[HN Gopher] The baffling intelligence of a single cell: The stor...
___________________________________________________________________
The baffling intelligence of a single cell: The story of E. coli
chemotaxis
Author : jsomers
Score : 359 points
Date : 2024-03-21 11:29 UTC (11 hours ago)
(HTM) web link (jsomers.net)
(TXT) w3m dump (jsomers.net)
| PcChip wrote:
| Excellent writeup, i love the interactive animation
| ehmorris wrote:
| If you're interested the code for the simulation all lives
| here: https://github.com/ehmorris/ecoli-
| chemotaxis/tree/main/ecoli...
| dbrgn wrote:
| The random spin followed by a run reminds me a bit of the first-
| generation Roomba logic...
| 082349872349872 wrote:
| or VC's between fads and during fads
| api wrote:
| Economies are ecological systems and behave a lot like
| systems of organisms.
| objektif wrote:
| VCs are pure momentum investors. There is not much
| intelligence there.
| swader999 wrote:
| Incredible to think how something this intricate with so many
| interdependent parts and integrated systems could have evolved.
| beders wrote:
| 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.
| FartyMcFarter wrote:
| It's still incredible despite all that. Not in the sense that
| one chooses not to believe it, but in the sense that it's
| hard to fathom that it actually happened.
| singularity2001 wrote:
| First you need the incredible machinery to enable mutations
| in the first place
| prmph wrote:
| So if a monkeys bangs on keys forever it will eventually
| produce Shakespeare? I'm quite skeptical
| FartyMcFarter wrote:
| There's no selection pressure when a monkey bangs their
| hands on a keyboard. It's just randomness without any
| consequence. The letters are not interacting with each
| other or their environment in any significant way.
| IncreasePosts wrote:
| Evolution wasn't evolving towards the specific point we are
| at now. It was just doing its own thing all the time, with
| no plans for the future.
|
| So, a better (but still not great) question, would be, if a
| monkey bangs on keys forever would they ever produce _any_
| kind of story at all?
|
| But, that's still not good enough, because evolution is
| iterative, and would pick out very short stories that
| worked a bit, and that page kept getting duplicated out to
| new monkeys who would start typing from the end of that
| story
| tasty_freeze wrote:
| 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.
| mrguyorama wrote:
| 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.
| nyc111 wrote:
| There is a section at the end "How did we figure all this stuff
| out?". Really amazing.
|
| And the scale invariance of nature is clearly visible here. The
| cell is "small" compared to human scale but it is as complicated
| as any machine existing in human scale. There is no absolute
| small or big in nature.
| beders wrote:
| 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.
| roenxi wrote:
| 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.
| fartsucker69 wrote:
| 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
| graemep wrote:
| 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.
| dotnet00 wrote:
| Technically humans are also made by humans :)
| janpmz wrote:
| I would love to understand how individual cells come together to
| form functioning organs with clear boundaries.
| dustingetz wrote:
| 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
| janpmz wrote:
| Thats a nice view. Packages of chemical ingredients that
| react. And they are in an environment together with gradients
| of molecules that start reactions at specific concentrations.
| swayvil wrote:
| Self-organizing brownie swarms manage the whole process from
| the ethereal plane.
| seatac76 wrote:
| Fantastic read! If y'all are into this kind of stuff I highly
| recommend reading "The Song of the cell" by Siddhartha
| Mukherjee[1], it is one of the best books I've read that made the
| topic of biology approachable.
|
| [1] https://www.amazon.com/Song-Cell-Exploration-Medicine-
| Human/...
| ramraj07 wrote:
| What does this book talk about that his previous book the Gene
| doesn't?
| sublimefire wrote:
| 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
| verisimi wrote:
| > How did we figure all this stuff out?
|
| > _We don't yet have the technology to just observe all of the
| activity inside a living cell_. That Goodsell painting above that
| shows the crowded cytoplasm packed with proteins is an artistic
| composite--backed by rigorous research to be sure--because
| there's no way to capture all the different players in situ at
| once.
|
| > A group at University of Illinois at Urbana-Champagne uses
| atomic-scale molecular dynamics _simulations, in software_ , to
| understand structural details
|
| > It's a world that's hard to see; sometimes _you just have to
| imagine what's going on down there_ , and back up those
| imaginings with the right experiments.
|
| > One reason I'm particularly attracted to studies of E. coli
| chemotaxis is that it's an early star of what's been called _"in
| silico" biology_. It's been the subject of many _computer
| models_.
|
| Honest, at least.
| burnished wrote:
| 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.
| wslh wrote:
| If you like this, there is a book about the complexity of a
| single neuron of the brain "Information Processing in Single
| Neurons" [1].
|
| [1] https://www.amazon.com/Biophysics-Computation-Information-
| Co...
| stephc_int13 wrote:
| Imagine a microscopic, fully autonomous and self-replicating
| Roomba that is also able to adapts at the individual and
| population levels.
|
| We're still quite far from replicating this kind of tech.
| agumonkey wrote:
| yes evolution/nature .. life .. did a lot with very few long
| ago, any insect is a technological marvel if you look at it
| right
| CyberEldrich wrote:
| > 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.
| retskrad wrote:
| From a laymans perspective, can human beings create our own
| version of DNA, let's say with the use of transistors instead of
| biological cells, long into the future? Or is DNA just magic and
| we can't recreate it inside solid state objects like a robot made
| out of transistors?
| dweekly wrote:
| Not sure if it's what you meant, but DNA Computing is a whole
| field!
|
| https://en.m.wikipedia.org/wiki/DNA_computing
| retskrad wrote:
| Thank you, that sounds interesting
| two_handfuls wrote:
| It's not magic, we can synthesize DNA. But we don't yet have
| the kind of nanotechnology that cells do.
| burnished wrote:
| 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.
| bell-cot wrote:
| On the one hand, this is extremely cool science.
|
| OTOH, English really needs another word, meaning "like
| intelligence, but it could be simulated by an analog computer
| with a good handful of of discrete components".
| Jensson wrote:
| 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.
| bell-cot wrote:
| Article subtitle: The story of E. coli chemotaxis
|
| I'm not thinking of simulating the whole cell. And last I
| heard, a DC full of computers can't fully simulate one
| sucrose molecule.
| Jensson wrote:
| E. coli does a lot more things than what is described in
| the article, the article just gives an extremely simplified
| view of the cells intelligence. They react to all sorts of
| substances in reality and decides where to go based on all
| of those, not just a simple "go towards good place"
| behavior. It is cool that they mapped out how it behaves in
| a simple environment, but you can do the same thing with
| humans, if you put a human in a simple experiment you can
| create similarly simple rules for human behavior.
|
| And even if you just look at the behavior described in the
| article that would still require quite a bit of components
| since you would need to accumulate signals and normalize
| them and then turn that to oscillating control signals.
| Computing via chemical processes like cells do makes the
| computations a lot simpler.
| bell-cot wrote:
| Um...I'm suspecting that you want to argue with someone
| whose worldview is rather unlike mine. And our notions of
| how many components are in a "good handful" may also
| differ rather widely. Thanks, OO.
| Jensson wrote:
| > I'm suspecting that you want to argue with someone
| whose worldview is rather unlike mine.
|
| Probably, but I can only respond to the words you write
| and not your internal thoughts. To me a handful is 10 or
| less, from fingers, but I guess a handful could also be
| hundreds like hundreds of rice grains which makes more
| sense but I haven't seen anyone use handful for more than
| 10.
| dekhn wrote:
| Sure, a DC full of computers can fully simulate a sucrose
| molecule at a detailed level of description. You wouldn't
| need a DC- it could be done on a single machine. The real
| question is, why would you need to model things at the
| molecular level of detail if that detail is not necessary
| to recapitulate the behavior of a cell?
|
| One thng I've learned from over a decade of simulating
| proteins and nucleic acids is that those methods, while
| mathematically interesting, don't provide useful data given
| the amount of resources they require. Instead, reduced
| models (effectively embeddings) and careful statistical
| methods are much, much more productive.
| FrustratedMonky wrote:
| Think the issue is what constitutes 'intelligence' at all.
| Forget computers.
|
| This article breaks down how the cell behaves down the the
| molecules. Once each part is pulled apart and examined, where
| did the 'intelligence' go.
|
| The single cell, looks 'intelligent'. But, when it is all
| pulled apart we don't find it. It is just chemicals,
| reactions, physics.
|
| Then, scale that up to multi-cellular organism, then human,
| its all just mechanistic, chemicals, physics. So where did
| the intelligence come from? Humans are also just twitching
| flagella.
|
| This article just makes it a more stark idea, because a
| single cell appears 'intelligent', but we can pull it apart
| and examine the constitutive parts, the chemical, molecules.
|
| So there is not much wiggle room for philosophy or souls. It
| looks intelligent, but look, we can peer under a microscope
| and don't see the intelligence.
| Jensson wrote:
| > This article breaks down how the cell behaves down the
| the molecules
|
| No, just for a single molecule. The cell does a lot more
| than that. Can read this if you want to learn a bit more.
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6194112/
|
| > So there is not much wiggle room for philosophy or souls.
| It looks intelligent, but look, we can peer under a
| microscope and don't see the intelligence.
|
| Sure, but we still can't replicate its behavior in a
| natural environment, just simple lab environments.
| RetroTechie wrote:
| The intelligence is in the parts' interactions.
|
| Compare with an OS kernel: individual code snippets are
| useless / meaningless.
|
| Executed by some CPU or VM, each snippet can be seen to
| modify that machine's state.
|
| Snippets put together may be observed, and understood as
| implementing some specific algorithm. Again: useless /
| meaningless in isolation.
|
| Some snippets may be seen to address I/O, and so it may be
| assumed to be part of a subsystem that controls (or is
| controlled by) a peripheral device.
|
| Now put all those parts together, and you have an intricate
| piece of machinery that shows flexible, adaptable, goal-
| oriented behaviour. Behaves in a 'smart' way (for varying
| definitions of 'smart').
|
| Where did the intelligence come from? The parts'
| properties, how they're put together, and their
| interactions (among themselves & their environment).
|
| As science progresses, I think we'll come to realize it's
| just that: a matter of scale & how the many parts and
| variables interact with their environment. No magic (but
| fascinating & wonderful nonetheless).
| jvanderbot wrote:
| 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
| whelp_24 wrote:
| How many simple physics combinations until you get
| intelligence? Remember that you are made of cells, and
| everything you do (probably) can be reduced to a group effect
| of your cells.
| jvanderbot wrote:
| Complexity is not magic. It's just a long search for the
| right combo. In fact we have untold trillions of branching
| iterations in evolution.
| whelp_24 wrote:
| This does not answer the question.
| taneq wrote:
| If it's more than physics at all, what's the extra bit?
| jvanderbot wrote:
| Well, I guess a fancy narrative.
| a_gnostic wrote:
| Even that is physics.
| jvanderbot wrote:
| You used my own point to "gotcha", so I guess that's
| Hackernews!
| whelp_24 wrote:
| I think intelligence is the correct word. Why not?
| bell-cot wrote:
| Useful languages can succinctly distinguish things which are
| qualitatively quite different. Describing everything in the
| world as "intelligent" sounds kinda cool and Zen, and may
| reflect some peoples' worldviews - but it also make
| "intelligent" pretty useless as an adjective.
| whelp_24 wrote:
| Why is intelligence a bad descriptor?
| bell-cot wrote:
| If "hot" described any temperature from "the dark side of
| Pluto" to "the core of a brand-new neutron star" - then
| how useful a word would "hot" be, for communication
| between humans?
| HarHarVeryFunny wrote:
| Because:
|
| 1) It's a poorly defined word that means different things
| to different people
|
| 2) The word "mechanism" perfectly describes what it is
|
| At the end of the day it's just using the detection of
| food, to switch from "tumble" (try a random direction to
| find food) to "run" (assume we're near, or in, a patch of
| food, and move forward to consume more).
| burnished wrote:
| Intelligence is not well defined enough for a succinct
| distinguishment. At least, not colloquially.
|
| But also we're in a context where acknowledging the
| intelligence of other life forms is pretty radical so
| distinguishing them as 'lesser' than human would be
| precisely opposite of the point. The baseline world view is
| that human intelligence is magically different than other
| animal intelligences.
| HarHarVeryFunny wrote:
| Why not just use something descriptive like "food finding
| mechanism".
|
| It's also seems odd to call it "baffling" when they 100%
| understand how it works!
| tempaway112751 wrote:
| "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
| singularity2001 wrote:
| These ribbons look a bit like wires, transforming the information
| of an attached molecules through the membrane through physical
| tension
| gilleain wrote:
| 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
| londons_explore wrote:
| > We don't yet have the technology to just observe all of the
| activity inside a living cell.
|
| How close are we to being able to make a map of all atoms within
| a cell? There are 1E23 atoms in 1 ml of water, and an ecoli is
| about 500nmx500nmx1um. That means there are only about 2E10 atoms
| in the whole cell!
|
| Would it be possible to somehow freeze a whole cell, then use an
| electron beam to knock off and identify (via mass) every atom
| there?
| koeng wrote:
| 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
| talkingtab wrote:
| The way I think about this comes from reading John Holland's
| "Hidden Order". If you read that book not as a book but as a way
| to build a Complex Adaptive System, then it comes down to a few
| essentials. An environment, a bunch of entities, a read/write
| messaging bus so the entities can interact. The entities need a
| set of rules and sensors. Put it together and what have you got?
| Thinking. Or intelligence. Try building one. Is the RIP routing
| protocol a complex adaptive system?
|
| Part of our problem is the way we think. I am a person. I am not
| a complex adaptive system. And yet I am. I am made of entities.
| There is a messaging bus, the entities sense, act and interact.
| But I don't think of myself as a CAS or talk about We. Wecellfs?
|
| Perhaps this a Sapir-Whorf thing. Our language limits what we can
| think. What is the difference between a pile of ants and an ant
| colony? A colony is collection of entities, but what do we call
| the entity that is the colony? Are the ants smart or is the
| colony smart.
| swayvil wrote:
| 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.
| Jensson wrote:
| > Individuals are smart, committees are dumb.
|
| But a human isn't a bunch of individual cells, it is a cell
| that cloned itself many times. Those cells all have the same
| base code and can thus become an intelligent committee.
| swayvil wrote:
| So the more identical the committee members are, the
| smarter the committee?
| Jensson wrote:
| At least a committee of 10 identical members wont be
| dumber than a single member most of the time. A committee
| of clones is just scaling up compute in order to solve
| larger problems. Imagine if you could clone yourself with
| your knowledge and mental state, much more useful than
| trying to cooperate with another human.
| swayvil wrote:
| But the committee-thinking is still constrained by the
| language. Any committee-thoughts must be coarser and
| slower than the member thoughts.
|
| We're trading depth for breadth, or something like that.
| GirkovArpa wrote:
| According to Condorcet's jury theorem, a committee of 10
| identical members may be smarter than a single member.
| procgen wrote:
| This seems obvious to me, as there'd be ten times more
| computational resources.
| genman wrote:
| No, it is because the probability of arriving to a
| correct answer increases when there are more members in
| the group, but only when the individual probability to
| arrive to a correct conclusion is higher than 50%. Group
| of smart people is smarter than an individual. The
| opposite is true too. If the individual probability is
| less than 50% then the group of people is dumber than the
| individual.
| inductive_magic wrote:
| I always felt that the decrease in intelligence is a side
| effect of the necessary consensus mechanisms.
|
| 10 genius clones would still take on various
| roles/positions in the system, requiring some
| optimization with respect to alignment under time/energy
| constraints.
| tshaddox wrote:
| > 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_.
| falcor84 wrote:
| It reminds me of this paper from MIRI a few years ago
| discussing models which treat themselves as an explicit part
| of the environment. I think it's a very productive approach -
| https://arxiv.org/abs/1902.09469
| medstrom wrote:
| Wow, wish more papers were so well written and pleasing to
| read!
| nxobject wrote:
| This is wild projection, but it reminds me of the good
| advice I got when writing undergrad philosophy papers -
| map out your tree of arguments (especially if they're
| logically complicated), and structure your writing around
| that; talk in as conversational prose as you can because
| it mercilessly exposes jargon; highlight when you
| introduce new concepts.
| aradox66 wrote:
| Yes - all of our conscious reality, including both the
| environment and our sense of self, are experiences of
| perception formed inside the mind by the body and brain. Our
| sense of an "external" world is very much an "internal"
| reality, and the boundary between self and world is a mental
| construct.
| wslh wrote:
| > 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.
| pas wrote:
| it's hard to forget about others in a city though. you have
| neighbors, traffic, etc. that's why the whole 'cabin in the
| woods' experience can be sold as a relative luxury nowadays.
|
| that said, based on the status quo we definitely don't spend
| enough resources on making sure we can peacefully and
| sustainably live next to others.
| fnord77 wrote:
| Sapir-Whorf is bunk
| mrkstu wrote:
| 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.
| Balgair wrote:
| Just to be clear here, are you talking about the 'left-brain,
| right-brain' thing? Because I thought that was pretty well
| debunked.
|
| Also, I think you are talking about the corpus callosum for
| the 'bus' right?
| gHA5 wrote:
| He's probably talking about split brain patients. Here's a
| video by CGP Grey about them:
| https://www.youtube.com/watch?v=wfYbgdo8e-8
| mrkstu wrote:
| Yep.
| smaddox wrote:
| AFAIK, the part that's been debunked is that there's a
| complete separation of concerns between the two
| hemispheres. From studies on split-brain patients, there
| does appear to be some specialization, but it's much
| fuzzier than "right brain does art, left brain does
| analysis" or anything like that.
| treprinum wrote:
| When Covid hit me, it felt like having a stroke and the
| effect was that I suddenly perceived that I don't have enough
| energy to sustain vision, instead I could perceive the
| delineation between object localization, object recognition,
| character-to-text conversion etc. It was like the brain was
| an engine that suddenly lacked fuel (I could force individual
| parts to "work" at the cost of immense pain) and dissolved
| into individual services competing for resources. The
| experience was both frightening and awesome. Not sure how I
| survived that (it took over 3 years to get back to normal).
| Diffuse MRI didn't find anything anyway.
| cmrx64 wrote:
| had a relatable but almost opposite experience (no obvious
| infection, but it was winter 20/21), where I noticed that
| objects in my visual field seemed to be differentiating
| themselves away from the background and "competing" for my
| attention when previously I had to go hunt for them.
| anal_reactor wrote:
| > The experience was both frightening and awesome.
|
| Basically LSD.
|
| It feels so weird to just... I don't know, have a different
| personality for a while. And when your normal self clicks
| back it's so relieving.
|
| This made me appreciate what a miracle it is that my brain
| is fully working most of the time, and realize what a
| horrible disease dementia is.
| hosh wrote:
| 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.
| ta8645 wrote:
| > I never liked the way biology was taught in high school. It was
| too much about the names of things. A subject so vast is spoiled
| by a textbook, which can only point at the endless parade of
| stuff-there-is-to-know.
|
| Amen. You could easily teach quite intricate biology in grade
| school, if you focused on a fascinating example or two. How many
| more people would be inspired, rather than bored?
| m3kw9 wrote:
| 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
| lostemptations5 wrote:
| Or maybe it wasn't done maliciously -- rather that's the way
| they thought it should be taught...
| atticora wrote:
| 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
| magicalhippo wrote:
| We had a student in class which was so brilliant at
| memorizing stuff.
|
| But each test had one or two questions where you had to put
| together the knowledge, not just regurgitate, and that
| student consistently failed those question on each and every
| test.
|
| Yet the student got top scores on each and every test,
| because the accumulated number of points was enough to get
| them into the top bracket.
|
| I was so annoyed with that, asking the teacher how they could
| get top scores while clearly demonstrating they didn't
| understand the subject matter. Of course, all in vain.
|
| edit: Great read BTW
| Balgair wrote:
| 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.
| kerowak wrote:
| So, just to simplify your argument, you're saying that grade
| school students should not be taught biology in a way that GP
| finds more engaging, because:
|
| > 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.
| gfjx45234 wrote:
| > Biology is just astoundingly complicated, especially micro-
| bio.
|
| Do you mean _molecular biology_ instead, which includes the
| study of central dogma?
|
| (That's a common terminology hiccup, lots of people get this
| wrong)
| dekhn wrote:
| Modern biology is very much not an exception to the central
| dogma; it still remains central. Don't mistake the vehemence
| of the RNA biologists (of which I used to be one) for impact
| or significance (for example, the central dogma had no
| opinion of whether the ribosome was a protein machine, or an
| RNA machine, or a protein-RNA machine where RNA formed the
| critical core components).
|
| The only really important detail that wasn't in the original
| dogma is reverse transcriptase, and they added a dotted line
| to support that once it was found in physical form.
| jmyeet wrote:
| So I have three thoughts about this.
|
| The first is cell specialization, particularly neurons. It seems
| like nature really came up with a universal neuron. There aren't
| neurons for eyesight vs thinking, etc. They've experimented with
| this on frogs where they've reweired the optic nerve to a
| different part ofd the brain and the frog seems to see just fine.
| They've even added an eye and the frog seems to cope and use it
| just fine.
|
| The second is the OpenWorm project [1]. This is an attempt to
| simulate a relatively simple organism with IIRC ~280 neurons.
| Despite lots of effort, the simulated version just doesn't match
| up to the real thing. In artificial neural networks we have a
| stupidly simplified model of neurons that tends to get reduced to
| a binary signal and an activation function. Thius can do a lot
| but it's clearly wholly inadequate for any realistic modelling.
| The protein interactions in a cell are mind-bogglingly complex.
|
| The third is the three-body problem. To summarize, we have a
| general solution for the grvity interactions of two bodies. Add
| one more and we don't. We have classes of solutions but no
| general solution. This is why JPL needs to use supercomputers to
| calculate flight plans with a relatively low number of bodies. We
| see a relatively simple set of interactions lead to massive
| complexity with protein folding. I imagine that it just won't be
| computationally viable to simulate even a single realistic cell
| given all th einteractions that go on. We're simply left to make
| estimations.
|
| [1]: https://openworm.org/
| m3kw9 wrote:
| 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
| dekhn wrote:
| 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.
| javajosh wrote:
| _CheA phosphorylates CheY to become CheY-p, and CheZ
| dephosphorylates it back to CheY; CheW couples CheA to the
| receptors, and CheR methylates those receptors' struts; CheB,
| meanwhile, "clips off" the methyl groups added to the struts by
| CheR._
|
| I guess 'naming things' isn't just hard in CompSci.
| the-mitr wrote:
| I was introduced to the idea of even single cells can exhibit
| "learning" and "culture" via John Bonner excellent book The
| Evolution of Culture in Animals.
|
| Instead of thinking in terms of a discontinuity between animals
| or putting humans categorically different, Bonner builds this
| idea of a continuum instead for both culture and learning. Of
| course there are differences,
|
| https://press.princeton.edu/books/paperback/9780691023731/th...
|
| This post of course goes deep in the rabbit hole so to speak.
| yehosef wrote:
| Am I allowed to think this is too complicated to be an accident?
| wiz21c wrote:
| 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.
| voidmain0001 wrote:
| I read a quote once that said "Simple bacteria can divide
| about every 20 minutes and have many hundreds of different
| proteins, each containing 20 types of amino acids arranged in
| chains that might be several hundred long. For bacteria to
| evolve by beneficial mutations one at a time would take much,
| much longer than three or four billion years, the time that
| many scientists believe life has existed on earth." I haven't
| performed the math to back up the quote. As well would it
| change the time required if the bacteria mutate in parallel
| rather than in series?
| pishpash wrote:
| It's called the plasmid exchange. The search is
| parallelized to however many individuals there are, which
| is arbitrarily large, then the result is shared.
| jjk166 wrote:
| It's the "one at a time" that is the issue here. Evolution
| is a massively parallel process. If a beneficial mutation
| happens once every million gnerations, and a generation is
| 20 minutes, that's a beneficial mutation every 38 years. If
| you have a million cells, that's a beneficial mutation
| every 20 minutes. If you have a billion cells, that's 1000
| beneficial mutations every 20 minutes. In your body there
| are around 40 trillion cells. There are something like
| 10^31 cells on earth.
| Jensson wrote:
| 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.
| arkey wrote:
| But doesn't that reduce to a point where something useful
| becomes from separate useless components?
|
| In your case, why would a flagella be useful if it's not
| propelling something? A flagella is only useful as a
| component of something, but not by itself.
| jjk166 wrote:
| Flagella only exist as components of something, they do not
| need to and shouldn't exist by themselves. If flagella
| spontaneously popped into existence and cells picked them
| up, that would be quite difficult to explain without
| design, but cells producing flagella because they are
| useful components makes perfect sense on its own.
| lebek wrote:
| I think he's saying, random mutation wouldn't produce all
| required components at once. One mutation gives you a bit
| of a flagella, another gives you bit of a nose, but how
| does the flagella mutation survive to coexist with the
| nose mutation that makes it useful.
|
| I suspect the answer is that having flagella without a
| nose is still better than having no flagella. If so it
| suggests evolution isn't good at accessing groups of
| mutations that aren't individually beneficial.
| jjk166 wrote:
| Evolution doesn't produce 1st part of the flagellum,
| second part of the flagellum, third part of the
| flagellum.
|
| It produces shitty flagellum, better flagellum, good
| flagellum.
|
| But the problem is we don't see the intermediate forms.
| So right now you might see a complicated flagellum that
| has a lot of highly specialized parts that all need
| eachother, but that is merely a refinement that took
| place after all the pieces were already there. Like once
| an arch is complete, all the scaffolding that was holding
| it up is now vestigial and if it is removed the arch will
| remain standing.
| crudcodersare wrote:
| It seems you may have misunderstood the original
| argument. The iterative approach suggests increments so
| minute at each step that they wouldn't significantly
| impact an organism's survival at any given time. Also
| given the extremely slow process of evolution and the
| relatively short number of iterations it is infeasible to
| suggest such a solution. If a person would like to create
| an iPhone it's easy to tell them to start with a shitty
| scrap of metal and work from there. You can make that
| sort of argument as a solution for creating anything but
| it is clearly not feasible.
| mrguyorama wrote:
| >so minute at each step that they wouldn't significantly
| impact an organism's survival at any given time.
|
| That's the thing. Evolution isn't "survival of the
| fittest" or even "driven by more efficient _anything_ ",
| evolution is simply; if you die before you pass on your
| genes, you don't pass on your genes. Over long enough
| time scales, with large enough populations, with tight
| enough tolerances and strict enough niches, the system
| roughly approximates a directed iteration of more
| efficient parts.
|
| Nothing about evolution prevents carrying forward
| explicitly negative mutations! Nothing about evolution
| prevents carrying completely unused functionality and
| features! Nothing about evolution guarantees
| monotonically increasing fitness!
|
| The giraffe has a certain nerve that goes from it's
| brain, all the way down around it's aorta, back up it's
| neck, to it's tongue. It does this, because in the fish
| we all evolved from, such a detour was less than a
| centimeter longer than an "optimal" path, and as each
| next generation went in different directions, it's just
| not that big a deal. A few hundred extra calories in
| development, and rare instances of a negative injury
| outcome are just not going to get fixed, because
| evolution is almost never vigilant. Most higher level
| animals have mating behaviors that explicitly favor
| "wasted" energy, including the long neck of giraffes!
| Sexual selection has a stronger influence on most animals
| than evolutionary pressure.
|
| > Also given the extremely slow process of evolution and
| the relatively short number of iterations it is
| infeasible to suggest such a solution
|
| This is silly. The vast majority of the ground work for
| complex life was developed by single celled organisms
| that produced a new generation every half hour, there
| were billions of these little creatures experiencing
| basically any possible mutation all the time, and a water
| droplet with a billion short lived single cells is
| exactly the kind of tight tolerance, competitive
| atmosphere where evolution is most prominent!
|
| Evolution is not iteration. Evolution is pruning bad
| branches in your breadth first tree based algorithm.
| jjk166 wrote:
| No, I understand the argument, it is just built on a
| false assumption about how the iterations work. That a
| change is small does not make its effects insignificant.
| A single codon change could profoundly alter the protein
| it encodes, and even a small change to a protein or its
| expression can have a massive effect on the organism.
| It's not the structures of an orgnaism that mutate, it's
| the instructions that generate those structures which
| mutate. Imagine for example a typo on a blueprint - where
| there was supposed to be a " instead there is a ' and
| suddenly instead of an 8 inch air vent, now you have an 8
| foot door. There is no intermediate step where you have a
| useless 2 foot hole.
|
| Evolution is not a slow process, it is an irregular
| process. The odds of a useful mutation popping up at any
| given time is low, but once it pops up it's there
| immediately. Yes, an evolutionary process could never
| make an iphone, but no is claiming that evolution
| produced the iphone. The complex systems evolution
| produces are things where all the changes are
| individually useful.
| satvikpendem wrote:
| > _significantly_
|
| Why not? People think in such a short time and amount
| scale such that we cannot comprehend trillions of cells
| spending billions of years, iterating. Even a small
| change can be significant at those scales.
| lebek wrote:
| I understand that, but it seems like even the MVP
| "shitty" flagellum would require many mutations that
| individually have no benefit. But I suppose with enough
| generations/parallelism you get enough stacking of
| useless mutations to reach the useful ones.
| jjk166 wrote:
| That's the thing most people have difficulty wrapping
| their head around. What you need to remember is it's not
| the structures evolving, it's the instructions evolving.
| If for example you have a small molecular pump that the
| cell uses to suck up sodium ions, and a mutation causes
| the part of the rotor sticking out of the cell to just be
| longer, which might be due to a single change to the gene
| controlling the length of the rotor, then congrats, you
| now have a shitty flagellum. The mutations don't even
| need to be useful for the eventual purpose. For example
| the highly dexterous fingers which enable complex tool
| use that humans used to conquer the world and with which
| I type this comment now started out as structural
| reinforcement for fish fins, absolutely useless for
| object manipulation. And those reinforcements in turn are
| just extremely bastardized version of a calcite growth
| which offered some protection to a soft body organism
| hundreds of millions of years before.
| martythemaniak wrote:
| 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.
| basil-rash wrote:
| It's funny, because the creationists generally feel the exact
| same about evolutionists.
|
| Both are faith based responses to questions we cannot answer
| any other way. Getting caught up in absolutes thinking your
| interpretation is the gold standard is a sign of an unrefined
| critical thinking process.
| crudcodersare wrote:
| God designing us in an emergent manner or through a static
| blueprint are the same thing. Someone had to create the
| laws, the genetic algorithm idea itself and all of these
| components and the environment for it to operate within
| never mind things like colors, matter etc. Evolutionists
| cant see the forest for the trees.
| Kerb_ wrote:
| Then that's not believing in creationism, that's
| believing in evolution. You wouldn't "not believe in
| fusion theory" because you believe God created the sun
| through the process of inventing a universe that sustains
| nuclear reactions. You would just believe in fusion, as a
| part of God's creation.
| satvikpendem wrote:
| > _Someone had to create the laws_
|
| This is unknown and a quite anthropomorphic view on the
| universe. Just because we can create things doesn't mean
| we ourselves were created, even in the way you're talking
| about in the First Mover argument.
| burnished wrote:
| Oh they really aren't. Its sort of a tired rhetorical ploy
| pitting them as faith based beliefs on equal intellectual
| footing though.
|
| Both are theories about the world. 'Creationism' as a
| theory really only became pure faith very recently as most
| specific claims attributable to it have been disproven or
| better explanations have been found. For a long time it was
| a perfectly cogent theory.
| basil-rash wrote:
| This is objectively false. Evolution explains absolutely
| nothing creationism doesn't, and creationism explains a
| whole lot that evolution cannot. For instance, universal
| origins and the formation of cells.
| dekhn wrote:
| Could you show us an experiment that would demonstrate
| creationism is a better explanation than evolution (and
| random chance) for the formation of cells? If you can't
| come up with an actual experiment, there's really no way
| to say that creationism "explains" something.
| Kerb_ wrote:
| That's cool and all, but do you give an equal amount of
| credit to Young Earth Creationists and regular
| creationists? Because both are equally based in faith. It
| is equally possible some holy being made fake dinosaur
| bones 6000 years ago to fool us, and no amount of
| scientific rigor can compete with a being with the
| foresight to know exactly how we would test the bones. At
| what point is "umm we obviously have evidence these bones
| are over 6000 years old" thinking in absolutes? In the
| meantime, I'm willing to be disrespected for thinking both
| forms of creationism are equally woo-woo in comparison to
| evolutionary theory.
| basil-rash wrote:
| It's important to understand why we think the bones are
| over 6,000 years old, and especially consider what
| assumptions we make in determining that age. Most
| importantly, the time invariance of physics.
|
| Really it boils down to whether you believe the laws of
| physics we observe now have been constant throughout
| time. If you do you're called an evolutionist, if you
| don't you're called a creationist. Neither side has any
| proof, nor is any proof fundamentally possible.
| IncreasePosts wrote:
| No, evolution is not faith based. If you want something
| faith based, which creationism purports to resolve, it
| would be if someone has a strong belief on how abiogenesis
| actually happened, since that is something that is still
| not well understood. But, we see evolution happening all
| around us, all the time.
| basil-rash wrote:
| It most certainly is. Evolutionists believe in the time
| invariance of the laws of physics with no proof,
| creationists believe the processes by why things have
| changed in the universe ("physics", broadly) _have_
| changed over time, also with no proof. That there is some
| external influence that we cannot directly observe that
| has some massive impact on the development of the
| universe in ways we cannot explain.
|
| (Funnily, physics have come to acknowledge the same, but
| they call it dark matter and say it's all very
| scientific, whatever it is. But this is unknown enough to
| be not worth much discussion.)
|
| Regarding the evolution we see around us all the time, I
| and many creationists besides me have full confidence in
| the idea that micro-evolution does occur. That there is a
| stochastic gradient decent process that hones in on time-
| varying local maxima over generations cannot really be
| denied. But that provides absolutely no answer to the
| questions of abiogenesis and speciation en-masse.
| dekhn wrote:
| The reason we believe in time invariance of the laws of
| physics is based on observation of old structures in the
| universe (at least we only have to look back about 4
| billion years to the beginning of evolution on earth). So
| far we have not found any convincing evidence that the
| laws have changed (either new or different interactions,
| or the strength of the interactions).
|
| I will say all of science is based on faith- the faith
| that the human mind can perceive the universe as it truly
| is, using rational thought and experimental data
| collection. For some reason this really bothers some
| scientists and they like to treat science as an
| unquestionable objective truth, but realistically, we
| can't exclude any number of hypotheses, but merely state
| them as improbable based on our understanding.
| pmayrgundter wrote:
| If you do an accounting of all the organ functions, and then ask
| if the cell has this function independently, nothing is left
| out... but only if you allow that intelligence arises from the
| cells.
|
| So I believe intelligence arises from the cells and is an
| essential function of life, not only an emergent phenomena. The
| organs serve as division of labor amongst the cells in community
| for what they are already originally capable of themselves.
|
| More musings in this direction
| https://sites.google.com/site/pablomayrgundter/mind
| photochemsyn wrote:
| Great writeup. Here's a full-text review that contains all the
| math needed to build a model of this process (2013):
|
| "Quantitative modeling of bacterial chemotaxis: Signal
| amplification and accurate adaptation, Yuhai Tu"
|
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737589/
|
| The main points are:
|
| * Both receptor cooperativity and accurate adaptation can be
| described quantitatively by simple mathematical models.
|
| * An integrated model (the "standard model"), which contains both
| signal amplification and adaptation, is developed to predict
| responses of it E. coli cells to any time-dependent stimuli
| quantitatively.
|
| * Exponential ramps induce activity shifts, which depend on the
| ramp rate through the methylation rate function F(a).
|
| * Responses to oscillatory signals reveal that E. coli computes
| time-derivative in the low-frequency regime.
|
| * E. coli memorizes the logarithm of the ligand concentration and
| the Weber-Fetcher law holds in E. coli chemotaxis.
|
| It also goes into cooperative phase transitions in the receptor
| complexes as a means of signal amplification, using the same
| model as in Ising ferromagnetic spin-spin interactions in
| physics.
| begueradj wrote:
| > An individual E. coli has no brain, obviously, and is even many
| orders of magnitude simpler than a human cell, and yet already it
| possesses something like a sense of smell, drive, even a memory.
|
| A person is billions of billions of more effective cells than an
| E.coli cell: still our sense of smell, drive and memory do not
| seem to be billions of billions times more efficient.
| chahex wrote:
| Haha. I know you try to persuade me that consciousness as life
| force intelligence does not exist. But as far as I am concerned,
| I am and I am sentient and that is the only thing in my life I do
| not need any proof.
| oersted wrote:
| The video embedded in the article is a great and more brief
| explanation of what's written:
| https://www.youtube.com/watch?v=LgPDOSou1tw
| crudcodersare wrote:
| God designing us in an emergent manner or through a static
| blueprint are the same thing. Someone had to create the laws, the
| genetic algorithm idea itself and all of these components and the
| environment for it to operate within never mind things like
| colors, matter etc. Evolutionists cant see the forest for the
| trees.
| ihumanable wrote:
| 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.
| pinkmuffinere wrote:
| > " 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.
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