The mechanism of mutation is reported to involve transcription rather than DNA replication. The mutation would take place for DNA when its is copied to RNA after opening of the DNA double strand. The mutations would have occurred during the period when neurons replicate and the mutation history can be read by studying the distributions of changes in the genome.
This brings in mind the finding that "knockout", that is removing a part of gene does not affect transcription (see the earlier blog posting). This suggests that the dark DNA is not changed in these modifications and mRNA is determined by the dark DNA, which would serve as a template for transcription rather than ordinary DNA. If this were the case also for neurons, the mutations of neuronal genes should not affect the gene transcription at all, and there would be no negative (or positive) effects on brain function. This seems too conservative. The mutations should have some rmore active role.
One can consider also different interpretation. The mutations of DNA could be induced by the dark DNA. As dark DNA changes, ordinary DNA associated with it is forced to change too - sooner or later. Especially so when the genome is in a state in which mutations can take place easily. Neurons during to replication stage could have such quantum critical genomes.
Evolution would not be mere selection by a survival of random mutations by external environment in the time scale much longer than lifetime of individual - but a controlled process, which can occur in time scale shorter than lifetime and differently inside parts of say brain. This is what the idea TGD inspired biology suggests. The modified DNA could be dark DNA and and serve as template for transcription and also induce transformation of ordinary DNA associated with it.
Whether this change can be transferred to the germ cells to be transferred to the offspring remains of course an open question. One can imagine that dark DNA strands (magnetic flux tubes) can penetrate germ cells and replace the earlier dark DNA sections and induce change of ordinary DNA. Or is a more delicate mechanism involving dark photons in question. With inspiration coming from the findings reported by Peter Gariaev I have proposed a model of remote DNA replication suggesting that DNA can be replicated remotely if the needed nucleotides are present: the information about DNA could be transferred as dark photons, which can be transformed to ordinary photons identified as
bio-photons. Could Lysenko have been at least partially right despite that he was a swindler
basing his views on ideology?
In any case, TGD inspired biology allows to imagine a controlled evolution of DNA in analogy to that what occurs in R&D departments of modern technological organizations. The notion of dark DNA suggests that biological systems indeed have a "R&D department" in which new variants of DNA studied as "dark DNA" sequences realised as dark proton sequences - same about dark RNA, and amino-acids and even tRNA. The possibility to transcribe RNA from dark DNA would mean that the testing can be carried in real life situations.
There indeed exists evidence that traumatic - and thus highly emotional - memories may be passed down through generations in genome . Could the modifications of brain DNA represent long term memories as the above described experiment suggests? Could the memories be transferred to the germ cells using the mechanism sketched above?
For background see the new chapter Dark matter, quantum gravity, and prebiotic evolution or the article "Direct Evidence for Dark DNA?!".
For a summary of earlier postings see Links to the latest progress in TGD.