4 ms·

If all you had was unix kernel machine code, could you really use it to engineer the hardware required for it to go inside of?

nsxwolf 9y ago
That’s a good analogy. So it seems the cell evolves separately. But this doesn’t seem to be talked about as much, at least not amongst laypersons.
- 100ideas 9y ago
  You might enjoy: Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9186-91. doi:10.1073/pnas.0914771107. Epub 2010 May 3. https://www.ncbi.nlm.nih.gov/pubmed/20439753 https://www.ncbi.nlm.nih.gov/pubmed/20439753
  - 100ideas 9y ago
    Also: Istrail S, De-Leon SB, Davidson EH. The regulatory genome and the computer. Dev Biol. 2007 Oct 15;310(2):187-95. Epub 2007 Aug 10. Review. PubMed PMID: 17822690. Full-text: http://www.sciencedirect.com/science/article/pii/S0012160607012547 http://www.sciencedirect.com/science/article/pii/S0012160607... Abstract: > "The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are “wired” together in large networks that control major processes such as development; they constitute “genomic computers.” Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers. Here we consider the operating principles of the genomic computer, the product of evolution, in comparison to those of electronic computers. For example, in the genomic computer intra-machine communication occurs by means of diffusion (of transcription factors), while in electronic computers it occurs by electron transit along pre-organized wires. There follow fundamental differences in design principle in respect to the meaning of time, speed, multiplicity of processors, memory, robustness of computation and hardware and software. The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life."
  - DoctorBit 9y ago
    That was interesting, but I think their conclusion about the linux kernel being comparatively top-heavy with relatively few "work horses" was probably greatly influenced by the fact that they only analyzed the linux kernel, not linux kernel + device drivers. IMO, device drivers should be considered part of the OS - really, the work horses of the OS, not called by any other code.
- dkural 9y ago
  Actually it's a very misleading analogy. In biology, that's precisely what is happening: The "kernel code" i.e. our genome in fact does have all the instructions on how to build a cell, how to build tissues, how everything communicates, etc. (my education: BA in math, PhD in Biology)
  - 100ideas 9y ago
    The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate and environment. Perhaps it may be possible to derive or infer these requirements through simulation and analysis of the OS or genome, or perhaps not. I guess it depends on the degree to which the "code" defining the system is abstracted from its operational embodiment, i.e. is the operating system in question encoded in the form of a Hardware Description Language [1], FPGA IP cores, or more abstract high-level source code? I assume it would be more difficult/impossible to work out the hardware requirements for an OS given the just the high-level source code (are compilers included?) vs a low-level or "bottom"-level (hardware-level?) code. Likewise for a genome, I don't think the sequence of As, Gs, Cs, & Ts specified in an organism's reference genome [2] entail the chemical and physical particulars needed to instantiate the genome in an environment (physical, virtual, whatever) such that it functions. On the other hand, if you gave me an actual genome comprised of purified genomic DNA, then I'm getting a big hint about how the code needs to be physically instantiated for it to work. From this hint, maybe a near-omnipotent reverse-engineer could infer the biochemical requirements (i.e. cell-free expression system or a donor cell) needed to boot up the organism. Am I just being pedantic or do you see what I'm trying to get at? [1]: https://en.wikipedia.org/wiki/Verilog https://en.wikipedia.org/wiki/Verilog [2]: https://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=graph&log$=seqview https://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=grap...
    - AstralStorm 9y ago
      No, genome contains almost all of the information about the running environment. The epigenome is the rest. Both of these even contain information about build environment. Given high genetic mastery you would be able to figure out the conditions for the whole organism to grow, including required feedback loops. Of course, we're not even close. Generic code is somewhat close to a quine if you look right at it.
haihaibye 9y ago
This is a bad analogy - the instructions for making everything in the cell is in the dna, so you also have the blueprints for the hardware fabrication plant.
- crusso 9y ago
  Don't some features of the cell that you get from your mother replicate themselves, like your mitochondria? Granted, mitochondria have their own DNA - but aren't considered part of the human chromosome. Besides mitochondria, isn't there a whole cellular bootstrap environment that the DNA doesn't specifically encode for?
- rleigh 9y ago
  No, it's a pretty reasonable analogy. For the original point, if all we had was machine code, and that code had a complete description of the machine which could run it and how to create it, it would still be useless without a machine to process it. The code on its own would not be sufficient to create the machine. You can't make use of DNA without all the complex machinery required to transcribe it, translate RNA and replicate it. There's a chicken and egg problem. The DNA does indeed encode the instructions to make and assemble all the rRNA, tRNA and protein sequences to do this, but you have to already have the machinery in place to do so. Kind of like compiling a compiler. You need an initial manual bootstrap, which in the case of life as we know it, took place many millions of years in the past. Just as the code for a compiler is just so much meaningless ones and zeroes without a working compiler to process it, so is DNA in the absence of the translation machinery. Without any context for how to process it, it's just a meaningless jumble of bases. One thing to think about. If we discovered intact dinosaur remains with non-degraded DNA, could we resurrect it? We don't have the machinery since it was lost with the death of the organism. But we could potentially bootstrap it by placing it in the cell of a related species, e.g. a reptile. But if it was a completely different form of life, we wouldn't even know where to begin.
  - haihaibye 9y ago
    >> if all we had was machine code, and that code had a complete description of the machine which could run it and how to create it That's a reasonable analogy but it's not what the original poster said.

nsxwolf 9y ago

That’s a good analogy. So it seems the cell evolves separately. But this doesn’t seem to be talked about as much, at least not amongst laypersons.

100ideas 9y ago
You might enjoy: Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Yan KK, Fang G, Bhardwaj N, Alexander RP, Gerstein M. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9186-91. doi:10.1073/pnas.0914771107. Epub 2010 May 3. https://www.ncbi.nlm.nih.gov/pubmed/20439753 https://www.ncbi.nlm.nih.gov/pubmed/20439753
- 100ideas 9y ago
  Also: Istrail S, De-Leon SB, Davidson EH. The regulatory genome and the computer. Dev Biol. 2007 Oct 15;310(2):187-95. Epub 2007 Aug 10. Review. PubMed PMID: 17822690. Full-text: http://www.sciencedirect.com/science/article/pii/S0012160607012547 http://www.sciencedirect.com/science/article/pii/S0012160607... Abstract: > "The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are “wired” together in large networks that control major processes such as development; they constitute “genomic computers.” Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers. Here we consider the operating principles of the genomic computer, the product of evolution, in comparison to those of electronic computers. For example, in the genomic computer intra-machine communication occurs by means of diffusion (of transcription factors), while in electronic computers it occurs by electron transit along pre-organized wires. There follow fundamental differences in design principle in respect to the meaning of time, speed, multiplicity of processors, memory, robustness of computation and hardware and software. The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life."
- DoctorBit 9y ago
  That was interesting, but I think their conclusion about the linux kernel being comparatively top-heavy with relatively few "work horses" was probably greatly influenced by the fact that they only analyzed the linux kernel, not linux kernel + device drivers. IMO, device drivers should be considered part of the OS - really, the work horses of the OS, not called by any other code.
dkural 9y ago
Actually it's a very misleading analogy. In biology, that's precisely what is happening: The "kernel code" i.e. our genome in fact does have all the instructions on how to build a cell, how to build tissues, how everything communicates, etc. (my education: BA in math, PhD in Biology)
- 100ideas 9y ago
  The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate and environment. Perhaps it may be possible to derive or infer these requirements through simulation and analysis of the OS or genome, or perhaps not. I guess it depends on the degree to which the "code" defining the system is abstracted from its operational embodiment, i.e. is the operating system in question encoded in the form of a Hardware Description Language [1], FPGA IP cores, or more abstract high-level source code? I assume it would be more difficult/impossible to work out the hardware requirements for an OS given the just the high-level source code (are compilers included?) vs a low-level or "bottom"-level (hardware-level?) code. Likewise for a genome, I don't think the sequence of As, Gs, Cs, & Ts specified in an organism's reference genome [2] entail the chemical and physical particulars needed to instantiate the genome in an environment (physical, virtual, whatever) such that it functions. On the other hand, if you gave me an actual genome comprised of purified genomic DNA, then I'm getting a big hint about how the code needs to be physically instantiated for it to work. From this hint, maybe a near-omnipotent reverse-engineer could infer the biochemical requirements (i.e. cell-free expression system or a donor cell) needed to boot up the organism. Am I just being pedantic or do you see what I'm trying to get at? [1]: https://en.wikipedia.org/wiki/Verilog https://en.wikipedia.org/wiki/Verilog [2]: https://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=graph&log$=seqview https://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=grap...
  - AstralStorm 9y ago
    No, genome contains almost all of the information about the running environment. The epigenome is the rest. Both of these even contain information about build environment. Given high genetic mastery you would be able to figure out the conditions for the whole organism to grow, including required feedback loops. Of course, we're not even close. Generic code is somewhat close to a quine if you look right at it.

haihaibye 9y ago

This is a bad analogy - the instructions for making everything in the cell is in the dna, so you also have the blueprints for the hardware fabrication plant.

crusso 9y ago
Don't some features of the cell that you get from your mother replicate themselves, like your mitochondria? Granted, mitochondria have their own DNA - but aren't considered part of the human chromosome. Besides mitochondria, isn't there a whole cellular bootstrap environment that the DNA doesn't specifically encode for?
rleigh 9y ago
No, it's a pretty reasonable analogy. For the original point, if all we had was machine code, and that code had a complete description of the machine which could run it and how to create it, it would still be useless without a machine to process it. The code on its own would not be sufficient to create the machine. You can't make use of DNA without all the complex machinery required to transcribe it, translate RNA and replicate it. There's a chicken and egg problem. The DNA does indeed encode the instructions to make and assemble all the rRNA, tRNA and protein sequences to do this, but you have to already have the machinery in place to do so. Kind of like compiling a compiler. You need an initial manual bootstrap, which in the case of life as we know it, took place many millions of years in the past. Just as the code for a compiler is just so much meaningless ones and zeroes without a working compiler to process it, so is DNA in the absence of the translation machinery. Without any context for how to process it, it's just a meaningless jumble of bases. One thing to think about. If we discovered intact dinosaur remains with non-degraded DNA, could we resurrect it? We don't have the machinery since it was lost with the death of the organism. But we could potentially bootstrap it by placing it in the cell of a related species, e.g. a reptile. But if it was a completely different form of life, we wouldn't even know where to begin.
- haihaibye 9y ago
  >> if all we had was machine code, and that code had a complete description of the machine which could run it and how to create it That's a reasonable analogy but it's not what the original poster said.