Sunday, June 19, 2016

Two proposals for physical realization of genetic code predicting correctly the numbers of codons coding given amino-acid

The view about evolution as a random process suggests that genetic code is pure accident. My own view is that something so fundamental as life cannot be based on pure randomness. TGD has led to several proposals for genetic code, its emergence, and various realizations based on purely mathematical considerations or inspired by physical ideas (see this). One can argue that genetic code is realized in several manners just like bits can be represented in very many manners. Two especially interesting proposals have emerged. The first one is based on geometric model of music harmony involving icosahedral and tetrahedral geometries. Second model having two variants is based on dark nuclear strings. Both models predict correctly the numbers of DNA codons coding for a given amino-acid.

For the successful options entire codons rather than letters are represented. The difference between letter-wise representation and codon-wise representations is analogous to that between spoken and written languages. In spoken languages words are not analyzed further to letters.

  1. The geometric theory of harmony (see this) represents codons as 3-chords without assigning fixed notes to A,T,C,G and explains also DNA-amino-acid correspondence.

  2. For the first variant of dark nuclear string serves as analog of DNA strand. The map of codons to the dark nucleon states of dark nucleon consisting of dark u and d type quarks does the same and also predicts the degeneracies successfully.

    This model can be modified by replacing u and d by dark nucleon states p and n without any change in predictions related to genetic code. The evidence that DNA codons indeed couple to dark nucleon states (see this) supports this option.

Geometric Theory of Harmony ond Genetic Code

The idea that the 12-note scale could allow mapping to a closed path going through all vertices of icosahedron having 12 vertices and not intersecting itself is attractive. Also the idea that the triangles defining the faces of the icosahedron could have interpretation as 3-chords defining the notion of harmony for a given chord deserves study. The paths in question are known as Hamiltonian cycles and there are 1024 of them (see this. There paths can be classified topologically by the numbers of triangles containing 0, 1, or 2 edges belonging to the cycle representing the scale. Each topology corresponds to particular notion of harmony and there are several topological equivalence classes.

In the article (see this) I introduced the notion of Hamiltonian cycle as a mathematical model for musical harmony and also proposed a connection with biology: motivations came from two observations. The number of icosahedral vertices is 12 and corresponds to the number of notes in 12-note system and the number of triangular faces of icosahedron is 20, the number of amino-acids. This led to a group theoretical model of genetic code and replacement of icosahedron with tetra-icosahedron to explain also the 21st and 22nd amino-acid and solve the problem of simplest model due to the fact that the required Hamilton's cycle does not exist. The outcome was the notion of bioharmony.

All icosahedral Hamilton cycles with symmetries(Z6,Z4, Z2rot, and Z2refl turned out to define harmonies consistent with the genetic code. In particular, it turned out that the symmetries of the Hamiltonian cycles allow to to predict the basic numbers of the genetic code and its extension to include also 21st and 22nd amino-acids Pyl and Sec: there are actually two alternative codes - maybe DNA and its conjugate are talking different dialects! One also ends up with a proposal for what harmony is leading to non-trivial predictions both at DNA and amino-acid level.

The conjecture is that DNA codons correspond to 3-chords perhaps realized in terms of dark photons or even ordinary sound. There are 256 different bio-harmonies and these harmonies would give additional degrees of freedom not reducing to biochemistry. Music expresses and creates emotions and a natural conjecture is that these bio-harmonies are correlates of emotions/moods at bio-molecular level serving as building bricks of more complex moods. Representations of codons as chords with frequencies realized as those of dark photons and also sound is what suggests itself naturally. This together with adelic physics involving hierarchy of algebraic extensions of rationals would explain the mysterious lookin connection between rational numbers defined by ratios of frequencies with emotions.

Mapping DNA and Amino-Acids to Dark Nucleon States

Could dark nuclear strings provide a representation of the genetic code. The answer was totally unexpected: the states of dark nucleons formed from three quarks can be grouped to multiplets in one-one correspondence with 64 DNAs, 64 RNAS, and 20 amino-acids and there is natural mapping of DNA and RNA type states to amino-acid type states such that the numbers of DNAs/RNAs mapped to given amino-acid are same as for the vertebrate genetic code.

The dark model emerged from the attempts to understand water memory (see this) . The outcome was a totally unexpected finding: the states of dark nucleons formed from three quarks connected by color bonds can be naturally grouped to multiplets in one-one correspondence with 64 DNAs, 64 RNAS, 20 amino-acids, and tRNA and there is natural mapping of DNA and RNA type states to amino-acid type states such that the numbers of DNAs/RNAs mapped to given amino-acid are same as for the vertebrate genetic code.

The basic idea is simple. The basic difference from the model of free nucleon is that the nucleons in question - maybe also nuclear nucleons - consist of 3 linearly ordered quarks - just as DNA codons consist of three nucleotides. One might therefore ask whether codons could correspond to dark nucleons obtained as open strings with 3 quarks connected by two color flux tubes or as closed triangles connected by 3 color flux tubes. Only the first option works without additional assumptions. The codons in turn would be connected by color flux tubes having quantum numbers of pion or η.

This representation of the genetic would be based on entanglement rather than letter sequences. Could dark nucleons constructed as string of 3 quarks using color flux tubes realize 64 DNA codons? Could 20 amino-acids be identified as equivalence classes of some equivalence relation between 64 fundamental codons in a natural manner? The codons would be not be anymore separable to letters but entangled states of 3 quarks.

If this picture is correct, genetic code would be realized already at the level of dark nuclear physics and maybe even in ordinary nuclear physics if the nucleons of ordinary nuclear physics are linear nucleons. Chemical realization of genetic code would be induced from the fundamental realization in terms of dark nucleon sequences and vertebrate code would be the most perfect one. Chemistry would be kind of shadow of the dynamics of positively charged dark nucleon strings accompanying the DNA strands and this could explain the stability of DNA strand having 2 units of negative charge per nucleotide. Biochemistry might be controlled by the dark matter at flux tubes.

The ability of the model to explain genetic code in terms of spin pairing is an impressive achievement, which I still find difficult to take seriously.

  1. The original model mapping codons to dark nucleon states assumed the overall charge neutrality of the dark proton strings: the idea was that the charges of color bonds cancel the total charge of dark nucleon so that all states uuu, uud,udd, ddd can be considered. The charge itself would not affect the representation of codons. Neutrality assumption is however not necessary. The interpretation as dark nucleus resulting from dark proton string could quite well lead to the formation the analog of ordinary nucleus via dark beta decays (see this) so that the dark nucleus could have charge. Isospin symmetry breaking is assumed so that neither quarks nor flux tubes are assigned to representations of strong SU(2).

    There is a possible objection. For ordinary baryon the mass of Δ is much larger than that of proton. The mass splitting could be however much smaller for linear baryons if the mass scale of excitations scales as 1/heff as indeed assumed in the model of dark nuclear strings (see this and (see this).

  2. The model assumes that the states of DNA can be described as tensor products of the four 3-quark states with spin content 2⊗ 2⊗ 2= 4⊕ 21⊕ 22 with the states formed with the 3 spin triplet states 3⊗ 3= 5⊕ 3⊕ 1 with singlet state dropped. The means that flux tubes are spin 1 objects and only spin 2 and spin 1 objects are accepted in the tensor product. One could consider interpretation in terms of ρ meson type bonding or gluon type bonding. With these assumptions the tensor product (2⊗ 2 ⊗ 2) ⊗ (5⊕ 3) contains 8× 8=64 states identified as analags of DNA codons.

    The rejection of spin 0 pionic bonds looks strange. These would however occur as bonds connecting dark codons and could correspond to different p-adic length scale as suggested by the successful model of X boson (see this) .

    One can also ask why not identify dark nucleon as as closed triangle so that there would be 3 color bonds. In this case 3⊗ 3⊗ 3 would give 27 states instead of 8 (⊕ 1). This option does not look promising.

  3. The model assumes that amino-acids correspond to the states 4× 5 with 4 ∈{4⊕2⊕ 2} and 5∈{5⊕ 3}. One could tensor product of spin 3/2 quark states and spin 2 flux tube states giving 20 states, the number of amino-acids!

  4. Genetic code would be defined by projecting DNA codons with the same total quark and color bond spin projections to the amino-acid with the same (or opposite) spin projections. The attractive force between parallel vortices rotating in opposite directions serves as a metaphor for the idea. This hypothesis allow immediately the calculation of the degeneracies of various spin states. The code projects the states in ( 4⊕ 2⊕ 2)⊗ (5⊕ 3) to the states of 4× 5 with same or opposite spin projection. This would give the degeneracies D(k) as products of numbers DB∈ {1, 2, 3, 2} and Db∈ {1, 2, 2, 2, 1} : D= DB× Db. Only the observed degeneracies D= 1, 2, 3, 4, 6 are predicted. The numbers N(k) of amino-acids coded by D codons would be

    [N(1), N(2), N(3), N(4), N(6)]=[2, 7, 2, 6, 3] .

    The correct numbers for vertebrate nuclear code are (N(1), N(2), N(3), N(4), N(6))= (2, 9, 1, 5, 3). Some kind of symmetry breaking must take place and should relate to the emergence of stopping codons. If one codon in second 3-plet becomes stopping codon, the 3-plet becomes doublet. If 2 codons in 4-plet become stopping codons it also becomes doublet and one obtains the correct result (2, 9, 1, 5, 3)!

    It is difficult to exaggerate the importance of this simple observation suggesting that genetic code is realized already at the level of dark or even ordinary nuclear physics and bio-chemistry is only a kind of shadow of dark matter physics.

Mapping DNA and Amino-Acids to Dark 3-Nucleon States

The assumption that entire codon rather than letter corresponds to a state of dark proton does not conform with the model for the origin of purines as DNA nucleotides (see this) assuming that purines and in fact all nucleotides are combined with dark proton unless one assumes that 3 nucleotides combine with the same dark proton. This looks somewhat artificial but cannot be excluded.

Amazingly, the arguments of the model involve only the representations of rotation group and since p and n have same spin as u and d, the arguments generalize to 3- nucleon states (ppp,ppn,pnn,nnn) connected by two color bounds and organized to linear structures. Concerning genetic code, exactly the same predictions follow in the recent formulation of the model. In this case quark color is not present. One could however use the 1-dimensionality and the ordering of dark nucleons as already described.

This variant has several nice features. The model is consistent with the model for dark nucleon strings consisting of nucleons and color bonds between them. There is no need to introduce Δ type nucleon states and colored states are not needed in fermionic sector. Color bonds must be colored if one wants ordinary bosonic statistics for flux tubes but here braid statistics might help. Colored bonds could of course have some important function.

An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems and in the article About physical representations of genetic code in terms of dark nuclear strings.

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

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