The newly discovered spatial grammar of DNA from the TGD perspective

The essential feature of spatial grammar is that transcription factors are effective only when they are attached to preferred positions of DNA. It has been thought that transcription factors can act as activators of repressors. The new finding is that most active transcription factors can also act as repressors. Moreover the removal of the activator need not lead to the loss of the activity. It was also found that the function of the activators is highly position dependent. In particular, the ambience, that is the spacing between transcription factors and their position relative to where a gene s transcription began, determined the level of gene activity.

This conforms with the TGD view of how genes and proteins, now transcription factors interact. The key ideas of the TGD view are as follows.

The TGD based view of space-time and quantum are essential for the TGD inspired quantum biology.

1. Ordinary DNA and also RNA, mRNA, tRNA, and proteins are accompanied by dark variants (see for instance this, this, this andthis) with a non-standard value of effective Planck constant h_eff, which can be understood in the number theoretic view of TGD (see this and this). The dark variants are realized as dark proton sequences at the monopole flux tubes parallel to the ordinary DNA, RNA, or amino-acid considered. Also tRNA has a dark variant.

   The monopole flux tubes carry sequences of dark codons realized as dark proton triplets associated with closed monopole flux tubes at a larger long monopole flux tube. Also neutrons can be considered but whether they are needed is still unclear. In any case, in the case of DNA the codons would consist of dark protons.

2. The dark codons at the monopole flux tube would bind to form dark genes behaving as quantum coherent units. Both DNA, RNA and tRNA are obtained. One can form a representation of the genetic code based on the dark proton states and one also obtains a representation assignable to amino-acids. The dark protons can be characterized by cyclotron frequencies assignable to the magnetic fields at closed flux tubes at which they reside.

1. Dark codon corresponds to a triplet of cyclotron frequencies and a given transition between different 3-proton states induces an emission of a dark photon triplet. Even more: entire dark genes with N codons can emit 3N-triplets of dark photons and in communications these can give rise to 3N-resonance so that only similar gene sequences can interact resonantly. Also partial resonance can be considered.
2. Icosa tetrahedral realization of the genetic code is in terms of cyclotron frequency triplets. This realization corresponds to a completely unique tessellation of the hyperbolic space H³ (light-cone proper time= constant hyperboloid) involving not only single platonic solid but tetrahedrons, octahedrons and icosahedrons as building bricks of the fundamental domain. This would be a universal realization of the genetic code, which could appear in all scales, not only in biology.

   In this realization, 60 codons of the dark DNA correspond to 3 different Hamiltonian cycles of icosahedron and 4 codons to the unique Hamiltonian cycle of the tetrahedron. Each icosahedral cycle gives 20 codons identifiable as 20 triangles as faces of the icosahedron.

3. This view emerged from a geometric model for music harmonies. Musical 12-note scale is realized using a closed icosahedral Hamiltonian path going through all 12 icosahedral vertices. One can realize the notes of the cycle by assuming that for a given step of the path, the frequency is scaled by factor 3/2 and then scaled to the basic octave (octave equivalence). Since the music expresses and induces emotions, the interpretation is that various bioharmonics defined by different combinations of Hamiltonian cycles correspond to different emotional states at the molecular level \cite{btart}{emotions}.
4. There are a large number of Hamiltonian cycles and therefore many realizations of the genetic codons in terms of frequency triplets associated with the faces of icosahedron and tetrahedron. These realizations are obtained as fusions of three Hamiltonian cycles with symmetry Z₆ (only one cycle), Z₄ (2 cycles) and Z_2,R or Z_2,rot corresponding to reflections and rotations (larger number of cycles). They would correspond to different molecular moods (see this).
5. Icosahedron gives 20+20+20 codons for a given bioharmony and the number of DNAs coding a given amino acid are obtained correctly. The tetrahedral cycle gives the remaining 4 codons.

1. In the icosa tetrahedral realization of the DNA and RNA codons, amino acids correspond to the orbits of a given triangle of the icosahedron under the action of the symmetries of the Hamiltonian cycle. This strongly suggests that the representation in terms of dark proton triplets makes sense also for the amino-acids.
2. The problem is that amino-acids do not have a constant charge density of -3e per amino-acid. Could ordinary protons associated with the amino-acids transform to dark protons only when this is needed?

   The dark protons of dark DNA and RNA are ordinary protons transferred to the monopole flux tubes. This charge separation means that the ordinary DNA becomes negatively charged. This is just the Pollack effect and requires metabolic energy feed as photons but also other energy sources are possible.

   Could most protons of the amino-acids be ordinary? This would save metabolic energy since the increase of h_eff requires energy and h_eff tends to decrease spontaneously. When protein is just a geometric building brick, this would be natural. Could the amino-acids be dark only when they are active, that is serve as a biocatalyst, in particular as a transcription factor? The activation would mean that the ordinary protons of the active portion of the amino acid are kicked by the Pollack effect to the magnetic body of the protein and the protein looks negatively charged. This serves as a killer test for this idea.

3. 3N-cyclotron transition to a smaller subset of 3N dark protons makes possible a communication mechanism by 3N-cyclotron resonance (see this). Pieces of dark DNA, RNA, trNA, and dark amino acids can communicate resonantly. This is like tuning the radio to a correct wavelength: now there would however be several wavelengths defined by the codon sequences or a sequence of amino-acids. This would also be the basic mechanism of biocatalysis.
4. 3N-frequency would serve as an address in these communications and the modulation of the cyclotron frequencies by varying the magnetic field strength, or equivalently the monopole flux true thickness, makes possible a coding of information to the frequency modulation. Therefore a given modulation generates a characteristic sequence of pulses analogous to nerve pulses: this mechanism would be involved also with communications of sensory data from the neuronal membrane to the magnetic body of the brain (see for instance this, this and this). Fractally scaled variants of the same communications would occur also at the level of the ordinary cells (see this).
5. Also dark-ordinary communications are possible but require the transformation of dark 3-N photons from dark molecules to ordinary photons.
6. A natural proposal is that the cyclotron frequencies assignable to dark amino-acids are the same as those associated with DNA codons coding from them. This would mean that a given protein can attach by 3N-resonance to all DNA sequences for which the codons code for it. This correspondence is testable and would mean an enormous amount of information about how the biocatalysis for the basic information molecules works.

See the chapter The realization of genetic code in terms of dark nucleon and dark photon triplets or the article with the same title.