If all you had was a genome, could you really use it to engineer the cell required for it to go inside of?
So - they bootstrapped that genome using machinery of the empty cell w/o the genome, but from that point on, the new genome produced everything needed for many other cells & itself. (Venter's papers creating synthetic life)
In fact, following that, the same team refactor that genome to create a minimum viable genome, the MVP of genomes if you will, just to see how few genes you can get away with!
Here's an article: http://www.nature.com/news/minimal-cell-raises-stakes-in-rac...
Definitively no if you consider multi-cellular organisms. And that's not just me being pedantic. Consider that every cell in your body, from the white blood cells to skin cells to neurons, has the same DNA. It's entirely non-genetic factors (epi-genetics like methylation of genes, but also hormones and existing intra-cellular structures) that leads to a neuron acting like a neuron instead of a liver cell.
DNA in a cell is ~2 meters long (rolled up it's 6 microns across) http://www.sciencefocus.com/qa/how-long-your-dna * ~40 trillion cells (https://www.smithsonianmag.com/smart-news/there-are-372-tril...) ~= 8e13 meters ~= 5 * 10 ^ 10 miles or ~50 billion miles.
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.
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/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."
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
[2]: https://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=grap...
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.
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.
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?
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.
That's a reasonable analogy but it's not what the original poster said.