I encountered last year a highly interesting article about "dark DNA" hitherto found in the genome of gerbils and birds, for instance in the genome of of the sand rat living in deserts. I have written about this in another book but thought that it might a good idea to add it also here.
The gene called Pdxl related to the production of insulin seems to be missing as also 87 other genes surrounding it! What makes this so strange that the animal cannot survive without these genes! Products that the instructions from the missing genes would create are however detected!
According to the ordinary genetic, these genes cannot be missing but should be hidden, hence the attribute "dark" in analogy with dark matter. The dark genes contain A lot of G and C molecules and this kind of genes are not easy to detect: this might explain why the genes remain undetected.
A further interesting observation is that one part of the sand rat genome has many more mutations than found in other rodent genomes and is also GC rich. Could the mutated genes do the job of the original genes? Missing DNA are found in birds too. For instance, the gene for leptin - a hormone regulating energy balance - seems to be missing.
The finding is extremely interesting from TGD view point, where dark DNA has very concrete meaning. Dark matter at magnetic flux tubes is what makes matter living in TGD Universe. Dark variants of particles have non-standard value heff=n× h0 (h= 6h0 is the most plausible option) of Planck constant making possible macroscopic quantum coherence among other things. Dark matter would serve as template for ordinary matter in living systems and biochemistry could be kind of shadow of the dynamics of dark matter. What I call dark DNA would correspond to dark analogs of atomic nuclei realized as dark proton sequences with entangled proton triplet representing DNA codon. The model predicts correctly the numbers of DNA codons coding for given amino-acid in the case of vertebrate genetic code and therefore I am forced to take it very seriously (see this and this).
The chemical DNA strands would be attached to parallel dark DNA strands and the chemical representation would not be always perfect: this could explain variations of DNA. This picture inspires also the proposal that evolution is not a passive process occurring via random mutations with survivors selected by the evolutionary pressures. Rather, living system would have R&D lab as one particular department. Various variants of DNA would be tested by transcribing dark DNA to ordinary mRNA in turn translated to amino-acids to see whether the outcome survives. This experimentation might be possible in much shorter time scale than that based on random mutations. Also immune system, which is rapidly changing, could involve this kind of R&D lab.
Also dark mRNA and amino-acids could be present but dark DNA is the fundamental information carrying unit and it would be natural to transcribe it to ordinary mRNA. Of course, also dark mRNA could be be produced and translated to amino-acids and even dark amino-acids could be transformed to ordinary ones. This would however require additional machinery.
What is remarkable is that the missing DNA is indeed associated with DNA sequences with exceptionally high mutation rate. Maybe R&D lab is there! If so, the dark DNA would be dark also in TGD sense! Why GC richness should relate to this, is an interesting question.
See the chapter Quantum criticality and dark matter.