# re: Yudkowsky on biological materials

I was asked to respond to [this comment](https://www.lesswrong.com/posts/8viKzSrYhb6EFk6wg/why-yudkowsky-is-wrong-about-covalently-bonded-equivalents?commentId=22wNnGvZErLnmRRm7) by Eliezer Yudkowsky. This post is partly redundant with [my previous post](https://www.lesswrong.com/posts/FijbeqdovkgAusGgz/grey-goo-is-unlikely).

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> Why is flesh weaker than diamond?

When trying to resolve disagreements, I find that precision is important. Tensile strength, compressive strength, and impact strength are different. Material microstructure matters. Poorly-sintered diamond crystals could crumble like sand, and a large diamond crystal has lower impact strength than some materials made of proteins.

> Even when the load-bearing forces holding large molecular systems together are locally covalent bonds, as in lignin (what makes wood strong), if you've got larger molecules only held together by covalent bonds at interspersed points along their edges, that's like having 10cm-diameter steel beams held together by 1cm welds.

> lignin (what makes wood strong)

That's an odd way of putting things. The mechanical strength of wood is generally considered to come from it acting a composite of cellulose fibers in a lignin matrix, though that's obviously a simplification.

If Yudkowsky meant "cellulose fibers" instead of "lignin", then yes, force transfers between cellulose fibers pass through non-covalent interactions, but because fibers have a large surface area relative to cross-section area, those non-covalent interactions collectively provide enough strength. The same is true with modern composites, such as carbon fibers in an epoxy matrix. Also, there generally are some covalent bonds between cellulose and lignin and hemicellulose.

> Bone is stronger than wood; it runs on a relatively stronger structure of ionic bonds

Bone has lower tensile strength than many woods, but has higher compressive strength than wood. Also, they're both partly air or water. Per dry mass, I'd say their strengths are similar.

Saying bone is stronger than wood because "it runs on a relatively stronger structure of ionic bonds" indicates to me that Yudkowsky has some fundamental misunderstandings about material science. It's a non sequitur that I don't know how to engage with. (What determines the mechanical strength of bonds is the *derivative* of energy with length.)

> But mainly, bone is so much weaker than diamond (on my understanding) because the carbon bonds in diamond have a regular crystal structure that locks the carbon atoms into relative angles, and in a solid diamond this crystal structure is tesselated globally.

This seems confused, conflating molecular strength and the strength of macroscopic materials. Yes, perfect diamond crystals have higher theoretical strength than perfect apatite crystals, but that's almost irrelevant. The theoretical ideal strength of most crystals is much greater than that of macroscopic materials. In practice, composites are used when high-strength materials are needed, with strong fibers embedded in a more-flexible matrix that distributes load between fibers. (Crystals also have low toughness, because they can fracture along smooth planes, which requires less energy than complex fractures.)

> But then, why don't diamond bones exist already?  Not just for the added strength; why make the organism look for calcium and phosphorus instead of just carbon?

> The search process of evolutionary biology is not the search of engineering; natural selection can only access designs via pathways of incremental mutations that are locally advantageous, not intelligently designed simultaneous changes that compensate for each other.

Growth or removal of diamond requires highly-reactive intermediates. Production of those intermediates requires extreme conditions which require macroscopic containment, so they cannot be produced by microscopic systems. Calcium phosphate, unlike diamond, can be made from ions that dissolve in water and can be transported by proteins. That is why bones are made with calcium phosphate instead of diamond. The implication that lack of diamond bones in animals is a failure of the evolutionary search process is very wrong.

> There were, last time I checked, only three known cases where evolutionary biology invented the freely rotating wheel.  Two of those known cases are ATP synthase and the bacterial flagellum, which demonstrates that freely rotating wheels are in fact incredibly useful in biology, and are conserved when biology stumbles across them after a few hundred million years of search.  But there's no use for a freely rotating wheel without a bearing and there's no use for a bearing without a freely rotating wheel, and a simultaneous dependency like that is a huge obstacle to biology, even though it's a hardly noticeable obstacle to intelligent engineering.

This conflates microscopic and macroscopic wheels, which should be considered separately.

Wikipedia has [a whole page](https://en.wikipedia.org/wiki/Rotating_locomotion_in_living_systems) on this topic, which is a decent starting point.

For macroscopic rotation:
- Blood vessels cannot rotate continuously, so nutrients cannot be provided to the rotating element to grow it.
- Without smooth surfaces to roll on, rolling is not better than walking.

On a microscopic scale, rotating proteins are floating in cytosol, so connecting them to resources isn't a problem. Evolution seems perfectly able to make variants of them; there are several types of ATPase and flagellar motors. ATPase may:
- use H+ ions, or Na+ ions
- attach to different membranes
- mainly produce or consume ATP

Flagellal motors can often reverse direction for run-and-tumble motion, and there are quite a few variants.

The reason you don't see many rotating elements in proteins is...they're just not normally very useful. Oscillating protein conformations are generally both smaller and easier to evolve, so you see lots of ping-pong mechanisms and few rotational ones. In the cases where rotation is useful, you see rotation:
- Flagellal motors are used because rotation of flagella is useful for propulsion.
- For ATP synthase, rotation is good because it allows coupling a gradient to a reaction with a variable ratio (of transports to ATP) as long as free energy is negative.
- Unwinding DNA involves rotation, so DNA helicases can rotate.
- RNA polymerase has a rotational nanomotor.
- TrwB uses rotation to move DNA across membranes.
- The bacterial [Rho factor](https://en.wikipedia.org/wiki/Rho_factor) is basically a RNA helicase that causes transcription termination.
- RecA family proteins use rotary nanomotors for DNA repair and recombination.
- Many viruses use molecular motors to package their genome into procapsids. It was previously believed that eg the phi29 motor and T4 DNA packaging motor rotate, but they're now understood to use DNA revolution around a (slightly larger) channel without rotation.
- etc

> How much evolutionary advantage is there to stronger bone, if what fails first is torn muscle?

Bones with higher specific strength could have the same strength with less mass, which would be a nontrivial evolutionary advantage.

> (Analogously, the collection of faults that add up to "old age" is large enough that a little more age resistance in one place is not much of an advantage if other aging systems or outward accidents will soon kill you anyways.)

I have the impression I disagree with Yudkowsky about the main causes of aging. See eg [my post on Alzheimer's](https://www.bhauth.com/blog/biology/alzheimers.html).

> I don't even think we have much of a reason to believe that it'd be physically (rather than informationally) difficult to have a set of enzymes that synthesize diamond.

That is very wrong. Diamond is hard to make with enzymes because they can't stabilize intermediates for adding carbons to diamond.

> It could just require 3 things to go right simultaneously, and so be much much harder to stumble across than tossing more hydroxyapatite to lock into place in a bone crystal.  And then even if somehow evolution hit on the right set of 3 simultaneous mutations, sometime over the history of Earth, the resulting little isolated chunk of diamond

"3 mutations" is not particularly difficult relative to some things that have evolved. It's also not sufficient for making diamond.

> Talking to the general public is hard.

I think I feel your pain right now.

> Then why aren't these machines strong like human machines of steel are strong?  Because iron atoms are stronger than carbon atoms?  Actually no, diamond is made of carbon and that's still quite strong.  The reason is that these tiny systems of machinery are held together (at the weakest joints, not the strongest joints!) by static cling.

When strength was important, strong materials have evolved. Spider silk aligns covalent bonds along its length, and can have higher tensile strength than steel per volume. Cellulose fibers are strong; wood is fairly strong and they're only a fraction of its volume. The actual structural elements of wood can have better tensile strength per mass than steel.

> And then the deeper question:  Why does evolution build that way?  And the deeper answer:  Because everything evolution builds is arrived at as an error, a mutation, from something else that it builds.

Per the above, evolution has done better than Yudkowsky seems to think.

> If somebody says "Okay, fine, you've validly explained why flesh is weaker than diamond, but why is bone weaker than diamond?" I have to reply "Valid, iiuc that's legit more about irregularity and fault lines and interlaced weaker superstructure and local deformation resistance of the bonds, rather than the raw potential energy deltas of the load-bearing welds."

Again, Yudkowsky is conflating mechanical strength at different scales, and the strength of composites with pure materials. He keeps putting forth diamond as an ultimate material, but tensile strength of 6mm wide 0.25mm thick CVD diamond films ranged from [230 to 410 MPa](https://pubs.aip.org/aip/jap/article-abstract/78/8/5177/1260/Tensile-strength-of-synthetic-chemical-vapor). Larger composites of those would obviously be significantly weaker. Larger diamond crystals would also be weaker, closer in strength to the worst samples than the best ones. Carbon fiber has better, cheaper, and more-reliable strength than CVD diamond. Large diamonds are not even necessarily stronger than strong wood in terms of tensile strength per mass.