The Beauty of the Genetic Code 2
16 Mar 2010
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 .
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 .
The Beauty of the Genetic Code .
22 Feb 2010
The present TerraIII genetic code is elegantly optimized to give the most robustness possible per unit of information .
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 .
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) .
Consider the ways of Gaia .
Linear and Sideways evolution .
The standard , gene and chromosome based inheritance
Equivalent to Beth(1+x) in our notation .
1>= x >=0
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 .
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 !