5 ms·

But physics is the 'runtime' for everything at some level of interpretation. I point out this other hypothetical system because it's possible for 'higher-level'

But physics is the 'runtime' for everything at some level of interpretation. I point out this other hypothetical system because it's possible for 'higher-level' runtimes to emerge from lower-level physicals rules, and this looks like it might be one of those cases. (To clarify, by 'emerge', I mean another consistent set of behaviors appears which are capable of formal description and which can be viewed as consequences of a lower-level system without actually resembling that system.)

mygo 9y ago
But I mean, depending on how you look at it, at some level of interpretation everything can be a higher-level runtime. Yes, protein-protein interactions are a higher-level runtime emerging from lower-level physical runtimes. But on the same vein, Hacker-news is a higher-level runtime emerging, in part, from protein-protein interactions, emerging from lower-level physical runtimes. Can we describe the runtime without invoking some notion of purpose nor questioning free will?
- westoncb 9y ago
  > at some level of interpretation everything can be a higher-level runtime. I don't see how everything can be considered a higher-level runtime. The concept of an execution environment just doesn't map to everything, unless you want to use a definition of it so general as to make it useless. If someone drops a glass and it shatters, would a higher level system describing the mechanics of glass shattering be a runtime? I don't see it. > Yes, protein-protein interactions are a higher-level runtime emerging from lower-level physical runtimes. That's pretty different from what I was describing. See my other comment for more details: https://news.ycombinator.com/item?id=16235639 https://news.ycombinator.com/item?id=16235639 > ... Hacker-news is a higher-level runtime emerging, in part, from protein-protein interactions, emerging from lower-level physical runtimes. I think we disagree on the meaning of the word 'runtime'. I would not consider Hacker News to be a runtime. I do agree with your main point there, though, if you just replaced 'Hacker News' in your statement with, say, the Java runtime environment, then yes, I think it is a higher-level system, usefully described as a runtime, which has emerged as a consequence of the laws of physics doing what they always do. > Can we describe the runtime without invoking some notion of purpose nor questioning free will? My usage of 'runtime' does not involve free will nor purpose.
  - mygo 9y ago
    > If someone drops a glass and it shatters, would a higher level system describing the mechanics of glass shattering be a runtime? I don't see it. It can be a runtime, if some interface is built on top of the phenomenon of the shattering of glass. Because humans.
chillacy 9y ago
I had a discussion about this a few days ago. If the current state of DNA programming is done at the physical level, that's like writing your code by doing photolithography on silicon: not very productive. A level up, maybe the Von Neumann architecture for genetic engineering is the world of DNA and the various proteins like transcriptase. When will we come up with the equivalent Structured Programming? Or Object Orientation? Or Operating Systems? Each represents an abstraction over the others, and increases productivity.
- jfarlow 9y ago
  It's what we do! https://serotiny.bio/notes/pinecone/ https://serotiny.bio/notes/pinecone/ :: http://biologylabs.utah.edu/jorgensen/wayned/ape/ http://biologylabs.utah.edu/jorgensen/wayned/ape/ as C :: assembly We'd even hope it's a bit like 'basic' rather than C, to the point where motivated non-scientists could even start to use it: https://serotiny.bio/notes/support/tutorials/ https://serotiny.bio/notes/support/tutorials/
- westoncb 9y ago
  My understanding is we got programmable computers in large part because: 1) a bunch of scientific/engineering advances we were in a position to make were bottlenecked by massive amounts of 'boring' calculations 2) Some of those affected areas related to the war effort in critical ways, so lots of money and resources were poured into solving the problem. Seems like we're in a similar position with '1' above, in connection with genetic engineering, so demand exists to abstract over and automate the boring stuff. But maybe the problem is significantly harder, or maybe we're just lacking the pressure that would lead to focused/cooperative effort and lots of resources pouring in, like we had in '2'.
  - jfarlow 9y ago
    > lacking the pressure that would lead to focused/cooperative effort and lots of resources pouring in Until literally a few months ago, hacking at the level of the protein abstraction was relegated to academics. Then Chimeric Antigen Receptors cured children of cancers, and were approved by the FDA. And so in August, Kite got bought by Gilead for $12B. Then in November Gilead bought another class of multi-domain protein biotherapeutics called SynNotch for $0.5B from an 18 month old startup. And Juno got purchased yesterday for $9B again for their work on CARs - multi-domain protein biotherapeutics. We'd like to think that such cooperative effort and resources are just starting to pour in. But up until very recently, it was not obvious what the commercial value was when working at such an abstraction layer.

mygo 9y ago

But I mean, depending on how you look at it, at some level of interpretation everything can be a higher-level runtime. Yes, protein-protein interactions are a higher-level runtime emerging from lower-level physical runtimes. But on the same vein, Hacker-news is a higher-level runtime emerging, in part, from protein-protein interactions, emerging from lower-level physical runtimes. Can we describe the runtime without invoking some notion of purpose nor questioning free will?

westoncb 9y ago
> at some level of interpretation everything can be a higher-level runtime. I don't see how everything can be considered a higher-level runtime. The concept of an execution environment just doesn't map to everything, unless you want to use a definition of it so general as to make it useless. If someone drops a glass and it shatters, would a higher level system describing the mechanics of glass shattering be a runtime? I don't see it. > Yes, protein-protein interactions are a higher-level runtime emerging from lower-level physical runtimes. That's pretty different from what I was describing. See my other comment for more details: https://news.ycombinator.com/item?id=16235639 https://news.ycombinator.com/item?id=16235639 > ... Hacker-news is a higher-level runtime emerging, in part, from protein-protein interactions, emerging from lower-level physical runtimes. I think we disagree on the meaning of the word 'runtime'. I would not consider Hacker News to be a runtime. I do agree with your main point there, though, if you just replaced 'Hacker News' in your statement with, say, the Java runtime environment, then yes, I think it is a higher-level system, usefully described as a runtime, which has emerged as a consequence of the laws of physics doing what they always do. > Can we describe the runtime without invoking some notion of purpose nor questioning free will? My usage of 'runtime' does not involve free will nor purpose.
- mygo 9y ago
  > If someone drops a glass and it shatters, would a higher level system describing the mechanics of glass shattering be a runtime? I don't see it. It can be a runtime, if some interface is built on top of the phenomenon of the shattering of glass. Because humans.

chillacy 9y ago

I had a discussion about this a few days ago. If the current state of DNA programming is done at the physical level, that's like writing your code by doing photolithography on silicon: not very productive. A level up, maybe the Von Neumann architecture for genetic engineering is the world of DNA and the various proteins like transcriptase. When will we come up with the equivalent Structured Programming? Or Object Orientation? Or Operating Systems? Each represents an abstraction over the others, and increases productivity.

jfarlow 9y ago
It's what we do! https://serotiny.bio/notes/pinecone/ https://serotiny.bio/notes/pinecone/ :: http://biologylabs.utah.edu/jorgensen/wayned/ape/ http://biologylabs.utah.edu/jorgensen/wayned/ape/ as C :: assembly We'd even hope it's a bit like 'basic' rather than C, to the point where motivated non-scientists could even start to use it: https://serotiny.bio/notes/support/tutorials/ https://serotiny.bio/notes/support/tutorials/
westoncb 9y ago
My understanding is we got programmable computers in large part because: 1) a bunch of scientific/engineering advances we were in a position to make were bottlenecked by massive amounts of 'boring' calculations 2) Some of those affected areas related to the war effort in critical ways, so lots of money and resources were poured into solving the problem. Seems like we're in a similar position with '1' above, in connection with genetic engineering, so demand exists to abstract over and automate the boring stuff. But maybe the problem is significantly harder, or maybe we're just lacking the pressure that would lead to focused/cooperative effort and lots of resources pouring in, like we had in '2'.
- jfarlow 9y ago
  > lacking the pressure that would lead to focused/cooperative effort and lots of resources pouring in Until literally a few months ago, hacking at the level of the protein abstraction was relegated to academics. Then Chimeric Antigen Receptors cured children of cancers, and were approved by the FDA. And so in August, Kite got bought by Gilead for $12B. Then in November Gilead bought another class of multi-domain protein biotherapeutics called SynNotch for $0.5B from an 18 month old startup. And Juno got purchased yesterday for $9B again for their work on CARs - multi-domain protein biotherapeutics. We'd like to think that such cooperative effort and resources are just starting to pour in. But up until very recently, it was not obvious what the commercial value was when working at such an abstraction layer.