TGD leads to 3 basic realizations of the genetic code. One can also consider 3 realization also for bio-harmony. The question is which of them is the realistic one or whether several options can be considered. In this article these ideas are discussed critically and open problems are summarized.
The three genetic codes correspond to a fundamental realization in terms of dark proton sequences (dark nuclei) with 3-proton representing codon. Second realization is the chemical realization and the third realization is in terms of dark photon 3-chords mediating the interaction between various realizations. Frequency resonance is very natural interaction between dark levels and energy resonance between dark level and chemical level. The possibility to modify the value of heff for flux tube makes possible to have for given codon single resonance energy.
The homonymy of the genetic codes at various levels is discussed. At the dark level the fact that icosahedral harmonies can have common 3-chords implies the first homonymy. The basic difficulty of Pythagorean scale realized in terms of quint cycle realized already by Pythagoras becomes the solution of this problem. The well-known homonymies in RNA-tRNA correspondence and even in RNA-AA correspondence can be understood in the model in which dark photon 3-chords mediate the interactions.
See the article An overall view about models of genetic code and bio-harmony or the chapter of "Genes and Memes: Part II" with the same title.
For a summary of earlier postings see Latest progress in TGD.