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Chromosomes and Sexual Rproduction
bacillus:
Hmmm....what about making a cap on the number of vectors in the DNA proportional to body size?
I gave this some more thought today, and thought this could play out nicely:
-Chromosomes
These have no particular internal structure. They are discrete eg. you can't have start/stop commands randomly floating around, but mutations can 'physically' break and recombine chromosomes (as real block mutations do). In place of genes, chromosomes have inline logic. This minimizes the deviation from the current code while still maintaining the rough structure of real chromosomes.
-Plasmids
These will be the conventional cond/start/stop genes. Plasmids can reproduce and eject themselves independently (eg. viruses), and are separated from the chromosomes. This means that primitive species can still function with only plasmid DNA, and will also provide full compatibility with the current code.
Sexrepro will mix chromosomes as in traditional meiosis (not sure what happens with plasmids, I guess you just mix and match somehow), repro will duplicate the individual as in mitosis, and viral commands and delgene will take over the plasmid controls.
The main idea is that chromosomes control the cell's defining functions, while the plasmids are extra generic pieces of DNA, such as viruses, or something like poison genes.
I guess the no real pressure to keep DNA length small - but mutations very rarely cause insanely large strands to appear out of nowhere (with the exception of polyploidy, which is fatal in animals and usually causes sterility in others), so DNA growth is mainly caused by viruses - a virus inserting itself into a host is usually fatal, terminating that strand. The only real growth in DNA is caused by broken viruses-and I think junk DNA is supposed to make up very large chunks of our DNA, on which no pressure acts...
There is some physical limitations on the amount of DNA, I guess. Space is the ultimate one (although only relevant when a virus undergoes extreme amplification-Ebola comes to mind), but within limits of reason, a cell can only produce so much proteins and other materials to read and execute DNA - like having a computer with a billion processors all running from the same battery, to use your analogy.
Numsgil:
--- Quote from: ikke on August 18, 2010, 12:49:38 AM ---
--- Quote from: Numsgil on August 17, 2010, 06:27:40 PM ---There's probably some selection pressure to keep DNA length small(ish), but I don't know what it might be. Bacteria genomes are orders of magnitude smaller than eukaryote genomes, so whatever it is it's less pronounced in eukaryotes.
--- End quote ---
As I understand it dna and cell size correlate (on a species level). Organisms are selected based on optimal cell size (be it bigger or smaller) and therefore insertions or deletions are selected
--- End quote ---
Hmm, we could probably tie DNA length to some sort of minimum cell volume. More DNA = larger cell. I'll have to think through what sort of consequences this might have. At some level you need some downward pressure on DNA length, because real life computer resources aren't infinite. But on the other side if the costs are too high you end up with grey goo. And I don't know a good way to figure out what too high is until after you have grey goo.
Along the same line if we could tie some sort of "efficiency" to cell size vs. DNA length, that might be interesting too. Like in times of trouble the cell can condense itself to preserve resources, but at the cost that it's basically putting itself in some sort of hibernation. To actually execute and metabolise code and stuff you need your DNA "unraveled" with lots of working room. But I don't know how to do that with a discretely executed DNA. If cells could run at different clock rates (eg: say 100 cycles pass before your DNA is executed again (cycles would represent smaller chunks of time probably)), that might work. I dunno, some food for thought.
@bac:
If viruses are chromosomes, you don't need cond, start, stop, etc. to define them anyway. Virus production just becomes "duplicate this chromosome". So if you've defined a nice way in which conflicting chromosomes interact (eg: average their store values or something) then this part of it at least becomes quite manageable. You also don't have to worry about trying to balance how DNA gets injected in to existing DNA strands (eg: inside the middle of a gene is usually doubly damaging).
--- Quote ---There is some physical limitations on the amount of DNA, I guess. Space is the ultimate one (although only relevant when a virus undergoes extreme amplification-Ebola comes to mind), but within limits of reason, a cell can only produce so much proteins and other materials to read and execute DNA - like having a computer with a billion processors all running from the same battery, to use your analogy.
--- End quote ---
Yeah, that's a good way to look at it actually.
bacillus:
--- Quote ---@bac:
If viruses are chromosomes, you don't need cond, start, stop, etc. to define them anyway. Virus production just becomes "duplicate this chromosome". So if you've defined a nice way in which conflicting chromosomes interact (eg: average their store values or something) then this part of it at least becomes quite manageable. You also don't have to worry about trying to balance how DNA gets injected in to existing DNA strands (eg: inside the middle of a gene is usually doubly damaging).
--- End quote ---
Ah, but viruses are not chromosomes - in this model, viruses would instead be plasmids, floaty chunks of DNA separate from the main body of DNA eg. chromosomes. I suppose you could also insert them into the chromosomes, but then you have to define the gene within the chromosome, which otherwise would not be necessary; this way also gives some limited degree of DB2 code.
In summary, I think I'm somehow missing your point...
Numsgil:
--- Quote from: bacillus on August 19, 2010, 02:13:02 AM ---
--- Quote ---@bac:
If viruses are chromosomes, you don't need cond, start, stop, etc. to define them anyway. Virus production just becomes "duplicate this chromosome". So if you've defined a nice way in which conflicting chromosomes interact (eg: average their store values or something) then this part of it at least becomes quite manageable. You also don't have to worry about trying to balance how DNA gets injected in to existing DNA strands (eg: inside the middle of a gene is usually doubly damaging).
--- End quote ---
Ah, but viruses are not chromosomes - in this model, viruses would instead be plasmids, floaty chunks of DNA separate from the main body of DNA eg. chromosomes. I suppose you could also insert them into the chromosomes, but then you have to define the gene within the chromosome, which otherwise would not be necessary; this way also gives some limited degree of DB2 code.
In summary, I think I'm somehow missing your point...
--- End quote ---
Well what is a chromosome? Basically a large floaty chunk of DNA. Functionally there's no reason to treat chromosomes separately from plasmids, so make them the same thing. When you get infected with a virus, the virus just becomes a new chromosome. It gets replicated during reproduction, tries to get matched during meiosis, all that fun stuff. Then virus replication doesn't need to rely on any special gene tags. It just literally copies the entire chromosome, since the entire chromosome is the virus.
Mutations later on can maybe merge chromosomes to provide some downward pressure on the number of them.
bacillus:
The main reason to treat chromosomes differently to plasmids is that they are the only determinants in sexual repoduction. Plasmids do not define a species - they just float in the cell, acting completely independently of the chromosomes. This also means that infected cells don't suddenly have huge reproduction complications - viral plasmids simply replicate their own DNA (a virus doesn't copy huge chunks of random DNA, just itself) without messing up the reproduction system. It also means you don't have to trim DNA to pressure downwards - you can just can, say, half the plasmids from each parent or something like that, which would provide serious issues with chromosomes.
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