Tuesday, March 16, 2010

The Beauty of the Genetic Code 2

The Beauty of the Genetic Code 2
Andre Willers
16 Mar 2010

Hi ,

See ""Rewriting life in four-letter words" , NewScientist 20 Feb 2010 p14.
I just read it (16 Mar 2010) , as I get New Scientist in a haphazard fashion via the library .

See para 2 of original post below
"2.Make 4-Base Codon Cell-Machinery .
A real remake . Not within human capability at the moment ."

I was wrong .
It has already been done by Jason Chin and colleagues at the University of Cambridge . They successfully redesigned some ribosomes and transfer RNA(tRNA) to manufacture a novel amino acid (a novo-calmodulin protein) , expressed via E.Coli .

Important note:
This worked so easily because it worked parallel to the three-Base expression without noticeable inerference .
This hints that the meta-controls (see Phene-system posts) already has provisions for 4-Base cell-machinery .

1.See "Pandora bacteria acts as one organism" , NewScientist 27 Feb 2010 , p11.
Electron-conducting protein nanowires link oxygen-poor sub-mud sulfur eating bacteria on the seafloor in an interactive network suggestive of a neural net .

The manufacture of such a protein nanowire would almost certainly require 4-Base Codon cell machinery . Hence the the existence of parallel meta-controls .

Room-temperature organic superconductors seem to be a distinct possibility .

2.Many old-age and degenerative diseases seems reminiscent of 4-Base Codon cell machinery activating over time .

But what do I know .

It is your poblem now .
I hope your molecular shamans are better than your climatologist shamans .

Andre .

-----Original Message-----

The Beauty of the Genetic Code .
Andre Willers
22 Feb 2010

The present TerraIII genetic code is elegantly optimized to give the most robustness possible per unit of information .

Discussion :
You have to be familiar with the concepts in:
1. http://andreswhy.blogspot.com "NewTools:Reserves" and Beth(n) orders of Randomness .
2.NewScientist of 23 Jan 2010 p34 "Another kind of evolution"

Brief recap of Reserves argument :
We take any identifiable entity , slice and dice it with an order of randomness like that of a coin (ie Beth(0) ) . We then calculate a minimum reserve (which is equivalent to the least errors of all possible Beth(0) paths per benefit . )
This works out at 1/3 on the average over Aleph(0) infinities .

The Beauty of the Genetic Code :
Four Base pairs (A,U,C,G) in triplet codons give a possible 4*4*4 = 64 codons .
But together , they code only for 20 amino acids , plus a Stop and a Semi-Start .

This gives
20/64 = 31.22% for 20 amino acids
21/64 = 32.81% for 20 amino acids + Stop
21.3333…/64 = 33.3333… for 20 amino acids + Stop + Semi-Start
22/64 = 34.375 %

Stop = (UGG) , (UGA) , (UAG) ,
Start = (AUG) , but this also codes for methionine . Hence the decimal notation . The system cannot come closer to 1/3 because of quantal considerations . Try it and see .
This also is the portal for the Epigenetic System ( note use of methiolization) .

Beautiful !!

Consider the ways of Gaia .

Linear and Sideways evolution .
Linear :
The standard , gene and chromosome based inheritance
Equivalent to Beth(1+x) in our notation .
1>= x >=0

Sideways :
Genetic material exchanged without going through all that genotype-phenotype procedures .
Equivalent to Beth(1-x) in our notation .
1>= x >=0

Note that the system could not possibly get as close to the optimum reserve without this stage .

The Breeder , genetic engineer .
Equivalent to Beth(2+x) in our notation . Humans or proto-humans .
Infinity>= x >=0

This gives a full spectrum of Beth capabilities .
(Negative Beth is outside the scope of this discussion)

You will notice that the system becomes chaotically unstable as x->0 from any direction . At that point , the system will exhibit symptoms of great stress and bifurcation . Once over the hump , it steadies either in an evolutionary manner (in
Probability = 1 - ( Beth(n+1)/Beth(n) ) ^0.5 . Admittedly a rough estimate .)

Or in a devolutionary manner , evolutionary manner here described as degrees of complexity .

Stable Gene Engineering :
1.Keep the same Triple-Base Codon Cell-Machinery .
The easiest . Existing cells can be used . Increase the number of bases to 5 .
Then we can optimally reliable make 1/3*5^3 = 40 amino acids + stop + semistart .
Different kinds of Stop and Start would be advisable .
So , maybe 18 new amino acids + 2 different types of Stop + SemiStarts

This would not even be hard .
Well within present technological capability .
(Wanna make an animal with a Kevlar skin ? Well , you can using this method .)

The system would even be self-assembling under the right condition . The main thing is the optimal stability .

This is already evolving as we speak . There a fifth base occasionally involved . So there is a fruitful interaction point .

2.Make 4-Base Codon Cell-Machinery .
A real remake . Not within human capability at the moment .

3.General :
nAminoAcids + nStops + nStarts = 1/3 * ( (nDNA-bases) ^ (nBasesPerCodon) )
where the prefix n denotes "number of"

A further stability would be introduced if nStarts ~ 1/3 * nStops in a fractal fashion .
This because life-forms evolve in a pedal-to-the-metal fashion . The problems are the brakes .

There is a relationship between the Beth level and the nBasesPerCodon . The minimum number sufficient for Beth(2+) is nBasesPerCodon=3 .
Else there is insufficient complexity .

Now go out there and evolve !

Andre .

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