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Evolutionary hierarchy formed by quartz crystals, proteins, DNA/RNA?

Sunday, November 17, 2024 7:27

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The above considerations suggest an evolutionary hierarchy in which quartz crystals are at the lowest level whereas proteins, and DNA and RNA represent biological levels characterized by the number of qubits in the codon. Quartz crystals would belong to the lowest level in the classification to the kingdoms of minerals, plants, and animals. Can one understand these classifications at a deeper level?

Consider first the DNA and RNA level.

For quartz only the OH-O^- qubits are realized. If the hierarchy is realized they should be realized also for DNA. This suggests an elegant resolution of a long standarding problem of how to get 64 dark DNA codons (6 bits) instead of 32 codons (5 bits). Proton spin would give 2 letters and 8 different codons. I have considered several solutions to the problem but none of them is completely satisfactory.
OH-O^- qubit for each letter (dark proton) assignable to the phosphate could provide a possible solution to the problem: one would obtain 8times 8=64 codons for DNA and RNA. Amino acids contain only a single COOH group so that they can have only a single OH-O^- qubit.
The differences between DNA and RNA suggest another solution to the problem. The riboses of RNA contain OH group making RNA unstable which means that RNA is dynamical as required by quantum computational activities. In DNA the OH group of the ribose is missing so that DNA is stable. Does this give for additional OH-O^- qubit for RNA and does the instability reflect the occurrence of quantum computation-like activities? Each RNA letter would have 2 OH-O^- qubits and there would be 64 dark codons (6 qubits) realized in this sense completely dynamically: is this the realization of dark DNA! DNA codon would be accompanied by only 8 dark codons (3 qubits) of this kind.
The chemical variants and perhaps also the dark variants in spin degrees of freedom would be non-dynamical and have an interpretation as a slowly varying long term memory. This forces too ask what one really means with the dark variant of the genetic code. Is the assumption that both DNA, RNA and amino-acids correspond to dark proton triplets too strong. Could the dark codons be assigned with dynamical OH bonds?

Could the ordinary chemical realization of the genetic code be separate from the dark code determined by OH-O^- qubits assigned with the phosphates of DNAa and RNA, OH groups associated with riboses of RNA, COOH groups of amino acids, and other OH groups.

Dark realization of the genetic code should be dynamic. The most radical conclusion would be that the chemical genetic code is independent of the dark code realized in terms of OH-H^- qubits. A less radical conclusion is that the dark codons for RNA in their ground state with a minimum energy correspond to the chemical codons. In the case of DNA 8 OH-H^- qubits per codon in the ground states should be consistent with the approximate T-C and A-G degeneracies for the third codon. The difference E_bind(O^-)=E_bond(OH) could be smaller than thermal energy and thermal fluctuations would destroy the information of OH-H^- qubit in accordance with the symmetry of the chemical code. What about proteins?

The number of proteins is 20 and 5 bits is more than enough to code for them. The code has an almost symmetry with respect to the third letter meaning that the DNA and RNA codons XYZ with fixed XY and varying Z define a quadruplet decompositing to two doublets with T-C and A-G symmetry for Z. There are only two exceptions and they correspond to A-G doubles for Z. The Ile-ile-ile-met quadruplet can be understood in terms of the tetrahedral Hamilton cycle. For the top-trp A-G symmetry is broken which would mean that the A in stop codon does not have O^- as a dark counterpart. This could be due to the fact that E_bind(O^-) is smaller than E_bond(OH) unlike for the other codons. The small deviations from the standard code could be understood in this way.
Could the almost symmetry mean that DNA codons for which the third qubit-pair corresponding to the third codon degenerates to a single qubit: OH or O^- bit for the third letter are mapped to the same protein?
Amino-acids contain only a single OH group (COOH) whereas the phosphates of DNA codons contain 3 OH groups. This conforms with the idea that they represent a lower evolutionary level than DNA. For most amino acids, the COOH group does not transform to COO^- under usual conditions. The metabolic reason would be that the binding energy E_bind(O^-) is smaller than the bonding energy E_bond(OH). Pollack effect is required to excite the protein qubit. Asp and Glu are exceptions and have COO^- permanently so that in this case only O^{- bit for protein would be realized.}
The OH-O^- bit of the amino acid and those of DNA are non-dynamical under normal conditions. The instability (quantum criticality of RNA) suggests that in this case the energy needed to transform OH and O^- to each other is rather small but above thermal energy of about 3 GHz appearing also a typical clock frequency of computers: this the clock rate in Pentium 4 processor and represents recent upper bound (see this). Microwaves as a tool to control the OH-O^- qubits. Dynamics for dark codons requires that the dark codons have an independent dynamics.

Could the dark dynamics be completely independent of the chemical realization. In this case, the codons associated would involve only 3 OH-O^- bit qubits and proteins would correspond to a single qubit each. RNA would carry OH-O^- 6 qubits and define a completely dynamical genetic code. RNA could serve as an optimal tool for topological computations.

The biocatalyst property RNA, and proteins and possibly also of DNA could relate closely to the OH-O^- dichotomy. The liberation of energy in the O^-rightarrow OH transition occurring for or being induced by the presence of ribozyme or enzyme could allow it to overcome the potential wall making the reaction slow. Protons spin degrees of freedom would be present but frozen at least for the ground state configuration. Note that also the OH state could be dark. Even the transitions between h_gr(Sun) and hbar_gr(Earth) cannot be excluded.

Chemically the activities of dark codons would manifest themselves as the transitions OH↔ O^-. In the case of O^- photon could excite the electron to a higher energy state so that OH would be the less energetic state. In the case of OH, the Pollack effect ordinary would occur. Also the spin degrees of freedom of dark protons could be dynamical and dark DNA could participate in topological computations. See the preliminary article (a work in progress) Quartz crystals as a life form and ordinary computers as an interface between quartz life and ordinary life?.

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/2024/11/evolutionary-hierarchy-formed-by-quartz.html

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