I don't share your reversion to creating the primitives to allow for self DNA inspection or manipulation. In fact, as above, I think it is critical to someday allowing the evolution of reproduction and mutation mechanisms outside the simulator. IMHO, we want an organism to at least have the capability to copy thier own DNA, to copy it inperfectly if selection favors this, to perform their own error analysis or virus infection analysis, to self correct, to evolve virual resistance and so on. IMHO, the genomorph should absolutely be a battle ground over which evolution presides.
My main concerns are:
1. Bots will be able to effectively eliminate or destroy foreign DNA in a more effective and cheap way than using slime to prevent virus infection, or whatever methods we care to add. Right now, slime costs a great deal more energy, and is far less effective, than delgene'ing a virus.
2. Self policing DNA protecting itself against viruses will tend to get shorter over time. The less to patrol, the easier the job. This shortening effect will reduce the "wiggle" room for new adaptations. Real DNA is
huge. Gigabytes and gigabytes of data, a large percentage of which is just along for the ride, and doesn't really do anything one way or another. That is, self policing DNA creates an implicit cost for DNA length, wether we like that or not. And costs generally have a simplifying effect on complexity.
3. Viruses end up with too much power. Whatever tools we give DNA to police itself, we have to give viruses too. The result is a powerstruggle between native DNA and viruses where huge swaths of DNA get deleted. The whole process is destructive, but struggles like this in nature tend to be constructive. The large sections of dead viruses in our DNA are evidence of this. Things don't get deleted very often. Usually they just get turned off.
I disagree here too. The whole concept of a virus is of a bit of essentially pure information that hijacks the machinery of more physical organisms to do its dirty work, replication cheif amoung that. Isolating viruses into their own module or thinking of them as somehow self contained and distict of otherwise "different" from the host DNA cuts against this IMHO.
This I agree with. Viruses need to be undifferentiated from any native DNA. Or that should be the goal at any rate.
Viruses should be able to hijack existing DNA sequences inside the genes or even hijack entire sets of genes of their host, redirecting that logic to their own ends. Selection will favor shorter viruses, ones that can take advantage of more existing host DNA so as not to contain that logic themselves. Many biological viruses do this including HIV, the Flu and all the Herpes variants. To this end, viruses need some some sort of fine grain mechanism to control where they get inserted in the host genome (a mechanism subject to mutation and selection) and what's more, host organisms must have some way to combat virual infection I.e. to evolve resistance to specific virus strains.
The problem with existing DNA is that it's very serial. Gene A is executed before gene B, resulting in a long assembly-line like progression from the start of the DNA to the end. The problem with this structure is that problems up stream can totally break things downstream. And anything at the very end of the DNA can override anything done earlier in the process. The whole genome is so tightly coupled that changes, from viruses or mutations, cause catastrophic failures in any but the simplest DNA.
Jaron's world (seriously read this article if you haven't before continuing my post) recently talked about synthetic biology's potential, relating it to software and hardware. I've been thinking a lot about this recently, and the conclusion I've come to is that the reason software progresses so slowly is that it's so tightly coupled. You can't grab microsoft word and throw it into world of warcraft to make an in-game text editor.
So what I'm trying to suggest for DNA is that we move away from the serial strand and move towards a more parallel structure, where genes form an interconnected web, communicating with each other only indirectly through the byproducts of their actions. I don't know if a purely parallel structure is even possible, but it's an ideal I'd like to move towards. By specifically limiting what a gene can know about other genes, we force them to decouple.
In such a system, the idea of coupling a virus to a set of genes is bogus. Genes are always in a state of flux, potentially changing from organism to organism through mutations, or whatever. Genes are black-boxes to other genes, and don't know or care about each other's existance. Instead, the virus can hijack existing pathways by meddling in the same collective soup that other genes use to communicate. If gene A produces X, and gene B regulates body growth by a feedback with X, a virus can cause mischief by metabolizing X, or producing more X. The virus *might* be somewhat coupled to the pathway, but it neither knows nor cares about what genes use X.
The way I'm presently imagining such a system working is to have several strands that run in serial inside the strand, but that communicate with each other through this web structure of ins and outs in parallel. A virus would just be a strand that can build a virus shot for itself and climb inside.
