Protein catalysis and reaction pathways look extremely complex (see this) as compared to replication, transcription, translation, and DNA repair. Could simplicity emerge if biomolecules are identified as chemical shadows of objects formed from dark nuclear strings consisting of dark nucleon triplets and their dynamics is shadow of dark stringy dynamics very much analogous to text processing?
What if bio-catalysis is induced by dark catalysis based on reconnection as recognition mechanism? What if contractions and expansions of U-shaped flux tubes by heff increasing phase transitions take that reactants find each other and change conformations as in the case of opening of DNA double strand? What if codes allowing only the dark nucleons with same dark nuclear spin and flux tubes spin to be connected by a pair of flux tubes?
This speculation might make sense! The recognition of reactants is one part of catalytic action. It has been found in vitro RNA selection experiments that RNA sequences are produced having high frequency for the codons which code for the amino-acid that these RNA molecules recognize (this). This is just what the proposal predicts!
Genetic codes DNA to RNA as 64→ 64 map, RNA to tRNA as 64→ 40, tRNA to amino-acids with 40→ 20 map are certainly not enough. One can however consider also additional codes allowed by projections of (4⊕ 21⊕ 22) ⊗ (5⊕ 3 (⊕ 1)) to lower-dimensional sub-spaces defined by projections preserving spins. One could also visualize bio-molecules as collections of pieces of text attaching to each other along conjugate texts. The properties of catalysts and reactants would also depend by what texts are "visible" to the catalysts. Could the most important biomolecules participating biochemical reactions (proteins, nucleic acids, carbohydrates, lipids, primary and secondary metabolites, and natural products, see this) have dark counterparts in these sub-spaces.
The selection of bio-active molecules is one of the big mysteries of biology. The model for the chemical pathway leading to the selection of purines as nucleotides (see this) assumes that the predecessor of purine molecule can bind to dark proton without transforming it to ordinary proton. A possible explanation is that the binding energy of the resulting bound state is higher for dark proton than the ordinary one. Minimization of the bound state energy could be a completely general criterion dictating which bio-active molecules can pair with dark protons. The selection of bio-active molecules would not be random after all although it looks so. The proposal for DNA-nuclear/cell membrane as topological quantum computer with quantum computations coded by the braiding of magnetic flux tubes connecting nucleotides to the lipids wlead to the idea that flux tubes being at O=-bonds (see this).
An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Nuclear string model and in the article About physical representations of genetic code in terms of dark nuclear strings.