How could the representations of genetic code as dark 3-chords and nucleotide triplets relate?

One of the poorly understood aspects of the model is how the various representations of the code relate.

Frequency coding of nucleotides is not possible

Frequency coding of nucleotides would look natural but it is easy to see that it is in conflict with bio-harmony.

1. The representations as dark proton triplets and dark photon triplets do not involve decomposition to ordered triplet of letters as the ordinary chemical representation does. Dark protons are entangled and one cannot order them and there is no obvious ordering of the frequencies of dark photons.
   

   This is not a problem for the correspondence between dark proton triplets and dark photon triplets and one can even imagine assignment of dark cyclotron photons with 3 parallel flux tubes acting as wave guides. This could mediate the interaction between dark variants of basic biomolecules with same value of h_eff as frequency resonance.
   
   

2. The interaction between ordinary DNA/RNA/tRNA and its dark variant should involve the transformation of dark photon triplet associated with flux tube triplet emanating from dark bio-molecule to ordinary photons (possibly bio-photons) and energy resonance would be involved. Is the energy resonance involved with the formation of the dark-ordinary pairs or with the sustainment of these pairings? The example of benzene suggests sustainment.
   
   
3. The assumption that energy resonance is involved with dark-ordinary pairing indeed leads to problems. The first guess would be that ordinary photon triplet somehow carries information about the position of nucleotide in the codon. The 4 nucleotides would correspond to 4 frequencies with frequency scale depending on the position inside the codon. There are indeed 12 frequencies in the 12-note scale so that 3 frequency scales with 4 frequencies associated with each of them would give 64 combinations of frequencies.
   

   Frequency coding of nucleotides however leads to a problem. The first two letters of the codon are known to determine the amino-acid coded by it to a high degree since the third letter typically distinguishes between 1 or 2 amino-acids only, and labels codons at the orbit of DNA codon defining amino-acid. Therefore for DNA codons coding same amino-acid the first two frequencies should be same. This is not the case for bio-harmony for the simple reason that the frequencies of 3-chords along the orbit defining amino-acids are different. Only the frequency ratios defining the type of the chord are same along the orbit.
   

   The frequency ratios determine the correspondence so that the correspondence can be only between entire dark and ordinary codons, and cannot be reduced to correspondence between frequencies and letters. Holism does not reduce to reductionism.
   
   

Does the impossibility of frequency coding of nucleotides lead to problems with the models of replication and transription?

This becomes a potential problem in the model for DNA replication and transcription to RNA.

1. The basic picture about bio-catalysis in TGD framework is following. U-shaped magnetic flux tubes emanate from the reactants and can reconnect to form a pair of flux tubes connecting the reactants. The shortening of the flux tube pair by a reduction of h_eff brings the reactants together and liberates the energy needed to kick the reactants over the potential wall making the reaction rate extremely low otherwise.
   

   The U-shaped flux tubes or flux tube triplets would be associated with dark codons of dark DNA accompanying DNA strand, and would be formed as the flux tube pair(s) connecting the strands split by the reversal of reconnection. The h_eff associated with resulting U-shaped flux tubes associated with replicating strands would increase requiring metabolic energy. They would get longer and could act as tentacles scanning the environment to spot similar flux tubes assignable to nucleotides or codons by resonance.
   
   

2. In the standard picture one assumes that nucleotides defining the letters of the codons appear as non-correlated molecules in the environment, and that each codon is built by a stepwise process in which letters attach to it. The letters can respond only to single frequency and cannot "know" which position to attach to. Thefrequency coding is not consistent with the idea that dark photon triplet assigned with the dark codon gives rise to energy resonance with the letters one by one.
   

   Could the triple resonance occur as single step and attach all 3 nucleotides in single step? Or could the triple resonance be a collective frequency resonance with dark codon already attached to the ordinary codon in the environment. Ordinary-dark pairing by energy resonance would sustain rather than generate DNA strand since otherwise the Coulomb repulsion due to the large negative charge of DNA does not allow stability.
   
   

3. The problem is that it is nucleotides seem to appear in the environment rather than codons. Could the nucleotides of the environment actually form loose codons connected to dark codons by long flux tubes with large value of h_eff? Could the reduction of h_eff bringing nucleotides together induce the reduction of flux tube lengths giving rise to ordinary codon? If the reduction of h_eff for flux tubes occurs nucleotide-by nucleotide, one would have consistency with the standard picture. The simplest picture is following.
   

   Dark codons are paired with the loose variants ordinary codons. The opening of DNA double strand leads to the splitting of the flux tube pairs connecting the ordinary codons of strands to U-shaped flux tubes, which reconnect with U-shaped flux tubes coming dark codons paired with loose ordinary codons. The reduction of h_eff d pairs nucleotides of loose codons with those of ordinary codons.
   
   

4. The pairs of dark codons and loose codons would be analogous to tRNA molecules. One can imagine even pre-tRNA molecules with loose coupling of RNA and amino-acid so that replication and transcription would be very similar topological processes. Also RNA transcription and translation of RNA to amino-acids would rely on similar mechanism. The only difference would be that only the second - active - strand would form U-shaped flux tubes connecting with dark RNA codons.
   
   

What about remote DNA replication?

This model could also explain remote replication of DNA for which Montagnier et al have reported evidence. Also remote transcription is predicted to be possible. I have already earlier considered a model of remote replication in an article written together with Peter Gariaev who has reported this kind phenomenon already earlier. I have also discussed the findings of Montagnier et al.

1. The experiment involves two vessels, call them A and B. A contains genes and B only nucleotides - at least according to the standard picture. There is irradiation using 7 Hz frequency not far from the lowest Schumann frequency having a nominal value of 7.8 Hz. What happens is that the replicas of genes appear in B. It is also reported that the DNA generates em radiation possibly responsible for the information transfer.
   
   
2. The proposed model for the ordinary DNA replication generalizes easily to describe also remote replication. The new element would be that the U-shaped flux tubes from A would extend to B - here 7 Hz radiation could be essential - , would be parallel to each other, and have same average length, which is natural if they have same value of h_eff. Also the experimental arrangement could favor parallel flux tubes. In B the dark codons paired with loose codons formed from ordinary nucleotides would be present, and their U-shaped flux tubes would reconnect with those coming from A. Remote replication could take place: here it is essential that the U-shaped flux tubes are parallel and have very nearly the same length.
   

   The TGD interpretation would be that the Earth's magnetic body is involved and generates quantum coherence in the length scale at least the size of the system studied. The reported em radiation would naturally relate to the dark photon triplets representing the codons.
   
   

Is ZEO needed to understand the replication?

In TGD one must give up thinking in terms of standard ontology of bio-chemistry in which the process is a kinetic process governed by differential equations for the populations of molecules and proceeding in step-wise manner nucleotide by nucleotide. ZEO suggests temporal holism - at least at the level of single dark codon, which cannot be built building brick by building brick.

1. An open question is in which time scale this temporal quantum holism holds true: in the time scale of addition of single codon or in the time scale of replication of gene or something else? In the following the possibility that temporal holism holds in the time scale for the pairing of dark codons.
   
   
2. In ZEO one could have state function reduction in which initial state corresponds to dark codon plus population of nucleotides and final state to dark codon paired with the ordinary codon formed from 3 nucleotides in energy resonance with the codon formed from nucleotides. What matters are only the initial and final states.
   
   
3. If "big" state function reduction (BSFR) is in question, the final state would correspond to a superposition of deterministic time evolutions leading from the outcome of the reduction to geometric past, possibly but not necessary to a state in which nucleotides do not form codon paired with the dark codon.
   
   
4. The process would create strong correlations between the position of nucleotides of the codon and between
   the positions of codon and its dark variant and therefore a generation of entanglement. Unitary evolutions followed by "small" state function reductions (SSFRs) would generate a state as a superposition of the states satisfying the criteria of the desired final state and other states and BSFR would select the desired final state. It could be followed by BSFR returning the original arrow of time but doing nothing for the state.
   
   

See the article An Overall View about Models of Genetic Code and Bio-harmony or the chapter with the same title.

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

Articles and other material related to TGD.