The model of DNA as topological quantum computer was originally motivated by the idea that quantum biology in TGD Universe might teach something about quantum computation like processes possibly taking place in living matter. It turned out that the model of DNA as topological quantum computer began to give lessons about quantum biology. In particular, one must assign 4-color to braid strands represented as flux tubes connecting DNA nucleotides A,T,C,G to lipids of nuclear or cellular membranes. In TGD Universe this color is naturally represented in terms 2 quarks u,d and their antiquarks (scaled up variants of ordinary quarks with large hbar and residing at flux tubes of "wormhole" magnetic fields defining the braid strands).
This sounds definitely something very weird for anyone still inhabiting the simple standard model universe and not gone through 28 year lasting process of discovery starting from the basic idea of TGD and ending up with the recent highly refined picture about how TGD Universe differs from that of standard model. Recall however that the discovery of Barbara Shipman that the patterns of honeybee dance can be understood in terms of the mathematics of color group SU(3) of strong interactions, led her to suggest that quarks are directly involved with cognition and memory. This makes sense since DNA as tqc using 4-colored braids is expected to be closely involved with cognition and memory.
The model led to the prediction that coding regions of DNA might be characterized by a breaking various symmetries at quark level, that is breaking of matter antimatter symmetry, isospin asymmetry, and asymmetry between uuc and ddc type matters (c refers to charge conjugation taking matter into antimatter) could take place at level of coding sequences. Three parameters should characterize this breaking.
I made some sample calculations and found support for the breaking of matter antimatter and symmetry and the generation of anomalous em charge implied by this. Yesterday I learned (thanks go to Dale Trenary for crucial references) that simple basic facts about DNA which can be found from Wikipedia support the proposed vision about symmetry breaking although details were not quite correct.
- Chargaff's rules, which I already knew, imply an approximate but not complete matter antimatter symmetry at the level of the entire genome and one can find nice examples about the small breaking. Depending on the explicit corresponds of A,T,C,G with quarks. The breaking of matter antimatter symmetry is quite generally below per cent. The anomalous em charge per nucleon, which depends on scenario (2 options and their charge conjugates) is typically below .1 units per nucleotide. The following table gives representative examples about values of various parameters (anomalous em charge per nucleotide for two options, isospin per nucleotide, quark number per nucleotide, G+C/A+T ratio).
- The deviation of C+G/A+T from unity used to classify genomes characterizes the asymmetry between uuc and ddc type matters. C+G/A+T increases as the length of coding sequence increases.
- Szybalski's rules state that matter antimatter symmetry and isospin symmetry are broken for coding regions of DNA. The breaking pattern is however more intricate than I had expected. The coding part of the DNA decomposes in fifty-fifty manner into regions in which either matter or antimatter dominates and the directions of transcription and selection of template DNA are different for these regions so that mRNA breaks matter antimatter symmetry and always in the same manner. By the way, I had always thought that the template DNA is always the same. The structural matter antimatter asymmetry of mRNA is obviously translated to a functional asymmetry of DNA. A possible reason is that otherwise DNA would not be stable since it would generate too high anomalous em charge. One can wonder whether the matter antimatter asymmetry for mRNA is compensated by the opposite asymmetry for some other type of RNA inside cell nucleus.
It thus seems that DNA as tqc and the coding of braid color by quarks allows to understand the poorly understood empirical rules about the distribution of codons in DNA. Many fascinating questions and working hypothesis can be considered besides those proposed already earlier.