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The point I was trying to illustrate was that neither operating systems nor genomes contain the information needed to specify their required operating substrate

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.
- 100ideas 9y ago
  If you’d care to share your reasoning I’d be interested to understand why you think so.
gilleain 9y ago
I'm not sure if you could work out from a genome what the cell should look like - probably not. An important point is that cells are always born of other cells. In other words, a cell replicates by dividing itself, building the parts as it goes along. So there is never such a thing as a 'naked' genome in biology. There are things like viruses, that hijack cell machinery. There are sperm cells, that carry some DNA into an egg and use that. There is the DNA in mitochondria that rely on the host cell for some proteins. If you trace backwards, the genome and it's substrate (the cell) have co-evolved to work together. The existing cell acts as the template for the organisation of a new cell, while reading the genome for the structure of its parts. Of course, the genome contains information about when to make the parts, and how to regulate them.

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.

100ideas 9y ago
If you’d care to share your reasoning I’d be interested to understand why you think so.

gilleain 9y ago

I'm not sure if you could work out from a genome what the cell should look like - probably not. An important point is that cells are always born of other cells. In other words, a cell replicates by dividing itself, building the parts as it goes along. So there is never such a thing as a 'naked' genome in biology. There are things like viruses, that hijack cell machinery. There are sperm cells, that carry some DNA into an egg and use that. There is the DNA in mitochondria that rely on the host cell for some proteins. If you trace backwards, the genome and it's substrate (the cell) have co-evolved to work together. The existing cell acts as the template for the organisation of a new cell, while reading the genome for the structure of its parts. Of course, the genome contains information about when to make the parts, and how to regulate them.