It’s #3. (B.Sc. in biochemistry, did my Ph.D. in proteomics.)
First, the set of polypeptide sequences that have a repeatable final conformation (and therefore “work” biologically) is tiny in comparison to the set of all possible sequences (of the 20-or-so naturally amino acid monomers). Pick a random sequence of reasonable length and make many copies and you get a gummy mess. The long slow grind of evolution has done the hard work of finding useful sequences.
Second, there is an entire class of proteins called chaperones) that assist macromolecular assembly, including protein folding. Even so, folding is a stochastic process, and a certain amount of newly synthesized proteins misfold. Some chaperones will then tag the misfolded protein with ubiquitin, which puts it on a path that ends in digestion by a proteasome.
Aaronson used to blog about instances where people thought they found nature solving a hard problem very quickly, and usually there turns out to be a problem like the protein misfolding thing; the last instance I remember was soap films/bubbles perhaps solving NP problems by producing minimal Steiner trees, and Aaronson wound up experimenting with them himself. Fun stuff.
It’s #3. (B.Sc. in biochemistry, did my Ph.D. in proteomics.)
First, the set of polypeptide sequences that have a repeatable final conformation (and therefore “work” biologically) is tiny in comparison to the set of all possible sequences (of the 20-or-so naturally amino acid monomers). Pick a random sequence of reasonable length and make many copies and you get a gummy mess. The long slow grind of evolution has done the hard work of finding useful sequences.
Second, there is an entire class of proteins called chaperones) that assist macromolecular assembly, including protein folding. Even so, folding is a stochastic process, and a certain amount of newly synthesized proteins misfold. Some chaperones will then tag the misfolded protein with ubiquitin, which puts it on a path that ends in digestion by a proteasome.
Thank you, Cyan. It’s good to occasionally get someone into the debate who actually has a good understanding of the subject matter.
Aaronson used to blog about instances where people thought they found nature solving a hard problem very quickly, and usually there turns out to be a problem like the protein misfolding thing; the last instance I remember was soap films/bubbles perhaps solving NP problems by producing minimal Steiner trees, and Aaronson wound up experimenting with them himself. Fun stuff.