The based view about dark matter at the level of molecular biology

We have written together with Reza Rastmanesh several articles related to biology, neuroscience, and TGD during this year. Language is indeed what distinguishes us from the other animals in a radical manner and therefore a challenge for any theory of consciousness and life. There are 3 articles related to the origin of language involving one preparatory article explaining the role of magnetic body (MB) in biochemistry - the topic of this posting - and a 2-part article about a model of language.

I decided to put the introductions of the articles to blog. Articles can be found also in Research Gate and hopefully sooner or later also at my homepage (my communizations to homepage have been continually terrorized during the summer).

The basic idea of the TGD based vision about living matter is that dark matter having effective Planck constant h_eff=nh₀ (h=6h₀) located at the flux tubes of magnetic body controls ordinary matter: MB would be the boss and biological body the slave. This hypothesis can be justified by number theoretic vision about TGD, which unifies ordinary physics as physics of sensory experience described by real number based physics and the physics of cognition based on p-adic number fields: real and various p-adic number fields are fused to adele.

Physical motivations for the TGD notion of dark matter

The notion of dark matter as control of biomatter emerged before its number theoretic justification.

1. The findings of Blackman et al about the effects of ELF radiation (in EEG (electroencephalogram) frequency range) on vertebrate brain led to the hypothesis that besides protons also ions have dark variants having h_eff=nh₀ with h_eff=h_gr.
2. Also electrons could have these phases but now the value of h_eff would be much smaller and satisfy generalized Nottale hypothesis h_eff=h_em, where h_em is the electromagnetic analogue of h_gr assignable to flux tubes assigned with valence bonds. This leads to a model of valence bond (see this) predicting that the value of h_eff/h₀=n=h_em increases along the rows of the periodic table. This would explain why the molecules such as proteins containing atoms towards the right end of the rows serve as carriers of metabolic energy and why biologically important ions like C⁺⁺ are towards the left end of the rows.

   The energy scale of dark variants of valence electrons is proportional to 1/heff² so that the orbital radii are scaled up and the identification as a Rydberg atom is the only possibility in the standard physics picture: could dark valence electrons be in question? There is empirical evidence known for decades for the mysterious disappearance of valence electrons of some rare earth metals. The article " Lifshitz transition from valence fluctuations in YbAl3 by Chatterjee et al published in Nature Communications (see this) discusses the phenomenon for Yb.

   The finding (see this) about misbehaving Ruthenium atoms supports the view that covalent bonds involve dark valence electrons. Pairs of Ru atoms were expected to transform to Ru dimers in thermo-dynamical equilibrium but this did not happen. This suggests that valence electrons associated with the valence bond of Ru dimers are dark in TGD sense and the valence bonded Ru dimer has a higher energy than a pair of free Ru atoms. TGD based explanation (see this) could be justified by a resonant coupling of the dark electron with an ordinary Rydberg state of the valence electron. In the lowest approximation dark valence electron has energies in the spectrum of ordinary valence electrons so that a resonant coupling with Rydberg states can be considered. The evidence found by Randell Mill (see this) for atoms with an abnormally large scale of binding energy suggests the formula h= 6h₀ (see this). Adelic physics (see this) predicts h_eff hierarchy and allows to understand the findings.

3. Nottale hypothesis (see this) introduces the notion of gravitational Planck constant hbar_gr= GMm/v₀ and is in the TGD framework identified as a particular value of h_eff assignable to gravitational flux tubes (see this). One trivial implication reflecting Equivalence Principle is that the cyclotron energy spectrum E_c= nhbar_greB/m= nGMeB/v₀ does not depend on the mass m of the charged particle and is thus universal. The energies involved are proposed to be in the range of biophoton energies (at least) suitable for control of the transitions of bio-molecule.

In biochemistry the density of dark protons would be much stronger and Pollack effect it in which the irradiation of water in presence of gel phases generates exclusion zones (EZs) as negatively charged regions by transferring every 4^th proton to dark proton at flux tubes forming dark proton sequences as dark nuclei. Also dark ions become important in biochemistry, at least positively charged ions would have an important control role in TGD based view about biochemistry.

Realization of the vision about MB as controller of ordinary biomatter

M⁸-H duality (see this) concretizes the general vision. This duality states the representability of space- times as a 4-D surfaces in either complexified M⁸ or H=M⁴× CP₂. n=h_eff/h₀ has interpretation as dimetinsion of extension of rationals and would the degree of a polynomial determining the space-time surface in M⁸ as a root of polynomial of degree n. Roots would correspond to different sheets of n-sheeted space-time surface and Galois group of extension would permute the sheets with each other and act as a number theoretic symmetry group. Dark matter states at the flux tubes of B_end would be in representations of Galois group and Galois confinement (see this) forcing n-particle states to behave as single unis like hadrons as color confined states.

The model of bio-harmony (see this and this) based on the icosahedral and tetrahedral geometries in turn predicts that genetic codons correspond to dark photon triplets as 3-chords of lights. The representation of 12-note scale as a sequence of quints reduced by octave equivalence fixes the harmony for a given Hamiltonian cycle and realizes the symmetries of the harmony defined by some subgroup of the icosahedral group.

Combination of 3 icosahedral harmonies with 20 chords and having different symmetries with tetrahedral harmony with 4 chords gives bioharmony 20+20+20+4=64 chords assigned to DNA codons. Amino-acids are identified as orbits of 3-chords under the symmetries of a given harmony, and one obtains 20 amino acids. DNA codons coding for a given amino acid correspond to the chords at the corresponding orbit and the numbers of DNA codons coding for a given amino acid come out correctly.

Bio-harmony assigns the binary aspects of information to the 6 bits of codon and emotional aspects to the bio-harmony characterized by allowed chords fixed by a given Hamiltonian cycle at icosahedron and the unique tetrahedral cycle. The model of bio-harmony requires that the values of B_end correspond to those associated with Pythagorean scale and defined by quint cycle.These frequencies would correspond to energies that a molecule must have to serve as a candidate for a basic biomolecule.

In the model of genetic code (see this) identifying codons as dark proton triplets, the numbers of dark proton triplets correspond to numbers of DNA, RNA, tRNA codons and amino acids and one obtains correctly the numbers of DNA and RNA codons assignable to given amino-acid in the vertebrate genetic code. Genes would correspond to sequences of dark proton triplets. Dark proton triplet would be analogous to baryon and Galois confinement (see this) would force it to behave like a single quantum unit. Dark codons would in turn bind to Galois confined states of the Galois group of extension of the extension associated with the codons.

Galois confinement would be realized also for the dark photon triplets as representation of genetic codons and also for the sequences of N dark-photon representing genes as dark 3N-photon states. Genes would serve as addresses in the communications based on dark 3N-photon resonances. For communications between levels with the same value of h_eff there would be both energy and frequency resonance and for levels with different values of h_eff only energy resonance. It is an open question whether for dark-ordinary communications dark photon 3N-plets transforms to single ordinary biophoton.

The basic hypothesis is that both DNA, RNA, tRNA, and amino acids are paired with their dark analogs, and that energy resonance mediates the interaction between the members of pairs. In this article the goal is to clarify the dark-ordinary pairing and the interaction between the members of the pairs. To achieve this, we first propose some questions below and then synthetize the answers to them.

Questions

In the sequel we will address the following questions about the roles of MB in the biochemistry of the basic biomolecules.

1. Do dark protons appear already in non-organic chemistry? Does acid/base tend to give/bind with a dark proton? The basic process is OH → O^- +H⁺. Water represents the basic example containing ions H₃O⁺ and OH^-: the dark proton from H₂O would bind to the second H₂O acting in the role of base. pH characterizes the fraction of protons equal to 10^-7 for pH=7.

   Does the transition to biochemistry mean Pollack effect (see this) in which the fraction of dark protons becomes 1/4 corresponding to pH= log₁₀(4). This would be the case for DNA, RNA, amino-acids, and tRNA also? Are the transitions between dark and ordinary states a key element of biochemistry. Could the gravitational flux tubes of MB take an active role in biochemistry?

2. Could the proton in hydrogen bond be dark? Could length of the hydrogen bond vary corresponding to different values of h_eff=h_gr. Could this explain the behavior of water below 100 C, in particular at physiological temperatures, challenging the standard thermo-dynamical model.
3. Do dark electrons play a role in chemistry as suggested (see this)? Does oxidation/reduction mean almost giving/receiving a dark valence electron in the valence bond? REDOX reactions are central also in biochemistry. The basic example is combustion in which O==O in presence of hydrocarbon such as sugar C_nH_2n gives rise to CO₂ and H₂O and C_n-1H_2n-2. O is reduced so that it almost receives valence electrons from C and H and C and H are in turn oxidized. The notion of electronegativity parametrizes the tendency to receive an electron. Is it possible to state that in inorganic and organic chemistry the electromagnetic part of MB is by far more important than the gravitational part of MB whereas in biochemistry also the gravitational part becomes important.

   Also ions are proposed to appear as dark variants and one can wonder whether the valence electrons of positively charged biologically important dark ions like Ca⁺⁺ are actually dark.

1. Does the energy resonance for dark proton triplets and even for their sequences between biomolecules and their dark variants select the basic biomolecules like DNA, RNA, tRNA, and amino-acids having dark proton counterparts? Base pairs in DNA double strand involve also hydrogen bonds. Could these hydrogen bonds have also dark variants?
2. Dark proton triplets would neutralize the negative charges assignable to the phosphates of DNA and RNA nucleotides and could be imaged as coming from POH→ PO^- +H⁺ by a transformation of proton to dark proton by the analog of Pollack effect making DNA negatively charged.

   What about the cell membrane, whose lipids have also phosphate ions at their ends? Could this give a higher level representation of the genetic code and genes at cell membrane level making possible dark 3N-photon communications between genome and cell membrae? Or do the dark protons serve at least as an energy storage? In fact, it has been proposed that cell membranes could involve a genetic code (see this).

   Microtubules are accompanied by negatively charged GTP molecules possibly associated with tubulins. 6-bit code defined also by DNA codons has been proposed by Hameroff et al as a memory code (see this). Could it be associated with genetic code represented using dark proton triplets?

3. The amino-acids in proteins should pair with dark variants of amino-acids by energy resonance. Amino-acid backbone does not however carry negative charge. Are the dark protons coming from NH₂ and COOH neutralized by electrons so that one would have dark hydrogens?
4. Also the ATP molecule has a negative charge of 3 units. Is it neutralized by a dark proton triplet serving as a temporary storage of metabolic energy? Could this energy at least partially explain the somewhat questionable notion of the high energy phosphate bond (also dark valence electrons would contribute)? Could ATP→ ADP liberate metabolic energy by splitting one dark valence bond and transforming one dark proton to ordinary one? Do the dark protons assigned with the proteins serve as metabolic energy storage besides valence electrons, whose reduced Coulombic binding energies also give rise to higher than expected bond energies?