8 ms·

In the beginning, there was computation

63 points by yarapavan 2y ago

kitd 2y ago
I was astounded when I read Matt Ridley's book "Genome" at just how mechanical cellular life is. The nucleus, loaded with DNA, is functioning like a ready-programmed CNC machine, or robot, or other programmable piece of hardware that interacts with the physical or chemical world.
- roywiggins 2y ago
  I know it's lame to link to video, but I saw this pair of videos recently which I thought made an interesting counterargument to the cell-as-machine idea: https://www.youtube.com/watch?v=zpIqQ0pGs1E https://www.youtube.com/watch?v=zpIqQ0pGs1E https://www.youtube.com/watch?v=jPhvic-eqbc https://www.youtube.com/watch?v=jPhvic-eqbc Referenced paper: https://philpapers.org/archive/NICITC.pdf https://philpapers.org/archive/NICITC.pdf The author's notes on genetics: https://www.subanima.org/mendel/ https://www.subanima.org/mendel/
  - quonn 2y ago
    It‘s an evolved machine, meaning that the parts are not designed to be easily understandable or maintainable or to develop or even necessarily particularly easy to evolve. But the videos are good, thank you.
    - roywiggins 2y ago
      the thing about cells is that even labeling bits of them as discrete "parts" seems like it might be misleading, eg this from the linked paper: > recent research on the cellular architecture demands that we look more carefully at what we have previously assumed were well-defined structures and reconsider them as stabilized processes. Because processes are temporally extended, it follows that they can only be understood by giving time due consideration... The structure of a machine, after all, can be grasped in abstraction from time (as it is not constantly changing), whereas the structure of, say, a whirlpool or a stream cannot. This explains why, when we have started using techniques that allow us to examine the cellular architecture in real time, we have found that many of the cell’s compartments and organelles are not fixed machineries at all, but stable macromolecular fluxes.
      - quonn 2y ago
        Okay, „parts“ for me was just a word to refer to the machine, it is also okay if it is only a single part. It still remains a machine in the sense that it performs a task it should perform and does so using the same approach across all instances. That the „parts“ do not only perform a specific function is not really surprising, because the machine does not need to be comprehensible or understandable. I would expect single-purpose parts only if that helps the function or if it helps evolvability (in the sense of not creating dead ends).
        roywiggins 2y ago
        The paper covers this also. Cells don't behave predictably: > The variable flickering of transcriptional activity in different cells is one of the major causes of heterogeneity in isogenic populations. But where exactly does this cell-to-cell variability in transcriptional activity come from? The answer becomes apparent when we remember that gene expression is a molecular process, and like all molecular processes, it is inherently stochastic, given that it takes place in an environment that is subject to the chaotic dynamics of Brownian motion. Each step in the process relies on fortuitous encounters between molecules that are randomly moving about as a consequence of thermal agitation. Evidently, these molecules must be at the right place and at the right time—not to mention in the right vibrational state—for them to be able to participate in the appropriate reactions. The unpredictability of the whole process is further amplified by the fact that the participating molecules in each step are present in the cell in very low copy-numbers, as this decreases the chances of successful interactions between them... > as research into the non-genetic heterogeneity of cells continues, evidence for the biological importance of this phenomenon is mounting ever-rapidly. We now know that non-genetic heterogeneity plays key roles in both microbial and eukaryotic cells, in embryonic development, and in evolution. For one thing, it is a crucial generator of phenotypic diversity, which enables cell populations to adapt rapidly to changing environmental conditions. It does so by permitting the implementation of probabilistic diversification strategies within a population, such as bet-hedging and divisions of labour, which can confer considerable fitness advantages... > One very important theoretical implication of the probabilistic nature of cellular behaviour and the observed heterogeneity of cell populations is that, quite literally, every cell (in an organism and elsewhere) is a unique entity. No two cells are identical, given that no two cells respond to a stimulus in the exact same way—even if they are genetically the same.
  - wvbdmp 2y ago
    I fully believe the biological details presented in the videos, sure, but there’s a certain clickbaitiness about them that leaves a bad taste. The one about genetics seems to force conclusions that are palatable to modern sensibilities. How does Mendel accidentally fudging his results using eugenics prohibit “talk of good genes and bad genes”? There clearly are good and bad genes, this is obvious to anyone. It’s practically the whole point of the olympics to showcase people who have the best genetic prerequisites for their discipline. None of the technical minutiae of inheritance prevent us from breeding better sprinters. In fact we’ve done it with several animals. Whether or not any of this is ethical is not the field of biology’s concern. The video about cells has a similar problem, where it acts like it wants to invalidate higher levels of abstraction because reality is more complicated. Of course biology doesn’t operate like a designed and manufactured apparatus, but omitting complexities irrelevant to the question at hand is the entire point of making diagrams. Does the thing turn methane into methanol? Yes, it does. There is no problem here. These could be great educational videos if they weren’t strawmanning so hard. This is especially obvious in his carefully designed definition of a machine. Biology is just stupidly stochastic, but this stuff is akin to “nooooo, systems don’t »prefer« low energy states, they’re not conscious qq”. Like, okay, use a different verb if that makes you happy??
  - FrustratedMonky 2y ago
    Had to stop watching those videos after so many errors. Saying Gene's aren't machines, because Machines are rigid bodies?? That is wrong, that seems to be the crux of his arguments, that gene's flex, and can become different shapes. Hello, machines do this.
    - roywiggins 2y ago
      Do you know any machines where single constituent parts can have hundreds of functions and will switch between them at random?
      - FrustratedMonky 2y ago
        Do you know any Proteins that do that? The examples given were for a 'few' modalities. Not thousands. My fishing rod is flexible. And I can cast over hand, or underhand, or side arm it under some trees.
        roywiggins 2y ago
        I mean, the video says that inherently disordered proteins make up a quarter of mammalian proteins, they don't even have a small set of conformations that they switch between. They're just flopping around all the time.
        FrustratedMonky 2y ago
        Sure. But to say something is floppy, and serves multiple functions, means it is not a machine, is a stretch. They made the argument multiple times about machines not flexing, and that is just no where in the definition of a machine.
        roywiggins 2y ago
        I think the video does dwell on that a bit too much. The paper he's pulling from defines machines like this: > First, machines can be described in terms of a list of parts and a blueprint indicating how those parts fit together, meaning that someone who has never seen a particular kind of machine should in principle be able to assemble any number of copies—each virtually identical in appearance and performance—provided they can consult the machine’s design specifications. Second, as machines are designed to perform highly specific functions, their operation is tightly constrained, which is why it is possible to predict and control their behaviour. Third, machines are highly efficient in what they do because they always follow the exact same sequence of steps in every cycle of their operation. And fourth, the operation of machines is not continuous; their functioning can be interrupted and their parts examined without thereby jeopardizing their structural integrity. And argues that cells look more like this: > according to this alternative view, the cellular architecture is regarded as a fluid, self-organizing process; protein complexes are considered to be transient, pleomorphic ensembles; intracellular transport is deemed to result from the harnessing of Brownian motion; and cellular behaviour is viewed as a probabilistic affair, subject to constant stochastic fluctuations. And > Viewing the cell as a machine allows us to think of its organization in terms of modular, solid-state circuits that can be approached reductionistically, and it also gives us the confidence to expect that when we eventually work out how all of the cell’s parts fit together, we will be able to completely predict its behaviour. If, on the other hand, we view the cell as a highly integrated, self-organizing, fluid system composed of densely interconnected processes ever-subject to stochastic fluctuations, we no longer have reasons to suppose that achieving such epistemic goals is even possible, let alone feasible. The stark contrast between these two outlooks is exemplified by their strikingly different ways of understanding causation in the cell (Bizzarri et al., 2019), and it serves to explain why some researchers find it easier than others to obtain funding and publish their work. https://philpapers.org/archive/NICITC.pdf https://philpapers.org/archive/NICITC.pdf
- api 2y ago
  These are all very rough analogies though. Everything interacts with everything. Proteins go back and 'flag' DNA with epigenetic flags, control how DNA is transcribed, control how other proteins are folded, etc. Sometimes cells even edit their own DNA, and not just during sexual reproduction. Then there's viruses, virus-like patterns within genomes, etc. Computational or mechanical analogies are not totally wrong but they're dangerously over-reductive.
  - exe34 2y ago
    > but they're dangerously over-reductive I never used to understand this position, until I saw right wing snowflakes getting triggered over a woman looking too manly at the Olympics. They confidently explained XX and XY to whomever would read their little meltdowns, and even rode back on their usual line that genitals determine gender - suddenly they care about hormone levels. So I'm having to come around to the idea that over-reductive can be a real thing. Although I'm not sure that the sort of dumdum that dive off the deep end with these things would do any better.
    - api 2y ago
      It's particularly dangerous with biology. A biology professor of mine put it this way: pretend you are reverse engineering alien technology. The stuff you are trying to understand was not designed by human minds. It was designed by evolution over billions of years, literally an alien intelligence that doesn't "think" anything like you do. A big difference between biology and human engineering is that humans like one-part-one-function and linear chains of cause and effect. Biology isn't like that at all. It's an analog causal matrix where everything affects everything else to varying degrees and most parts have multiple simultaneous functions.
      - medstrom 2y ago
        Bit like a codebase where different parts slowly accrete extra features that presume the presence of the other parts, so that you eventually have to read the whole to follow anything.
- bitwize 2y ago
  I was explaining mRNA vaccines to my dad, and I found myself describing the cell's ribosomes as reading RNA and 3D-printing proteins based on the instructions in the RNA. Not the best analogy, but I figure not a terrible one either.
empath75 2y ago
https://latecomermag.com/article/a-holistic-view-of-the-cell/ https://latecomermag.com/article/a-holistic-view-of-the-cell... There are isolated aspects of cells that are analogous to computation, but it would be extremely misleading to try and think of the cell as a computer or life as a computer, it is far messier than that, and in particular, the analogy implies some teleology or purpose that just isn't there.
- swayvil 2y ago
  Society's technological obsession of the hour invariably dominates philosophical discourse. The metaphors are clearly visible and within easy reach, so it makes perfect sense. Hunting, fishing, agriculture, clockwork, steam, electronics, software... such rich sources. (And then the metaphors are invariably taken literally, hilarity ensues...)
swayvil 2y ago
According to ChatGPT, computation is the foundation of reality. I think he's being serious here. No irony.
roywiggins 2y ago
I have to say I'm immediately skeptical when someone with a background in computation confidently declares that X (for any value of X) is fundamentally computation.
- fsckboy 2y ago
  > someone with a background in computation confidently declares that X (for any value of X) is fundamentally computation. I have to say I'm skeptical when anybody with a background solely in the monasteries of the "materialist interpretation" of the Matrix declares that even energy is a form of matter. There's even a guy in the Matrix who says that so many Matrices have been built within the Matrix experimentally, that with all probability he lives in one of those. (I'm not just making a formulaic joke; I believe the informational/computational universe is a much better explanation of everything we see. I'm not saying digital computers, or quantum computers, not trying to shoehorn anything; the computer has the nature of our universe. But you know how when we shake hands, at a particle level we have to reinterpret to where our hands don't actually touch, our electrons repel each other, and perhaps some jump the gap? that is more informational than it is material; there is no need for the imagining of material quantum-bollards interacting; we do physics with math (abstract) not billiard balls (physical). Mind-body problem? there is no mind-body problem if the body is as abstract as the mind. Or rather, there still are some mind-body questions, but they doesn't seem as intractable.)
  - roywiggins 2y ago
    I'm just saying, if someone works with hammers every day, and publishes some writing about how everything is nail-shaped, this might be more influenced by their experience with hammers than you'd like
  - discreteevent 2y ago
    A naturalist account of the limited, and hence reasonable, effectiveness of mathematics in physics. - Lee Smolin (he's a physicist) https://arxiv.org/abs/1506.03733 https://arxiv.org/abs/1506.03733
_f9cu 2y ago
Yaar apa ivan. In the beginning there was light. Don't change the facts, untill you find the counter part of computation. For example, when I say, in the beginning there was light, Einstein law of light to matter and matter to light holds true. Same way, how can or which other part can you relate computation to?
hggh 2y ago
https://web.archive.org/web/20240902180048/https://nautil.us/in-the-beginning-there-was-computation-787023/ https://web.archive.org/web/20240902180048/https://nautil.us...
the_panopticon 2y ago
This is a good read. Dr. Blaise Agüera y Arcas was a keynote speaker at https://attend.ieee.org/newera/program/ https://attend.ieee.org/newera/program/ here in Seattle a week ago but he didn't really get a chance to delve deeply into his position. During his slot there ended up being a lot of back-and-forth about whether AGI truly achieved or just seeing ACI, etc, among the folks from MS, Meta, Google, UW, and even https://www.dia.mil/ https://www.dia.mil/ rep.
bbor 2y ago
Oh my god that is maybe the most unexpected turn of all time. I almost hesitate to spoil it… suffice to say that the author is not who you think they are! I was reading through to validate that it’s all pretty basic stuff without citations to any philosophers, which is true, but it’s great for what it is. No disagreements here. They even summarized the Imitation Game correctly, which is quite rare! (Most people frame it as “a computer is conscious when it can fool a human”, which is, somewhat impressively, missing the point in two ways at once)
Animats 2y ago
At the beginning, it looked like this was headed for Wolfram land. Wolfram has the idea that, down at the bottom, the universe is a cellular automaton, like the Life game. He's done a lot of work on that, but hasn't reached any connection with the physical universe. But no. It's off into early Turing and von Neumann land, which is more philosophical than useful.
- ggm 2y ago
  Sorry.. you're drawing a distinction between modelling the world as cellular automota, turing machines, and Von Neumann architectures? Some cellular automota (not all I read) are turing complete. Von Neumann architectures are definitionally turing complete. It's turtles all the way down.
- theGnuMe 2y ago
  Wolfram talks about Turing machines in his book. They are interesting in that they produce similar complicated behavior. Using the brainf*ck language is interesting to us though because we can read the language to understand what is going on and reason about it... that is way better than just applying logical operations on cells... that is a step above what Wolfram has done in my opinion... it is sort of hinted at by mathematical equations and arithmetic computations (which Wolfram also discusses)... Also the article discusses CA, just more fancy and see the same behavior: >Alex Mordvintsev created a two-dimensional bff-like environment where each of a 200×200 array of “pixels” contains a tape, and interactions occur only between neighboring tapes on the grid. The tapes are interpreted as instructions for the iconic Zilog Z80 microprocessor, launched in 1976 and used in many 8-bit computers over the years (including the Sinclair ZX Spectrum, Osborne 1, and TRS-80). Here, too, complex replicators soon emerge out of the random interactions, evolving and spreading across the grid in successive waves. This is amazing. I think the next step is to build a compiler that compiles into cellular automata.
bschmidt1 2y ago
> We are made out of functions Not really true, our minds create approximate models of reality and in doing so divides the world into discrete objects that we can play with, but there's no reason to believe those discrete objects actually exist "out there" independent of our senses. In this regard, even something as seemingly fundamental as arithmetic is just language. There's not really "two" "oranges". I can write a function that explains what happens when a ball bounces off concrete, but nothing about that function is the ball bouncing off the concrete - the bouncing ball is not made of the function, nor is the function even a part of it. It's a totally outside replica that isn't even fully 1:1. Any attempt to completely model the ball or the concrete or the bouncing will fall short - they'll always be reductions. So we're not made of functions. We don't know what we are. We use functions to model what's happening, but they're approximations or reductions of what it really is.
- hateful 2y ago
  I don't think the author was referring to thinking or consciousness itself, but things like the processes within cells and the replication of DNA.
- kaashif 2y ago
  > Any attempt to completely model the ball or the concrete or the bouncing will fall short - they'll always be reductions. I don't like it when people assume perfect descriptions of reality are possible, but I also don't like it when people baselessly assume they're impossible. Maybe one day we'll have a theory of everything and a solar system sized computer capable of perfectly simulating a bouncing ball at all levels, with no reduction. Or maybe it's impossible. We just don't know, and I don't know if it's possible to know you have the full picture.
  - bschmidt1 2y ago
    There are things that are simultaneously true/false depending on how you look at it - and looking at something 1 way makes the other incompatible. Thought experiment: I live on a planet near Star A and you live 6 trillion miles away on a planet near Star B. Each of us can see each other's host star as a bright star in our respective skies. Suddenly, both of our host stars supernova and burn out at the exact same time. However, survivors on my planet observe that Star A supernova'd, and then about 1 year later Star B supernova'd (due to how long the light takes to reach Star A from Star B). And survivors on your planet observe the opposite: That Star B blew up first, and 1 year later Star A followed. Only an observer precisely equidistant from both stars would have observed the stars burn out simultaneously. But there's nothing special about this vantage point - this vantage point isn't "the truth" either. This means that a concept like the order of events is not an absolute measurement. To come up with a new function that explains what "really happened" here, accounting for relativity and lightspeed, would be to leave out at least that detail. Each additional function that answers new mysteries abstracts further and leaves out other details by necessity. I think of it like fine-tuning a model to increase accuracy, it necessarily de-tunes it in other ways. > simulating a bouncing ball at all levels, with no reduction It wouldn't fully be the same thing (although could be a very good approximation).
toisanji 2y ago
The human mind is an autonomous interlinked model building database of the world https://blog.jtoy.net/the-human-mind-is-an-autonomous-interlinked-model-building-database/ https://blog.jtoy.net/the-human-mind-is-an-autonomous-interl...
dr_dshiv 2y ago
“ It now seems clear, though, that by unifying thermodynamics with the theory of computation, we ought to be able to understand life as the predictable outcome of a statistical process, rather than regarding it uneasily as technically permitted, yet mysterious. Our artificial life experiments suggest that, when computation is possible, it will be a “dynamical attractor,” because replicating entities are more dynamically stable than non-replicating ones, and, as von Neumann showed, computation is required for replication”
jekude 2y ago
Is it only academia and Google Research that is funding these kind of artificial life passion papers? Wondering if anyone knows of real-world applications / companies working on them.
- theGnuMe 2y ago
  I mean you can do these yourselves. These guys wrote in branf*ck.. it's fascinating to see the system evolve replicators. Perhaps the gliders in CAs are little replicators trying to escape.
ankurdhama 2y ago
This is a prime example of the fallacy where a "conceptual model" is considered reality. Humans always have created many models/abstractions to understand things around us but that doesn't mean that reality is those models/abstractions.

63 points by yarapavan 2y ago

kitd 2y ago

I was astounded when I read Matt Ridley's book "Genome" at just how mechanical cellular life is. The nucleus, loaded with DNA, is functioning like a ready-programmed CNC machine, or robot, or other programmable piece of hardware that interacts with the physical or chemical world.

roywiggins 2y ago
I know it's lame to link to video, but I saw this pair of videos recently which I thought made an interesting counterargument to the cell-as-machine idea: https://www.youtube.com/watch?v=zpIqQ0pGs1E https://www.youtube.com/watch?v=zpIqQ0pGs1E https://www.youtube.com/watch?v=jPhvic-eqbc https://www.youtube.com/watch?v=jPhvic-eqbc Referenced paper: https://philpapers.org/archive/NICITC.pdf https://philpapers.org/archive/NICITC.pdf The author's notes on genetics: https://www.subanima.org/mendel/ https://www.subanima.org/mendel/
- quonn 2y ago
  It‘s an evolved machine, meaning that the parts are not designed to be easily understandable or maintainable or to develop or even necessarily particularly easy to evolve. But the videos are good, thank you.
  - roywiggins 2y ago
    the thing about cells is that even labeling bits of them as discrete "parts" seems like it might be misleading, eg this from the linked paper: > recent research on the cellular architecture demands that we look more carefully at what we have previously assumed were well-defined structures and reconsider them as stabilized processes. Because processes are temporally extended, it follows that they can only be understood by giving time due consideration... The structure of a machine, after all, can be grasped in abstraction from time (as it is not constantly changing), whereas the structure of, say, a whirlpool or a stream cannot. This explains why, when we have started using techniques that allow us to examine the cellular architecture in real time, we have found that many of the cell’s compartments and organelles are not fixed machineries at all, but stable macromolecular fluxes.
    - quonn 2y ago
      Okay, „parts“ for me was just a word to refer to the machine, it is also okay if it is only a single part. It still remains a machine in the sense that it performs a task it should perform and does so using the same approach across all instances. That the „parts“ do not only perform a specific function is not really surprising, because the machine does not need to be comprehensible or understandable. I would expect single-purpose parts only if that helps the function or if it helps evolvability (in the sense of not creating dead ends).
      - roywiggins 2y ago
        The paper covers this also. Cells don't behave predictably: > The variable flickering of transcriptional activity in different cells is one of the major causes of heterogeneity in isogenic populations. But where exactly does this cell-to-cell variability in transcriptional activity come from? The answer becomes apparent when we remember that gene expression is a molecular process, and like all molecular processes, it is inherently stochastic, given that it takes place in an environment that is subject to the chaotic dynamics of Brownian motion. Each step in the process relies on fortuitous encounters between molecules that are randomly moving about as a consequence of thermal agitation. Evidently, these molecules must be at the right place and at the right time—not to mention in the right vibrational state—for them to be able to participate in the appropriate reactions. The unpredictability of the whole process is further amplified by the fact that the participating molecules in each step are present in the cell in very low copy-numbers, as this decreases the chances of successful interactions between them... > as research into the non-genetic heterogeneity of cells continues, evidence for the biological importance of this phenomenon is mounting ever-rapidly. We now know that non-genetic heterogeneity plays key roles in both microbial and eukaryotic cells, in embryonic development, and in evolution. For one thing, it is a crucial generator of phenotypic diversity, which enables cell populations to adapt rapidly to changing environmental conditions. It does so by permitting the implementation of probabilistic diversification strategies within a population, such as bet-hedging and divisions of labour, which can confer considerable fitness advantages... > One very important theoretical implication of the probabilistic nature of cellular behaviour and the observed heterogeneity of cell populations is that, quite literally, every cell (in an organism and elsewhere) is a unique entity. No two cells are identical, given that no two cells respond to a stimulus in the exact same way—even if they are genetically the same.
- wvbdmp 2y ago
  I fully believe the biological details presented in the videos, sure, but there’s a certain clickbaitiness about them that leaves a bad taste. The one about genetics seems to force conclusions that are palatable to modern sensibilities. How does Mendel accidentally fudging his results using eugenics prohibit “talk of good genes and bad genes”? There clearly are good and bad genes, this is obvious to anyone. It’s practically the whole point of the olympics to showcase people who have the best genetic prerequisites for their discipline. None of the technical minutiae of inheritance prevent us from breeding better sprinters. In fact we’ve done it with several animals. Whether or not any of this is ethical is not the field of biology’s concern. The video about cells has a similar problem, where it acts like it wants to invalidate higher levels of abstraction because reality is more complicated. Of course biology doesn’t operate like a designed and manufactured apparatus, but omitting complexities irrelevant to the question at hand is the entire point of making diagrams. Does the thing turn methane into methanol? Yes, it does. There is no problem here. These could be great educational videos if they weren’t strawmanning so hard. This is especially obvious in his carefully designed definition of a machine. Biology is just stupidly stochastic, but this stuff is akin to “nooooo, systems don’t »prefer« low energy states, they’re not conscious qq”. Like, okay, use a different verb if that makes you happy??
- FrustratedMonky 2y ago
  Had to stop watching those videos after so many errors. Saying Gene's aren't machines, because Machines are rigid bodies?? That is wrong, that seems to be the crux of his arguments, that gene's flex, and can become different shapes. Hello, machines do this.
  - roywiggins 2y ago
    Do you know any machines where single constituent parts can have hundreds of functions and will switch between them at random?
    - FrustratedMonky 2y ago
      Do you know any Proteins that do that? The examples given were for a 'few' modalities. Not thousands. My fishing rod is flexible. And I can cast over hand, or underhand, or side arm it under some trees.
      - roywiggins 2y ago
        I mean, the video says that inherently disordered proteins make up a quarter of mammalian proteins, they don't even have a small set of conformations that they switch between. They're just flopping around all the time.
        FrustratedMonky 2y ago
        Sure. But to say something is floppy, and serves multiple functions, means it is not a machine, is a stretch. They made the argument multiple times about machines not flexing, and that is just no where in the definition of a machine.
        roywiggins 2y ago
        I think the video does dwell on that a bit too much. The paper he's pulling from defines machines like this: > First, machines can be described in terms of a list of parts and a blueprint indicating how those parts fit together, meaning that someone who has never seen a particular kind of machine should in principle be able to assemble any number of copies—each virtually identical in appearance and performance—provided they can consult the machine’s design specifications. Second, as machines are designed to perform highly specific functions, their operation is tightly constrained, which is why it is possible to predict and control their behaviour. Third, machines are highly efficient in what they do because they always follow the exact same sequence of steps in every cycle of their operation. And fourth, the operation of machines is not continuous; their functioning can be interrupted and their parts examined without thereby jeopardizing their structural integrity. And argues that cells look more like this: > according to this alternative view, the cellular architecture is regarded as a fluid, self-organizing process; protein complexes are considered to be transient, pleomorphic ensembles; intracellular transport is deemed to result from the harnessing of Brownian motion; and cellular behaviour is viewed as a probabilistic affair, subject to constant stochastic fluctuations. And > Viewing the cell as a machine allows us to think of its organization in terms of modular, solid-state circuits that can be approached reductionistically, and it also gives us the confidence to expect that when we eventually work out how all of the cell’s parts fit together, we will be able to completely predict its behaviour. If, on the other hand, we view the cell as a highly integrated, self-organizing, fluid system composed of densely interconnected processes ever-subject to stochastic fluctuations, we no longer have reasons to suppose that achieving such epistemic goals is even possible, let alone feasible. The stark contrast between these two outlooks is exemplified by their strikingly different ways of understanding causation in the cell (Bizzarri et al., 2019), and it serves to explain why some researchers find it easier than others to obtain funding and publish their work. https://philpapers.org/archive/NICITC.pdf https://philpapers.org/archive/NICITC.pdf
api 2y ago
These are all very rough analogies though. Everything interacts with everything. Proteins go back and 'flag' DNA with epigenetic flags, control how DNA is transcribed, control how other proteins are folded, etc. Sometimes cells even edit their own DNA, and not just during sexual reproduction. Then there's viruses, virus-like patterns within genomes, etc. Computational or mechanical analogies are not totally wrong but they're dangerously over-reductive.
- exe34 2y ago
  > but they're dangerously over-reductive I never used to understand this position, until I saw right wing snowflakes getting triggered over a woman looking too manly at the Olympics. They confidently explained XX and XY to whomever would read their little meltdowns, and even rode back on their usual line that genitals determine gender - suddenly they care about hormone levels. So I'm having to come around to the idea that over-reductive can be a real thing. Although I'm not sure that the sort of dumdum that dive off the deep end with these things would do any better.
  - api 2y ago
    It's particularly dangerous with biology. A biology professor of mine put it this way: pretend you are reverse engineering alien technology. The stuff you are trying to understand was not designed by human minds. It was designed by evolution over billions of years, literally an alien intelligence that doesn't "think" anything like you do. A big difference between biology and human engineering is that humans like one-part-one-function and linear chains of cause and effect. Biology isn't like that at all. It's an analog causal matrix where everything affects everything else to varying degrees and most parts have multiple simultaneous functions.
    - medstrom 2y ago
      Bit like a codebase where different parts slowly accrete extra features that presume the presence of the other parts, so that you eventually have to read the whole to follow anything.
bitwize 2y ago
I was explaining mRNA vaccines to my dad, and I found myself describing the cell's ribosomes as reading RNA and 3D-printing proteins based on the instructions in the RNA. Not the best analogy, but I figure not a terrible one either.

empath75 2y ago

https://latecomermag.com/article/a-holistic-view-of-the-cell/ https://latecomermag.com/article/a-holistic-view-of-the-cell... There are isolated aspects of cells that are analogous to computation, but it would be extremely misleading to try and think of the cell as a computer or life as a computer, it is far messier than that, and in particular, the analogy implies some teleology or purpose that just isn't there.

swayvil 2y ago
Society's technological obsession of the hour invariably dominates philosophical discourse. The metaphors are clearly visible and within easy reach, so it makes perfect sense. Hunting, fishing, agriculture, clockwork, steam, electronics, software... such rich sources. (And then the metaphors are invariably taken literally, hilarity ensues...)

swayvil 2y ago

According to ChatGPT, computation is the foundation of reality. I think he's being serious here. No irony.

roywiggins 2y ago

I have to say I'm immediately skeptical when someone with a background in computation confidently declares that X (for any value of X) is fundamentally computation.

fsckboy 2y ago
> someone with a background in computation confidently declares that X (for any value of X) is fundamentally computation. I have to say I'm skeptical when anybody with a background solely in the monasteries of the "materialist interpretation" of the Matrix declares that even energy is a form of matter. There's even a guy in the Matrix who says that so many Matrices have been built within the Matrix experimentally, that with all probability he lives in one of those. (I'm not just making a formulaic joke; I believe the informational/computational universe is a much better explanation of everything we see. I'm not saying digital computers, or quantum computers, not trying to shoehorn anything; the computer has the nature of our universe. But you know how when we shake hands, at a particle level we have to reinterpret to where our hands don't actually touch, our electrons repel each other, and perhaps some jump the gap? that is more informational than it is material; there is no need for the imagining of material quantum-bollards interacting; we do physics with math (abstract) not billiard balls (physical). Mind-body problem? there is no mind-body problem if the body is as abstract as the mind. Or rather, there still are some mind-body questions, but they doesn't seem as intractable.)
- roywiggins 2y ago
  I'm just saying, if someone works with hammers every day, and publishes some writing about how everything is nail-shaped, this might be more influenced by their experience with hammers than you'd like
- discreteevent 2y ago
  A naturalist account of the limited, and hence reasonable, effectiveness of mathematics in physics. - Lee Smolin (he's a physicist) https://arxiv.org/abs/1506.03733 https://arxiv.org/abs/1506.03733

_f9cu 2y ago

Yaar apa ivan. In the beginning there was light. Don't change the facts, untill you find the counter part of computation. For example, when I say, in the beginning there was light, Einstein law of light to matter and matter to light holds true. Same way, how can or which other part can you relate computation to?

hggh 2y ago

https://web.archive.org/web/20240902180048/https://nautil.us/in-the-beginning-there-was-computation-787023/ https://web.archive.org/web/20240902180048/https://nautil.us...

the_panopticon 2y ago

This is a good read. Dr. Blaise Agüera y Arcas was a keynote speaker at https://attend.ieee.org/newera/program/ https://attend.ieee.org/newera/program/ here in Seattle a week ago but he didn't really get a chance to delve deeply into his position. During his slot there ended up being a lot of back-and-forth about whether AGI truly achieved or just seeing ACI, etc, among the folks from MS, Meta, Google, UW, and even https://www.dia.mil/ https://www.dia.mil/ rep.

bbor 2y ago

Oh my god that is maybe the most unexpected turn of all time. I almost hesitate to spoil it… suffice to say that the author is not who you think they are! I was reading through to validate that it’s all pretty basic stuff without citations to any philosophers, which is true, but it’s great for what it is. No disagreements here. They even summarized the Imitation Game correctly, which is quite rare! (Most people frame it as “a computer is conscious when it can fool a human”, which is, somewhat impressively, missing the point in two ways at once)

Animats 2y ago

At the beginning, it looked like this was headed for Wolfram land. Wolfram has the idea that, down at the bottom, the universe is a cellular automaton, like the Life game. He's done a lot of work on that, but hasn't reached any connection with the physical universe. But no. It's off into early Turing and von Neumann land, which is more philosophical than useful.

ggm 2y ago
Sorry.. you're drawing a distinction between modelling the world as cellular automota, turing machines, and Von Neumann architectures? Some cellular automota (not all I read) are turing complete. Von Neumann architectures are definitionally turing complete. It's turtles all the way down.
theGnuMe 2y ago
Wolfram talks about Turing machines in his book. They are interesting in that they produce similar complicated behavior. Using the brainf*ck language is interesting to us though because we can read the language to understand what is going on and reason about it... that is way better than just applying logical operations on cells... that is a step above what Wolfram has done in my opinion... it is sort of hinted at by mathematical equations and arithmetic computations (which Wolfram also discusses)... Also the article discusses CA, just more fancy and see the same behavior: >Alex Mordvintsev created a two-dimensional bff-like environment where each of a 200×200 array of “pixels” contains a tape, and interactions occur only between neighboring tapes on the grid. The tapes are interpreted as instructions for the iconic Zilog Z80 microprocessor, launched in 1976 and used in many 8-bit computers over the years (including the Sinclair ZX Spectrum, Osborne 1, and TRS-80). Here, too, complex replicators soon emerge out of the random interactions, evolving and spreading across the grid in successive waves. This is amazing. I think the next step is to build a compiler that compiles into cellular automata.

bschmidt1 2y ago

> We are made out of functions Not really true, our minds create approximate models of reality and in doing so divides the world into discrete objects that we can play with, but there's no reason to believe those discrete objects actually exist "out there" independent of our senses. In this regard, even something as seemingly fundamental as arithmetic is just language. There's not really "two" "oranges". I can write a function that explains what happens when a ball bounces off concrete, but nothing about that function is the ball bouncing off the concrete - the bouncing ball is not made of the function, nor is the function even a part of it. It's a totally outside replica that isn't even fully 1:1. Any attempt to completely model the ball or the concrete or the bouncing will fall short - they'll always be reductions. So we're not made of functions. We don't know what we are. We use functions to model what's happening, but they're approximations or reductions of what it really is.

hateful 2y ago
I don't think the author was referring to thinking or consciousness itself, but things like the processes within cells and the replication of DNA.
kaashif 2y ago
> Any attempt to completely model the ball or the concrete or the bouncing will fall short - they'll always be reductions. I don't like it when people assume perfect descriptions of reality are possible, but I also don't like it when people baselessly assume they're impossible. Maybe one day we'll have a theory of everything and a solar system sized computer capable of perfectly simulating a bouncing ball at all levels, with no reduction. Or maybe it's impossible. We just don't know, and I don't know if it's possible to know you have the full picture.
- bschmidt1 2y ago
  There are things that are simultaneously true/false depending on how you look at it - and looking at something 1 way makes the other incompatible. Thought experiment: I live on a planet near Star A and you live 6 trillion miles away on a planet near Star B. Each of us can see each other's host star as a bright star in our respective skies. Suddenly, both of our host stars supernova and burn out at the exact same time. However, survivors on my planet observe that Star A supernova'd, and then about 1 year later Star B supernova'd (due to how long the light takes to reach Star A from Star B). And survivors on your planet observe the opposite: That Star B blew up first, and 1 year later Star A followed. Only an observer precisely equidistant from both stars would have observed the stars burn out simultaneously. But there's nothing special about this vantage point - this vantage point isn't "the truth" either. This means that a concept like the order of events is not an absolute measurement. To come up with a new function that explains what "really happened" here, accounting for relativity and lightspeed, would be to leave out at least that detail. Each additional function that answers new mysteries abstracts further and leaves out other details by necessity. I think of it like fine-tuning a model to increase accuracy, it necessarily de-tunes it in other ways. > simulating a bouncing ball at all levels, with no reduction It wouldn't fully be the same thing (although could be a very good approximation).

toisanji 2y ago

The human mind is an autonomous interlinked model building database of the world https://blog.jtoy.net/the-human-mind-is-an-autonomous-interlinked-model-building-database/ https://blog.jtoy.net/the-human-mind-is-an-autonomous-interl...

dr_dshiv 2y ago

“ It now seems clear, though, that by unifying thermodynamics with the theory of computation, we ought to be able to understand life as the predictable outcome of a statistical process, rather than regarding it uneasily as technically permitted, yet mysterious. Our artificial life experiments suggest that, when computation is possible, it will be a “dynamical attractor,” because replicating entities are more dynamically stable than non-replicating ones, and, as von Neumann showed, computation is required for replication”

jekude 2y ago

Is it only academia and Google Research that is funding these kind of artificial life passion papers? Wondering if anyone knows of real-world applications / companies working on them.

theGnuMe 2y ago
I mean you can do these yourselves. These guys wrote in branf*ck.. it's fascinating to see the system evolve replicators. Perhaps the gliders in CAs are little replicators trying to escape.

ankurdhama 2y ago

This is a prime example of the fallacy where a "conceptual model" is considered reality. Humans always have created many models/abstractions to understand things around us but that doesn't mean that reality is those models/abstractions.