Saturday, January 20, 2018

About the Correspondence of Dark Nuclear Genetic Code and Ordinary Genetic Code

The idea about the realization of genetic code in terms of dark proton sequences giving rise to dark nuclei is one of the key ideas of TGD inspired quantum biology (see this). This vision was inspired by the totally unexpected observation that the states of three dark protons (or quarks) can be classified to 4 classes in which the number of states are same as those of DNA, RNA, tRNA, and amino-acids. Even more, it is possible to identify genetic code as a natural correspondence between the dark counterparts of DNA/RNA codons and dark amino-acids and the numbers of DNAs/RNAs coding given amino-acid are same as in the vertebrate code. What is new is that the dark codons do not reduce to ordered products of letters.

During years I have considered several alternatives for the representations of genetic code. For instance, one can consider the possibility that the letters of the genetic code correspond to the four spin-isospin states of nucleon or quark or for spin states of electron pair. Ordering of the letters as states is required and this is problematic from the point of view of tensor product unless the ordering reflects spatial ordering for the positions of particles representing the letters. One representation in terms of 3-chords formed by 3-photon states formed from dark photons emerges from the model of music harmony (see this). By octave equivalence the ordering of the notes is not needed.

Insights

The above observations inspire several speculative insights.

  1. The emergence of dark nuclei identified as dark proton sequences would relate to Pollack's effect in which irradiation of water generates in presence of gel phase bounding the water what Pollack calls exclusion zones (EZs). EZs are negatively charged and water has effective stoichiometry H1.5O. EZs deserve their name: somehow they manage to get rid of various impurities: this might be very important if EZs serve as regions carrying biologically important information. The protons of water molecules must go somewhere and the proposal is that they go to the magnetic body of some system consisting of flux tubes. The flux tubes contain the dark protons as sequences identifiable as dark nuclei.

  2. Since nuclear physics precedes chemistry, one can argue that prebiotic life is based on these dark biomolecules serving as a template for ordinary biomolecules. To some degree biochemistry would be shadow dynamics and dark dynamics would be extremely simple as compared to the biochemistry induced by it. In particular, DNA replication, transcription, and translation would be induced by their dark variants. One can even extend this vision: perhaps also ordinary nuclear physics and its scaled up counterpart explaining "cold fusion" are parts of evolutionary hierarchy of nuclear physics in various scales.

  3. Nature could have a kind of R&D lab allowing to test various new candidates for genes by using transcription and translation at the level of dark counterparts of the ordinary basic biomolecules.

Conditions on the model

The model must satisfy stringent conditions.

  1. Both the basis A, T, C, G and A, U, C, G as basic chemical building bricks of RNA and DNA must have emerged without the help of enzymes and ribozymes. It is known that the biochemical pathway known as pentose-phosphate pathway generates both ribose and ribose-5-phosphate defining the basic building brick of RNA. In DNA ribose is replaced with de-oxiribose obtained by removing one oxygen.

    Pyrimidines U, T and C having single aromatic ring are are reported by NASA to be generated under outer space conditions (see this). Carell et al have identified a mechanism leading to the generation of purines A and G, which besides pyrimidines C,T (U) are the basic building bricks of DNA and RNA. The crucial step is to make the solution involved slightly acidic by adding protons. TGD inspired model for the mechanism involves dark protons (see this).

    Basic amino-acids are generated in the Miller-Urey type experiments. Also nucleobases have been genererated in Miller-Urey type experiments.

    Therefore the basic building bricks can emerge without help of enzymes and ribozymes so that the presence of dark nuclei could lead to the emergence of the basic biopolymers and tRNA.

  2. Genetic code as a correspondence between RNA and corresponding dark proton sequences must emerge. Same true for DNA and also amino-acids and their dark counterparts. The basic idea is that metabolic energy transfer between biomolecules and their dark variants must be possible. This requires transitions with same transition energies so that resonance becomes possible. This is also essential for the pairing of DNA and dark DNA and also for the pairing of say dark DNA and dark RNA. The resonance condition could explain why just the known basic biomolecules are selected from a huge variety of candidates possible in ordinary biochemistry and there would be no need to assume that life as we know it emerges as a random accident.

  3. Metabolic energy transfer between molecules and their dark variants must be possible by resonance condition. The dark nuclear energy scale associated with biomolecule could correspond to the metabolic energy scale of .5 eV. This condition fixes the model to a high extent but also other dark nuclear scales with their own metabolic energy quanta are possible.

Vision

The basic problem in the understanding of the prebiotic evolution is how DNA, RNA, amino-acids and tRNA and perhaps even cell membrane and microtubules . The individual nucleotides and amino-acids emerge without the help of enzymes or ribozymes but the mystery is how their polymers emerged. If the dark variants of these molecules served as templates for their generation one avoids this hen-and-egg problem. The problem how just the biomolecules were picked up from a huge variety of candidates allowed by chemistry could be solved by the resonance condition making possible metabolic energy transfer between biomolecules and dark nuclei.

Simple scaling argument shows that the assumption that ordinary genetic code corresponds to heff/h=n=218 and therefore to the p-adic length scale L(141)≈ .3 nm corresponding to the distance between DNA and RNA bases predicts that the scale of dark nuclear excitation energies is .5 eV, the nominal value of metabolic energy quantum. This extends and modifies the vision about how prebiotic evolution led via RNA era to the recent biology. Unidentified infrared bands (UIBs) from interstellar space identified in terms of transition energies of dark nuclear physics support this vision and one can compre it to PAH world hypothesis.

p-Adic length scale hypothesis and thermodynamical considerations lead to ask whether cell membrane and microtubules could correspond to 2-D analogs of RNA strands associated with dark RNA codons forming lattice like structures. Thermal constraints allow cell membrane of thickness about 5 nm as a realization of k=149 level with n= 222 in terms of lipids as analogs of RNA codons. Metabolic energy quantum is predicted to be .04 eV, which corresponds to membrane potential. The thickness of neuronal membrane in the range 8-10 nm and could correspond to k=151 and n=223 in accordance with the idea that it corresponds to higher level in the cellular evolution reflecting that of dark nuclear physics.

Also microtubules could correspond to k=151 realization for which metabolic energy quantum is .02 eV slightly below thermal energy at room temperature: this could relate to the inherent instability of microtubules. Also a proposal for how microtubules could realize genetic code with the 2 conformations of tubulin dimers and 32 charges associated with ATP and ADP accompanying the dimer thus realizing the analogs of 64 analogs of RNA codons is made.

See the chapter About the Correspondence of Dark Nuclear Genetic Code and Ordinary Genetic Code or the article with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

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