Quartz crystals as a life form and ordinary computers as an interface between quartz life and ordinary life?

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. At the highest level would be the magnetic bodies of the Earth and Sun. Can one understand these classifications at a deeper level?

OH-O^- qubits at DNA and RNA level

Consider first the DNA and RNA level.

1. For quartz only the OH-O^- qubits are realized. If the hierarchy is realized, OH-O^- qubits 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 only 3 bits and 8 different codons for a single DNA strand. I have considered several new physics 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 represent 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 of codons are non-dynamical and could have an interpretation as a slowly varying long term memory. This forces us to ask what one really means with the dark variant of the genetic code. The simplest assumption is that the dark codons correspond to dynamical OH bonds able to transform to O^-?

   The ordinary chemical realization of the genetic code would be separate from but in some sense 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. What is the relation between the chemical code and OH-O^- code? The assumption that the chemical genetic code is completely independent of the dark code realized in terms of OH-O^- qubits seems unrealistic. A more realistic assumption is that the ground states of minimum energy for the dynamical OH-O^- qubits or more plausibly, the entire codons consisting of entangled OH-O^- qubits for the letters of the codon are entanglement associated with DNA base pairs and RNA codons, correspond in 1-1 manner to the chemical codons.

Symmetries of the chemical code in relation to OH-O- code

It is interesting to consider the symmetries of the genetic codon required to reduce the number of amino acids from 61 to 20.

1. In the case of single DNA strand 3 OH-O^- qubits per codon in the ground states should be consistent with the approximate T-C and A-G degeneracies for the third codon. For DNA T↔C and A↔G exchanges for the third codon correspond to very slightly broken symmetries (see this).

   The T-C↔A-G exchange permutes the DNA strands and is exact only when all codons XYZ, Z\in \{T,C,A,G\ code for the same amino acid (see this). This symmetry is analogous to a broken isospin symmetry.

2. What about the interpretation of these symmetries? T-C↔A-G exchange is analogous CP conjugation in the sense that the passive character of the conjugate strand in DNA transcription is analogous to the invisibility of the antimatter. This symmetry would therefore permute the strands. A testable naive guess is that for the passive strand the ground state codons have OH in the phosphate of the third letter. A stronger testable hypothesis is that T-C↔A-G exchange corresponds to O-O^- permutation for all phosphate bonds. The situation would be similar in RNA.

   For this option, the T↔C and A↔G exchanges would define an analog of almost exact strong isospin symmetry. One could however as whether the situation

3. The origin of the symmetries could be thermodynamic. The difference E_bind(O^-)-E_bond(OH) for the codons coding for the same amino acid estimated to be .33 eV under normal conditions could be smaller than thermal energy of about .15 eV at physiological temperatures and thermal fluctuations would destroy the information of OH-O^- qubit and also information about the difference of T-C and A-G doublets.

OH-O^- qubits in proteins

OH-O^- qubits appear also in 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 OH-O^--qubit pair corresponding to the third letter 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 differs sufficiently from the thermal energy.

   Wien's law for the wavelength distribution of blackbody radiation for the wavelength at the maximum of the wavelength distribution of photons at temperature T reads as λ_max = 2.898 10^-3mK/T. At room temperature 300 K this gives E_th=0.146 eV and infrared frequency f=3.43× 10⁴ GHz. Photons having energy sufficiently above or below E_th are not thermally masked. The estimated energy difference e=E_bind(O^-)-E_bond(OH) =.33 eV is more than twice E_th so that there would be no thermal masking. Raising the temperature by a factor of ≈ 2.26 to about 600 K would cause thermal masking. This explains why biological functions fail at low temperatures.

   One expects that the critical temperature at which Pollack effect occurs should be around the bodily temperature 313 K (40 degrees Celsius) prevailing in fever causing hallucinations. A possible identification is that this energy absorbed by the electron of O^- reduces the E_bind(O^-)-E_bond(OH) near thermal energy and induces the instability of O^- ions of phosphates of DNA and RNA against transformation to OH. Second possibility is that this transformation transforms protons of OH to gravitational magnetic body as in the Pollack effect.

   Note that microwaves with frequency 3000 GHz have energy about .013 eV by factor ≈ 1/11 lower E_th so that they are not thermally masked (see this) Note also that the clock frequency of Pentium 4 processor is 3000 GHz and represents recent upper bound (see this).

5. The biocatalyst property RNA, of proteins and presumably also of DNA could relate closely to the OH-O^- dichotomy. The liberation of energy in the OH-O^- 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.

   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).

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.

How the field bodies control control the chemical activity of biomolecules

The value of e= E_bond(OH)-E_bind(O^-) characterizes the level of quantum criticality of the biomolecules and the nearer this parameter is to the thermal energy, the more sensitive the system is to sensory input and more capable to perform chemical activities. Besides pH also the presence of electric field affects the energy of the electron of O^- and could induce the instability of dark codons and electric fields associated with the electric body of the system (see this) could serve as tools controlling how "quantal" DNA, RNA and proteins are.

A good example is provided by microtubules which define a 2-D quantum computer like system organized into helical strands of OH-O^- qubits. Tubulin proteins are collections of OH-O^- qubits and the surface of the microtubule involves GPTs molecules accompanied by phosphates accompanied by OH-O^- qubits.

Microtubules have a longitudinal electric field and the second end of the microtubules is highly unstable inducing a continual decay and regeneration of the microtubule. This could be due to the reduction of the energy difference e= E_bond(OH)-E_bind(O^-) to energy near the thermal energy. In the case of DNA this could be achieved by irradiation using photons with energy which reduces e≈ .33 eV to about e_th≈ .15 eV. The needed energy would be about .18 eV.

Quite generally, the body of the organism carries an electric field in the head-tail direction (see this. For the TGD based interpretation of Becker's findings (see this). Becker's electric field plays a key role during the growth of the organism and also in healing of wounds and addition of external electric field affects these processes. If the energy e= E_bond(OH)-E_bind(O^-) is nearer to the thermal energy for the growing or healing cells, they would be more capable of changing.

See the article Quartz crystals as a life form and ordinary computers as an interface between quartz life and ordinary life? 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.