313 karma · joined July 8, 2025
But speed isn’t all that useful, here. Neuronal activity is slow, but you can cancel it out, and control it mid firing. You have subdendritic and sub-axonal processing, so you can shoot off a signal, then tamp it down as it’s traveling, or ramp it up for some stretches of your axon, etc. Getting message fastest from cell A to cell B isn’t what we’ve needed. Rather, you get rich information that can have all kinds of impacts on cells along the way.
But it isn’t. Every neuron runs the core circadian transcription-translation feedback oscillations. Every neuron is on a roughly 24 hour loop, synchronized by the master circadian oscillator, a clump of about 20k cells called the Suprachiasmatic nucleus.
The faster oscillations nest under that one, including the oscillations in firing rates.
Jet lag is when the synchrony and phase hierarchy breaks. Shift work does the same.
Now the brain doesn’t have a fast global clock like a chip. But that’s very much part of the evolutionary design. It’s not very energy efficient to have a fast global clock. And in a system like the brain, what purpose would it serve? In the brain, timing is information. You want the slow arrival of some signal to be slow so you can actually assign some meaning to it. A fast global clock would throw those gaps away.
In fact, there are neuromorphic and RACE logic chips that dump the global clock for the same efficiency reasons.
We’re finding out though that the brain is, yes, a fluid dynamic system, an electromagnetic system (though we know way less about the magnetism that we’d like), AND a mechanical system. Wonder how many more ands we’d have to add by the time we figure it out.
I don’t think these studies quite rest the case. As Buzsaki comments in the article, the action is in the cells to create these waves. Do the waves themselves get measured and impact what happens next? The issue at hand is: synaptic currents are stronger and we know neurons respond to them. The wave behavior is in the extracellular fluid as well, and that part we have evidence neurons don’t respond much to.
That said, thing the article doesn’t talk about is astrocytes. Especially in the cortex, most synapses are tripartite. There’s an astrocytic end foot that sheathes the synapse and regulates how much of the bulk extracellular space has access to the synapse. And one astrocyte can touch thousands of synapses and in humans, hundreds of thousands. They also form a syncitium, through gap junctions/electrical synapses.
Do astrocytes respond to the extracellular wave behavior, which potentially changes the extent and behavior of the syncitium, and thus impact the neurons they touch?
That’s still an open question but that’s what I’d be interested to find out more about.
No such equivalent prompt saying “reproduce” can be found for evolution. And plenty of evolutions “products” in fact don’t reproduce, by choice or because they don’t find a mate who’ll take em, or because they have fundamental issues in their reproductive biology.
This is all aside from comparing a process that’s played out for about 4 billion years and declaring we’ve matched it because we got some agents to stay active for a bit of time by telling them to and giving them the energy they need, no questions asked. Certainly, evolution doesn’t give us any such comforts to carry out any “prompts” you can imagine it giving us, yet here we all are.
“ it runs continuously and makes decisions on its own (within the boundaries you’ve set)”
More importantly, this setup of any other, is feeding in time externally. The agents themselves have no internal sense of time.
Pretty much all of biology has endogenous rhythms at various timescales (some bacteria and archaea, that live very short lives, may not, but even they may have their metabolism under a rhythm. Viruses definitely don’t have one). These rhythms continue to tick even when external time signals (light availability in day vs night being the big one, and tidal forces, for marine life) are removed. That is, in constant conditions, the rhythms keeps ticking.
This temporal awareness is baked into every cell in our bodies. And entirely absent in AI models. Which is why all kinds of higher level things we hear about, like consciousness, feeling, knowledge… they don’t make sense for AI. A foundational aspect of agency in biology has been nixed out and we keep ignoring this.
> They're called agents because they can act on our behalf. Which they do.
That’s not how most AI companies describe their agents. They describe them as being capable of acting on their own behalf.
I get that in computers, you can have, say, a “user agent” that deterministically provides certain information or takes some action on behalf of the user.
AI companies clearly do not mean this when they say their models are “agentic”, otherwise calling them “rogue” would make no sense. A user agent that screws up didn’t do so for its own purposes did it?
The answer is a very clear no. And yet, these companies pretend like this fundamental fact is meaningless to the concept of agency.
The issue comes to the fore when you try to give these agents a prompt that allows them to stay active for long. Long range agency requires long range loops of activity.
Within such loops, these so called “agents” are curtailed by their context window, or, in multi agent scenarios, by the fact that their memory is a system of external notes, that they need to add to their context to make sense of, and depending on the content of these memories, this can take arbitrarily long time periods.
In dynamics, none of this matches any biological agent, down to a bacterium. Perhaps a viral life cycle has information dynamics that come close.
To me, it’s beyond odd we call these thing agents without acknowledging the clear differences in the dynamics of their behavior. We keep expecting them to have “human like” behavior, but that is entirely unfounded given the substrate differences between biological and artificial systems.
The sooner we learn the difference and explore the ways in which it matters, the better we’ll get at dealing with these systems without bias tinted glasses where what we want these systems to be blinds us to what they actually are.
This is always a problem when one tries to view biology through an engineering lens. The functions we see today emerged well after the genes themselves started on the path that allowed them to support these specific functions in us. Nor are the genes restricted to exactly identical functions even when their sequence is identical. The context of each cell matters.
Rather than beginning from external function and going down to find energy, replication and cancer/escape from multicellularity as factors affecting these organ’s behavior, it’s a lot better to go cell up, where metabolism, DNA replication, waste clearance, and cell to cell communication and cell-microenvironment sensing are all constantly having to be balanced.
The functions we see from ensembles of cells are composed of these cell level behaviors multiplexing.
And when we look at the eukaryotic cell, we don’t just see linear DNA. We also see mitochondria. Our mitochondria reproduce and proliferate in all cells, depending on energy requirements. The process also produces a lot of reactive oxygen species which need to be kept tamped down to prevent damage.
And the mitochondrial endosymbiotic event also potentially explains why we have linear DNA in a separate compartment. From first eukaryotic common ancestor (FECA) to the last eukaryotic common ancestor (LECA), you had two genomes inside one cell, and by the time we got to LECA a bunch of DNA from the alphaproteobacter that became mitochondria migrated to the core genome, leaving the mitochondrial genome to remain circular.
The exact time and reason for linearization of DNA is (as yet) lost to deep time. But we can see a path from two circular genomes to one linear one circular and construct a fairly believable hypothesis to why you got linearization: as cell type increased, you needed more transcript copies, and access to different transcripts at different times at different rates. A linear genome is much better able to accommodate these requirements. And this has resulted in prokaryotes also partially or fully linearizing some of their genomic material when the need arises (Cyanobacteria, the first autotrophs, have some strains with linear ends, and Lyme disease and streptococcus also break from full circularity).
This linearization is also critical for mitosis and meiosis.
As far as the exact causal chain, we are, at the moment, groping in the blind, since the FECA->LECA transition occurred some 2 billion years ago, and we don’t have candidate fossils. They are reconstructed from genomic puzzle pieces, which is why we have these holes.
In that transition timetable, it is possible commitments were made that shape everything we see today.
Beyond doubt, those commitments had to thread everything a single cell has to thread.
And then came multicellularity, which had its own tradeoffs.
Teleology doesn’t help because none of these early commitments were being made with the specifics of our current lifestyle in mind, or even that complex beings like us could exist.
Evolution is a blind watchmaker. Ignore that and you’ll end up with nice sounding ideas that may not quite fit what we see.
But the first complex multicellular life only appears about 1.6 BYA, and sexual reproduction and cell differentiation only about 1.2 BYA.
And no, I wouldn’t say eukaryotes have evolved faster or further, just differently. It’s questionable they’d be able to do any of this without the mitochondrial and chloroplast endosymbiotic events, and microbiomes have existed since the beginning as well. Framing it as a contest misses the point, in the end.
In some ways, it’s wrong to imagine the branches of life are actually branches. Loki archea and alphaproteobacter together gave us the last eukaryotic common ancestor, and then bacteria continued to live around and in eukaryotes.
That said, mitochondria can’t be called prokaryotes within us. They’ve given up too many genes, and can’t survive on their own.
Of course, the rest of us can’t survive without them either, so it’s a complete mutual situation.
However, we have ATP Synthase. That’s also an ion driven molecular rotary engine. Of course, we use it to convert ionic gradients to energy (ATP).
Both are exceptionally efficient molecules for their tasks.
Rodriques is CEO of Edison scientific, which is going all in on agentic biology. These problems are all benchmarkable, and have been selected to allow for agentic exploration. That is, the tool is driving the problem selection more than genuine value to the field in solving these problems.
Still, if someone takes any of this up and manages something, it’ll be cool.
The brain is a composit of cells from two lineages that separate very early in development and reflect a deeper spatial and functional separation deep in the history of metazoan (read: animal) evolution.
Tying all this to humans specifically is just confusing. This is something that’s seen in a substantial portion of animals, and as such has nothing to do with “ poetry, mathematics and wondering about our own origins”. These features of humans evolved hundreds of millions of years after this two lineage composite organization of animal brains evolved.
I wish the article hadn’t gone out of its way in confusing these issues to push the “relevance” of the research. It’s a pretty remarkable finding anyway.
However, the United States isn’t just a group of humans. It’s also a group of bison. Wild horses. Flies. Bacteria. Bats. Dung beetles. And whatever entity occupies the White House.
If the United States is conscious, it’s unclear why it’s consciousness stops at its fictitious, human imagined border. Except for humans, no other animal cares or knows when they cross the border.
So a much better claim can be made for the Earth and the entire web of life.
At which point we’re at Gaia hypothesis/Earth Systems science territory, and I’m fine with that too.
I still remain a materialist. And don’t consider the United States to be particularly conscious as an entity.
But yes, the I suppose a call to study ocean creatures can be more compelling with that’s name.
The interconnections between genes has led to proposals of “omnigenic” models, the idea that all genes expressed in a cell affect every given trait of the cell, to some extent.
When it comes to something like autism, it’s a word covering a vast number of traits and behaviors of many different cells that gives rise to that set of effects as seen from outside.
And the issue with genetic testing is, we often only look at specific regions of the genome. Even when we do whole genome tests, and compare whole genomes of autistic folks, what we find is no single origin but many overlapping patterns. No definitive set is found because we are looking at complex processes that have many nodes where mutations can mildly tweak the function. Many such functionally relevant mutations can chain together to give you the signatures of autism, and no two are the same.
All these reasons also point to why we are increasingly realizing autism isn’t a “disease” with a “cure”. It’s a way in which people can be people. It’s time society accepted that and expands itself to accommodate.
You mean sleep? Actually the answer is pretty complicated. Your body clock is very much on during sleep. It responds to temperature changes. Sound and light responsiveness is obviously dampened, but hardly absent.
You are unaware of wall clock time. You’re in an altered state of consciousness that needs your eyes closed after all. However, you are not timeless, nor is the entirety of your body and brain unaware of environmental signals for time.
> Humans don't do this either. You use context clues from the world around you. If I lock you in a room with no windows or a dark cave your timing senses can go all fucky really quick.
Again, that’s wall clock time. Our time perception does indeed get fucked up in total darkness. But our internal clock ticks on. I’d recommend reading about the Aschoff Bunker experiments, which first proved this rigorously.
> I mean, so is an agents harness. You can make as many loops as you'd like here.
An agents harness doesn’t touch its weights. A figure 8 on paper is a loop. That doesn’t mean it’s the same as a dynamical loop that’s self sustaining and internally organized.
Are you just reading the words and randomly grabbing related concepts to say nothing here is meaningful?
You and I are clusters of about 36 trillion cells that are all able to individually keep time. They synchronize and orchestrate their timekeeping, and entrain to the external environment, and there is a cluster of cells, the suprachiasmatic nucleus, that is the master orchestrator of circadian time, sitting right behind the eyes as light is the main signal it uses to tell external time.
We know its function can get dampened with age.
However, please note this is not how we perceive time, in the sense of being able to count 60 seconds and have it match the wall clock. That’s a subsystem. But the internal temporal order of your body is cell by cell, not dictated from one spot in your body.
Is that all it needs to do? A rock, in response to a sound signal (make it as informative as you want) can also be said to go from state A (molecules at rest) to state B (molecules vibrating in response to the sound). Is the rock a cognitive system?
Or let’s go up a level of complexity. Is a thermostat a cognitive system? It doesn’t just go from state A to B but measures changing stages against a reference. Is it a cognitive system?
> The time interval between these states can be arbitrary, it seems to me (setting aside problems with disconnecting the mind from its substrate, which does of course need rhythms at various frequencies; oxygen at a higher frequency than sugar, and so on)
Not sure how you land on this. Going from A to B, in your definition, is a purely internal state transition, right? If the motivation to go to state B is external (as will often be the case with a conscious agent), and the system is offline entirely while it switches from A to B, how is it to reverse or stall its transition if external signals contradict the earlier decision?
It’s a very bizarre definition of consciousness, that you don’t need to be in time. Seems to break the word beyond meaning, and allows it to be applied to any system capable of change.
> I'm not sure that going from A to B quickly, or slowly, or with intervals of a thousand years affects that entity's consciousness in of itself
It’s not about the speed of transition from A to B. Instead it’s about the internal processes being temporally commensurate, and entrainable to environmental periodicities.
All of biology (plants and many bacteria included) has its dynamics are organized around an internally generated rhythm. This rhythm entrains to the external environment, shifting its phase to match (mismatch leads to issues like jet lag: a place where your consciousness shows its temporal boundaries as it is abruptly subjected to an environment out of sync with its current phase tethered to another location). Crucially, the internal rhythm continues to run in isolated conditions (total darkness), and have been measured to be around 24 hours, but slightly off, within and across species (and the same holds for endogenous tidal rhythms, which also don’t exactly track tidal period left to themselves).
Everything, including learning and memory, but also sleep, sensory and locomotor function, shows organization around this internal temporal axis. The key advantage this gives, evolutionarily, is anticipation. The sunflower rises to face the east, not in reaction to sunrise, but in advance of it (many lovely YouTube videos of this), so it can maximally extract the nutrition it needs from whatever sunlight it can get. A purely reactive system would waste a ton of time after sunrise getting subsystems ready to respond.
Now, there is no broadly agreed theory of consciousness that points to these oscillations as the source. For one, Cyanobacteria and plants have them, a too much of science has rested on the baseless assumption of consciousness being some unique, or advanced thing.
But the evidence is rather overwhelming that consciousness is very much shaped by these internal oscillations. Deep cave experiments have shown what happens to cognition, and consciousness, when the clock free-runs (that is, keeps cycling with no entraining light or temperature signals from the environment). Studies have also shown that restoring the amplitude of these rhythms in patients with “diseases of consciousness” leads to improvement of symptoms.
There’s also a LOT of molecular evidence showing how the circadian clock affects learning and memory. Most critically, actual synapses are never static. Major components are on a 24 hour cycle, and recent research has shown that major clock proteins are at the synapse organizing its dynamics, and synaptic proteins critical to learning and memory loop back to affect the clocks phase and amplitude.
Timing is, beyond doubt, a huge aspect of what biology is. And every bit of evidence we have, from the molecular level to observable behavior we can feel ourselves, says that consciousness is fundamentally linked to how the body organizes its internal rhythms and responds to external time.