I think it's easier to understand if you rephrase it as "evolution doesn't encapsulate." Just because a bunch of smaller proteins fold into a bigger quaternary protein structure doesn't mean that those smaller proteins become "private" members of the new protein "class". Any chemical binding sites that are still exposed on the surface of the complex protein will still be chemically active and affected by evolutionary pressure. Even if you have a protein A made up of B, C, and D that all evolved together to metabolize fructose, an exposed binding site from protein C on A can still effect some completely unrelated biochemistry. At the same time, protein C could also be a critical component of a new protein E.

If the evolutionary pressures on E (or C individually) are greater than on A, C could evolve completely out from under A to the point where A is no longer functional or foldable. As such, evolution can't "rely" on abstractions like "protein C" because their "source code" can be changed nonlocally and their function is dependent on very local conditions like temperature, pH, and surrounding molecules. Abstracting away g(h(i(x))) as f(x) in Mathematica is pointless when your packet sniffer can arbitrarily change the meaning of "h(x)" to "nop".

>>evolution doesn't encapsulate.

I'm not a biologist or geneticists but from everything that I've read about cellular biology and genetics I get the strong feeling that there is a lot of encapsulation going on. Sure, it isn't 100% percent perfect but there is still encapsulation going on. Evolution would probably be way harder without it.

One hint is the human body, there are lots of encapsulations: eyes, heart, kidneys, digestive system, etc.

Evolution can repurpose an existing system for a completely different use with just some tweaking.

I think that's a misleading observation though. It is squinting at the macro structure of the body and saying "ah ha, encapsulation!". When you look closer the apparent encapsulation seems less and less like an accurate notion. For example the newer research showing how the gut affects cognition. [0]

This is a bit off-topic but I think paleo-ontologists fall into a similar trap, at least based on popular writing about e.g. sharks. Claims that they haven't evolved in 100M years because they're the same shape as they used to be completely ignore all the other aspects of the shark that could change without affecting the overall shape.

0. https://www.ncbi.nlm.nih.gov/pubmed/24997042

Or perhaps it's like code where everything is in therl global scope. New code may add global variables and/or rely on existing ones, or even change existing ones. In code like, changing one line of code could have far reaching and unexpected consequences.

Great explanation (even though you're not OP), makes sense now!

It's not a great example, and I'm sorry for it. Let me try another one. In the study of eukaryotic cell cycle, there's a notion of a checkpoint. For example, if you damage the DNA of a yeast cell severely, it will continue its cell cycle until some point and then arrest instead of arresting directly, and you can find mutants that don't arrest. There's a whole set of mutants that were used to figure out the checkpoints in the cell cycle.

Of course there's no little physical switch. This is a giant mass of molecules bouncing around. A fellow I know did some interesting work on replacing simple checkpoint models with entrained oscillators. But this makes the checkpoints look like an abstraction.

That's our view of it, though. It's not an abstraction. It's something that looks like one.

Presumably they mean that material evolution doesn't involve ideas, which is what abstractions are.

This is a physicalist line to take which implies that the universe is entirely material, and abstraction is just something human minds perceive.

> ...abstraction is just something human minds perceive.

This itself is a physical phenomenon :)

Makes things tricky, doesn't it? We utilize abstraction to make theories of a world that doesn't have abstractions.

For physicalists, yes.

DNA is spaghetti code where modularization happens by accident.

Reminds me of our corporate codebase after 10 years of A/B testing

Still growing strong I assume:)

We decided we had enough so we rewrote it! Well, most of it, there were some abandoned servlets that brought in enough money that we kept the old codebase running as well. :)

Yeah, great comment. Definitely a "best of HN comments" candidate.

Isn't abstraction just the emergence of simpler, lower fidelity, and higher density structures of information? Are we not a part of nature?

Did you ever read "Mote in God's Eye"? It's like Motie engineering.