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

The considerations of the earlier post 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.

1. For quartz only the OH-O^- qubits are realized. If the hierarchy is realized they should be realized also for DNA and RNA. 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). If codons correspond to 3 dark protons, proton spin would give for single DNA strand only 3 bits and 8 different codons. I have considered several solutions to the problem but none of them is completely satisfactory.
2. Could OH-O^- qubit for the proton defining spin qubit given an additional qubit for each DNA letter (dark proton) assignable to the phosphate provide a solution to the problem: one would obtain 8× 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. There is however a problem. The spins of electron and dark proton sum up to spin 0 had one cannot speak of proton spin as a degree of freedom. Could one consider the entire DNA double strand as a realization of the genetic code so that each base pair would correspond to two OH-O^- phosphate qubits?
3. What about RNA? 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 unless entire double strands represents the dark code. Does the ribose OH give an 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!
4. The chemical variants are non-dynamical and could have an interpretation as a slowly varying long term memory. This forces to ask what one really means with the dark variant of the genetic code. Suppose that the dark codons correspond to dynamical OH bonds able to spontaneously transform to O^- or vice versa?

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

5. Dark realization of the genetic code should be dynamic. However, the conclusion that the chemical genetic code is independent of the dark code realized in terms of OH-H^- qubits seems unrealistic. A more realistic conclusion would be that the dark codons for DNA base pairs and RNA in their ground state having a minimum energy correspond to the chemical codons. In the case of DNA strands 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?

1. 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.
2. Could the almost symmetry mean that DNA base pair 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? If the energy difference between these bits is below thermal threshold this is the case.
3. 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.}
4. 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 could serve as a tool to control the OH-O^- qubits.

   Could the dark dynamics be completely independent of the chemical realization. In this case DNA double strand and RNA would carry OH-O^- 6 qubits and define a completely dynamical genetic code and would serve as ideal tool for topological quantum computations (see this, this and this).

5. The biocatalyst property RNA, and proteins and presumably also of DNA could relate closely to the OH-O^- dichotomy. The liberation of energy in the O^-↔ 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 ℏ_gr(Sun) and ℏ_gr(Earth) cannot be excluded.
6. Chemically the activities of dark codons would manifest themselves as the transitions OH↔ O^- for dark codons whose ground states correspond to the chemical codons. 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 ordinary Pollack effect would occur. DNA double strands and RNA strands could participate in topological computations under suitable metabolic conditions and chemical parameters such as pH making the OH↔ O^- transition energy small but not smaller than thermal energy.

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.