Author Topic: Policeing Mutations/ error repear  (Read 3828 times)

Offline Botsareus

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Policeing Mutations/ error repear
« on: April 19, 2005, 06:46:50 PM »
Num Quote:
Quote
And to be honest, trying to police mutations is impossible. There'll always be mutations we deem 'pointless' that fall through any cracks we leave. And some 'pointless' mutations are actually worth developing. Just let them do whatever you can possibly imagine. Something interesting is bound to develop.

Is the real dna writtin in a sertain way that its possible to police some easy errors?like:

Quote
cond
30
20
>
start
is the same as:
Quote
cond
4
1
>
start

Offline shvarz

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Policeing Mutations/ error repear
« Reply #1 on: April 19, 2005, 08:01:56 PM »
Real DNA is a total mess from any programmer's point of view :)

There are no conditions and no commands and everything is analog, not digital.  I am not sure what you mean by your question, but if I understand you right then the answer is "No, there is no easy way for organism to monitor its own mutations, no matter how silly they are".

Look at genetic code:  Say you want to encode an aminoacid cysteine.  Then you write:

UGU

this is the code for cysteine

But then it mutates into

UGC

What happens?  Nothing.  Because UGC is also a code for cysteine.

Then it mutates into

UGG

And now what happens?  Now it means Tryptophan.

Then it mutates to

UGA

Now what happens?  Now it means "STOP", so that any commands that go after it are not read at all.

Does that answer your question?
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Botsareus

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Policeing Mutations/ error repear
« Reply #2 on: April 19, 2005, 08:09:35 PM »
Thx Shvartz , I forgot that real Dna has no conditions at all...

Offline Numsgil

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Policeing Mutations/ error repear
« Reply #3 on: April 19, 2005, 11:17:38 PM »
Well, to say real DNA has no conditions isn't exactly accurate.

The DNA itself doesn't have conditions, but there are regulatory proteins that bind to the DNA to prevent transcription under certain circumstances.

Also, the enzymes that are produced can have built in regulation sites that limit the activity.

Offline shvarz

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Policeing Mutations/ error repear
« Reply #4 on: April 20, 2005, 12:32:15 AM »
Yeah, you are right.  But it is so much more complicated than simple condition that I did not want to go into explaining all that.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Zelos

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Policeing Mutations/ error repear
« Reply #5 on: April 22, 2005, 12:49:15 AM »
shvarz, what you showed aint DNA, its RNA. DNA is made up of A,T,C and G. while RNA is the same exept that T have become you
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline shvarz

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Policeing Mutations/ error repear
« Reply #6 on: April 22, 2005, 11:21:15 AM »
DNA on its own makes little sense.  If you want to make protein, you have to go through RNA.  That is why genetic code is usually written using A, C, G and you (instead of T).  For any biologist T and you are so interchangable that one can use either one and will be understood.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Zelos

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Policeing Mutations/ error repear
« Reply #7 on: April 24, 2005, 04:48:32 AM »
I know shvarz, but the code for everything is ATCG not AUCG, thats for the messager ;)
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline Numsgil

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Policeing Mutations/ error repear
« Reply #8 on: April 24, 2005, 10:42:10 AM »
That's not exactly accurate.  If you trace the development of DNA and RNA, you see that RNA is the thing, and DNA is just the backup hard copy.

Offline Zelos

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« Reply #9 on: April 24, 2005, 12:55:10 PM »
RNA is nothing in the lifeforms we know today, it was the DNA in begining (they think). but cause the dna is more stable than RNA it become the storage of information. now RNA is used to put aminoacids toghater and transmit information from the DNA, its mRNA, and what are the other ones?
When I have the eclipse cannon under my control there is nothing that can stop me from ruling the world. And I wont stop there. I will never stop conquering worlds through the universe. All the worlds in the universe will belong to me. All the species in on them will be my slaves. THE ENIRE UNIVERSE WILL BELONG TO ME AND EVERYTHING IN IT :evil: AND THERE IS NOTHING ANYONE OF you CAN DO TO STOP ME. HAHAHAHAHAHAHAHA

Offline AZPaul

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Policeing Mutations/ error repear
« Reply #10 on: April 24, 2005, 03:27:37 PM »
Quote
RNA is nothing in the lifeforms we know today, it was the DNA in begining (they think). but cause the dna is more stable than RNA it become the storage of information. now RNA is used to put aminoacids toghater and transmit information from the DNA, its mRNA, and what are the other ones?

I'd have to research for specifics but as I remember there are a large number of RNA types with the three most important being mRNA, rRNA & tRNA.

mRNA is the messenger carrying the codon codes (the three letter genetic code that corresponds to a specific amino acid to be used to build a protein) from DNA. rRNA is the ribosomal RNA which, together with lots of other proteins, is the actual work site for building the protein from the mRNA. tRNA is the transport mechanism to carry the appropriate amino acid for the protein being made onto the ribosome.

I am always amazed at the structure of tRNA. It is an elegant molecule shaped like a "V" (with different angles and twists for each type of tRNA) with an anti-codon on one arm and an amino acid on the other. When the anti-codon finds its codon match on the mRNA the shape of the tRNA puts the other end in exactly the right position for the ribosome to grab the amino and hang it on the building protein. Each codon on the mRNA has its own corresponding type of anti-codon match triplet on one end and exactly the right amino sitting on the other end of the tRNA molecule.

I can almost understand why Creationists insist some purposful itellegent design is at work here. The tRNA is indeed a most elegant work of chemical engineering.
« Last Edit: April 24, 2005, 03:31:30 PM by AZPaul »

Offline Ulciscor

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Policeing Mutations/ error repear
« Reply #11 on: June 06, 2005, 05:08:23 PM »
Hey everyone! I'm new to the boards and to DB in general lol but this post is really interesting so I thought I'd poke my nose in lol.

Like [shvarz] said isn't the only method of correction in DNA the redundancy of code? Like lots of different groups of letters encode the same protein? But things can go seriously crazy with shifting point mutations where a letter is deleted and all the groups change? I read somewhere that's how the diversity of blood groups came about. But DB doesn't just delete letters it deleted entire lines doesn't it? And even if it did delete letters it would make no sense 99% of the time.

Lol I haven't actually said anything of any help but just thought it'd be something interesting to say.

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Offline shvarz

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Policeing Mutations/ error repear
« Reply #12 on: June 06, 2005, 05:14:18 PM »
welcome to DBs, Ulc!

You are absolutely correct, if the mutation algorithm worked by deleting and/or inserting single letters, then the chances of getting any meaningful mutation would be very low.  It's not to say that the program would not work, it's just that simulations would take  very long time.  So we just assume that any mutation that results in a defunct programming code is lethal and we don't even bother to create a bot with it.  Well, actually we don't bother even to create a mutation like that.  It is really just a shortcut, but it works very well!
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Ulciscor

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Policeing Mutations/ error repear
« Reply #13 on: June 06, 2005, 05:43:18 PM »
What if there was a really big population with a small genome? Wouldn't it be easier to get lots of mutations there, some of which are bound to be useful?
Also what is the point of a mutation deleting parts of a gene? Should altering or copying be the only two operations, as I would have thought this would be less likely to mess the bot up.

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Offline Numsgil

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Policeing Mutations/ error repear
« Reply #14 on: June 06, 2005, 11:19:51 PM »
That's more or less how I feel.  I've had alot more success with insertions and slight changes than with deletions.

But the beauty is you can decide the liklihood of any mutations, so you're free to experiment in a deletion free universe, or a deletion only univierse.

Mutating single letters is at least technically possible.  DB DNA is stored as an array of three bytes per unit, so all you have to do is shift a bunch of bytes down the strand.  But as shvarz said, there isn't alot of useful mutations that arise this way.

Still, if there's a demand, I can probably work soemthing out.
« Last Edit: June 06, 2005, 11:22:17 PM by Numsgil »