Wednesday, September 03, 2008

Dark nuclear strings as analogs of DNA-, RNA- and amino-acid sequences and baryonic realization of genetic code

In the earlier posting I considered the possibility that the evolution of genome might not be random but be controlled by magnetic body and that various DNA sequences might be tested in the virtual world made possible by the virtual counterparts of bio-molecules realized in terms of the homeopathic mechanism as it is understood in TGD framework. The minimal option is that virtual DNA sequences have flux tube connections to the lipids of the cell membrane so that their quality as hardware of tqc can be tested but that there is no virtual variant of transcription and translation machinery. One can however ask whether also virtual amino-acids could be present and whether this could provide deeper insights to the genetic code.

  1. Water molecule clusters are not the only candidates for the representatives of linear molecules. An alternative candidate for the virtual variants of linear bio-molecules are dark nuclei consisting of strings of scaled up dark variants of neutral baryons bound together by color bonds having the size scale of atom, which I have introduced in the model of cold fusion and plasma electrolysis both taking place in water environment. Colored flux tubes defining braidings would generalize this picture by allowing transversal color magnetic flux tube connections between these strings.

  2. Baryons consist of 3 quarks just as DNA codons consist of three nucleotides. Hence an attractive idea is that codons correspond to baryons obtained as open strings with quarks connected by two color flux tubes. The minimal option is that the flux tubes are neutral. One can also argue that the minimization of Coulomb energy allows only neutral dark baryons. The question is whether the neutral dark baryons constructed as string of 3 quarks using neutral color flux tubes could realize 64 codons and whether 20 aminoacids could be identified as equivalence classes of some equivalence relation between 64 fundamental codons in a natural manner.

The following model indeed reproduces the genetic code directly from a model of dark neutral baryons as strings of 3 quarks connected by color flux tubes.

  1. Dark nuclear baryons are considered as a fundamental realization of DNA codons and constructed as open strings of 3 dark quarks connected by two colored neutral flux tubes. DNA sequences would in turn correspond to sequences of dark baryons. It is assumed that the net charge of the dark baryons vanishes so that Coulomb repulsion is minimized.

  2. One can classify the states of the open 3-quark string by the total charges and spins associated with 3 quarks and to the two color bonds. Total em charges of quarks vary in the range ZB Î {2,1,0,-1} and total color bond charges in the range Zb Î {2,1,0,-1,-2}. Only neutral states are allowed. Total quark spin projection varies in the range JB=3/2,1/2,-1/2,-3/2 and the total flux tube spin projection in the range Jb = 2,1,-1,-2. If one takes for a given total charge assumed to be vanishing one representative from each class (JB,Jb), one obtains 4×5=20 states which is the number of amino-acids. Thus genetic code might be realized at the level of baryons by mapping the neutral states with a given spin projection to single representative state with the same spin projection.

  3. The states of dark baryons in quark degrees of freedom can be constructed as representations of rotation group and strong isospin group. The tensor product 2Ä2Ä2 is involved in both cases. Physically it is known that only representations with isospin 3/2 and spin 3/2 (D resonance) and isospin 1/2 and spin 1/2 (proton and neutron) are realized. Spin statistics problem forced to introduce quark color (this means that one cannot construct the codons as sequences of 3 nucleons!).

  4. Second nucleon spin doublet has wrong parity. Using only 4Å2 for rotation group would give degeneracies (1,2,2,1). One however requires the representations 4Å2Å2 rather than only 4Å2 to get 8 states with a given charge. One should transform the wrong parity doublet to positive parity doublet somehow. Since open string geometry breaks rotational symmetry to a subgroup of rotations acting along the direction of the string, the attractive possible is add a stringy excitation with angular momentum projection L=-1 to the wrong parity doublet so that parity comes out correctly. This would give degeneracies (1,2,3,2).

  5. In flux tube degrees of freedom the situation is analogous to construction of mesons from quarks and antiquarks and one obtains pion with spin 0 and r meson with spin 1. States of zero charge correspond to the tensor product 2Ä2=3Å1 for rotation group. Drop the singlet and take only the analog of neutral r meson. The tensor product 3Ä3=5Å3Å1 gives 8+1 states and leaving only spin 2 and spin 1 states gives 8 states. The degeneracies of states with given spin projection for 5Å3 are (1,2,2,2,1). Genetic code means projection of the states of 5Å3 to those of 5 with the same spin projection.

  6. Genetic code maps of ( 4Å2Å2)Ä(5Å3) to the states of 4×5. The most natural map maps the states with given spin to state with same spin so that the code is unique. This would give the degeneracies D(k) as products of numbers DB Î {1,2,3,2} and Db Î {1,2,2,2,1}. The numbers N(k) of aminoacids coded by D(k) 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, 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)!

The conclusion is that genetic code can be understand as a map of stringy baryonic states induced by the projection of all states with same spin projection to a representative state with same spin projection. Genetic code would be realized at the level of dark nuclear physics and perhaps also at the level of ordinary nuclear physics and that biochemical representation would be only one particular higher level representation of the code.

For details see chapters Homeopathy in Many-Sheeted Space-time of "Bio-Systems as Conscious Holograms" and The Notion of Wave-Genome and DNA as Topological Quantum Computer of "Genes and Memes"

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