Sunday, October 04, 2015

Do neurons have their private genomes?

Genetics is experiencing a revolution as the information technology has made possible new research methods and old dogmas must be given up. Before continuing, thanks for Ulla for giving links (see this and this) explaining the results of the article discussed in more detail: this led to a correction of some misunderstandings. See also this for a background.

It has been discovered that brain cells have a mosaic like distribution of genomes (see this, this, and this). In standard framework this mosaic should be created by random mutations.

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.


Ulla said...

I put the links here for future.

Ulla said...

Also this. a review article. said...

Thank you for the links. Very valuable!

Ulla said...

Maybe some ideas concerning gravitational lensings would be useable?

Ulla said...

Actually the creation of negative refraktion is a clue to this? How does it invoke on the 'negative energy' concept?

Ulla said...

This is about regulating DNA loops, which has bothered me much. Maybe the loops are like gravitational lenses??? Smiley. It would explain the dark matter regulation? said...

That topology is involved with DNA regulation is very interesting. I am however unable to say anything interesting except that magnetic flux loops should be involved as in any bio-control. Reconnections, length change induced by change of h_eff, etc… A lot of mechanisms. Dark matter as large h_eff phases would be certainly involved should be certainly involved in TGD Universe.

The idea about gravitational lensing does not look compelling;-) to me (why it would be needed?) although h_eff= h_gr identity means that flux tubes mediating gravitational interactions - at least those between dark matter - should be involved with biology.

h_eff=h_gr is nice for other reasons: the Compton long length does not depend on particle mass and the energy spectrum of dark photons is universal - in the range of biophotons, which is in visible and UV and corresponds to molecular transition energies. Dark photons can induced transitions of biomolecules and the control by magnetic body becomes possible. said...

Negative energy concept is basic element at all levels of
self hierarchy. Also DNA. Translated to a theory of consciousness it says that sequences of self-its time reversal-self-… are fundamental. This is new and I have not yet found a manner to express is mathematical result in a manner appealing to intuition. Re-incarnation is familiar notion but how I could make re-incarnations as time reversal with sensory input somewhere in geometric past understandable. We are used to think that time has always the same arrow: how to overcome come the this barrier?

New theories lead to highly counterintuitive predictions, if they are really new theories. If they are also working theories these predictions turn out to be correct! Jury has to decide;-)

Ulla said...

It is the gravitational hierarchy, as Plancks constant that made me think of a 'blowed up state' like a gravitational lens for the regulation and for quantum states. In a way this would give Einstein right? said...

Einstein was right in certain resolution: when you approximate many-sheetedness with single sheet with single piece of curved Minkowski space- like replacing sandwich with single infinitely thin sheet- Einstein was right. Also his two principle - general coordinate invariance and equivalence principle hold still true albeit in different framework. Even better they are consistent with special relativity. TGD is more Einsteinian that Einstein himself!;-)