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It’s interesting that throughout history we have tended to characterize the behavior of biological systems in terms of the dominant technology of the time. At o

• angiosperm 3y ago
  Michael Levin appears to be demonstrating that cells have a goal-seeking intelligence operating more or less independently of directions from the nucleus. Since literally every cell on earth arose by fission from another cell, the lineage of this intelligence goes back in an unbroken line to their first common ancestor billions of years ago, with natural selection operating on it directly by success at solving problems of survival and reproduction in real time, not just via selection of genes. In a similar way, every membrane in every cell came from extending and then splitting an existing membrane, again more or less independently of the nucleus. Natural selection has operated directly on those membranes, besides its role in adapting the genes that code for subunits of the membranes. The nucleus might be thought of as mainly a library of apparatus that the cell's goal-seeking capacity may draw upon as needed. This analogy is necessarily limited because there are innumerable feedback control cycles encoded in genes and repressor and promoter proteins they encode, and enzymes to methlylate or de-methylate start and stop codons. But something is in charge that operates on a shorter scale than those can. We understand very, very little about that intelligence. It is far more capable than we could ever have guessed. It barely seems possible, with as few moving parts as we know about.
  • ace2358 3y ago
    Lovely insight
  • crotchfire 3y ago
    the lineage of this intelligence goes back in an unbroken line to their first common ancestor billions of years ago, Nonsense. If cell walls ever had the ability to replicate themselves, totally autonomously, without the rest of the cell -- they've very certainly lost that ability. That loss of self-sufficient replication is quite a big "break" in the line. Your argument might apply to ribosomes, however. The nucleus needs the ribosome for replication every bit as much as the ribosome needs the nucleus. And the ribosomal DNA is one of the very, very rare things that has hardly changed at all in the history of life -- humans and yeast have 75%-identical ribosomal DNA. Yeast! https://en.wikipedia.org/wiki/Ribosomal_DNA https://en.wikipedia.org/wiki/Ribosomal_DNA
    • angiosperm 3y ago
      I think you miss the point. Every scrap of membrane in every cell in every known organism -- and cells have a lot of different membranes in them -- was once part of a membrane in the parent cell, or was one of several in a parent cell that became part of this or that daughter cell. We don't know of any organism that constructs any membrane for any purpose de novo. In a very real sense, life may be defined as a membrane with apparatus to aid in growing it. So, in that sense, every evolutionary change is ultimately a refinement to enable growing more membrane. You, personally, are a lot of membranes all folded and wrapped up and carrying around a skeleton.
  • zmgsabst 3y ago
    > In a similar way, every membrane in every cell came from extending and then splitting an existing membrane, again more or less independently of the nucleus. Can you elaborate? As I understand it, the manufacturing of the cell membrane and coordination of splitting with other features (eg, intracellular features that pull it apart) requires the DNA transcription and is regulated by particular genes. That is, depends on the nucleus.
    • angiosperm 3y ago
      Proteins are certainly involved wherever membranes are grown, and proteins are coded for in the nucleus. But the membranes are always there first. No cell anywhere in nature, as far as we know, just makes any membrane from one lipid and then another; membranes are only made by extending an existing membrane.
      • zmgsabst 3y ago
        The hypothesis is that coding molecules predate cell membranes. So we have “every current cell membrane requires the nucleus” and “the coding portion came first”; nobody is disputing that membranes build on membranes, just pointing out they integrally depend on the nucleus to operate (coding for proteins) — and always have. > again more or less independently of the nucleus Ie, this is wrong.
        • angiosperm 3y ago
          There was a time when there was no nucleus, and no DNA. But there were membranes and RNA.
  • dekhn 3y ago
    everything about cell membranes splitting would need to be encoded in the germ plasm of the embryo (because all cells derive from that one). Can you point to the information-encoding information in the germ plasm which is not in the nucleus? Everything we know about cell biology currently suggests that everything required for cell membranes is implemented by proteins controlled by regulated expression of DNA. For natural selection to operate directly on membranes would be a fantastic discovery but would require some pretty challenging experiments to demonstrate convincingly.
• pjio 3y ago
  The code analogy is right in this aspect: The data has a quantized form. But to know the storage format does not explain the higher emergent properties. Those are not comparable to programming languages, which are optimized for human understanding.
  • darkwater 3y ago
    And you, or (almost) nobody else, would have never made this example (quantized, emergent properties etc) just 15 years ago. GP point still stands.
    • thaumasiotes 3y ago
      15 years ago it was 2009; those concepts were widespread at the time.
      • darkwater 3y ago
        I knew someone would nitpick on the chosen time-range, missing the point. Let say 25, or 30, or whatever.
        • thaumasiotes 3y ago
          > The philosopher G. H. Lewes coined the term "emergent" in 1875, distinguishing it from the merely "resultant" https://en.wikipedia.org/wiki/Emergence https://en.wikipedia.org/wiki/Emergence The word is 150 years old; the concept is older than we can determine.
• alexey-salmin 3y ago
  The thing is, the code analogy still holds up pretty well if you ask me. The linked article tells us how this code is self-generating and self-modifying, how the interpreter of this code is more complex than you may expect from a 4-word language, how this code reads from external inputs when it runs. Well OK, sounds very reasonable to me. No one promised the code will be easy. The problem with the code analogy at our current level of understanding is not that it's untrue and not that it's too simplistic, but on the contrary that it's too complex to be applied on practice. What we do now is akin to debugging running linux system by analyzing bit sequences in the kernel image. Surely it's all code and data, surely the bit sequences of the kernel image do determine the kernel behavior within the environment of hardware. This framework is correct but not powerful enough produce good results.
  • thaumasiotes 3y ago
    > how the interpreter of this code is more complex than you may expect from a 4-word language It's not a 4-word language. It's a 64-word language. That's been known for about as long as we've known what DNA was.
    • alexey-salmin 3y ago
      4 or 64, neither is a good description of how it works outside of protein building. Same as saying that C++ is a 100-word language because it's the size of the ASCII alphabet: correct but not helpful
      • thaumasiotes 3y ago
        That's only correct in the same sense that it's "correct" to say DNA is a four-word language. It's not "correct in an unhelpful way", it's just incorrect.
        • alexey-salmin 3y ago
          Well so is the 64-word concept if you insist. It only applies to protein transcription which is 1-2% of human DNA, so it's wrong 98% of the time
• Gooblebrai 3y ago
  It tends to happen. Think of spacetime in Physics. Is a mathematical structure that, saving some small issues, works pretty well to describe reality. That doesn't mean that is fundamental but if you ask people nowadays many will believe it as a fundamental truth
• TeMPOraL 3y ago
  > At one point, it was mechanical automata. Then it was hydraulics. Then it was electrical circuits. Now it is computers. Those analogies aren't equivalent. At each step, they got more accurate. Computing analogies may be flattering to programmer's ego, but it doesn't change the fact that they're also qualitatively different than what came before, because computer science is effectively a branch of physics now. First, computer science gives us fully abstract mathematical framework that describes calculation independent of the medium - the same CS applies to silicon-based computers, meat-based distributed systems (aka. bureaucracy, societies), neural compute, biochemical compute, substance-less compute implemented using photon interference, whatever. Whatever something is, if we can identify a few patterns we care about, we can view it as a computer. And, like with every math-backed science, as long as the assumptions hold, results of our calculations apply to real-world systems. Secondly, researchers also found fundamental connection between information and energy, computing and thermodynamics. That means we can take an abstract computer and establish bounds on its energy use - like how much energy it takes to flip a bit - conditioned on some environment (IIRC it's temperature-dependent, at least). This is the part where CS becomes effectively a branch of physics. Science and mathematics made qualitative jump in the last 100-200 years; we're not making crude analogies to other observed processes now, but rather abstract models with known preconditions and a set framework for reasoning within them. This makes viewing biology through lens of computing a good, useful thing. The important bit is to remember that "all models are wrong, some are useful". If we see that our computing analogies are failing us, perhaps it's time to rethink how we map them to territory. Maybe the most useful computing systems are to be demarked differently, or elsewhere.
  • Kim_Bruning 3y ago
    Ah, putting it this way connects a few of my brain-cells together that weren't previously connected. ;-) Thanks you so much!
• vonjuice 3y ago
  > It’s interesting that throughout history we have tended to characterize the behavior of biological systems in terms of the dominant technology of the time. "In the beginning was the Word", says the book.
• FrustratedMonky 3y ago
  DNA does have error correction. It is a fundamental building block. I'm not sure this article is tossing it out of the window. Just that it can be modified. Epigenetics, how environment of the host changes the DNA. That doesn't mean DNA is suddenly not valuable because we also found that it has capacity for modification. Still need something to modify. Or, like code, it can be updated.
• persolb 3y ago
  As an analogy, I like to think of it as us only having access to the compiled/minified/processed code; except it is massive, no libraries were used, and we can’t even fully describe the hardware. Yeah… technically that code is controlling what happens (along with whatever hardware inputs exist). But the raw HEX is also near impossible to use in a productive way.