12 ms·

> The source is elegant, but the programs are even more amazing, in my humble opinion. Makes me curious about the 'runtime' which makes their impressive execut

> The source is elegant, but the programs are even more amazing, in my humble opinion. Makes me curious about the 'runtime' which makes their impressive execution possible—granting that the analogy has definite limitations and could be misleading. The aspect of a 'runtime' which I see carrying over is that once the 'source' is 'compiled' into proteins, something makes the interesting behavior of those proteins what it is. I think where the analogy could be misleading is that the architecture of programming language runtimes tends to be a single coherent system with definite separation from programs executing within; whereas in the case of proteins, a large part of what provides for their biologically interesting behavior is just their general chemical properties (which are sort of contained within the 'programs' themselves, rather than in a separate external system). But there are probably aspects of the environment into which the proteins are released that systematically influence their behavior in a way that could be abstracted and studied (at which point it might have some loose resemblance in role to language runtimes). Maybe?

jfarlow 9y ago
In that regard, the protein programs exist and interact with each other in a runtime environment/OS that is 'physics'. Which is cool. Especially, because those programs, when run together, along with all sorts of other small molecule/lipid/temperature conditions are sufficient to output, well, me.
- westoncb 9y ago
  I was somewhat avoiding bringing that up just because, in theory, every physical 'system' in the universe just boils down to physics—and this question gets pretty close to the line between where it's useful to start talking about a higher-level system, versus thinking in terms of chemistry (and/or physics). So it could get confusing. If there is a higher level system analogous to a runtime-environment which could be abstracted from actual genetic machinery, I would bet the rules of its operation would still be at least partially in terms of chemical rules (in other words, you couldn't abstract over it entirely). My justification for it is that I think the system is split between the decentralized behavior of proteins and enzymes etc. just following the rules they always follow, combined with the external 'system' which sets up conditions constraining and otherwise directing the proteins. That second system could maybe be higher level, but it's still central to its operation that it interfaces with a 'raw' chemical system. (Just an idea of course—my confidence that it means anything is ~12%). Edit: another analogy to maybe clarify (or confuse) things. I see the proteins/enzymes etc. which I described as decentralized as operating like a cellular automaton (e.g. Conway's GoL), but then the 'external'/centralized system as like another layer of rules which sort of pushes around clusters of cells in the grid in various significant ways, while all those clusters are still locally just executing the simple automaton rules.
  - jfarlow 9y ago
    Very much. We've actually tried to capture some of those runtime variables within proteins and break down the programs into smaller compossible units. And start to keep track of which conditions are required for particular functionalities of which components. Life has already made a bunch for us to look at. Ultimately, in our hands, those properties are strongly linked to physical associations, locations within a cell, enzymatic capabilities, and i/o (light, heat, chemical concentrations, force, etc.). Then you start (re)building little i/o robots from reusable components for use by and within cells that are regulated by their location and associations (in a wet Brownian environment). All by coding using that same genetic source.
mygo 9y ago
Your 'runtime' is physics. A protein is a chain of concatenated amino acids. The chain will "ball up" into a 3-dimensional shape. Its shape = its function. Why does the balled-up chain function the way that it functions? Because other balled-up protein chains bump up against it in a certain way and suddenly an iron molecule can be contained within the confines of this mega-structure that has formed, and you now have hemoglobin. Why does the chain ball up the way it does? Can we predict how a protein chain will ball up? Well, protein folding is an NP-Complete problem. Solve it and you will get at least $1M USD, change the world, etc. - Software Engineer with a B.S. Degree in Biological Science w/ a focus on genetics + minor in Chem.
- westoncb 9y ago
  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.
leoc 9y ago
Reflections on Trusting Trust...
sporkologist 9y ago
Wouldn't the ribosome be the compiler, that translates codes to proteins?
- jacquesm 9y ago
  Yes.
jacquesm 9y ago
> Makes me curious about the 'runtime' which makes their impressive execution possible https://en.wikipedia.org/wiki/Ribosome https://en.wikipedia.org/wiki/Ribosome
- yorwba 9y ago
  If DNA is the source code and proteins are the compiled programs, the Ribosome is the compiler, not the runtime.
  - jacquesm 9y ago
    It's an analogy. You could also say that DNA is the program, the Ribosome is the interpreter and proteins are the output, which is much closer to the truth.

jfarlow 9y ago

In that regard, the protein programs exist and interact with each other in a runtime environment/OS that is 'physics'. Which is cool. Especially, because those programs, when run together, along with all sorts of other small molecule/lipid/temperature conditions are sufficient to output, well, me.

westoncb 9y ago
I was somewhat avoiding bringing that up just because, in theory, every physical 'system' in the universe just boils down to physics—and this question gets pretty close to the line between where it's useful to start talking about a higher-level system, versus thinking in terms of chemistry (and/or physics). So it could get confusing. If there is a higher level system analogous to a runtime-environment which could be abstracted from actual genetic machinery, I would bet the rules of its operation would still be at least partially in terms of chemical rules (in other words, you couldn't abstract over it entirely). My justification for it is that I think the system is split between the decentralized behavior of proteins and enzymes etc. just following the rules they always follow, combined with the external 'system' which sets up conditions constraining and otherwise directing the proteins. That second system could maybe be higher level, but it's still central to its operation that it interfaces with a 'raw' chemical system. (Just an idea of course—my confidence that it means anything is ~12%). Edit: another analogy to maybe clarify (or confuse) things. I see the proteins/enzymes etc. which I described as decentralized as operating like a cellular automaton (e.g. Conway's GoL), but then the 'external'/centralized system as like another layer of rules which sort of pushes around clusters of cells in the grid in various significant ways, while all those clusters are still locally just executing the simple automaton rules.
- jfarlow 9y ago
  Very much. We've actually tried to capture some of those runtime variables within proteins and break down the programs into smaller compossible units. And start to keep track of which conditions are required for particular functionalities of which components. Life has already made a bunch for us to look at. Ultimately, in our hands, those properties are strongly linked to physical associations, locations within a cell, enzymatic capabilities, and i/o (light, heat, chemical concentrations, force, etc.). Then you start (re)building little i/o robots from reusable components for use by and within cells that are regulated by their location and associations (in a wet Brownian environment). All by coding using that same genetic source.

mygo 9y ago

Your 'runtime' is physics. A protein is a chain of concatenated amino acids. The chain will "ball up" into a 3-dimensional shape. Its shape = its function. Why does the balled-up chain function the way that it functions? Because other balled-up protein chains bump up against it in a certain way and suddenly an iron molecule can be contained within the confines of this mega-structure that has formed, and you now have hemoglobin. Why does the chain ball up the way it does? Can we predict how a protein chain will ball up? Well, protein folding is an NP-Complete problem. Solve it and you will get at least $1M USD, change the world, etc. - Software Engineer with a B.S. Degree in Biological Science w/ a focus on genetics + minor in Chem.

westoncb 9y ago
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.

leoc 9y ago

Reflections on Trusting Trust...

sporkologist 9y ago

Wouldn't the ribosome be the compiler, that translates codes to proteins?

jacquesm 9y ago
Yes.

jacquesm 9y ago

> Makes me curious about the 'runtime' which makes their impressive execution possible https://en.wikipedia.org/wiki/Ribosome https://en.wikipedia.org/wiki/Ribosome

yorwba 9y ago
If DNA is the source code and proteins are the compiled programs, the Ribosome is the compiler, not the runtime.
- jacquesm 9y ago
  It's an analogy. You could also say that DNA is the program, the Ribosome is the interpreter and proteins are the output, which is much closer to the truth.