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HGT

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shvarz:
1.  If a bot "wants" to accept DNA, then it does - no problem there, right?  This may be advantegeous for a bot for "sex" or if it is doing very poorly and it wants to pick up some DNA in hope that it will pick up a beneficial gene.  If a bot does not want to accept DNA (infection by a virus, or a DNA shot fired by a competitor to mess it up), then there should be a gradient of succeptability.  The more specific is the virus the better are the chances of infection.  Bots may respond by mutation of "specificity sites", but it should not be "all or nothing".  It should be "the more mutations in the recognition site the less likely is the bot to get infected".

2. Both insertion and replacement should be possible.  I think that if incoming DNA can be aligned with bots DNA, then it should be replacement.  If you can't find what to replace, then you just insert.  Maybe add some probabilities to these decisions.

I think that the system I described above more or less fits both of these ideas.

Numsgil:

--- Quote from: shvarz ---1. If a bot "wants" to accept DNA, then it does - no problem there, right?
--- End quote ---

 right.
 
 
--- Quote ---This may be advantegeous for a bot for "sex" or if it is doing very poorly and it wants to pick up some DNA in hope that it will pick up a beneficial gene. If a bot does not want to accept DNA (infection by a virus, or a DNA shot fired by a competitor to mess it up), then there should be a gradient of succeptability. The more specific is the virus the better are the chances of infection. Bots may respond by mutation of "specificity sites", but it should not be "all or nothing". It should be "the more mutations in the recognition site the less likely is the bot to get infected".
--- End quote ---

 I don't know if I like the idea of the HGT DNA being compared to the bots' explicitly.  I understand where you're comming from, but it just doesn't jive with me.
 
 Real viruses etc. seem to (I'm generalizing here) attach themselves to specific protein markers on the cell membrane that are tricked into accepting it.  Perhaps we should first find a reason for and model this membrane transportation mechanism.
 
 If we tie it into the Mebo system, you could have viruses that mimic the numerical bit pattern of a substance.  If the bot pumps in that substance while the virus/HGT is "stuck" on the cell wall, there'd be some chance of ingesting the particle.
 
 Perhaps viral coats are made up of these substances the virus/HGT is mimicing?
 
 
--- Quote ---2. Both insertion and replacement should be possible. I think that if incoming DNA can be aligned with bots DNA, then it should be replacement. If you can't find what to replace, then you just insert. Maybe add some probabilities to these decisions.
--- End quote ---

 What about what I was suggesting where new codules replace old codules at specific locations.  I know you want to be more general than strictly codules, but would that fit with your idea?  If a bot doesn't have that codule (and hence this is a new gene) it would just be inserted into the codule array.

shvarz:

--- Quote ---Real viruses etc. seem to attach themselves to specific protein markers on the cell membrane that are tricked into accepting it. Perhaps we should first find a reason for and model this membrane transportation mechanism.
--- End quote ---

No need to follow the real nature down to such specifics.  In the end the viral envelope protein has to recognize a certain protein on cell membrane.  Both proteins represent genetic code of the cell and of the virus.  So in the end it is the comparison of two genetic codes.  The better they match, the easier it is for virus to get in.  The name for the co-evolution of virus and host is "genetic conflict" (just to strengthen my point).  

No need to bind it to transport molecules (are you thinking that virus gets transported by such proteins?  it is not so).  In real life viruses use a bunch of different proteins for this purposes - sensing proteins, connection proteins.  Hell, some viruses recognize lipids!  These are just markers that viruses use to hook up to the correct cell that they want to infect.  Besides, the infection is controlled even after virus gets into the cell, so this "ability to infect" is not determined just by the receptor molecule, but by othe cellular proteins as well.  

But in the end, it is still about the match between the genotypes of virus and of the cell.

2.  Yeah, maybe replacing codules might be the easiest thing to do.  I forgot, how many total codules are we going to allow?

Numsgil:
A base level of maybe 1000 possible codules is where I'm aiming at the moment, but there isn't any practical limit beyond the ability to easily call the goto command (so upwards of like 32000 codules).

I'm just not that comfortable with having the virus squirm its way into a resistant bot.  I'd like the bot to, at least implicitly, grant the virus entrance into the cell.  It can be tricked, begged, cajoled, wheedled, anything but forced.

If a bot is quite stuborn and shuts down everything I'd like to see it be 100% resistant to viruses.  Sort of an isolationist policy

Elite:
Maybe make a gene that deals with energy shots mandatory. Force bots to specify wether thay want to accept a -2 shot.

ie.

cond
*.shflav -2 =
start
' accept the shot
stop

Or something like that. And guess what flavour viruses would show up as  

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