What about quantum entanglement between codons?
One could also imagine quantum entanglement (necessary negentropic in p-adic degrees of freedom) between codons. This NE could be between additional degrees of freedom or between spin degrees of freedom determining the codons. In the latter case complete correlation between dark and ordinary DNA codons would imply superposition of their tensor products too. This does not seem to make sense in PEO since the chemistries of codons are different) but could make sense in ZEO. McFadden has actually proposed this kind of quantum superposition for ordinary codons: I have compared this vision with TGD views as they were for years ago (see this). Now these views are somewhat out-of-date .
The NE between dark codons could also have a useful function: it could determine physically gene as a union of disjoint mutually entangled portions of DNA. Genes are known to be highly dynamical units, and after pre-transcription splicing selects the portions of the transcript translated to protein. The codons in the complement of the real transcript are called introns and are spliced out from mRNA after the pre-transcription (see this).
What could be the physical criterion telling whether a given codon belongs to exonic or intronic portion of DNA? A possible criterion distinguish between exons and introns is that exons have NE between themselves and introns have no entanglement with exons (also exons could have NE between themselves). Introns would not be useless trash since the division into exonic and exonic region would be dynamical(one can imagine also other reasons for them not being trash). The interpretation in terms of TGD inspired theory of consciousness would be that exons correspond to single self.
An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in
chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems and in the article About physical representations of genetic code in terms of dark nuclear strings.
For a summary of earlier postings see Latest progress in TGD.