This is my article on one of the dumbest and most obviously false claims Yudkowsky has ever made, about biology not using covalent bonds.

  • skillissuer@discuss.tchncs.de
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    1 year ago

    Organic chemist there

    bucket o' nitpicking incoming

    I think that chemistry 101 classification of bonds is a tad useless here. Instead, you can go from first principles: there are things that happen when atomic orbitals overlap (covalent bonds, metallic and such), there are interactions that are mostly electrostatic in nature (ionic, dipole-dipole, quadrupole-quadrupole - important biologically as pi-stacking, also ion-quadrupole etc) and there are things that are a result of exchange interaction (van der Waals and steric repulsion). Hydrogen bonds would be a mix of dipole-dipole and van der Waals interaction. You don’t have to transfer electrons in order to have ionic interaction, most of the time in biologically relevant situations it’s proton transfer, or charges just were there previously. Hydrophobic interactions are almost entirely a solvent effect and aren’t a bond strictly speaking

    In water, i’m pretty sure that proteins are mostly held by hydrogen bonds and hydrophobic interactions. EY is correct in that some proteins hold shape by mostly noncovalent interactions, but these are mostly hydrogen, ionic, hydrophobic interactions and the proteins that actually provide mechanical strength run in continuous covalent strands through entire length of them anyway (collagen, keratin). I don’t think that counting bonds and saying that something is 90% bound covalently is a meaningful metric, because long series of hydrogen bonds or even vdW forces (in things like UHMWPE fibers) can be stronger than single covalently bound strand, ie if you tried to pull out a single strand of kevlar or collagen from bulk material, above certain length you won’t pull it apart, you’d just break it because collective energy of hydrogen bonds will be greater than single covalent bond holding it together, that’s why these fibers are strong in the first place

    There is another kind of flexibility that you haven’t mentioned: proteins are made out of single covalently bound strand, yes, but these aren’t straight C-C chains. Making and especially breaking C-C bonds in controlled way is hard, proteins can be just hydrolyzed at amide bonds. If protein breaks in some way, and in real world everything breaks, it can be recycled into aminoacids (+ any cofactors etc) and then put back in a pretty straightforward way; you can’t do this with diamondoids, when it breaks, it breaks hard, and you’re done unless you’re picking everything apart atom by atom which would be much harder and more energy intensive. As it happens you can buy bulk adamantane, but it’s just made in conditions where C-C bonds are weak (high temperature) and it’s preferentially formed because it’s most stable thermodynamically among its isomers (that are starting materials). Conversely, if you use weaker bonds, you can make pieces conform to some template, or to each other without breaking everything at once - this is basis of dynamic combinatorial chemistry. There’s also entire field of self-healing materials that is based almost entirely on these either noncovalent or reversible covalent bonds

    As part of the process, parts of the enzyme actually shift and mold their structures around the incoming molecules in order to better catalyse reactions. I’m not sure how easily you could replicate this using stiff strictly covalent structures.

    You actually don’t have to do that, and there are some small organocatalysts that are entirely covalently bonded and do the same job. However you can’t make them from from aminoacids, these don’t have secondary structure (too small) and are generally less active. The bare minimum is to provide a receptor for transition state, and you can make it work without drastic changes in conformation. You could make your catalyst as stiff as you like, and it’ll even make activity higher - but only if none of these stiff parts interfere with binding of substrates, and your options are limited. It’s often better to leave some wiggle room. Short peptides aren’t really stiff enough in ways that matter there and instead it’s secondary and tertiary structure that puts important bits in the right place

    Feel free to pick my brain any time you like

    • titotal@awful.systemsOP
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      1 year ago

      Hey, thanks so much for looking through it! If you’re alright with messaging me your email or something, I might consult you on some more related things.

      With your permission, I’m tempted to edit this response into the original post, it’s really good. Have you looked over Yudkowsky’s word salad in the EA forum thread? Would be interested in getting your thoughts on that as well.

      • skillissuer@discuss.tchncs.de
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        1 year ago

        my DMs are open, but lemmy’s DMs seem to be janky, matrix should be more reliable

        I’m tempted to edit this response into the original post

        no issues with that

        Yudkowsky’s word salad

        i’ll have a closer look tomorrow, for now i’d just say that that steel chain protein analogy is okay, however if you wanted to convey directionality of hydrogen bonds, then every link is magnetized, and really these links are not welded shut, but instead bolted, so you can disassemble them and put them together again with some effort. continuing this analogy, diamondoids would be elaborate welded assembly of stiff H-beams or something like that

        i see that EY tries to “get” materials science from first principles, in true aristotelian fashion, never reading first year BSc level chemistry textbook, fails badly and can’t even comprehend that he can be wrong. in other words, another tuesday

      • skillissuer@discuss.tchncs.de
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        1 year ago

        Have you looked over Yudkowsky’s word salad in the EA forum thread? Would be interested in getting your thoughts on that as well.

        update 2: i’m not doing that, he sounds like a straight up cultist in this one

  • swlabr@awful.systems
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    1 year ago

    I’ve been looking through the replies in the crossposts. It illustrates your gullibility filter point completely.

    Also, if you need validation, you are a fantastic science communicator. You take research that isn’t accessible to me and present it in a form I can understand. You also provide enough disclaimers about gaps in your knowledge when you might be glossing over details while providing me with inroads to research those details themselves. You dispel fear and confusion stemming from the unknown while inspiring me to discover more.

    Yud doesn’t do any of those things and often does the opposite, but let’s forget about him for a moment. Good article!

    • titotal@awful.systemsOP
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      1 year ago

      Thanks! I strive for accuracy, clarity, humility, and good faith. Aka, everything I learned not to do from reading the sequences.