Hen-egg problem usually means that something is missing from the conceptual picture and TGD based quantum biology suggests what this missing piece could be. The general solution of the problem in TGD would be that dark analogs of information molecules emerged first simultaneously as Galois confined states of dark proton-triplets and dark photon-triplets.
This made possible resonance communications and the basic recognition mechanism by 3-resonance for dark 3-photons. DX-X pairing was based on energy resonance and these composites were able to find each other by resonance. The reduction of heff for connecting flux tubes in their shortening liberated energy making it possible to overcome the potential wall preventing chemical reactions to occur.
The challenge is to develop a more detailed picture around these basic ideas. I have already earlier considered several proposals for the first steps of the evolution of basic bio-molecules (see this, this and this) but without the recent, rather detailed, view about resonance mechanism combined with the notion of dark 3N-photon and 3N-nucleon as a dark analog of basic biomolecule (see this).
Did the DX-X pairing occur simultaneously for all basic biomolecules?
Consider first the pairing of basic information molecules X (DNA, RNA, tRNA codons and AAs). Their polymers are not considered in this section. The simplest vision is that the dark variants of basic biomolecules emerged by Pollack effect in water irradiated by solar light. This is discussed from the TGD point of view here).
- Pollack effect generated exclusion zones (EZs) as negatively charged regions. Part of protons were transferred to magnetic monopole flux tubes of MBs assignable to water clusters and created phases of water with a hexagonal lattice-like structure.
- An attractive possibility is that the notion of hydrogen bonds generalizes. The monopole flux tubes could be accompanied by hydrogen bonds. This predicts a length scale hierarchy of hydrogen bonds implying long range quantum correlations in arbitrarily long scales and allowing to understand the strange thermodynamic anomalies of water. The length of the dark flux tube is proportional to heff as also the total energy consisting of K\"ahler magnetic and volume contribution.
- Galois confinement as a universal bind mechanism would give rise to sequences of dark protons as bound states. The states of dark proton triplet correspond to DDNAs, DRNAs, DtRNAs and DAAs.
The pairing of the dark analogs of biomolecules with ordinary biomolecules to form pairs DX-X gave rise to the observed basic biomolecules. DX-X pairing requires that the ordinary biomolecules have transition energies, which correspond to the cyclotron transition energies of DX for the value of heff considered. Ordinary cyclotron transitions and vibrational transitions are good candidates in this respect.
- Energy resonance condition for the pairs gives powerful conditions and selects the allowed biomolecules. The selection has not been completely unique. In tRNA the third letter of the chemical codon paired with one of the 32 DtRNAs need not be an ordinary nucleotide and in some viruses adenosine (A) is replaced with 2-amino-adenine ("Z") (see this).
It is not at all clear whether the dark variants of the polymers of basic bio-molecules can emerge spontaneously. The problem is that the formation of valence bonds requires energy. This forces us to consider the TGD counterparts of the usual purely chemical proposals in which basic building bricks DNA, RNA and AAs form polymers. Now one considers an analog of polymerization at the level of DDA, DRNA, and DAA.
The findings of Montagnier et al discussed from the TGD view point in here suggests that remote DNA replication occurs in absence of DNA template but that the presence of DNA polymerase is necessary. Dark DNA sequences generated by remote replication would appear as a template. This suggests DDNA-DNA pairing could occur by polymerization and require the presence of enzymes and metabolic energy feed.
Could proteins (Ps) have served in the role of egg in the chemical sense in the TGD framework? Could the resonance mechanism together with the TGD view about bio-catalysis make it possible to generate DP-P pairs by a polymerization-like process using DP as a template?
- The large heff between DP and P would be shortened in a given polymerization step. Energy would be liberated as the dark flux tube bond between DP and P is shortened. This energy should make it possible to overcome the potential wall preventing the formation of the peptide bond and also provide the energy of the peptide bond, which is about .08-.16 eV and considerably smaller than metabolic energy quantum about .5 eV.
- The thermal energy at room temperature using the definition ET=kT is .025 eV. Second definition of thermal energy is as the energy for which the distribution of black-body radiation as function of energy is maximum: this gives the energy is ET \simeq .12 eV and rather near to the Josephson energy of the cell membrane for charge Z= 2e is about .1 eV.
- The energetic requirements for AA polymerization might be satisfied by using irradiation with photon energy around thermal energy at room temperature. An interesting possibility consider in \cite{allb/geesink} is that a cell membrane formed from lipids and acting as a Josephson junction was formed before the polymerization of AAs and the Josephson radiation from the cell membrane with energy of order .1 eV provided the metabolic energy for the polymerization process.
- In the case of DNA and RNA the carbon bond energy between two codons is about 3.2 eV and considerably larger so that the polymerization without enzymes looks highly implausible.
Also the formation of glycine peptides has been observed in laboratory conditions mimicking the interstellar medium (ISM). The following summarizes the results described in the article of Serge Krasnokutski et al published in Nature (see this). The following summarizes Krasnosutski's non-technical description of the results (see this).
- The ultra-low temperatures, common in astrophysical environments, have been believed to freeze out any chemistry in the dense areas of the ISM. Already the discovery of a high abundance of small organic molecules in molecular clouds was a great surprise. But also the formation of amino acids, nucleobases, lipids, and sugars in space has been confirmed.
- What about the polymers of AAs? It has been conjectured that the condensation of carbon atoms at the surface of dust particles make possible the formation of organic molecules. Serge Krasnokutski et al indeed demonstrated the formation of glycine polymers from amino ketenes (glycine corresponds NH2-CH2-COOH, aminoketene to NH2-CH-CO and polyglycine to NH-CH2-CO) under laboratory conditions simulating the ISM conditions at temperature T=10 K (see this). A spontaneous(!) formation of relatively short peptides (less than 10-11 monomeric units) was found. The polymerization of amino acids under energetic processing (e.g. heat, pressure, or UV irradiation) is known to occur. Therefore, a further increase in chain length can be expected in natural environments.
Moreover, by adding other species instead of a proton to the \alpha-carbon atom of amino ketene (nearest to the functional group) during the polymerization, a variety of different peptide chains can be formed. Furthermore, chemical and photochemical modifications of glycine residues in peptides into other amino acid residues were also demonstrated in many works. Thus, the glycine peptides observed in our experiments can be converted into different proteins.
- These findings fit nicely with the proposed mechanism for the formation of proteins (or at least short peptides). The mechanism is not chemical, and no radiation is needed since the generalized Josephson radiation would provide the energy of the AA-AA bond, and the formation rate does not vanish at ultralow temperatures.
For a summary of earlier postings see Latest progress in TGD.
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