The baffling intelligence of a single cell: The story of E. coli chemotaxis

I find this to be an incredibly bizarre thing to say. Nobody is stopping you from thinking anything, of course you're allowed and surely you know this very well.

I suspect what you're really saying is "Will you still respect me for being a creationist". And the answer is, LOL of course not. Nobody is entitled to have their wacky ideas be respected. A lot of the "free speech" complaints are really demands that other people treat your bullshit with respect, which is an absurd demand.

But if my suspicion above is way off, please tell me. I am curious why anyone would say what you said.

Yes, but that doesn't mean people will take you seriously.

In order to evolve such a system all you need is for the separate components to be useful. A cell laying still and multiplying is useful enough, so that is the baseline. Then adding a flagella to move randomly so it can move away from its waste product and keep hitting new nutrients is also useful. From there it can start to detect waste and move when it is near waste and stop moving when it is near food. Then yo just continue such steps, not very hard to imagine compared to imagining macro evolution.

Given the size of the universe and its age, I'd say we have waited long enough for probabilities to line up and produce such a complicated design.

As can be seen by the specializations between human brain hemispheres. There is a bus between them, but when that communication is cut, and you can see that a lot of what we perceive as a single thought process, is a bunch of independent computing entities with an OS layer on top creating the unity that doesn't really exist.

So as we add layers of language, intelligence goes down. (Of course, to the residents of that layer, only the residents of that layer are intelligent. The depths are inscrutable chaos. And further layers are ... Tools? Toys?)

Individuals are smart, committees are dumb.

Fundamental particles must be geniuses.

I am a person. I am not a complex adaptive system. And yet I am.

Your adaptive system has a very complex model of the environment. You can model yourself as an agent in the environment, and you identify as parts of that agent. I say “parts,” because there is a ton of thinking and actions that your adaptive system performs which you do not identify as you.

Part of our problem is the way we think. I am a person. I am not a complex adaptive system.

I agree that, in general, we humans, downgrade the importance of external stimulus and interactions with our environment (including other people). My two cents is that this is downplayed where we live in cities and don't move too much, once you move to very distanct places and cultures (and not assuming yours is the best one) more things tick in the brain.

But I don't think of myself as a CAS or talk about We. Wecellfs?

I am a collector of theories of consciousness :) assuming your quote above is making reference to the "scale" at which "self" is understood, you might be interested in this theory:

Information Closure Theory of Consciousness (2020) https://www.researchgate.net/publication/342956066_Informati...

This reddit comment sums it up better than the paper seems to be able to: https://www.reddit.com/r/MachineLearning/comments/dco3t1/com...

Consciousness (at least, consciousness(es) that we are familiar with) seems to occur at a certain scale. Conscious states doesn't seem to significantly covary with noisy schocastic activities of individual cells and such; rather it seems to covary at with macro-level patterns and activities emerging from a population of neurons and stuffs. We are not aware of how we precisely process information (like segmenting images, detecting faces, recognizing speeches), or perform actions (like precise motor controls and everything). We are aware of things at a much higher scale. However, consciousness doesn't seem to exist at an overly macro-level scale either (like, for example, we won't think that USA is conscious).

Going at it a bit sideways, there's also a sense of self that's constructed in which narratives forms around it ... and yet, there's a way of experiencing the world without that separate sense of self.

Complex adaptive systems can be nested. Human families, communities, societies, governments all form greater gestalts in which humans, themselves complex adaptive system are a part of.

Sapir-Whorf is bunk

How does a water droplet "know" the path downhill. How does electricity "know" the least resistance path.

All this language is just confusing. In a chemical gradient sense, molds and yeasts solve tough problems all the time, but it's not much more than physics

You can't simulate the intelligence of a cell using just a handfull of analogue components. Cell intelligence is still beyond us.

People tend to underestimated cells just like you do here.

I think intelligence is the correct word. Why not?

"like intelligence, but it could be simulated by an analog computer with a good handful of of discrete components"

dude, I am an analog computer with a good handful of discrete components and I'm definitely intelligent

I know. But this is very well understood and researched.

All it requires is mutations, time and selection pressure.

The Blind Watchmaker is still a good read.

Have you actually seen the results of things made with evolutionary algorithms? They ALWAYS produce "what the fuck, how could this be good" outcomes. From antenna that look like scifi props, to a computational system that somehow requires a supposedly unconnected transistor to be activated, evolutionary systems always find their way to a goal in an unimaginable fashion, because "random" mutations are basically the direct opposite of engineering something, so why does everyone always expect the outcome to look engineered?

Evolution producing a complicated, half non-working, incomprehensible, "everything interacts with everything else in a chaotic and unpredictable to us way", is the EXPECTED outcome.

It's similar to how many big programming projects become spaghetti messes of half integrations and barely functional parts hooked together half-hazardly where every feature relies on a bit of code nobody understands. It's an "iterate on the stuff that works" process, except the machinery inside a cell is way more effective and tolerant of such a regime than our stupidly strict programming languages and computers.

The thing that makes it difficult to imagine is that the large numbers involved are hard to imagine.

In a given teaspoon of ocean water in the top layer, there are millions of bacteria (in soil there can be up to 1 billion). Each one lives for a day or two before it either divides or is consumed, with a handful of mutations at each round of division. So ~200 divisions a year, for three billion years, with selection stochastically whittling out the few good mutations the crop up now and then, in a diversity of changing ecosystems and you end up with where we are today. Oh, and the occasional horizontal gene transfer for extra spice.

Obviously that is a large hand wave -- the numbers above are from today's environment; early on the biotic density was lower. But the large numbers swamp things. The only real mystery is how things initially got started. But again, it is hard to imagine the time scale involved and the wide variety of environments that exist over the time to imagine the happy accident where the first self-replicating molecule just happen in the right environment that was stable enough for long enough for that self replication to gain traction.

I cannot disagree more here.

Biology is just astoundingly complicated, especially micro-bio.

Lets look at the 'Central Dogma' of biology as a point to focus on a bit. It's the idea of 'information' transfer. DNA gets decoded into RNA which then gets decoded into Protiens, right? Easy peasy little discussion. You go into how DNA works a bit, it's structure, it's functions. Then you go a bit more into RNA and the various sub types, how the decoding proteins work, Slicer and Dicer, etc. You then talk about how three letter codons work to make amino acids, how you transport the mRNA out of the nucleus, etc. At each step you take a look at how the thing works and you mention some other launching off points for more research if the kids are interested. This is how a lot of education works, things like cooking, math, history, etc.

Except nearly none of what I just said about the 'Central Dogma' is considered true anymore. Sure, some of it is, but the vast majority of how proteins get made is not encompassed in it. Nearly the entirety of modern micro-biology is all about the 'exceptions' to the 'Central Dogma'. So much so that you can't really even say that there is any appreciable difference between RNA and proteins anymore. Every week, and I am not joking here, there is at least one new paper detailing some hybrid mess of RNA and proteins that has critical importance in how we understand how even the most common parts of a cell works. It's to the point that I would not call the 'Central Dogma' and outright lie, but more of a useful fiction.

Like saying that a 'for loop' is how the internet works. Yes, there are 'for loops' in the internet, yes they are critical, yes, you need to learn about them. But no, you cannot teach someone about the internet via a fascinating example or two about 'for loops'.

Understanding biology is Hard, it is the end result of 4+ billion years of literal life and death. It is not something that can be done in a few examples. Even an understanding at a 12 grade level does in fact take a full school year to get to, and even then, it's just the barest launching point into the wider field. The OP s wrong. Full Stop. You do need to learn the names of these things, you do need to get down and do the work of learning all the facts, you do need to fill your brain with these things that are going to affect you as the world gets more and more complicated, you do need to connect this incredibly vast amount of information together. It is going to affect you or the ones you love.

Edutaiment is not the way forward here. Hard work is.

There's a nice discussion of this in Surely You're Joking, Mr. Feynman!

I discovered a very strange phenomenon: I could ask a question, which the students would answer immediately. But the next time I would ask the question – the same subject, and the same question, as far as I could tell – they couldn’t answer it at all!

Then I say, “The main purpose of my talk is to demonstrate to you that no science is being taught in Brazil!”

https://v.cx/2010/04/feynman-brazil-education

It turns out the curriculum was made by a bunch of teachers that has been old school taught. Seniority and entrenchment, nobody in that group risking their heads to suggest any deviation from old beliefs

It is a lot more complex than anything made by humans, but it is nothing like as complicated as a human that consists of a huge number of cells.

I was about to post a very similar comment. That last section elevates the article from "interesting" to "wow, that was great". It isn't just revealed wisdom; the gentleman want to show the limits of the knowledge.

And the "in silico" experiments are probably a bit of a sleeper for people outside the field. It is really obvious how improvements in computing power will have/had a transformative impact on this field. To go from poking out random molecules and growing dangerous things in a pitri dish to fast computer simulations from DNA seems like quite a big jump in how quickly the field can learn.

there would be an absolute small, at planck scales (from what we know)

there's also an absolute big, known in cosmology, far beyond the scales of galaxies, galaxy clusters, etc... it's your mom

It is a highly evolved bacterium for sure. It still hasn't figured out how to form multi-cell clusters. And let's hope it stays that way ;)

Also scale is subject to physical limitations. Bones can only carry that much weight - chemical processes are limited by - for example - maximum energy dissipation rate.

Not sure if it's what you meant, but DNA Computing is a whole field!

https://en.m.wikipedia.org/wiki/DNA_computing

It’s not magic, we can synthesize DNA. But we don’t yet have the kind of nanotechnology that cells do.

DNA sequences are instructions that get printed on the spot and self assemble. This requires a great deal of flexibility so any reproduction would probably look much like what we find in nature.

Or did you understand that and were wondering if we'd ever coopt the bodies mechanisms to create familiar logic gate based compute? Personally I doubt that we'd use already familiar transistors because the process requires ultra pure materials that are modified in very thin layers using gasses to scrape or place individual layers, but maybe we'd find a mechanical analogue expressible via protein, or at that point use purpose built neurons instead.

Yeah I always appreciate that, I hate it when people shy away from honesty because they think some heckler won't understand the subtlety of the observations at play.

What does this book talk about that his previous book the Gene doesn’t?

He is a great storyteller, 2 other very successful and interesting books of his:

- The emperor of all maladies - about cancer research, for which he got a Pulitzer

- The gene - about the evolution of the field and the discoveries and what is the latest thinking

But of course, every neuron in the brain is bafflingly complex and we still don't know or understand how that complexity manifests itself in thought and intelligence.

Indeed.

Biophysics of Computation: Information Processing in Single Neurons challenges this notion, using richly detailed experimental and theoretical findings from cellular biophysics to explain the repertoire of computational functions available to single neurons. The author shows how individual nerve cells can multiply, integrate, or delay synaptic inputs and how information can be encoded in the voltage across the membrane, in the intracellular calcium concentration, or in the timing of individual spikes: https://www.amazon.com/Biophysics-Computation-Information-Co...

On the other hand, AI doesn't have to be intelligent to be dangerous. Think of viruses for example.

Brain is basically running a matrix-like simulation with a central person in it, for AGI we just need to simulate the thinking parts which is a simpler problem. But who knows how much simpler...

elemental cells also have clear boundaries ie the cell membrane, which evolved as a way to catalyze a chemical reaction by containing all the ingredients in one place. imagine a fatty globule that randomly happens to enclose a set of chemical ingredients that react; that reaction is now far more likely to occur

Self-organizing brownie swarms manage the whole process from the ethereal plane.

or VC's between fads and during fads

yes evolution/nature .. life .. did a lot with very few long ago, any insect is a technological marvel if you look at it right

Imagine a microscopic, fully autonomous and self-replicating Roomba that is also able to adapts at the individual and population levels.

Well, if the Roomba could exchange genetic information with the surrounding population and adapting to a changing environment would give the appearance of intelligence and design.

Key word here is activity. Even if you froze a cell and mapped it down to an atom, you'd need to do it again for a cell you somehow managed to freeze in the state immediately after the first one, and so on. What granularity would be significant? What branching of what process would you like to follow?

We’re pretty close. There’s TEM microscopy tech which basically tilts a sample to get a bunch of lines, which is then reconstructed as a 3d model.

It’s stupid expensive though, and you can only really identify whole proteins. But you can do that in context, which is massive

My one thought is that at the atomic level it is also “doing calculations” where by the interactions were evolved over eons to work they way it does. It’s like 3 body problem X a million, but it actually have a purpose and not chaos. If you know what I’m getting at

Are you sure JPL needs supercomputers to calculate flight plans? Please, if you know of more details, I'd like to see them. I was reading the NASA supercomputer complaint and it looks like trajectories can be calculated on extremely conventional small high performance computers now.

“ God designing us in an emergent manner or through a static blueprint are the same thing.”

Perhaps I’m misunderstanding you, but to me it seems like you have no argument with evolutionists. Your beliefs seem to permit evolution. I think your disagreement is actually with people that see evolution as evidence for atheism.

So your answer to "where did this complexity come from?" is to invent an even more complex celestial being that just did it.

Creationists can't see the forest for the trees.

the red helices? those are transmembrane helices, and i guess yes they can transmit information in some cases. there are receptors in the membrane of our cells that respond to mechanical force

If you're interested the code for the simulation all lives here: https://github.com/ehmorris/ecoli-chemotaxis/tree/main/ecoli...