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Why Yudkowsky is wrong about "covalently bonded equivalents of biology" (titotal.substack.com)
submitted 11 months ago by titotal@awful.systems to c/sneerclub@awful.systems
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This is my article on one of the dumbest and most obviously false claims Yudkowsky has ever made, about biology not using covalent bonds.

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[–] swlabr@awful.systems 16 points 11 months ago (1 children)

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.systems 14 points 11 months ago

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

[–] skillissuer@discuss.tchncs.de 11 points 11 months ago* (last edited 11 months ago) (1 children)

Organic chemist there

bucket o' nitpicking incomingI 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.systems 5 points 11 months ago (7 children)

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 9 points 11 months 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 7 points 11 months 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

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[–] corbin@awful.systems 9 points 11 months ago (2 children)

The paragraph about gullibility resonates strongly with me. One of the first things in organic chemistry (a course I repeatedly failed) is that carbon doesn't behave like the ions which we normally manipulate in undergraduate chemistry laboratories. Instead, carbon is like a Lego brick or K'Nex connector, with four ports which clip together in a variety of configurations. This is used to explain many quirks of biology, like why diamond or nanotubes can't be easily produced by enzymatic processes; as you explain, carbon's bonding process makes it very difficult to put into place atomically, and instead we need some sort of external force like immense pressure or heat to reconfigure large masses of carbon into carbon-only structures.

[–] GorillasAreForEating@awful.systems 7 points 11 months ago* (last edited 11 months ago)

I suppose when talking about science to a popular audience it can be hard not to make generalizations and oversimplifications and if it's done poorly that oversimplification can cross over into plain old inaccuracy (if I were to be charitable to Yud I would say that this is what happened here).

To wit: even the "K'nex connector with 4 ports" model of carbon doesn't really explain the bonding of aromatic molecules like benzene or carbon nanotubes; I've likewise seen people confidently make the generalization "noble gases don't react", apparently unaware of the existence of noble gas compounds.

[–] Soyweiser@awful.systems 9 points 11 months ago* (last edited 11 months ago) (1 children)

Thanks for all the effort, also that you post these on all the various LW-sphere related places. Interesting to see the various places react.

E: 18 hours later, I notice that on LW your 38 vote score went down to 30 while the amount of votes increased from 17 to 70, and on EA it also dropped from a higher positive (forgot how high) to a sad 9.

[–] GorillasAreForEating@awful.systems 6 points 11 months ago* (last edited 11 months ago) (9 children)
[–] blakestacey@awful.systems 15 points 11 months ago (2 children)

"If you take only the statements where I was vague instead of the ones where I was explicitly wrong and interpret my words in the way that I am now telling you to, you will see that I am right."

[–] blakestacey@awful.systems 10 points 11 months ago (1 children)

Yudkowsky:

Talking to the general public is hard.

Multiple commenters on FanFiction.net replying to chapter 23 of HPMOR: Genetics don't work that way. If magic were recessive, then wizard parents would always have wizard kids and there would be no such thing as squibs. Look, I drew the Punnett square....

[–] gerikson@awful.systems 5 points 11 months ago

Don't patronize fans, Yud.

[–] locallynonlinear@awful.systems 8 points 11 months ago

"I'm LessWrong than you're implying!!!"

[–] mountainriver@awful.systems 12 points 11 months ago (3 children)

I must have missed the class in material physics where they explained that all material has a generic "strength" that determine which material can cut which. Is it perhaps abbreviated STR?

[–] gerikson@awful.systems 9 points 11 months ago (1 children)

Only someone with high INT can discover this brilliant theory. As luck would have it, they have high CHR too!

[–] locallynonlinear@awful.systems 8 points 11 months ago

Unfortunately such characters tend to dump stat WIS.

[–] Soyweiser@awful.systems 8 points 11 months ago

He never played dwarf fortress confirmed, else he would be talking about shearing, compression, tearing, impact and whatever else values DF uses for materials.

[–] GorillasAreForEating@awful.systems 7 points 11 months ago (1 children)

The so called "experts" say that spider silk is stronger than steel, but steel beams can hold up bridges while I can break a spider web with my little finger. Looks like the "experts" are wrong and spider silk isn't very strong after all - probably because it's made of proteins held together by weak van der Waals forces instead of covalent bonds.

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[–] blakestacey@awful.systems 11 points 11 months ago* (last edited 11 months ago)

Quoth Yud:

I'm sort of skeptical that you could write something that works as science communication for a general audience, though lord knows I'm not necessarily succeeding either.

All the faux modesty of Tommy Tallarico saying "my mother is very proud".

The key valid ideas to be communicated are [made-up sci-fi bullshit about nanobots]

[–] YouKnowWhoTheFuckIAM@awful.systems 11 points 11 months ago (1 children)

I reply: Because the strength of the material is determined by its weakest link, not its strongest link. A structure of steel beams held together at the vertices by Scotch tape (and lacking other clever arrangements of mechanical advantage) has the strength of Scotch tape rather than the strength of steel.

This is sub-childishly false and he opens with it. Unbelievable.

[–] mountainriver@awful.systems 9 points 11 months ago (1 children)

He also writes: "The entire human body, faced with a strong impact like being gored by a rhinocerous horn, will fail at its weakest point, not its strongest point."

If a rhino comes at Yud, he can use his mighty cranium, which is not his weakest spot, to defend his weak meat parts. Since the rhino horn only impacts his head and not his weak points, his body can not fail, and thus he lives.

Reminds me of Cyrano de Bergerac's Travel to the Sun, where the protagonist encounters a thin chain carrying a great load. Since all links of the chain were equally strong, it couldn't break as chains always break in there weakest link. De Bergerac had the excuse of writing his sci fi in the 17th century (he also features some pre-Newtonian physics), Yud lacks such an excuse.

[–] YouKnowWhoTheFuckIAM@awful.systems 5 points 11 months ago

There are too many comments in here going for the stringy lean detail and not pointing out magnificent conceptual errors like this

[–] skillissuer@discuss.tchncs.de 10 points 11 months ago (1 children)

Bone is weaker than diamond, then, because... why?

Well, partially, IIUC, because calcium atoms are heavier than carbon atoms. So even if per-bond the ionic forces are strong, some of that is lost in the price you pay for including heavier atoms whose nuclei have more protons that are able to exert the stronger electrical forces making up that stronger bond.

i don't even know where to begin. stay in school, kids

[–] earthquake@lemm.ee 5 points 11 months ago

Guy with 4 wiki pages open, determined to win an argument, even if it means stacking shit until the other person stops responding.

[–] skillissuer@discuss.tchncs.de 9 points 11 months ago

this entire response reads like "diamond is the hardest metal" copypasta

[–] dgerard@awful.systems 8 points 11 months ago

"yeah but no also :words:"

[–] Amoeba_Girl@awful.systems 5 points 11 months ago (1 children)

Okay that's so much word vomit, and I know next to nothing about biology and medicine so I have to ask: is any of this actually relevant to pandemics, virulence, lethality or whatever was his initial point?

[–] GorillasAreForEating@awful.systems 9 points 11 months ago (1 children)

His argument, as I understand it, is that he knew about the covalent bonds between proteins but didn't mention them because he was simplifying things for a lay audience, and that those covalent bonds don't matter because they aren't the "load bearing" elements in flesh.

There are two problems I see

  1. His earlier statements suggest he actually had no knowledge of that whatsoever

  2. I think his revised explanation is still wrong, because the extracellular matrix that holds cells together and connective tissue are composed largely of proteins that have these covalent crosslinks and rely on them for strength. When you tear a ligment it's not just van der waals and hydrogen bonds being broken, those alone would be far too weak.

[–] Amoeba_Girl@awful.systems 5 points 11 months ago (1 children)

What I mean specifically is, he wrote:

The nanomachinery builds diamondoid bacteria, that replicate with solar power and atmospheric CHON, maybe aggregate into some miniature rockets or jets so they can ride the jetstream to spread across the Earth's atmosphere, get into human bloodstreams and hide, strike on a timer.

Would "diamondoid bacteria" be inherently, significantly better at killing us? Or wait is he imagining the bacteria literally slashing at us???

[–] Soyweiser@awful.systems 9 points 11 months ago* (last edited 11 months ago) (1 children)

From what I could understand is that he talks about diamondoid (and these other things) just because he has read one book about the subject. ‘Nanosystems’ by Drexler apparantly. (Never read it, can't say anything about it).

I'm not sure Yud is really engaging with what is being said vs just going on and on about how AGI can kill us all via nanomachines (son), because handwave theory something.

[–] blakestacey@awful.systems 11 points 11 months ago (1 children)

It's like he heard the phrase "flesh-eating bacteria" and decided they would be more scarier if they had tiny knives and forks.

[–] gerikson@awful.systems 7 points 11 months ago (1 children)

The worst part is when they start to season you with salt and pepper...

[–] locallynonlinear@awful.systems 8 points 11 months ago

When, arguing with people like yudkowsky, you can never decisively 'win' or change his mind, because he and other doomers can quickly retreat to the classic hole: "You can't prove X is impossible!! Nature isn't already perfectly optimal!!!" Searching for some kind of "hard limit" on how nature or technology can evolve will always end up empty handed. Lots of really awful things are possible. (Lots of super fascinating things are also possible.) Searching for some singular hard reason why nature as it is, is totally safe from future threats or change will always end up empty handed.

Capability, is not interesting. Capability, is not the real test. Economics, is the real master of it. And specifically, the open system economics of the entire environment in which something is embedded. It's why the Voyager, a technology planned, built, and launched with 80 year old techniques and knowledge is SOTA for space exploration and contribution to science, and Starship is still just a huge dark hole for money and talent.

if I want to understand historical biology, I do not go looking for the alien intelligence and engineering capability that built it, I look for the environmental forces that contributed to, and eventually supported the homeostasis of, it.

[–] NAXLAB@lemmy.world 8 points 11 months ago* (last edited 11 months ago)

It was in high school that I last learned about the different types of bonds. This one article actually gave me a better education than chemistry class, if I'm going to be very honest. (Though to be fair to my chemistry class, I probably wouldn't have the foundational knowledge to understand what was going on otherwise, so I'll give you both credit)

[–] blakestacey@awful.systems 7 points 11 months ago* (last edited 11 months ago) (1 children)

Quoth Yud:

Algae are tiny microns-wide solar-powered fully self-replicating factories that run on general assemblers, "ribosomes", that can replicate most other products of biology given digital instructions.

Ribosomes ... make proteins.

[–] skillissuer@discuss.tchncs.de 4 points 11 months ago

and not even finished proteins