- The first realization - proposed in the model for DNA as topological quantum computer (tqc) - maps the nucleotides A,G and T,C to dark quarks u,d and their anti-quarks assignable to the ends of magnetic flux tubes representing braid strands and connecting nucleotides to lipids of cell membrane.
- Second realization was discovered in the model of dark nuclei as strings of dark baryons. Dark baryons realize codons in terms of quantum entanglement and without decomposition to letters. Dark baryons are strings of 3 quarks connected by two color flux tubes. The neutral states of the dark baryon predicted by the model are in 1-1 correspondence with DNA, RNA, aminoacids. Candidates for the counterparts of tRNA anticodons are also obtained if one accepts that genetic code actually decomposes to 2 steps 64→40→20 such that there are 40 dark baryon counterparts for tRNA anticodons. The amazing finding is that vertebrate genetic code comes out correctly.
- The third realization is a physical realization for the divisor code proposed by Khrennikov and Nilsson. The realization relies on two integers labeling magnetic flux tubes containing dark matter. The dark magnetic flux tubes assignable to DNA codons and amino-acids could be labeled by these integers providing a representation of the genetic code consistent with the divisor code. Also a physical mechanism implying the physical equivalence of the dark baryon code and divisor code can be imagined.
The basic proposal is that dark baryon counterparts of basic bio-molecules and genetic code were present from beginning and gave rise to pre-biotic life at the magnetic flux tubes so that the evolution of biological life meant the development of translation and transcription mechanisms allowing to transform dark baryon variants of the codons to their chemical variants. These mechanisms would be still at work inside the living cell and allow the living matter to perform genetic engineering. This proposal is consistent with recent findings about large variations of genomes inside organism.
There is a strange experimental finding by a roup led by a HIV Nobel winner Montagnier giving support for this picture. A water solution containing human cells infected by bacteria is sterilized by a filtering procedure and healthy cells are added to the filtrate. Within few weeks the infected cells re-appear. A possible explanation is that dark baryon variant of the bacterial genome realized as nano-sized particles remains in the solution despite the filtering.
The codes are discussed from the point of view of DNA as tqc hypothesis and the model for protein folding and bio-catalysis. The basic selection rules of bio-catalysis could be based on the two integers assignable to the dark magnetic flux tubes. Only bio-molecules whose dark magnetic bodies contain a layer characterized by same integers can be connected by dark magnetic flux tubes. The reconnection of the dark magnetic flux tubes selecting the bio-molecules participating the catalytic reaction and the contraction of these flux tubes induced by a phase transition reducing Planck constant and forcing the bio-molecules near to each other would represent basic mechanisms of bio-catalysis.
For background see the new chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems of "Genes and Memes".