Iterated Boolean circuit diagram for a random instance of lazy sorting of 6-bit input 000101, with 1 bit signals highlighted. Atomic force microscopy image of an opened and flattened DNA nanotube performing the same computation. Images of other nanotubes performing other computations, each labeled with a 3-digit barcode, in the background.
Credit: Demin Liu (Molgraphics) and Damien Woods

Second Bit

Poet: I like that! A "self-assembly algorithm". A contradiction in terms. The dictates of randomness! The agency of the enslaved! A cookbook for creativity!

in the swirl of the whirlpool
we twirl, with Brownian abandon
at random, we join hands and link force;
the choices are ours, but step by step
and rule by rule, as we chart our course,
there is no free will for the molecule

Scientist: I really don't know what you're talking about.
Farmer: You've (cough) written better, my friend.
Philosopher: I think I get your point. If the assembly just follows instructions, like putting together an Ikea bookshelf, then there is no agency, no "self".
Computer Engineer: I don't buy it. That's like saying a self-driving car isn't self-driving because the transistors are telling it what to do. Or the programmer. The programmer is boss. But no. It is a self-driving car.
Scientist: Self-assembly is ubiquitous throughout nature, and it always follows rules, so I don't see any contradiction here either. Crystals are the purest sort of molecular self-assembly, and they always turn out exactly the same. For example, rock candy is crystallized sucrose. C12H22O11. It always grows into a crystal with the P21 symmetry group. In biology, you can find a remarkable variety of really astounding self-assembly processes. Multipart molecular motors self-assemble from dozens of exquisitely crafted proteins. The cellular cytoskeleton consists of self-assembled microtubules and self-assembled filaments. Viruses self-assemble from proteins that they trick the host cell into producing. They're all programmed by the genome. The molecules self-assemble according to plan.
Farmer: I don't like viruses.
Mathematician: But a plan is not the same as an algorithm. A plan lays out the whole thing, envisions the whole thing at once, like an architectural blueprint. Whereas an algorithm describes how to respond to different input; the same logical procedure is used, but with different input you do different things and get different output. So these examples of crystals that grow according to plan aren't really helping me understand what a "self-assembly algorithm" is.
Scientist: Well, then, with those definitions I'd say that a lot of biological self-assembly processes are more like algorithms than plans.
Poet: Excuse me?

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