Emergent Systems

[PurpleYouko]

Yeah that is a big number, but can't we rule out some commands as impossible?  Rule out others as duplicates?

Would this help reduce it a bit?

Oh I see what you mean.

I think the way I see it is that duplicates would be possible but not pre-determined. I think that could be left to chance mutation.

Also variations in a specific "bit pattern" DNA strand (called a Word hereafter for simplicity) would be mitigated or compounded by the strands before and after it such that a specif pattern would actually have different effects in different parts of the DNA.

I kind of visualize a system where some Words would be like switches that activate the Word immediately following it. Others would be more like actions but the actual action would be fully contained in the word itself or in a specified register. Others again would close a conditional loop. Nested loops would be possible so behaviours could get really complex.

A little like DB still but with a lot more variability in what can happen. Also a whole lot less readable DNA code.

[PurpleYouko]

PY I dont know what you are thinking, but take some time off, write a doc about what you have in mind, just skecth it roughly, we always get back to details latter. I would love to know (and help) what it is, but well I am not a mind reader!

I will at some point.

The way I work though is to think out loud a lot and gradually let things congeal into a real plan. I don't quite feel that I'm there yet.

Talking here is helping.

[Greven]

Also a whole lot less readable DNA code.

Forget about that! When we have an DNA interprenter, we can have the reverse, a DNA parser, whatever we will called doesnt matter. What matters is the outcome of this. You ideas sound better and better. I have to go to work now, but I will think of it to see if I can come up with something to.

[Ulciscor]

So basically you can't have the kind of DNA you are suggesting, even though it would give the most accurate representation of DNA in a sim?

But wait! I've just remembered something from a biology book I read...

DNA has an in-built redundancy to protect from catastrophic errors from mutations. Many different sequences of DNA code the same protein! Now that would definitely reduce all those possibilities. We could arbitrarily group variations together so that they code for the same environmental action.

How would that be?

[Greven]

It simple.

A codon (3 base pairs (each with 4 possible states)) give 64, there are only 20 aminoacides, the redundancy lies in the fact that many codon come for the same aminoacid.

EDIT: not come from, but code for the same aminoacid!

AH I hate when I type something wrong! :puke:

[Ulciscor]

OK cool, could that be introduced to this idea?

Meant 'How would that be' for would that apply to the sim idea.. but v interesting, thanks [Greven]!   :D

[PurpleYouko]

DNA has an in-built redundancy to protect from catastrophic errors from mutations. Many different sequences of DNA code the same protein! Now that would definitely reduce all those possibilities. We could arbitrarily group variations together so that they code for the same environmental action.

Not quite. We have to get away from anything arbitrary as much as possible.

Think of it more as a wider range of similar codes that do the same thing.

Possibly think a single specific protein being produced due to a certain combination of  bits within the Word. Say protein A will be made by any combination 1011101 found within the 32 bit Word. There exists the potential of this pattern appearing a lot of times in the 32 bits. They might even overlap.

Other bit patterns can do stuff like turning protein production on or off or redirecting available proteins to muscles or fat storage or all the other stuff an organism does.

To take this analogy a step further, the entire action/reaction could be controlled by the type and amount of these proteins that are present in the organism at the end of a given action cycle. The organism can then use these proteins to power movement or feed or whatever.

[Ulciscor]

Well hasn't it all become much much easier to do by making duplicate codes?

Other bit patterns can do stuff like turning protein production on or off or redirecting available proteins to muscles or fat storage or all the other stuff an organism does.

To hell with them for now! We would want code that is remotely readable, surely?

I'm getting thoroughly excited :D

[PurpleYouko]

To hell with them for now! We would want code that is remotely readable, surely?

Actually the way I see it, from a purely evolutionary point of view, readability of code is the last thing you really want.

We could probably rig up some kind of interpretter to allow a little bit of design and and debugging but this concept is aiming for maximum possibilities of action within a somewhat limited environment.

Basicly pure evo.

[Ulciscor]

Can't we just go with commands -> actions (visible ones) for now? Just to get it working?

[PurpleYouko]

Can't we just go with commands -> actions (visible ones) for now? Just to get it working?

But how can we do that?

Actions can only be performed once the actual DNA has been passed through an interpretter. That has been the gist of my entire point here (and elsewhere)  :banghead:

The Interpretter is the entire core of the program. without it the DNA cannot have any effect on the simulation or vice versa.

[Ulciscor]

The problem you are describing has apparently gone right over my head; I just don't see one at all. Sure it will take a while to list all commands, assign them codes and group them together, but that's doable.  :blink: Isn't it?

[Numsgil]

I would like to point out that while there are a finite number of amino acids used, the length of proteins constructed from these amino acids are thousands of amino acids long.

That may even be a conservative estimate.

And then there are the actual simulation problems, specifically that modelling chemical reactions realistically is really a simulation in and of itself.

So trying to get the DNA to actually cause physical changes beased on purely chemical motive forces is a bit unrealistic with the processing power available.

If that's what this thread is really about and I haven't wasted the last 10 minutes of my life reading it ;)

[Ulciscor]

Aha but I cleverly never mentioned chemicals merely substances. And a limited number of them at that.

In my head I imaginined there being more 'clumpy' substances like soil, air etc... it might be stupid but it would mean you wouldnt need to calculate chemical processes. You could simply state the rules of interaction instead of having to calculate them.

[Griz]

But the difference from Ulciscor and PY thought is:
I understand perfectly what Ulciscor is saying, while you PY have been vague in describing your ideas (no offense).
And--->
ULCISCOR that is exctractly what I am thinking!!!!!!!!!

Ulciscor's ideas = PY's ideas = Greven's ideas => PERFECT

It seems we all see it the same way, but have explain them differently, and we therefore have misunderstood each other.

Ulciscor, you have the power of the written text, or what ever I should call it! Thank you!

just found and began reading this thread.
so just to say ...
so far ... I am in total agreement with these ideas.
this, imo, is what is needed to 'begin'.