How the genetic code is realized at the level of the magnetic body of DNA double strand?

Suppose that the proposed view of the ITT realized at the level of the magnetic body (MB) of DNA is correct that dark genetic codons as induction of ITT from the MB of DNA have as a chemical counterpart of DNA or RNA double strand. How the more precise view of ITT affects the earlier model discussed in (see this).

First a couple of facts.

1. The numbers of (T,I,O) per vertex should be (20,12,10) if the T-I interface always involves O. Therefore also DNA codons correspond to faces of O:s and DNA sequences can be identified as a sequence of faces of O:s.
2. 10 DNA codons define the shortests DNA sequence for which the twist is a full multiple of 2π. One should have a sequence of triangles representing genetic codons and each codon should correspond to a face of I and to a 3-chord of a fixed Hamiltonian cycle defining a bioharmony.

This raises the following questions.

1. Does the sequence of 10 O:s correspond to a single ITT vertex and does DNA correspond to a sequence of ITT vertices such that each vertex corresponds to an O and associated 20 T:s and 12 I:s?
2. Do the two DNA strands correspond to separate dark strands or does a single dark strand correspond to both of them as the fact that the DNA strands are conjugates of each other as the latest proposal assumes. Assume this. Single O has 3+3 faces and has two disjoint triangular faces. Could these two faces correspond to DNA codon and its conjugate?
3. This sequence of 10 O:s corresponds to a sequence of 12 I:s. 2 I:s would be “empty” and would not correspond to dark proton triplet: what does this mean? Does this mean that all vertices of the I and T carry ordinary protons and the activation of the codon transforms the ordinary protons of the face to dark proton triplet. I have considered a possible interpretation of this. In the state in which DNA is opened (transcription) the 2 codons would become active and correspond to dark proton triplets.
4. What distinguishes between I and T type active codons? When the dark proton triplet is of T type and when it is of I type? Could the presence of the Hamilton cycle, the assignment of 3-chords to the faces, and resonance interaction allow us to understand this? Does the 3-chord assigned to the face determine whether the dark proton triplet belongs to the T or I type Hamiltonian cycle? Is there some symmetry breaking mechanism selecting from the T type conds the one while the remaining ones act as stop codons. Could the presence of I or T type Hamiltonian cycle in given I or T determine whether it can define an active codon and whether an associated ordinary proton triplet can be transformed to a dark one?

The cyclotron frequencies assignable to T type codons are different from those assignable to I type codons if the frequency ratio for two subsequent vertices of the cycle is 3/2 for the Hamilton cycle at I in the Pythagorean model.

Note that the basic problem of the Pythagorean model of harmony (known already by Pythagoras) is that the full Hamiltonian cycle, involving 12 frequency scalings by factor 3/2, does not give quite precisely a full multiple of octaves. One must allow irrational frequency scaling of 2^1/12 on a well-tempered 12-note scale to get rid of the problem. This might relate to the symmetry breaking.

For a tetrahedron with 4 vertices the frequency ratio should be also such that the cycle spans a multiple of octaves. This is not possible for rational scalings. In any case, I and T options are not consistent and this suggests that the 3-chords select between I and O options. The chords dictated by the character of the Hamilton’s cycle select whether the face is of type I or O. The presence of the Hamiltonian cycle would be necessary for the transformation of the ordinary proton triplets to dark proton triplets and only the I or T type cycle can be realized.

In the standard realization of the code there are 3 stop codons, which are transcribed to mRNA but are not translated to amino-acids. There are 4 codons of type T. There should be a symmetry breaking in the sense that 3 of them are not translated. This could be due to the failure of 3-chord resonance conditions so that there would be no tRNAs with the required resonance frequency triplest. Only a single tetrahedral codon would be translated for the standard realization of the code. This model also allows deviations from the standard realization of the code. Pollack effect and ATP→ ADP+P_i transformation

The molecules XP, where X ∈ {A,T,C,G} denotes DNA nucleotide, are basic building blocks of DNA. The molecules XP are stable unlikes the more complex molecules. The molecules ATP, ADP and GTP, GDP involving 2 or 3 phosphates ions. The latter molecules are essential for the metabolism and appear as carries of metabolic energy assigned in the TGD view to the dark protons at the magnetic body associated with the molecule. What distinguishes them from the mononucleotides appearing in DNA and RNA?

We talked with Ville-Einari Saari (a member of our Zoom group) about whether it might be possible to build stable negentropic systems with a large Planck constant h_eff. Without any stabilizing mechanism, large h_eff systems are unstable against the decrease in h_eff because their energies increase with h_eff, so as free systems they require a continuous energy input and only flow equilibrium is possible. This is the case in the case of XDP and XTP and this make for ADP and GTP to transfer metabolic energy.

In water, the Pollack effect is a fundamental process and produces dark protons that transform into ordinary ones in an attosecond time scale. This expectation comes from the observation of exotic phases of water with effective stoichiometry H_1.5O having attosecond life time. The explanation is that a phase transition in which every fourth proton becomes a dark proton at monopole flux tubes takes place under external energy feed. The negatively charged exclusion zone (EZ) created in Pollack effect by radiation is an example of this effect. The essential prerequisite for the Pollack effect is external energy feed and TGD has led to various generalizations of the Pollack effect. In particular formation of biomolecules generates binding energy and this could stabilize dark phase cite{btar/penrose,hem,QCs} and cold plasmas are excellent candidates for the carriers of stable dark phases.

An illustrative example is provided by transformation of chemical energy to a usable energy as a transition ATP→ ADP +P_i, where P_i is inorganic phosphorus. This process occurs spontaneously. The reverse process requires metabolic energy input and mitochondria are specialized to produce ATP from ADP. The process ADP→ ATP→ … can be seen as a kind of a karmic cycle.

1. The phosphorus P appearing in ATP and ADP ions is organic. It is not clear what this really means and biologists argue about a mysterious high energy phosphate bond which would carry the metabolic energy to the final uses as ATP transforms back to ADP + P_i. In the TGD framework, the interpretation is that ATP and also ADP involves a dark proton at the MB that neutralizes the negatively charged system and is generated by the generalization of the Pollack effect in the formation of ATP or ADP.
2. The conversion of the chemical energy into a usable form occurs in the mitochondria in a biochemical machine that resembles a rotating turbine of a power plant. 3 ATP are produced in one revolution of the turbine from three ADP. This would strongly suggest that a precursor of dark genetic codon as dark proton triplet is involved.

Google informs that the lifespan of the ATP varies enormously: when the environment needs energy, its lifespan is shortened. In vivo it varies from a few seconds to about 100 seconds whereas in vitro ATP can be almost stable. What about DNA and RNA?

1. DNA and RNA have a stable negative charge (as Google informs): there are a negative charge of 3 units per codon. A natural guess is that it corresponds to the exclusion zone (EZ) of the Pollack effect. This suggests that that there must be a stable positive charge in the form of dark proton triplets at the magnetic body associated with the DNA and the proposal is that these triplets define dark codons. What stabilizes the negative charge of DNA and therefore also the dark protons and makes the negentropic state stable
2. Bound states are formed between phosphates and DNA nucleotides. If their chemical binding energy is so high that the total binding energy, which is reduced by the energy of the dark proton, remains positive, the state is stable. I have suggested earlier (see this) that the formation of biomolecules as bound states can stabilize the dark protons, so the creation of biomolecules would also produce negentropy at the magnetic body. In fact, the formation of biomolecules as bound states during the biological evolution would have generated the dark protons at the monopole flux tubes of their magnetic bodies.

To sum up, negentropic states can be stabilized in this way and do not require a constant input of metabolic energy to maintain dark h_eff in the sense of flow equilibrium. DNA and RNA would be completely exceptional bio-molecules in this respect and would fully deserve the name information molecule. Does the presence of ITT at the MB reveal itself in the structure of DNA the surrounding water

Does the presence of ITT at the MB of DNA reveal itself in the structure of DNA and the surrounding water. How does the presence of O:s, T:s and I:s at the MB reflect itself in the properties of chemical DNA and possibly of water? Could the structure of water around DNa reflect the projection of hyperbolic tessellation at 3-D Euclidean space E³.

Do the octahedrons of the field body have any counterpart in the nearby environment of DNA.

1. Here Google tells that the water around DNA indeed involves octahedral structures besides tetrahedral structures which generally present. They occur in the form of hexahydrated metal cations, such as Mg[H₂O]_{62+ with positive charge of 2 units. Mg⁺²} ions are bosons and could form Bose-Einstein condensate like states? The 6 water molecules reside at the 6 vertices of O and whether its two opposite disjoint faces could correspond to dark codons.
2. These octahedral complexes are commonly found in the major groove or the phosphate backbone region of the DNA, where they are thought to shield the negative charges and stabilize the overall structure. This assumption is natural also in the TGD based view. Only 15 percent of Mg⁺² ions is estimated to touch phosphate oxygens directly. They would form a kind of cloud, which conforms with the idea that they serve as stabilizers. That they accompany the vertices of octahedron conforms with the idea that the vertices involve negative charges created as protons are transformed to dark protons.
3. Mg⁺² ions screen 88-89 percent of the negative DNA charge. If one can assign this kind of octahedron with a net charge of +2 units with each genetic codon, one unit of negative charge remains unscreened for both strands. Fraction 2/3 of total charge would be screened. This is considerably less than 88-89 percent so that not all Mg⁺² ions would be associated with the vertices of the octahedra.

What about tetrahedral structures, which also characterize water, around DNA? Here Google informs that in the hydration shell of DNA tetrahedral ordering is present and is essential for the stability of DNA. The presence of tetrahedral ordering could reflect the presence of ITT at the magnetic body associated with DNA and also a region of water environment. There is an enhanced tetrahedral ordering in the DNA grooves. DNA molecules imprints its helical structure to the tetrahedral structure of water,

Icosahedral structures associated with the water are not present. They would be present only at the magnetic body of DNA. Does this have any reasonable interpretation? The dark proton triplets at the icosahedral faces should originate from the tetrahedral structure of water. This could be the analog for the I-T faces of ITT identifiable also as octahedral faces?

Hen-egg questions related to the genetic code

Biology involves a long list of hen-egg questions (see this and this). What came first: metabolism, basic information molecules, bio-catalysis, or genetic code? Which biomolecules emerged first: RNA, DNA, or amino acids? TGD provides tentative general answers to these questions in terms of the dark genetic code, whose realization in terms of ITT was present from the beginning. It is instructive to consider these questions in the framework provided by the recent views about the realization of the genetic code in terms of ITT about the emergence of dark matter via the generalization of the Pollack effect. One can also try to develop an overall view.

1. The dark variants of DNA, RNA, tRNA, amino acids were present from the beginning and realized in terms of dark proton triplets assigned with ITTs at MBs. Stable dark realizations of the DNA, RNA and dark protons at MB were stabilized by the formation of corresponding biomolecules as bound states with the binding energy of the state compensating for the larger energy of the dark proton (see this). Hence one cannot say which came first.
2. The lifetimes of the basic biomolecules serve as guidelines in the attempts to build an overall view about whether the dark protons at the magnetic body of a biomolecule are relevant for its functioning.
   1. DNA is extremely long-lived: 521 years in bone. Also the negative charge associated with its phosphates is stable. The TGD based conclusion is that the dark protons at the magnetic body of DNA are stable. There is however a metabolic cost also in this case. The classical long range electric along DNA are a crucial aspect of DNA and make possible large values of h_em assignable to the DNA. Also the nuclear membrane potentials are crucial for the survival of the DNA nucleus. Metabolic energy feed is needed to preserve the charge separations generating the classical electric fields.
   2. Also the negative charge of RNA is stable but the lifetimes of RNA molecules vary in a wide range. mRNA has a lifetime from minutes to ours and the average lifetime of 2-20 mins. The lifetime can however be much longer, even days and can persist an organism’s lifetime. Special RNAs such as tRNA, rRNA, circular RNAs and nuclear RNAs are very stable and long-lived.

The finite life-time of RNA could be due to the instability of the -OH bond associated with the ribose making possible the transition to the -OH → O^- + dark proton at its magnetic body. This would be essential for the ability of RNA to act as a catalyst and could explain the varying lifetime. The stable negative charge of RNA serves as a signature for the presence of dark protons. The dark protons triplets would make possible the communications of RNA with dark DNA and dark tRNA by 3N-resonance.

Amino-acids (see this) do not possess a stable negative charge, which suggests that they do not have dark protons at their magnetic body stably. However, Google AI tells that, a C=O bond in a protein can be temporarily converted into a gem-diol structure C(OH)₂ intermediate in an enzyme’s active site during catalytic action. This process is a form of nucleophilic addition of water across the carbonyl double bond, which is often a key step in reactions such as the hydrolysis of peptide bonds (catalyzed by peptidases/proteases) or other reactions involving carbonyl-containing substrates. The 6 water molecules could be assigned with the 6 vertices of O and whether its two opposite disjoint faces could correspond to dark codons.

In the TGD framework this could mean that during the enzyme catalysis a proton from C-OH is transferred to the magnetic body of the protein and drops back later. ATP could quite generally provide the needed metabolic energy to achieve this.

The emergence of communications and control was a crucial step in evolution. Cyclotron frequency triplets as chords assignable to the ITT made possible resonant communications between field bodies by 3N-resonance involving both frequency and energy resonance. The communications between levels involving different values of h_eff (and different length scales) involved only energy resonance and very ×probably 3N-resonance was replaced by the ordinary resonance. This led to an automatic generation of communication and control networks between field bodies characterized by varying values of h_eff and biological bodies. Dark cyclotron radiation and frequency modulated dark Josephson radiation inducing a sequence of pulses at the receiver’s end are basic mechanisms suggested by TGD (see this).

Large h_eff stability possible for DNA and RNA led to a generation of intelligence based on algebraic complexity and to a control by MB. This led to an evolutionary explosion. The electric and gravitational field bodies assignable to the Earth and the Sun were in essential roles (see this).

The emergence of replication was a crucial step. At the chemical level replication reduces to the replication of DNA. A doubling of the DNA strand must occur. In the bio-chemistry approach replication is something which is just accepted.

In the TGD framework, the analog of the replication problem is encountered already at the level of particle physics. Fermion fields are free fields in H=M⁴× CP₂ as also the induced spinor fields at the space-time surfaces defined by them: how is fermion pair creation possible at all? The solution is simple and possible only in 4-D space-time: fermion makes a V-turn in time direction generalized (see this). The vertex of V corresponds to a 3-D edge of the space-time surface (see this), this) and this) at which the standard smooth structure has a defect (see this, this, and this). The magnetic body assignable to the dark DNA as a 3-surface would make a V-turn and induce DNA replication by transcription of the dark DNA to ordinary DNA.

What was the first replicator and when did it emerge? This classical question becomes obsolete in the proposed framework. The replication could be a general property of space-time surfaces and therefore of the 3-surfaces associated with the dark DNA molecules realizing ITT at the magnetic body of DNA. There are many interesting questions to be pondered. For instance, how to relate the usual view about the role of various catalysts involved with the replication and what is the role of “big” state function reductions (BSFRs) changing the arrow of time in the process. Could the BSFR have a V-turn as a classical counterpart?

What bio-catalysis is and how did it emerge?

1. In biocatalysis the reactants must find each other in a dense molecular crowd. How can they recognize each other’s presence? In the simplest picture the U-shaped monopole flux tubes emerging from the reactants reconnect to form flux tube pairs connecting them. The shortening of the flux tube pair would force the reactants together and could be induced by a reduction of h_eff shortening the flux tube lengths.
2. The potential wall preventing the bio-chemical reaction must be overcome. The shortening of the monopole flux tubes could liberate metabolic energy while the reduction of h_eff could help to overcome the potential wall. The attachment of a biocatalyst carrying large h_eff protons to the reacting system could also provide energy allowing it to overcome the potential wall.
3. How are biocatalysts generated? In general, biocatalysts are unstable. The instability can be inherent or their degradation can be programmed for metabolic reasons since they are needed only when used. If bio-catalysts provide energy to overcome potential walls, they must carry dark protons and their generation requires metabolic energy feed, which also raises the algebraic complexity, “IQ” of the catalysts so that it can take the role of a midwife. ATP is a universal way to provide metabolic energy and dark protons in a standardized way. An alternative option is creation of chemical binding energy making it possible to generate dark protons with large h_eff.
4. The dark proton of the catalyst should transform to an ordinary one in the reaction and liberate the energy needed to overcome the potential wall. Catalysts could be either inherently h_eff unstable or the instability could be induced in the reaction and induce the decay of the catalyst. Often the catalyst indeed decays after the reaction. Catalysts often have ATPs attached to them and ATP–&sectiogt;ADP is a basic aspect of catalysis.

Note that in the translation of mRNA to proteins mRNA serves as a template and degrades after the translation. This could be due to the catalysis of the translation requiring the reduction of h_eff inducing a chemical instability. The instability could relate to the -OH sidegroup of the ribose. See the article About honeycombs of hyperbolic 3-space and their relation to the genetic code or the chapter with the same title.

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.

Source: https://matpitka.blogspot.com/2025/12/how-genetic-code-is-realized-at-level.html