TGD diary: Quantum gravitational metabolism in contrast to the standard view about metabolism

In the TGD framework, the gravitational magnetic body would play a key role in metabolism. In the sequel this notion and also a concrete model for the somewhat mysterious high energy phosphate bond (HEPB), playing a fundamental role in the standard picture, is considered. The facts that DNA base pairs are connected by 2 or 3 hydrogen bonds (HBs) and nucleosides are accompanied by monophosphate ions suggest a possible application to DNA metabolism.

Gravitational magnetic body and metabolism

In the TGD framework magnetic body (MB) would serve as the controlling agent receiving sensory information as a frequency modulated dark Josephson radiation and controlling the cell by using dark cyclotron radiation coming as pulses corresponding to resonant receival of Josephson radiation.

The large value of h_eff=h_gr=GMm/v₀ implies that the dark cyclotron radiation in the EEG range would correspond to visible and UV energies.

The intuitive notion is that MB consists of U-shaped monopole flux tubes extending from the system considered and serving as kinds of tentacles. These flux tubes for two systems can reconnectand form a pair of flux tubes connecting the system if the cyclotron frequencies of the tubes are the same so that cyclotron resonance becomes possible.

The question of what the notion of gravitational MB does mean, was considered in here.

The dark flux tube would be gravitational with h_eff=h_gr. Gravitational flux tubes have lengths, which can be of the order of Earth size scale and the radii of gravitational Bohr orbits define a natural scale form them.
The elongated gravitational flux tubes could correspond to either hydrogen- or valence bonds. The loop-like bond could connect nearby atoms just like the ordinary bond. The delocalization of the charge to the flux tube leads to an effectively ionized donor atom.
All values of h_eff are possible. For electromagnetic flux tubes the values of h_eff/h are not very large. This picture leads to a view about hydrogen and valence bonds as bonds having h_eff/h>1 (see this). Also gravitational variants of hydrogen and valence bonds are possible. In this case, the proton or electron would be vertically delocalized in the Earth scale so that the donor atom would be effectively ionized. For instance, a phosphate ion could be an effective ion having a gravitational hydrogen bond with the hydrogen of a water molecule.
A gravitational valence bond, connecting a metal atom with an atom with an opposite valence, would lead to effective ionization of the metal atom. For instance, biologically important bosonic ions such as Ca⁺⁺, Mg⁺⁺, Fe⁺⁺ and Zn⁺⁺ associated with their oxides could correspond to effective ions like this.
The signature would be a pairing with a neutral oxygen atom by a gravitational valence bond. I have introduced the notion of dark ion to explain the findings of Blackman and others and dark ion could correspond to this kind of pair. Note that the original variant of the model assumed that the entire ion is dark, the later version assumed that the valence electron of free atom is dark, and the model considered here assumes that darkness is a property of bond.
The effective ionization requires energy Δ E to compensate the increment of the gravitational potential energy given by Δ E=(< V_gr(R)>-V_gr(R_E)). Here E_gr(R) is gravitational potential energy proton or electron, and R_E denotes the radius of Earth, and R is the distance of the point of flux tube from the center of Earth.
This estimate neglects the kinetic energy of the dark particle at the flux loop. This assumption is not consistent with the localization near the top of the loop so that the estimate can serve only as a rough order of magnitude estimate.
The maximal value for Δ E for electron Cooper pair (dark Cooper pair is at infinite distance) corresponds to V_gr(R_E)= .36 meV to be compared with the energy scale .3 meV defined by the temperature of 3 K microwave background and to the value .4 meV of the miniature potential. This suggests that, in the case of the electron, the reduction of kinetic energy contributes more than 10 per cent to the Δ E.
For a single dark proton one has V_gr(R_E)≈ .34 eV, which is below the nominal value of the metabolic energy currency about .5 eV. If a single dark proton is involved, the reduction kinetic energy should contribute at least 32 per cent to Δ E.
For a dark proton Cooper pair, one has the maximal value of Δ E= .68 eV somewhat above the metabolic energy quantum. These findings support the idea that both proton and electron Cooper pairs give rise to metabolic energy quanta. The challenge is to understand the mechanism for the formation of proton Cooper pairs.
The transformation of electrons and protons between ordinary and gravitationally dark states would be a key process of metabolism and biocatalysis. This conforms with the fact that proton and electron exchanges play a key role in biology. For instance, phosphorylation means that the receiving molecule gains phosphate, which can form gravitationally a dark hydrogen bond so that the system becomes metabolically active. This would correspond to the activation in bio-catalysis.
DNA base pairs are connected by 2 (A-T) or 3 (G-C) hydrogen bonds. If these strands can appear as dark gravitational strands, the maximum of 2 (3) metabolic quanta could be liberated in A-T (G-C) pairs via a transformation to ordinary hydrogen bonds. Could this serve as a yet-unidentified source of metabolic energy in the replication and transcription?
In the same way, in a redox reaction, the electron donor is oxidized and the electron receiver is reduced. Reduced molecule gains the ability to have a gravitationally dark electron, and therefore becomes metabolically active in the electronic sense. Redox reaction would be the electronic counterpart for phosphorylation.

Dark gravitational bonds, high energy phosphate bond, and DNA

How could the somewhat mysterious high energy phosphate bond (HEPB) associated with di-phospates (DP) and tri-phosphates (TP) relate to the gravitationally dark hydrogen bonds (HBs)?

HEPB (see this) is identified as the bond ...--O--... connecting to P atoms in ATP or ADP (see this). Hydrolysis involves also one H₂O molecule. The -O-P bond splits inducing the splitting of ATP to ADP and inorganic phosphate P_i. One cannot assign HEPBs to the monophosphates (MPs) associated with DNA so that the splitting of the O-P bond must play an essential role..
It is best to start by listing the facts about ATP\rightarrow ADP +P_i+2H⁺ reaction for which the Wikipedia article (see (see this) gives both graphical representation and the overall formula for the reaction.
In the initial state 4 O-atoms of ATP have a visible negative charge. The simplest assumption is that all ions O^- actually correspond to gravitationally hydrogen bonded O...H pairs with a delocalized proton charge so one should use the notation O^"-". The same assumption is natural also for ADP and AMP. This would define the meaning of organic phosphates. In the final state both P_i and ADP have visible charge -3 to give a total visible charge -6.
2H⁺ in the final state guarantees the conservation of the visible charge in the reaction.
The P(O^"-")₂ of the third phosphate transforms to an inorganic phosphate P_i. A natural interpretation is that the gravitationally dark protons become ordinary ones. This explains 2H⁺ in the final state. This reaction would liberate part of the metabolic energy.
One H₂O molecule is used in the reaction. The natural assumption is that one hydrogen of H₂O has a dark gravitational HB with the oxygen appearing in O-P of (O^"-"₂P=O)-O-P... so that it one has O^"-" visible charge -1. The bond ...P-O-...H becomes the effective oxygen ion of ...P-O^"-" of P_i so that P_i would not be completely inorganic. The remaining OH of the water molecule becomes one O^"-" of P of ADP. Also this reaction can liberate metabolic energy.

DNA base pairs are connected by 2 (A-T) or 3 (G-C) HBs: what could this mean from the point of view of DNA energy metabolism?

If these strands can appear as dark gravitational strands, the maximum of 2 (3) metabolic quanta could be liberated in A-T (G-C) pairs via a transformation to ordinary HBs. Could this serve as a yet-unidentified source of metabolic energy in the replication and transcription?
Could the dark/organic mono-phosphates of the double DNA strand serve as a source of metabolic energy for DNA transferred to the HBs connecting base pairs?
Suppose that the DDNA parallel to DNA corresponds to a sequence of gravitational HBs B_gr as loops associated with the organic phosphates. Codon would correspond to a bound state of dark protons associated with three dark gravitational HBs.
Consider an ordinary HB A_ord associated with a base pair and B_gr associated with the corresponding dark/organic phosphate. Can one transform A_ord to A_gr to achieve the transfer of metabolic energy?
Two reconnections for a HB pair (A_ord,B_gr) can transform the pair to (A_gr,B_ord). The gravitational dark proton and metabolic energy would be transferred to basepair from the organic phosphate, which itself would become an organic phosphate ion P₁^-.
Note: Also the phospholipids of the cell membrane are accompanied by a monophosphate group. Also microtubules are accompanied by GMPs. Could they serve as metabolic energy sources in the cell membrane using the above described mechanism?