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There's a couple of things that are slowly changing in the thinking of biologists related to this: 1. Genes are not loci. The "one gene = one protein" dogma of
by madhadron 8y ago
There's a couple of things that are slowly changing in the thinking of biologists related to this:
1. Genes are not loci. The "one gene = one protein" dogma of molecular biology (expanded: "one trait selectable in breeding experiments = one compact locus of the chromosome") was a priori wrong, but it's taken us decades to undo the damage. We were led astray because there are traits that do map to a single locus, or single mutations that were found to be able to control a trait, which is not the same thing as the trait.
2. Distributed representation. If I point to a sentence and ask "where is the sarcasm?" (assuming the sentence is sarcastic), there is no answer. It's certainly a trait of the sentence, just as, say, being red headed is a trait of the organism. But a linear model showing each word's contribution to sarcasm isn't helpful.
3. Perhaps a corollary of (2), humans have the concept of abstraction. There are many situations where you can get something like an abstraction from evolution. If a human engineered it, we'd call it a leaky abstraction, but please don't get caught up on that. Evolution doesn't abstract. But there are structures that emerge that can have similar properties, especially from repeated exaptation. Consider the MAP kinase pathways. Lots and lots of cell responses involve them, in all kinds of subtly different ways. We don't try to claim that a MAP kinase is the gene for anything in particular, any more than we would claim that the interrupt for triggering a system call on 32 bit Linux is the cause of certain behavior that a program is supposed to have in a particular domain.
- jds375 8y agoVery interesting comment, thanks! Could you elaborate on what you mean by ‘evolution doesn’t abstract’? I did not totally understand what the example given had to do with abstraction
- theoh 8y agoPresumably 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.
- tw1010 8y agoYeah, great comment. Definitely a "best of HN comments" candidate.
- civilitty 8y agoI 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".
- felipemnoa 8y ago>>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.
- telchar 8y agoI 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 https://www.ncbi.nlm.nih.gov/pubmed/24997042
- kristianov 8y agoDNA is spaghetti code where modularization happens by accident.
- foobarian 8y agoReminds me of our corporate codebase after 10 years of A/B testing
- kristianov 8y agoStill growing strong I assume:)
- foobarian 8y agoWe 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. :)
- inventtheday 8y agoIsn't abstraction just the emergence of simpler, lower fidelity, and higher density structures of information? Are we not a part of nature?
- carapace 8y agoDid you ever read "Mote in God's Eye"? It's like Motie engineering.
- madhadron 8y agoIt'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.
- pishpash 8y agoTo add to that, evolution does generate compositions, and some of the abstractions that do occur come from those.
- biot 8y agoI often think of that scene in Contact where they are trying to decrypt the alien message: https://youtu.be/HgPSUer1ujM https://youtu.be/HgPSUer1ujM Multiple genetic materials operating on multiple levels...
- deleted 8y ago[deleted]
- kevinwang 8y agoGreat comment, thanks!
- lisper 8y ago> Evolution doesn't abstract. That is a very profound observation. It suggests a way that one can distinguish between something that evolved vs something that was designed.
- resource0x 8y agoUnless it's designed to be obfuscated. Which is a very big "unless" IMO :)
- madhadron 8y agoI've spent a little time considering what this class of things would be. It's like trying to turn a forgetful functor into a homotopy transformation and having some kind of universal measure of the distance from the end of the transformation.
- fragsworth 8y agoBut we don't actually know if evolution doesn't abstract. It's possible that our genome has been around long enough to develop tendencies to cause mutations that change us in certain ways that might be considered "abstract". For instance, we might be able to mutate longer or shorter arms or legs. This notion should be supported by the fact that we don't mutate in completely random ways, and the fact that most mutations don't kill us.
- jlg23 8y ago4. Few biologists have dived into automata theory. The divide in background theoretic knowledge and thus language is too great for biology to directly profit from advances in automata theory.
- mrfusion 8y agoI’m interested. Explain more?
- skosuri 8y agoRe: 1: It wasn’t wrong. There are Mendelian traits and complex traits. We shouldn’t forget we’ve basically tracked down most Mendelian diseases since the human genome was published. Still some to go but we will hopefully have all soon. This is a huge accomplishment. Complex/quantitative traits on the other hand have been known for quite some time. I don’t think it’s anything new, but the landscape is becoming increasingly clear thanks to large scale GWAS and analyses from many groups including Pritchard’s.
- __s 8y agoPoint 1 draws parallels with machine learning's pixel attacks. That one pixel doesn't define the image, but it happens that changing it changes the classification of the whole
- bambamboom 8y agoPeople who downvoted thid- can you explain? I see this as a very nice simplification of point 1 and am glad that _s brought it up
- tome 8y ago> Evolution doesn't abstract What does this mean? Are cells, for example, not abstractions?
- coldtea 8y agoParent means it doesn't consciously abstract -- not that abstractions cannot result from it. In the same way the banana skin is a great packaging solution, but it wasn't created to serve as packaging for our consumption.
- coldtea 8y ago>If a human engineered it, we'd call it a leaky abstraction, but please don't get caught up on that. Evolution doesn't abstract. Why not? Humans are products of evolution too, and they abstract. I mean, what we consider conscious (e.g. human activity) and what we consider accidental (e.g. the result of evolutionary forces clashing) are not very well defined. Heck, we haven't even solved the determinism vs free will issue yet.
- ismail 8y ago“Distributes representation... there is no answer. It's certainly a trait of the sentence“ Thanks for this. Came here to post a comment and saw this Very similar view, with a different term. Another way to define this is: 1. The higher level object/thing has traits/properties that the parts do not have 2. Understanding each part does not necessarily = understanding these traits 3. The parts are interdependent 4. The traits/properties of the higher level is determined by the interaction of the parts ... which is the definition of a system.
- Ngunyan 8y agoI think this is called an emergent property.