https://matpitka.blogspot.com/2019/09/the-details-of-genetic-code-in-model.html

## Friday, September 20, 2019

### The details of the genetic code in the model based on bio-harmony

TGD suggests several realizations of music harmonies in terms of Hamiltonian cycles representing the notes of music scale, most naturally 12-note scale represented as vertices of the graph used. The most plausible realization of the harmony is as icosahedral harmony (see this and this).

1. Icosahedron (see this) has 12 vertices and Hamiltonian cycle as a representation of 12-note scale would go through all vertices such that two nearest vertices along the cycle would differ by quint (frequency scaling by factor 3/2 modulo octave equivalene). Icosahedron allows a large number of inequivalent Hamiltonian cycles and thus harmonies characterized by the subgroup of icosahedral group leaving the cycle invariant. This group can be Z6, Z4, or Z2 which acts either as reflection group or corresponds to a rotation by π.

2. The fusion of 3 icosahedral harmonies with symmetry groups Z6, Z4 and Z2 gives 20+20+20=60 3-chords and 3+1 + 5 + 10 =19 orbits of these under symmetry group and almost vertebrate genetic code when 3-chords are identified as analogs of DNA codons and their orbits as amino-acids. One obtains counterparts of 60 DNA codons and 3+1 + 5 + 10 =19 amino-acids so that 4 DNA codons and 1 amino-acid are missing.

3. The problem disappears if one adds tetrahedral harmony with 4 codons as faces of tetrahedron and 1 amino-acid as the orbit of the face of tetrahedron. One obtains 64 analogs of DNA codons and 20 analogs of amino-acids. I call this harmony bio-harmony. The predicted number of DNA codons coding for given amino-acid is the number of triangles at the orbit of given triangle and the numbers are those for genetic code.

4. How to realize the fusion of harmonies? Perhaps the simplest realization that I have found hitherto is based on union of tetrahedron of 3 icosahedrons obtained by gluing tetrahedron to icosahedron along its face which is triangle. The precise geometric interpretation of this realization has been however missing and I have considered several variants. I have proposed that the model could explain the two additional amino-acids Pyl and Sec appearing in Nature.

There is also a slight breaking of symmetries: ile 4-plet breaks into ile triplet and met singlet and trp double breaks into stop and trp also leu 4-plet can break in leu triplet and ser singlet (see this). This symmetry breaking should be understood.

The following argument suggests a more detailed solution of these problems than proposed earlier.
1. The copies of icosahedron would differ by a rotation by multiples of 2π/3 (Z3) around axis through the common triangular face. This face unlike the other faces remains un-affected. Also tetrahedron remains un-affected so that it is counted only once.

If the 3 copies of the icosahedral common face are counted as separate (this is important!), one obtains 20+20+20 faces from icosahedron. If also tetrahedral shared faces is counted as separate, tetrahedron gives 4 faces: 64 codons altogether as required. One obtains 19 orbits from the 3 icosahedra and 1 orbit from tetrahedron: 20 orbits as counterparts of amino-acids altogether.

2. But can one really counter the 4 common faces as separate? One must do so. Could these faces be interpreted as somehow special codons? Maybe as stop codons or start codons for the vertebrate genetic code which also corresponds to the realization of DNA, RNA ,tRNA, and amino-acids as dark proton triplets so that DNA sequences would correspond to dark proton sequences. Could the shared codons be assigned with various modifications of the vertebrate code involving also exotic amino-acids Pyl and Sec.

3. Consider first the tetrahedral face. If the common face is removed from the 4-face orbit of tetrahedron, the orbit has only 3 faces and correspond to an amino-acid coded by 3 DNA codons. ile is the only such amino-acid and the interpretation could be that one ile corresponds to the 3 tetrahedral faces and met acting as start codon to the fourth shared face.

4. Also 3 icosahedral amino-acids corresponding to orbits containing the shared face can lose 1 codon each. To nake this more concrete, one can look for the deviations from the vertebrate code.

1. There are 10 doublets if the doublet UAA, UAG acting as stop codons is counted as doublet coding for stop regarded formally as amino-acid.

2. The second member in the doublet UGA, UGG coding for tyr in code table could correspond to a common face and act as a stop codon.

3. For the modifications of genetic code UAG coding for stop can code for Pyl and UGA coding for stop can also code for Sec. UGA can also code for trp so that there would not be any symmetry breaking in this case. Could UAG and UGA correspond to common faces for two icosahedra?

4. There is also third icosahedral shared face. CUG coding for leu can also code for ser. Could this correspond to the third exceptional codon associated with the icosahedral part of the code?

5. If the answers to the questions are affirmative, all basic deviations from the vertebrate code can be understood. The translation of the codons associated with shared face would be unstable for some reason.

1. 3-chord representation is more fundamental than the chemical one. This could mean that the chords associated with the shared faces are very near to each other so that the correspondence between 3-chord representation and chemical representation of codons becomes unstable if based on triple resonance.

2. The proposal has indeed been that the 13th vertex implied by tetrahedron corresponds to a note very near to one of the notes of 12-note scale - this note is necessary since the 12-note scale defined by quints gives 12th note slightly more than octave under octave equivalence as discovered already by Pythagoras.

If this picture is correct, the symmetry breaking of the genetic code would be due to the presence of the face common to icosahedron and tetrahedron and reflect the problem discovered already by Pythagoras. The rational number based Pythagorean scale defined by quints is special: people with absolute pitch prefer it over the well-tempered scale involving powers of irrational number 21/12 requiring extension of rationals.

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.