that the brain is processing every second.   The languages we speak express a tiny fraction of what is conscious.  But the part outside of consciousness is immensely larger .  

I copied a few paragraphs that emphasize the immense amount of non-linguistic information that LLMs (Large Language Models) ignore. ..." - John F. Sowa 

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Last Updated

04/10/2026

Inside interoception: The hidden sense of how you feel inside

By: Katherine W. Isaacs 
MIT Technical Review:12/05/2026

Katherine W. Isaacs: Katherine W. Isaacs is a writer and senior lecturer at the MIT Sloan School of Management. Her teaching and research focus on the intersection of psychology, technology, and innovation. Originally trained as a biologist and later as a social psychologist, she is currently working on a book called Gut Feel, about intuition, interoception, and embodied decision-making.

...

Researchers are decoding how signals move between body and brain, with implications for how we understand and treat conditions from obesity to anxiety.

Your brain lives in the dark space of your skull. Yet it knows when the wind lifts the hairs on your skin, when your heart is racing, when your gut tightens with fear.

It’s also, right now, predicting what you’ll read next as your eyes move across this page. It’s picking up signals that help it make sense of what’s happening around you and prepare you to act if you need to stay safe. You aren’t usually aware that your brain is doing all that.

Our senses take in information at a staggering rate—roughly 11 million bits flood in every second from our skin, eyes, ears, and more. That’s nearly three paperback novels’ worth of data every second. Only a sliver reaches our conscious awareness. Researchers estimate that our conscious minds can process roughly 10 to 60 bits of information per second, about the rate at which you’re reading this sentence. That’s a ratio of about one conscious bit to hundreds of thousands of unconscious bits.

And that’s a mercy. As Moriah Thomason, a neuroscientist at NYU Langone, says, “Thank goodness we’re built like this. There’s a layer of what we have access to in conscious awareness. And then we have a right-under-the-surface amount. There is only a certain amount we are meant to ‘hold in mind’ in order to function successfully.” 

What you are aware of: Your stomach growling when you’re hungry. Your palms sweating before you speak in public. The breath you just took, if you pay attention to it. Even your heartbeat, which some people can sense from the inside without feeling their pulse in their wrist.

Scientists have a word for how we sense ourselves from the inside: interoception. 

The term was coined in 1906 by the British neurophysiologist Charles Sherrington. For most of the 20th century it remained largely confined to textbooks. Today, thanks to a 2021 Nobel Prize and new tools that can map the interoceptive system across the body, the study of this facility is suddenly quite hot. As researchers decode how signals move between body and brain, a clearer picture is starting to take shape—with implications for how we understand and treat conditions from obesity to chronic pain to anxiety.

The field began to take off in the 1990s. In 1994, the neurologist Antonio Damasio published a book with a pointed title: Descartes’ Error. He challenged the historical separation of thinking and feeling, arguing that our ability to choose and act is driven by feelings, and those feelings in turn are shaped by the body’s signals, such as your gut clenching or your skin going clammy. When we lose that connection between feeling and thinking, as one of Damasio’s patients did after surgery to treat a brain tumor, we may still be able to reason with perfect logic about the pros and cons of traveling on a Tuesday or a Wednesday. But without the emotional signals that help us predict what a choice will feel like, our reason spins and circles, and we cannot decide.

A contemporary of Damasio’s, the neuroscientist Bud Craig, spent his career asking one question: How do you feel? He charted how the brain builds an inner map of the body and updates it in real time every moment you are alive.

Think of the captain’s bridge on the USS Enterprise, where a live map displays the status of the ship’s critical systems: oxygen levels, energy availability, hull integrity, shield strength. Another set of indicators senses things outside the ship: asteroid belts, enemy ships, radiation, life signs, and spatial anomalies not yet understood.

Your brain, only about the size of your two fists pressed together, creates a map like this for your entire body, along with a map of the outside world, from data streaming in through your five senses. Together, they feed into your brain’s working model of you in the world, now and across time—where you are, who you are, your expectations for what’s about to happen (based on everything you know), and what all that means for you.

When someone asks “How are you doing?” we consult our maps and report back on our status. We might say we’re happy, depleted, anxious, or energetic. These feelings are always a braid of emotional and physical sensations. They’re what your interoceptive navigational system serves up to your awareness when you sense yourself from the inside.

As we grow up, we learn to interpret what these sensations mean—interpretations that, in turn, can alter our physiology, emotions, and behavior. Research by the psychologist Alia Crum shows that people who embrace a “stress is enhancing” mindset produce more growth hormones than people who have a “stress is debilitating” mindset. They also experience more positive emotions and greater cognitive flexibility.

Language also matters. We learn words for the textures of our feelings—words that then shape how we feel and act. The psychologist Marc Brackett points out that people low in "emotional granularity"—the ability to distinguish between closely related feelings—react more impulsively under stress and are less able to find meaning in difficult experiences.But mindsets and emotional intelligence are malleable. We can learn that “anxious” is different from “terrified,” and we can even reframe how we interpret our body’s sensations. Instead of thinking of the butterflies in our bellies as annoying, we can welcome them as our body’s way of preparing us for a peak performance.

Research by the neuroscientist Lisa Feldman Barrett, who discovered and named emotional granularity, suggests that it is not about describing or labeling emotions. It's about how our brains construct emotions with more or less specificity, often outside of awareness.

Scientists have long understood that the interoceptive information informing these lived experiences travels via two major systems: nerves and humors (blood and lymph). Now they’re actively studying a third system—the “interstitium,” a network of fluid-filled spaces woven throughout the body’s connective fascia that may also play a role in communication.

But until recently, scientific understanding of this interoceptive system looked like a high-level schematic that left out vital details—how information travels from the outside environment in, how it moves from your body to your brain, and how it is integrated and interpreted within your brain. Researchers are now racing to explore what the neuroscientist Catherine Tallon-Baudry calls this “new continent of awareness.”

The wandering highway

One of the most active areas of research centers on the vagus nerve, the main component of the parasympathetic nervous system and an information highway carrying news from your organs up to your brain and back down to your body. The vagus has become a celebrity nerve, ubiquitous in wellness podcasts and trauma therapy. “Tone your vagus nerve.” “Activate your parasympathetic system.” The language suggests a single thing you can target, like a muscle. The reality, as Steve Liberles at Harvard Medical School is discovering, is far more interesting.

Liberles has spent most of his career mapping what he calls “the great wide unknown” of one of our largest and longest nerves. He speaks the way he works—methodically, without overselling. But the questions driving him are huge. How do we sense our body’s inner state? What information flows through which channels? And how does the brain decide what to do with it?

“When I’m nervous giving a talk in front of a thousand people,” he says, “my heart might race. I might get butterflies in my stomach. I might get goosebumps on my skin.” We all know what he’s talking about.

“It’s bizarre,” he muses. “Your brain has to send a signal to the gut, and then the gut back to the brain, to tell you you’re nervous?” He pauses. “This just shows there is this intimate connectivity between the brain and the body that’s real.”

The vagus is often called the calming nerve, because it controls “rest and digest” functions that quiet our body after the sympathetic nervous system revs us up with “fight or flight” impulses to handle danger or stress. 

But it is also doing something else: It’s listening to us inside. Anatomists have known for over a century that roughly 80% of its fibers carry information upward, from body to brain. Think of it as a two-lane highway with far more traffic headed north. What scientists are just beginning to understand in detail is what those signals are saying. 

Liberles is decoding the vagus with molecular precision and finding that its messaging system is unexpectedly diverse. So far, his research has uncovered dozens of types of vagus nerve cells, each wired to a specific organ. Team Red relays information about the heart; Team Blue, the gut.

Within those teams, each courier has a unique job that’s different from those all its teammates perform. Liberles found 10 types in the lungs alone. Until then, only one lung reflex had ever been identified, in 1868. One nerve courier carries information about breathing rate; another the stretch of your lungs; yet another information about airway threats, like food going down the wrong pipe.

“It’s super exciting to think about what each of these neurons is doing,” he told me in a conversation last fall, a flash of intensity breaking through the calm. “Where does it go in the body? What is it sensing? What is it controlling?”

The doors of the cell

Liberles is mapping the vagus information highways. But highways need on-ramps for signals to enter. For years, one of neurobiology’s biggest mysteries was the molecular on-ramp for our sense of touch.

Somewhere, something in our bodies was converting physical force into an electrical signal that the nervous system could understand. But no one knew how. 

Solving that mystery required a scientist willing to trust a hunch when the data couldn’t show the way. 

Ardem Patapoutian grew up in Lebanon and fled the country’s civil war at 18, landing in Los Angeles, where he delivered pizzas and wrote horoscopes for a local newspaper before falling in love with science at UCLA.

In the 1990s, as a postdoc at the University of California, San Francisco, he became fascinated with our sense of touch—the last of the five major senses not yet understood at the molecular level. The lung stretch signal that Liberles’s vagus neurons carry to the brain? No one had ever figured out how that signal began.

“How do you feel the embrace of a loved one? How do your fingers distinguish one texture of hair from another?” Patapoutian invites us to wonder in his 2021 Nobel Prize lecture. The problem: Most cellular communication works through chemistry. But mechanical force offers no molecule to bind. How does the body translate physical pressure into the electrochemical language that neurons speak?

Scientists knew that the answer had to be an ion channel—a protein gate embedded in cell membranes that opens to let electrically charged particles into the cell. But tracking down the one responsible for touch turned out to be absurdly difficult. Ion channels are a hundred thousandth the size of a cell, invisible to ordinary microscopes. Worse, they don’t resemble each other. You can’t recognize one by its shape or its sequence of amino acids. Even with one right in front of you, nothing would tell you it was there.

At Scripps, where he works now, Patapoutian decided to try an unusual approach. He’d try to find cells that showed sensitivity to touch and destroy their internal genetic blueprint one gene at a time—hunting for the move that would make the cell go numb. It was tedious, expensive, and possibly a dead end. “A lot of people made fun of us,” he says.

Two years in, Patapoutian’s collaborator Bertrand Coste had burned through half his postdoctoral appointment with no results. Patapoutian said: Another 30 genes, and then we decide whether to continue.

What kept them going, Patapoutian told me, was informed intuition. “As you gain more experience, you have this sense of what’s going to work, what’s not going to work. Sometimes the data cannot answer the question of when to stop or when to continue. There has to be another process. If you start trusting it, it gives you an avenue to continue.”

Coste knocked out candidate gene 72. Flatline. The cell had gone numb.

They’d found it—the mechanism behind something you feel every day.

They named the protein they identified PIEZO, from the Greek piezi, meaning pressure. There are two variations, PIEZO1 and PIEZO2, each responsible for sensing different kinds of pressure in the body. They’re elegant in their design—over 2,500 amino acids folded into a three-bladed propeller-shaped gate embedded in cell membranes. When pressure stretches the membrane, the gate opens and electrically charged ions flood through, translating physical pressure into an electrical signal that the brain can understand—all within milliseconds.

Patapoutian calls scientific discovery a dream that survives reality. He won the Nobel Prize in medicine in 2021 for his discovery of PIEZO, sharing the award with David Julius of UCSF for his work on how cells sense temperature. Now researchers are finding PIEZO proteins everywhere—skin, organs, blood vessels, and even red blood cells, where they help the cells squeeze through narrow capillaries. They’re how your brain knows where your hand is in space without looking at it, a sense called proprioception. They’re in plants too, enabling roots to sense pressure as they push down into the earth.

PIEZO was just the beginning. With a $14.5 million grant from the US National Institutes of Health, Patapoutian and his collaborators are now mapping the body’s entire interoceptive system—as many internal senses as he can find, he says.

Patapoutian has translated his discovery into a unique form of public outreach. At scientific conferences, he sometimes rolls up his sleeve mid-lecture to reveal half his arm covered in ink—a gigantic PIEZO protein in exquisite anatomical detail, its blades spreading across his biceps. Then he flexes. The tattoo flexes with him, the structure bending exactly as the real protein does when pressure opens the gate.

“At a pub or a party,” he explains, smiling, “how else would I demonstrate this beautiful structure?”

Orchestrating the field

Steve Liberles is mapping a major interoception highway. Ardem Patapoutian discovered the gates of touch. Meanwhile, Wen Chen at the National Institutes of Health is pulling the field together, putting neuroscientists, immunologists, physiologists, and clinicians into the same room. The demand, she says, has been enormous.

She tested her pitch at a dinner party with NIH colleagues a few years ago. You’re hungry right now—that’s interoception. You’re thirsty—that’s interoception. Heads nodded as she pointed around the table.

“We can’t have just the brain or just the body,” she told me. “We need to look at the whole person.”

In 2018 she organized a symposium on interoception where Liberles was one of the invitees, along with researchers and practitioners of meditation and yoga. “It was not their thing,” she says, laughing as she recalls how uncomfortable some of the researchers looked. But the practitioners were excited to finally meet scientists who were studying the inner mechanisms of what they did.

That was followed by a series of NIH workshops on interoception that spanned topics from basic science to clinical practice. Patapoutian was the keynote speaker for the first one. 

The NIH began funding scientists to chart the neural circuits of interoception and bringing them together to talk about their findings. Partway through one of these meetings, the equipment failed for an hour. More than 1,000 people stayed online, waiting for it to come back.

“We were shocked at the turnout,” she says. “There was much bigger interest than we could have imagined.”

Chen is now building infrastructure to match the demand: a formal community, funding mechanisms, a venue where cardiologists and neuroscientists and clinicians can all find each other. And she’s redefining the field as she goes; interoception is not a one-way signal from body to brain but a continuous two-way communication system, each direction shaping the other in real time. 

Liberles’s nervousness on stage is that two-way loop in action. Signals from his racing heart and belly butterflies travel up to the brain, which weaves them into an interpretation: This is anxiety, and this is what to do to handle it. His actions produce fresh signals that the brain reads in light of its ongoing predictions about what will happen next. In the body-brain communication loop, each player constantly updates the other.

I asked Wen what her work on interoception might mean for another inner sense: intuition. “People talk about ‘gut feelings,’” I said. “How does that relate to interoception?”

“Intuition might be the bridge where interoception moves from unconscious processing to conscious awareness,” she answered. “If that’s true, then intuition is not magic. It’s physiology.”

But it depends on how we read the signals. Intuition is like pain. It tells you something, but it’s not always clear what. “Perhaps we can treat intuition as a source of data,” she says. “Meaningful, but probably not complete.”

“Maybe we can be grounded in both—in feeling and fact.”

Which raises a more personal question: What do you do with the signals your body is sending?

One avenue for exploration is therapeutic intervention—both pharmacological and neural stimulation. Vagal nerve stimulation has treated epilepsy and depression for four decades, but as Liberles puts it, it’s like pressing all the keys on the piano to hit one note. Weight-loss drugs like Ozempic act in part through vagal pathways but can cause nausea as a side effect, because the targeting isn’t precise enough. Map the body’s circuits with enough accuracy and you might hit the note you actually want.

Another area of active research is psychological and behavioral—teaching people how to detect and even shape interoceptive signals. Low interoceptive awareness is linked to mental-health disorders and stress-related physical conditions. But like emotional intelligence, it’s not fixed. Researchers are finding that people can boost their body awareness by, for example, learning to detect their heartbeats from the inside—now a common measure of interoceptive awareness. Other interventions focus on body-based therapies and conscious activation of the parasympathetic “rest and digest” system to improve emotional and physical well-being. The placebo effect is another example of the mind acting on the body through expectation alone.

The signals we once dismissed as vague feelings—when your gut tightens before you know why, when your body says yes or no before your mind catches up—those are real. How we interpret them and whether we act on them is another frontier.

It’s clear that gut feelings play a role in scientific research, especially when the path forward looks foggy. Patapoutian’s informed intuition kept him and his colleagues going long enough to find PIEZO, a reminder that major discoveries often start with a hunch that is later tested against evidence. Chen puts it well: Maybe we can be grounded in both feeling and fact.

Update

This story was updated to include information on Lisa Feldman Barrett's work.

...

Katherine W. Isaacs is a writer and senior lecturer at the MIT Sloan School of Management. Her teaching and research focus on the intersection of psychology, technology, and innovation. Originally trained as a biologist and later as a social psychologist, she is currently working on a book called Gut Feel, about intuition, interoception, and embodied decision-making.

5 amazing visuals show how the male fruit fly’s brain map is advancing neuroscience

Mike's Notes

The brain's structural complexity is fascinating.

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Last Updated

29/09/2026

5 amazing visuals show how the male fruit fly’s brain map is advancing neuroscience

By: Michał Januszewski & Viren Jain
News from Google: 03/09/2026, Updated 21/09/2026

Michał Januszewski: Research Scientist, Google Research.

Viren Jain: Research Scientist, Google Research.

...

A years-long project by HHMI Janelia, Google Research, and collaborators has built the first complete brain map for a male fruit fly, a key model organism in science.

Updated September 21, 2026

For the first time, scientists have mapped every single neural connection in the brain and central nervous system of an adult male fruit fly. In this years-long project by HHMI Janelia Research Campus, Google Research, a team in Cambridge, U.K., and collaborators from the scientific community, this map of the male fruit fly brain includes a record-breaking more than 166,000 neurons. It’s a big step in advancing neuroscience experiments on this key model organism.

AI is making it possible for scientists and researchers to exponentially scale projects in the field of connectomics, which precisely reconstruct the connections between brain cells. This new complete brain map, a first for a male fruit fly, builds on the earlier release of a complete female fruit fly brain map, and promises to be a foundational resource for neuroscience for years to come.

Today, we’re sharing five images from the project.

1. A record-breaking map: charting more neurons than ever before

Angled brain map of the male fruit fly

This image shows selected neurons in the male fruit fly’s brain and ventral nerve cord, which is analogous to a spinal cord.

Like humans, flies do most of their sensing using organs located on their heads, including two huge compound eyes and a retractable proboscis that extends to detect smell and ingest liquid food. Neurons in these sensing organs detect external information and pass the signal through pathways that eventually reach the motor neurons that control movement.

2. Brain + nerve cord: Connecting sensing to actions using AI

Male fruit fly brain map when viewed from above

When seen from above, the fruit fly’s massive eyes and central brain stand out. They connect via a thick cord of nerves to the body, where motor neurons control behavior. This map was created by taking thin sections of a fruit fly brain and body, imaging each slice, and then using computers and AI to combine millions of 2D images to create 3D neural shapes. Knowing the structure of the brain allows neuroscientists to understand the mechanisms behind brain function.

3. Inside the black box: Visualizing almost 11,700 types of neurons

Male fruit fly CNS cell types. 0:32

(Data acquired and analyzed by the FlyEM Project Team at HHMI-Janelia, the Cambridge Connectomics Group, and Google Research. Video by Philip Hubbard.)

This video shows some of the 11,691 types of neuron cells in the male fruit fly’s central nervous system, which includes the brain and ventral nerve cord. Neurons can be categorized by size, shape, function, gene expression, or other factors. This visualization begins with neurons at the core of the brain and body. It then gradually moves to outer layers and, finally, to neurons at the extremities. Computing and AI helped human experts classify more than 166,000 neurons.

4. Vive la différence: Brain differences between male and female fruit flies

Sexual dimorphism in the fruit fly central nervous system. 0:56

(Data acquired and analyzed by the FlyEM Project Team at HHMI-Janelia, the Cambridge Connectomics Group, and Google Research. Female data acquired by the FlyWire project. Video by Philip Hubbard and Isabella Beckett.)

While most neurons in male and fruit females are the same, or isomorphic, a minority are sex-specific. A third category of neurons are “dimorphic,” existing in both males and females but connecting to different neighboring neurons. These neighbors may be isomorphic, the same in both male and female, or sex-specific, or even dimorphic themselves. This video shows one example, for the neural type AOTU012 (blue) that plays a role in processing sensory and taste inputs. While paired AOTU012 neurons exist in both male (left) and female (right) fruit fly brains, the AOTU012 connect to both similar (green) and different (red, orange and yellow) neurons in male and female fruit flies.

5. Fly see, fly do: Connecting stimulus to motion

Example visual-motor pathway in the fruit fly. 0:51

(Data acquired and analyzed by the FlyEM Project Team at HHMI-Janelia, the Cambridge Connectomics Group, and Google Research. Video by Philip Hubbard and Alexandra Fragniere.)

The new brain map of the male fruit fly includes visual-motor pathways. These connect the visual neurons, which help the fly detect its environment, to motor neurons, which help it move in response. This video shows an example of such a pathway, going from the R1-R6 visual neurons (purple) to the DNg13 motor neuron (green). In between are several intermediate steps, including the male-specific LoVP92, named for the so-called “love spot,” that plays a role in courtship behavior.

Three companion studies also released today apply the new brain map to studying visual systems, taste, and social behavior. Read more about this groundbreaking project, and about our ongoing efforts to map full vertebrate brains, on the Neural Mapping website and in the Google Research Blog post.

Sizing Up the Ghosts in the Machines

Mike's Notes

Very true.

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Last Updated

15/09/2026

Sizing Up the Ghosts in the Machines

By: David Krakauer
Santa Fe Institute: 01/09/2026

David Krakauer: David Krakauer, President of the Santa Fe Institute.

...

A BEYOND BORDERS column by David Krakauer, President of the Santa Fe Institute.

...


Diagram of the Human Mind , Robert Fludd, 1617, via Public Domain Review

All of science is in the business of exorcism. When philosopher Gilbert Ryle coined “the ghost in the machine” in The Concept of Mind (1949), he was identifying an unnecessary explanatory entity in Cartesian dualism and expelling it. Descartes had posited a res cogitans, a thinking substance categorically distinct from the mechanical body. Ryle diagnosed this as a “category mistake,” and explained it away in the manner an Oxford professor does any superstition: like being shown the colleges, library, and playing fields of the university, and still asking the benighted question, “But where is the University?”

What Ryle did for mind, other sciences have done for their own spectral inhabitants. But the ghosts differ in kind, and so do their rites of exorcism. Physics exorcises supernumerary particles — unnecessary free parameters in pursuit of universality. Biology exorcises redundant processes — divine or teleological agencies. And the sciences of intelligence exorcise imposed patterns — transcendent sources of cognition. Each tradition seeks minimality, yet each means something profoundly different by it.

The deepest ambition of physics has always been to reduce the number of independent facts the universe requires us to accept. Theoretical physicist Eugene Wigner observed that symmetry and invariance principles act as filters on possible theories, eliminating free parameters with a scandalous efficiency. And Einstein’s general relativity derived gravitation from the minimal geometric postulate that spacetime curvature is gravity, eliminating Newton’s action-at-a-distance.

Biology’s ghost was never a free parameter but an agent. Before Darwin, the complexity of organisms demanded an intelligent designer the way a watch implied a watchmaker. On the Origin of Species (1859) performed an exorcism on the demiurge itself and replaced a transcendent creative process with a mechanical one. The ghost to be exorcised is the unnecessary rule, an act of God or Lamarckian inheritance. What remains after exorcism is not the universal parameterization of physics, but a universal mechanism (selection) that operates locally and iteratively.

Alan Turing showed in 1936 that a device of absurd simplicity consisting of a tape, a head, and a finite set of states could compute anything computable. Warren McCulloch and Walter Pitts demonstrated in 1943 that networks of binary threshold neurons could instantiate logical operations. Both of these exorcisms expelled patterns of architectural extravagance that Descartes and his followers had imposed on the mind. David Marr, in his 1969 model of cerebellar cortex, proposed a single, repeating architecture consisting of Purkinje cells trained by climbing-fiber error signals, that could learn arbitrary input–output mappings. Computation of near arbitrary complication could be solved through scale.

Computer scientists build architectures that seek to be spirit-proof. When physicists criticize biology for having too many parameters, they are applying parametric parsimony where processual parsimony is the goal. And when biologists accuse neuroscience of ignoring evolutionary constraint, they are importing processual parsimony into a domain governed by architectural parsimony. Each field is haunted by a different ghost, exists in a different intellectual bardo, each governed by its own rituals.

The old disciplinary ghosts aspired to be ontological, frightening entities posited to occupy ordered states of reality, from which ensuing and more skeptical generations banished them. We now have epistemic ghosts, patterns in large datasets, manifesting as regularities, correlations, and structures, that no human theorist seems to have previously named or noticed. LLMs suggest that we have been haunted by vast domains of regularity, in language, protein folding, weather, and genomics, that are simply too high-dimensional for human intuition to observe but not too complex for a sufficiently scaled statistical model to discern.

The ghosts are multiplying, many of them hallucinations, and scientific exorcists must learn new rites.

— David Krakauer

President, Santa Fe Institute

From the Summer 2026 edition of the SFI Parallax newsletter. Subscribe for our monthly e-Parallax, or email “news at santafe.edu” to request quarterly home delivery in print.

The curious life of a clever slime mold

Mike's Notes

Slime Moulds are one cell, yet perform tricks of memory. From Knowable Magazine.

This example from nature is one of the many reasons why Pipi is modelled on how biological cells work.

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Last Updated

10/09/2026

The curious life of a clever slime mold

By: Tim Vernimmen
Knowable Magazine: 11/02/2026

Tim Vernimmen: Tim Vernimmen is a freelance science writer based near Antwerp, Belgium. For this article, he was hoping to interview Physarum itself, but scientists are still working out how to do that.

...

In its quest to feed, avoid nasty substances and just generally live its life, the brainless, one-celled Physarum polycephalum performs some impressive tricks of learning and memory

...

Sixteen years ago, a brainless, unicellular organism blew our human minds. And it continues to fascinate and surprise researchers to this day.

Scientists had known that some slime molds of the species Physarum polycephalum consist of one giant, pulsating cell that keeps changing shape as it moves around and branches out to access food and avoid unpleasant things like salt or light. But it took a 2010 experiment led by Japanese biologist Toshiyuki Nakagaki of Hokkaido University to reveal the depths of its sophistication. When Nakagaki placed the oat flakes that Physarum likes in a pattern mimicking the cities surrounding Tokyo, the slime mold’s branches almost exactly reproduced the efficient transport connections between them that humans had taken years to develop.

From the center of a petri dish, the slime mold Physarum polycephalum extends branches to find food in this time-lapse video.

CREDIT: © DUSSUTOUR / CNRS

To Karen Alim, a theoretical physicist starting a postdoctoral project at Harvard University at the time, that study was a revelation. “I was like, ‘Wow, this is so crazy.’ A single cell that solves complex tasks appealed very much to me as a physicist.” Perhaps, Alim thought, she could apply her training to make sense of this clever creature with its network of contractile tubes and constantly pulsating currents.

So Alim and colleagues grew Physarum on a jelly-like substance called agar and carefully watched and recorded its behavior under the microscope. They measured the strength and direction of the fluid flow in its network of tubes. Then they simulated what they’d seen in mathematical models.

The result? Through studies like this, as Alim recounts in the Annual Review of Condensed Matter Physics, she has become convinced that the flow of fluid can be a way of transmitting information, and she’s working to understand the underlying mechanisms. Other researchers, meanwhile, are continuing to uncover new, intriguing behaviors in Physarum, a creature that appears able to learn, remember and make decisions — all without a brain.

Photograph of Karen Alim holding up a petri dish on which a slime mold is growing.

Researcher Karen Alim (right) and her colleagues grow Physarum polycephalum in petri dishes containing a nutrient-rich agar medium.

CREDIT: STEFAN WOIDIG / TUM

The flow of memory

Though Physarum is a single cell, the large body it forms can often be easily seen by the naked eye, growing to more than a foot in diameter under favorable conditions. It looks like a central blob from which a network of vein-like tubes emanates — larger tubes, then smaller tubes that fan out from them. Inside those tubes, cytoplasmic fluid is rhythmically flowing back and forth, supplying all parts of the cell with what they need. In nature, the slime mold is found in damp, dark spots like forest floors and decaying logs.

Many of the studies revealing Physarum’s unexpected skills revolve around its most important concern: finding food. Whenever Physarum encounters something edible, the outer wall of tubes near the food become soft. As a result — due to the pressure of the constantly moving fluid inside its tubes — that part of the body spreads out like a fan. This fan then slowly morphs into a network of even tinier tubes. Under the microscope, this looks like a river delta network of yellow slime feeding into the larger tubes of Physarum’s body.

How does it happen? Alim, who now works at the Technical University of Munich in Germany, figured out that encounters with food lead to an increase in local fluid flow within the tubes. This exerts greater shear force on the tube walls. The walls in that region grow thinner, allowing the tubes to expand.

Inside the slime mold Physarum polycephalum’s branching, pulsating body, currents of fluid flow back and forth to transport food and other molecules. These currents are key to the organism’s ability to move, change its shape and learn.

CREDIT: DELESCLUSE & DUSSUTOUR / CNRS

The opposite happens when Physarum encounters something awful like salt or light that it wants to get away from. In response to a repellent, the tube walls stiffen and contract, which redirects fluid flow elsewhere.

In sum, researchers now understand that where the flow is stronger, the tubes expand, and where the flow is weaker, they shrink. This interplay of shrinking and expansion in different areas of the body is what reorganizes the shape of Physarum’s tube network, causing it to approach food and avoid things like salt.

More recently, Alim and colleagues discovered just what creates a tube network as efficient as Tokyo’s transport links. It ties into something crucial about the fluid flow in Physarum’s body: Tube walls respond to changes in flow with some delay. First the flow increases. Then, slightly later, the tube expands in response, causing the flow to decrease. This causes the tube to shrink, again with some delay.

The result, Alim found, is that the best-positioned tubes will grow larger and larger and receive more and more flow, while others will fade away — and hence, over time, a super-efficient network of links will form.

Put another way, Alim adds, you could say that the shape of the network (and its underlying fluid flow dynamics) helps Physarum to remember. Appropriately sizing its branches in accordance with food sources it has encountered recently makes for a simple but effective way to recall where food can be found.

Recent work in Alim’s lab suggests it’s not just the shape of the network that helps Physarum remember, but also how, when and where it contracts the walls of its branches. For example, she says, putting food in a certain location leads the slime mold to respond with a certain pattern of contractions and move toward the food. Between experiments, the contraction pattern diminishes, but if food is put in the same spot, it reappears, more quickly than before. In one experiment, a persistent wave of contractions caused a slime mold to keep crawling in one direction for hours to get away from a light source, long after the light had been switched off, which suggests it still remembered it.

Like all of us, Physarum polycephalum has its food preferences, as this time-lapse video shows.

CREDIT: © DUSSUTOUR / CNRS

Salt and slime

The finding is reminiscent of a study by Audrey Dussutour, a biologist working on the same species, now at the National Centre for Scientific Research in France. In 2019, Dussutour had reported something interesting: After a few attempts, Physarum took less time to cross a nasty salty patch inside its dish while moving toward a food source — implying some kind of learning. The effect remained even after the slime mold had spent time in the dormant state it adopts under stressful conditions.

Since the slime mold absorbed and retained some salt, it’s possible that this lowered the shock of encountering it again and allowed it to move faster, says Dussutour. So in a recent experiment, as yet unpublished, she used light as the repellent instead. Physarum still shaved down its travel time with repeated exposures, even though light isn’t retained the same way salt is. Dussutour suspects that contraction patterns may persist and store information “similar to the way waves of activity in our brain can store information,” she says.

In addition to the information stored in the layout and contractions of its tubes, says Dussutour, Physarum has another way to “remember”: the trail of slime it leaves wherever it goes. “Avoiding slime is a convenient way to make sure it’s exploring new places rather than retracing its own trail,” she says.

In the wild, Physarum polycephalum is often found on dead plant material, as shown in this time-lapse video.

CREDIT: © DUSSUTOUR / CNRS

Dussutour was also able to show that slime molds can learn about each other: They are sensitive to aspects of each other’s behavior. “They will approach others that have access to food, and avoid ones that are starving or stressed,” she says. “Remarkably, they also prefer to approach young individuals.”

Older slime molds become very slow and fragile, she adds. “We have some in the lab that are now 5½ years old…. We hardly dare to use them anymore. But intriguingly, when they go through dormancy, or fuse with a younger individual, it’s as if they’re young again.”

For a better understanding of the slime molds’ mysterious ways, it would be very helpful to find out what exactly they’re up to in the wild, says behavioral ecologist Tanya Latty of the University of Sydney. “Almost everything we know about their behavior is based on experiments done in a lab,” she says — experiments that focus on the large, multi-nucleus forms of the creatures, not the single-nucleus, microscopic amoeba state in which they spend most of their lives.

So Latty’s research group has been collecting wild slime molds to investigate. “They’re often found on rotting logs, but we’ve also found them in the leaf litter just in front of our building. People have also found them on house plants. They’re everywhere,” she says.

Latty suspects that the large form, with its various ways of learning, allows Physarum to consume a lot more food in preparation for making the spores it needs to spread. Physarum may be far less clever in its microscopic form, she adds, if its surprising behavior really depends on its ability to branch and contract its tubes. “But who knows? We didn’t think they were capable of anything when we started to study them.”

10.1146/knowable-021126-1

Live 4K video of Earth and space: 24/7 Livestream of Earth by Sen’s 4K video cameras on the ISS

Mike's Notes

Just beautiful.

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25/04/2026

Live 4K video of Earth and space: 24/7 Livestream of Earth by Sen’s 4K video cameras on the ISS

By: Sen
Sen: 25/04/2026

Sen’s vision is to democratise space through video to inform, educate, inspire, and benefit all of humanity. Sen’s mission is to stream real-time video from space to billions of people, gathering news and information about Earth and space and making the data universally accessible and useful.

Watch Earth Live and in 4K from Sen's video cameras on the International Space Station, downlinked via NASA. This is the world’s first continuous 4K livestream from space, empowering you to see our planet like astronauts do.

Universe Is Not a Computer Simulation, New Study Says

Mike's Notes

I'm glad they finally figured this one out.

In case there are any other confused people out there, Nature is 100% analogue. 

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  • Mir Faizal et al. 2025. Consequences of Undecidability in Physics on the Theory of Everything. Journal of Holography Applications in Physics 5 (2): 10-21; doi: 10.22128/jhap.2025.1024.1118

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24/01/2026

Universe Is Not a Computer Simulation, New Study Says

By: News Staff
SciNews 30/10/2025

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A team of physicists from Canada, the United States, the United Kingdom and Italy has mathematically shown that our Universe is built on a type of understanding that exists beyond the reach of any algorithm.

“It has been suggested that the Universe could be simulated,” said Dr. Mir Faizal, a physicist at the University of British Columbia Okanagan.

“If such a simulation was possible, the simulated Universe could itself give rise to life, which in turn might create its own simulation.”

“This recursive possibility makes it seem highly unlikely that our Universe is the original one, rather than a simulation nested within another simulation.”

“This idea was once thought to lie beyond the reach of scientific inquiry.”

“However, our recent research has demonstrated that it can, in fact, be scientifically addressed.”

“Our research hinges on a fascinating property of reality itself.”

“Modern physics has moved far beyond Newton’s tangible ‘stuff’ bouncing around in space. Einstein’s theory of relativity replaced Newtonian mechanics. Quantum mechanics transformed our understanding again.”

Today’s cutting-edge theory — quantum gravity — suggests that even space and time aren’t fundamental. They emerge from something deeper: pure information.

“This information exists in what physicists call a Platonic realm — a mathematical foundation more real than the physical Universe we experience. It’s from this realm that space and time themselves emerge.”

The authors demonstrated that even this information-based foundation cannot fully describe reality using computation alone.

They used powerful mathematical theorems — including Gödel’s incompleteness theorem — to prove that a complete and consistent description of everything requires what they call non-algorithmic understanding.

“Think of it this way. A computer follows recipes, step by step, no matter how complex. But some truths can only be grasped through non-algorithmic understanding — understanding that doesn’t follow from any sequence of logical steps,” they said.

“These Gödelian truths are real, yet impossible to prove through computation.”

“Here’s a basic example using the statement, This true statement is not provable.”

“If it were provable, it would be false, making logic inconsistent. If it’s not provable, then it’s true, but that makes any system trying to prove it incomplete. Either way, pure computation fails.”

“We have demonstrated that it is impossible to describe all aspects of physical reality using a computational theory of quantum gravity,” Dr. Faizal said.

“Therefore, no physically complete and consistent theory of everything can be derived from computation alone.”

“Rather, it requires a non-algorithmic understanding, which is more fundamental than the computational laws of quantum gravity and therefore more fundamental than spacetime itself.”

“Since the computational rules in the Platonic realm could, in principle, resemble those of a computer simulation, couldn’t that realm itself be simulated?”

“No. But our work reveals something deeper.”

“Drawing on mathematical theorems related to incompleteness and indefinability, we demonstrate that a fully consistent and complete description of reality cannot be achieved through computation alone.”

“It requires non-algorithmic understanding, which by definition is beyond algorithmic computation and therefore cannot be simulated. Hence, this Universe cannot be a simulation.”

According to the team, the findings have profound implications.

“The fundamental laws of physics cannot be contained within space and time, because they generate them,” said Origin Project Foundation researcher Dr. Lawrence M. Krauss.

“It has long been hoped, however, that a truly fundamental theory of everything could eventually describe all physical phenomena through computations grounded in these laws.”

“Yet we have demonstrated that this is not possible. A complete and consistent description of reality requires something deeper — a form of understanding known as non-algorithmic understanding.”

“Any simulation is inherently algorithmic — it must follow programmed rules,” Dr. Faizal said.

“But since the fundamental level of reality is based on non-algorithmic understanding, the Universe cannot be, and could never be, a simulation.”

The study was published in the June 2025 issue of the Journal of Holography Applications in Physics.


Consequences of Undecidability in Physics on the Theory of Everything

By: Mir Faizal, Lawrence M. Krauss, Arshid Shabir, Francesco Marino
ArXiv: 29/07/2025

Abstract

General relativity treats spacetime as dynamical and exhibits its breakdown at singularities. This failure is interpreted as evidence that quantum gravity is not a theory formulated within spacetime; instead, it must explain the very emergence of spacetime from deeper quantum degrees of freedom, thereby resolving singularities. Quantum gravity is therefore envisaged as an axiomatic structure, and algorithmic calculations acting on these axioms are expected to generate spacetime. However, Gödel’s incompleteness theorems, Tarski’s undefinability theorem, and Chaitin’s information-theoretic incompleteness establish intrinsic limits on any such algorithmic programme. Together, these results imply that a wholly algorithmic “Theory of Everything” is impossible: certain facets of reality will remain computationally undecidable and can be accessed only through non-algorithmic understanding. We formalize this by constructing a “Meta-Theory of Everything” grounded in non-algorithmic understanding, showing how it can account for undecidable phenomena and demonstrating that the breakdown of computational descriptions of nature does not entail a breakdown of science. Because any putative simulation of the universe would itself be algorithmic, this framework also implies that the universe cannot be a simulation.

...

Groundbreaking visuals capture how our bodies repair damaged DNA

Mike's Notes

Nature is not digital. Beautiful work by animator Drew Berry.

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20/01/2026

Groundbreaking visuals capture how our bodies repair damaged DNA

By: Drew Berry
Aeon: 9/01/2026

The biomedical animator Drew Berry is known for his dazzling visualisations of biological processes that unfold on microscopic scales.

https://youtu.be/lWbXGIuCsmo?si=2w7e4uPwTKv5HQNP

The biomedical animator Drew Berry is known for his dazzling visualisations of biological processes that unfold on microscopic scales. As enlightening as it is arresting, his imagery straddles the line between science and art, as seen in his work as the in-house animator for the Walter and Eliza Hall Institute of Medical Research (WEHI) in Melbourne, Australia, and in his music video collaboration with Björk. This animation illustrates a process called homologous recombination, in which specialised proteins repair damaged DNA by using an intact copy as a template – failures of which can increase one’s risk of cancer. Through this glimpse into the worlds within us, Berry highlights the intricate biology that plays out inside each of us unseen, shaped by millennia of evolution.

Video by the Walter and Eliza Hall Institute of Medical Research

Animator: Drew Berry

A timeline of Earth's average temperature

Mike's Notes

This has to be one of the coolest visualisations.

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18/06/2025

A timeline of Earth's average temperature

By: Randall Munroe
xkcd: 12/09/2016




Moving Naturalism Forward

Mike's Notes

My friend James Miller sent me a link to this workshop recording. Three days of discussion on YouTube. 

Sean Carroll, Jerry Coyne, Richard Dawkins, Terrence Deacon, Simon DeDeo, Daniel Dennett, Owen Flanagan, Rebecca Goldstein, Janna Levin, David Poeppel, Massimo Pigliucci, Nicholas Pritzker, Alex Rosenberg, Don Ross, and Steven Weinberg are among the participants.

I have been watching the whole series.

This information comes from the website of physicist Sean Carroll.

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17/05/2025

Moving Naturalism Forward

By: Sean Carroll
YouTube: 08/05/2018

An Interdisciplinary Workshop - Oct. 25-29, 2012

Over four centuries of scientific progress have convinced most professional philosophers and scientists of the validity of naturalism: the view that there is only one realm of existence, the natural world, whose behavior can be studied through reason and empirical investigation. The basic operating principles of the natural world appear to be impersonal and inviolable; microscopic constituents of inanimate matter obeying the laws of physics fit together in complex structures to form intelligent, emotive, conscious human beings.

In the public sphere, debates continue between naturalism and spiritual or religious or dualistic worldviews, and those debates are worth having. But it is also important for those committed to naturalism to address the very difficult questions raised by replacing folk psychology and morality by a scientifically-grounded understanding of reality. We would like to understand how to construct meaningful human lives in a world governed by the laws of nature. Some specific questions include:

  • Free will. If people are collections of atoms obeying the laws of physics, is it sensible to say that they make choices?
  • Morality. What is the origin of right and wrong? Are there objective standards?
  • Meaning. Why live? Is there a rational justification for finding meaning in human existence?
  • Purpose. Do teleological concepts play a useful role in our description of natural phenomena?
  • Epistemology. Is science unique as a method for discovering true knowledge?
  • Emergence. Does reductionism provide the best path to understanding complex systems, or do different levels of description have autonomous existence?
  • Consciousness. How do the phenomena of consciousness arise from the collective behavior of inanimate matter?
  • Evolution. Can the ideas of natural selection be usefully extended to areas outside of biology, or can evolution be subsumed within a more general theory of complex systems?
  • Determinism. To what extent is the future determined given quantum uncertainty and chaos theory, and does it matter?

This workshop brought together a small number of researchers and writers to tackle the project of moving naturalism forward by making progress on these issues. We met for three days of focused discussion and debate at the Red Lion Inn in Stockbridge, Massachusetts. Full videos of the proceedings are freely available online.

Interview with James Miller

Mike's Notes

Here is a fascinating video interview I did with my friend James "Jim" Miller on 13 December 2024. Jim lives in Seattle, USA.

He wrote a series of essays, including Universal Evolution, Probability, and Life's Origins, which are available on his SubStack.

I published his essay previously.

Any errors in the interview are due to my still learning how to drive Zoom.

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18/04/2025

Interview with James Miller

By: Mike Peters
Zoom: 13/12/2024

Mike is the inventor and architect of Pipi and the founder of Ajabbi.

Interview