An improved version of the dark genetic code

The condition that the dark protons are stably dark implies that they cannot represent analogs of topological qubits formed by the pair of states -OH and -O^- plus dark proton at the monopole flux tube. The formation of dark nuclei would make dark proton sequences energetically stable and explain the negative charge of DNA and RNA strands and predict an evolutionary hierachy of values of electric Planck constant h_em assignable to the genes (see this, this, this and this). This forces to ask whether -OH and -O^- plus dark proton state pair can define an analog of topological qubit. Pollack effect would however play key role in metabolism and biocatalysis.

This forces to reconsider the model of the dark variant of the genetic code. The basic condition is that the dark codons are in 1-1 correspondence with the ordinary codons.

1. Each nucleotide (letter of the codon) should give rise to 2 bits. In the case of DNA codons the problem is that the only obvious quantum number for proton is its spin (I have earlier considered also other options but with no obvious success). The large value of h_eff=h_em would make proton spin a qubit and make possible quantum computation like activities.

   How to get the additional bit? I have already earlier proposed that the dark base pairs represent the letters of the dark codons. If the spins of the dark protons for codon and its conjugate are independent, this gives two bits and 4 letters. This would give an additional reason for why two DNA strands are necessary although the second strand is passive.

   I have also proposed that the dark codons make possible a kind of R\&D lab \cite{btart/evogene,icosacluster}. One can think that the spins of dark protons pairs can act as qubit pairs making possible quantum compution type activities. They would interact with the ordinary codons only when they correspond to the same codons. The interaction would be via dark cyclotron multi-photons transforming to ordinary photons and acting resonantly with the ordinary codons.

2. In the case of RNA one has only a single strand. Dark code would have only two letters so that the number of codons would be only 2³=8. I have proposed that the -OH group of the ribose ring distinguishes RNA from DNA transforms to -O^- plus a dark proton so that there would be two dark protons per letter.

   If the dark protons of mRNA letters are able to stay at the monopole flux during the transcription and translation, the needed two bits per letter are obtained for mRNA. The time scale of transcription is 2-3 minutes for a typical gene and 1 minute for translation. Could one think that in the case of ribozymes acting as catalysts the dark proton stays at the flux tube only the time necessary for the process to occur? Could metabolic energy feed induce Pollack effect kicking the dark protons of the first two RNA letters from the -OH group to the monopole flux tube?

   The first 2 2-bit RNA letters would have charge -2. The standard belief is that they have charge -1. It might be easy to test whether this is the case also during transcription and translation and ribozyme catalysis.

3. DNA codons have an almost symmetry. For most mRNA codons the codons for which the third letter is A or G code for the same amino acid. There is however a small violation of the A-G symmetry. In the standard code there are two exceptions. The AUA-AUG pair corresponds to an ile-met pair rather than an ile-ile pair. The UGA-UGG pair corresponds to stop-trp pair rather than a stop-stop pair.

   Met is exceptional in that it is coded by the start codon in the transcription. Also trp is considered as an exceptional, unique, and rare amino acid among the 20 standard amino acids. Trp is special due to its structural complexity, low abundance, high energy cost to synthesize, and its critical role as a precursor to vital bioactive compounds.

   Trp is found at critical locations in protein structures such as protein-protein interfaces and the lipid-water interface of membrane proteins. Could the additional dark proton serve as an additional bit informing about the existence of the interface?

See the article How the genetic code is realized at the level of the magnetic body of DNA double strand? or the chapter About honeycombs of hyperbolic 3-space and their relation to the genetic code .

For a summary of earlier postings see Latest progress in TGD.

For the lists of articles (most of them published in journals founded by Huping Hu) and books about TGD see this.