Mutation protection

[Numsgil]

Right, doing something like 10 .protect store is what I'm against.  You want that data attached to the actual base pairs instead of floating around in the DNA. (Though I do think using negative numbers in .mrepro to lower mutations during reproduction (higher cost?) would be cool).

Codules are essentially functions, except that they can't recurse (call themselves or anything that called them) and they operate on the stack instead of using arguments.  In their most abstract, they're essentially macros that you can use as custom commands, and are subject to mutation.  They can contain any (or none I suppose) DNA, from multiple genes to a single number, so they would provide a natural way of grouping like base pairs together, and it's on that level I think mutation multipliers should live.  I think Eric believes this is not fine enough control, and differing mutation probabilities are needed even within codules, should they be implemented.

[jknilinux]

...

But this second methodology breaks down if metadata (by which I mean tags that describe the DNA itself, such as changing the mutation rate for some basepairs or, if we had diploid DNA, changing the dominance/recessiveness of a gene) is itself actually a bead. It might be that after a few splices the tag that identifies a change in mutation rate is now modifying entirely different DNA. Which entirely defeates the purpose if you're a bot author and your goal is to make the reproduction gene, or whatever, non mutable.

...

Codules are essentially functions, except that they can't recurse (call themselves or anything that called them) and they operate on the stack instead of using arguments.  In their most abstract, they're essentially macros that you can use as custom commands, and are subject to mutation.  They can contain any (or none I suppose) DNA, from multiple genes to a single number, so they would provide a natural way of grouping like base pairs together, and it's on that level I think mutation multipliers should live.  I think Eric believes this is not fine enough control, and differing mutation probabilities are needed even within codules, should they be implemented.

Well, if I understood your argument against metadata correctly, you think that it would be useless to the coder if the mutation protection is itself mutatable, since it could easily be mutated to protect a different stretch of DNA, etc... However, if the mutation protection instruction could protect itself from mutations by having more than one argument, then this could be easily circumvented. For example:

10 5 5 .protect store

could mean "protect next 10 bps by giving them a 5% mutation rate, and give self a 5% mutation rate." Thus, it protects itself and can therefore be useful for protecting the coder's DNA.

In essence, your codule idea just sounds like

10 5 0 .protect store

Or "protect next 10 bps by giving them a 5% mutation rate, and give self a 0% mutation rate." In which case, the mutation protection is impossible to move or change, just like a codule.

I think this design is more flexible, since it can actually protect DNA in the long run, like you wanted, and it can be moved, added, or deleted through mutation, like what Eric and I wanted. It's all up to the coder.

---

NOTE: I've never written DBcode before, so don't laugh if I'm not allowed to have three arguments for a command. There are ways to circumvent this and use only one argument.

[bacillus]

I don't like the idea of changing the rate of mutation too much; if anything, it should be treated like internal slime eg. higher protection lasts for a less period of time, and wears down in relation to the amount of protection offered, and the amount of DNA protected. Maybe have something like X .mkenzyme store and Y .protect store, where Y is the amount of base pairs relative to the position of the current base pair to be protected, so that -10 .protect store will protect the previous 10 bps, while 10 .protect store protects the next 10 bps.

[jknilinux]

I don't like the idea of changing the rate of mutation too much; if anything, it should be treated like internal slime eg. higher protection lasts for a less period of time, and wears down in relation to the amount of protection offered, and the amount of DNA protected.

But that's nothing like real-world Biology. An organism doesn't get increased mutation rates after it lives a long time. Photosynthesis doesn't wear down if a tree lives for a thousand years, because an organism's mutation rate is not dependant on time, amount of DNA, or anything else.

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Numsgil:

By the way, if Metadata wasn't coded for inside the DNA in a real organism, where would it be stored?

[Numsgil]

It's either a property of the codon itself, (multiple codons, with different possible mutation probabilities, might code for the same amino acid), or it might be regulated by a regulatory protein which sits on the strand of DNA itself, like a glob of clay stuck on my string of beads analogy.

[jknilinux]

It's either a property of the codon itself, (multiple codons, with different possible mutation probabilities, might code for the same amino acid), or it might be regulated by a regulatory protein which sits on the strand of DNA itself, like a glob of clay stuck on my string of beads analogy.

Either way, the DNA still governs it's own mutation rate. Having an exon make a protein to protect another peice of DNA by sitting on it is just like saying

x .protect10 store

Or "protect the next X bases by giving them a 10% mutation rate". Whether it's done through proteins or not doesn't matter. Ultimately, in real biology, the DNA is protecting itself, and therefore does contain metadata.

[Numsgil]

No, it's quite different.  That protein might have come from anywhere in the genome.  It get's created, floats around a bit, finds its target, and latches on.  If its target moves, so does it.  If its target doesn't exist, it doesn't bind.  If there are multiple targets, multiple proteins may or may not bind to the site.  The protein may be encoded somewhere in the DNA, so in that regard you're right that the DNA includes it somewhere in itself, and thus regulates itself, but the actual mechanism is not embedded next to thing it wants to protect, which is my point.

Mind you this idea (that organisms can control their mutation rates voluntarily) are new in biological thinking.  They're not quite as dogmatic as some of the more central tenants of evolutionary theory.

[jknilinux]

No, it's quite different.  That protein might have come from anywhere in the genome.  It get's created, floats around a bit, finds its target, and latches on.  If its target moves, so does it.  If its target doesn't exist, it doesn't bind.  If there are multiple targets, multiple proteins may or may not bind to the site.  The protein may be encoded somewhere in the DNA, so in that regard you're right that the DNA includes it somewhere in itself, and thus regulates itself, but the actual mechanism is not embedded next to thing it wants to protect, which is my point.

Mind you this idea (that organisms can control their mutation rates voluntarily) are new in biological thinking.  They're not quite as dogmatic as some of the more central tenants of evolutionary theory.

I see your point. However, it sounds like it would be difficult to implement and difficult for evolution to take advantage of (since each "protect codule1" instruction must tie to a certain "codule1" exon, etc...).

How about having the protection instruction that Eric and I were talking about act like a protein, so it can be "glued" to the exon? That way, if one instruction in the exon moves, then the entire codule (including the mutation protection "protein" instruction) moves. You could also have multiple mutation protection protein instructions (MPPIs) for the same codule, like having

10 .protect5 store
9 .protect50 store

in which case the two MPPIs could "compete" for protecting the next exon within the next nine/ten lines***, just like how you said two or more proteins could be assigned the same exon to protect. Here, maybe one of the mutation rates could be randomly chosen out of the two, because the other MPPI couldn't bind to the exon before the first one did.

Or, the 9 .protect50 store could apply it's mutation rate to only the next nine bps, but let the 10 .protect5 store govern it's (the 9 .protect50 store's) mutation rate. This way, you can never 100% protect a certain exon (since even a 10 .protect0 store is subject to the outside mutation rate, so it could change to 10 .protect200 store) but you can get really close, just like real biology.

The only problem with this idea is that the protected exon must be directly behind the MPPI, like Numsgil pointed out. However, since the MPPI acts like a protein (it's basically an exon that makes a protein that attaches to the parent exon and the next x bps), this is still just like real-world biology. Besides, the fact that the MPPI is right before the exon it protects is not a big deal. Why make code somewhere else that protects code at another place? This does the same thing, evolutionarily speaking. Also, come to think of it, having code at one place protect code at another place sounds like a DB version of goto. Nesting them is a debuggers' nightmare.

Just one instruction, so it's easy to implement and easy for evolution (and coders) to use, but it also has most of the features Numsgil wanted (like binding specifically to one exon, and binding-site competition).
Plus, it can decrease or increase mutation rates, like by having 10 .protect200 store, which would double the mutation rate for the next 10 bps.

Everyone happy?

***- With this method, an MPPI could protect lines of code not directly behind it.

[Numsgil]

I don't like the idea of any sysvar or command influencing mutation rates (of a subset of the DNA anyway).  Having it use the stack and sysvars is not an improvement over just using a command.

What I'm thinking, in the short term, is something like this:

Code: [Select]

[x0]
cond
*.nrg 5000 >
start
50 .repro store
stop
[/x0]
The [] tags would let you specify meta data, that applies for all base pairs until you find the matching closing [/] tags.  (In this example, the x specifies a mutation multiplier, with 0 meaning mutation rates for this section get multiplied by 0).  It would get "compiled" into something like this:

Code: [Select]

(type: flow logic) (value: 1) (mutation multiplier: 0)
(type: sysvar) (value: 236 (or whatever .nrg is)) (mutation multiplier: 0)
etc.
etc.
That is, right now the DNA is stored in memory as a pair of numbers: one describes the type, the other describes what it actually is (cond, start, stop, else share a type but have different values).  To that tuple I would add a float that describes a mutation multiplier.  It defaults to 1.0, but can be modified by special tags.  If we really want, we could have these multipliers subject to mutations as well.  I'm not sure I like the idea (it would get really messy with evolved DNA), but I wouldn't be against it either.

It's not what I'll probably do for DB3, but I think it addresses both Eric and my concerns, with the added benefit that it can be done right now.  Not sure if it addresses your concerns, though.

[bacillus]

I don't like the idea of changing the rate of mutation too much; if anything, it should be treated like internal slime eg. higher protection lasts for a less period of time, and wears down in relation to the amount of protection offered, and the amount of DNA protected.

But that's nothing like real-world Biology. An organism doesn't get increased mutation rates after it lives a long time. Photosynthesis doesn't wear down if a tree lives for a thousand years, because an organism's mutation rate is not dependant on time, amount of DNA, or anything else.

Actually, more than you think. Internally, DNA is tended to by having enzymes which 'remember' certain assigned parts of DNA; if an error is found in these, eg. the sequence doesn't match, it is replaced by the version the enzyme is carrying. This doesn't mean that DNA is immutable though, the backup copy can always mutate. More protection simple means more backups.

[jknilinux]

I don't like the idea of any sysvar or command influencing mutation rates (of a subset of the DNA anyway).  Having it use the stack and sysvars is not an improvement over just using a command.

What I'm thinking, in the short term, is something like this:

Code: [Select]

[x0]
cond
*.nrg 5000 >
start
50 .repro store
stop
[/x0]
The [] tags would let you specify meta data, that applies for all base pairs until you find the matching closing [/] tags.  (In this example, the x specifies a mutation multiplier, with 0 meaning mutation rates for this section get multiplied by 0).  It would get "compiled" into something like this:

Code: [Select]

(type: flow logic) (value: 1) (mutation multiplier: 0)
(type: sysvar) (value: 236 (or whatever .nrg is)) (mutation multiplier: 0)
etc.
etc.
That is, right now the DNA is stored in memory as a pair of numbers: one describes the type, the other describes what it actually is (cond, start, stop, else share a type but have different values).  To that tuple I would add a float that describes a mutation multiplier.  It defaults to 1.0, but can be modified by special tags.  If we really want, we could have these multipliers subject to mutations as well.  I'm not sure I like the idea (it would get really messy with evolved DNA), but I wouldn't be against it either.

It's not what I'll probably do for DB3, but I think it addresses both Eric and my concerns, with the added benefit that it can be done right now.  Not sure if it addresses your concerns, though.

Well, if it's true that everyone else likes this idea, then I like this idea. Like I said, I think the most important thing is to get it coded. Once we've done that, then we can add features to make everyone happy. I would hate for this feature to go the way of Duke Nukem Forever.

EDIT: So, everyone, which method for Mutation Protection are you in favor of?

1: Numsgil's idea of having codules of the form "[xmutation_rate] ...protected BPs... [/xmutation_rate]"

2: Ericl's idea of having a new instruction, of the form "number_of_lines_to_protect .protect store"

3: A hybrid idea, like my MPPI instruction (Feel free to add another, but I'm not aware of any)

4: Something totally different

TELL US WHAT YOU THINK [a href=\'index.php?showtopic=2947\']HERE![/a]



I think the most important problem with this idea is that evolution will have a hard time taking advantage of it, since it seems more delicate than "10 .protectx store".
And besides, I don't see anything this can do that 10 .protectx store can't, or vise-versa. So, if they're equivalent, why not implement the easier one? See below.

But this second methodology breaks down if metadata (by which I mean tags that describe the DNA itself, such as changing the mutation rate for some basepairs or, if we had diploid DNA, changing the dominance/recessiveness of a gene) is itself actually a bead.

Sorry for bringing up an old post, but why would having metadata in the DNA break the second methodology? If you're afraid the Mutation Protection instruction will get separated from it's exon, then just "glue" it there, like in my MPPI-based idea above.

But, like I said, if everyone else likes this idea, I like it.

Maybe I'm just too tired to think clearly about it!  




Bacillus-
In that case, it's only dependent on the cell having, like, 5 ATP per month, to run that enzyme whenever a stray UV ray hits that DNA. I think that's negligible.
Besides, in relation to your original comment:

I don't like the idea of changing the rate of mutation too much. If anything...

The rate of mutation can change quite quickly in a population. For example, if memory serves me correctly, the average mutation rate in a bacteria culture will go up as the amount of food decreases, since the bacteria have "evolved to evolve" to find new food sources.

[Numsgil]

But this second methodology breaks down if metadata (by which I mean tags that describe the DNA itself, such as changing the mutation rate for some basepairs or, if we had diploid DNA, changing the dominance/recessiveness of a gene) is itself actually a bead.

Sorry for bringing up an old post, but why would having metadata in the DNA break the second methodology? If you're afraid the Mutation Protection instruction will get separated from it's exon, then just "glue" it there, like in my MPPI-based idea above.

But, like I said, if everyone else likes this idea, I like it.

Maybe I'm just too tired to think clearly about it!  

I have no idea   I've been a bit burned out lately, and my mind's felt like mush trying to work through anything left brain, so the reasoning might be full of holes.

[ikke]

Maybe I'm the outcast here, but I am not in favour of coding mutation rates. To me there two ways to mutaton protection: evolve it or program copy protection. In my evo sims the most fatal mutation I can track with the graphs is a breakdown of the reproduce condition, resulting in exploding population, and certain death of all the offspring (I use kilobody nrg with low energy levels, so a veggie needs a minimum body size to survive). I have seen strains evolve that don't break down explosively but bubble at regular intervals. Also I noticed that the explosions occur less and less often. With my current zerobot evolution I haven't seen this behaviour alltogether, which says something about the strenght of natural vs manmade code. I would be sad to see this gone by creationist intervention.

As for coding copy protection I would favour a command that allows for checking gene equality. A but has two copies of a gene and checks for equality. Or a gene has a a stored vs actual hashvalue, whatever. Die on inequality, or maybe even allow repairing if genes are identified as defects and the coder is smart enough to program the bot to figure out how to tget back to normal...

[jknilinux]

Maybe I'm the outcast here, but I am not in favour of coding mutation rates. To me there two ways to mutaton protection: evolve it or program copy protection. In my evo sims the most fatal mutation I can track with the graphs is a breakdown of the reproduce condition, resulting in exploding population, and certain death of all the offspring (I use kilobody nrg with low energy levels, so a veggie needs a minimum body size to survive). I have seen strains evolve that don't break down explosively but bubble at regular intervals. Also I noticed that the explosions occur less and less often. With my current zerobot evolution I haven't seen this behaviour alltogether, which says something about the strenght of natural vs manmade code. I would be sad to see this gone by creationist intervention.

As for coding copy protection I would favour a command that allows for checking gene equality. A but has two copies of a gene and checks for equality. Or a gene has a a stored vs actual hashvalue, whatever. Die on inequality, or maybe even allow repairing if genes are identified as defects and the coder is smart enough to program the bot to figure out how to tget back to normal...

Your copy protection just sounds like a universal halved mutation rate for that species, assuming every gene has a duplicate error-checker version.
If you want only some genes to have copies, then it's basically regular mutation protection only for those certain genes, but you're limiting the mutation protection to either the regular mutation rate or 1/2 the regular mutation rate, if I understand you correctly.

Also, this will be an added feature, not a requirement, so you could easily continue your evolved mutation protection sims by simply switching the feature off.

Thanks for the input, and let me know if I missed something.

[jknilinux]

I'm sending this topic over [a href=\'index.php?showtopic=2947\']here[/a], mainly so I could add a poll, but also because it's more of a suggestion for DB2 than DB3. Sorry for any inconvenience!