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Year 2015

Do neurons have their personal 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 chapter Quantum Mind, Magnetic Body, and Biological Body or the article "Direct Evidence for Dark DNA?!".

Psychedelic induced experiences as key to the understanding of the connection between magnetic body and information molecules?

There is a book about psychedelics titled as "Inner paths to outer space: Journies to Alien Worlds through Psychedelics and Other Spiritual Technics" written by Rick Strassman, Slawek Wojtowicz, Luis Eduardo Luna and Ede Frecska (see this). The basic message of the book is that psychedelics might make possible instantaneous remote communications with distant parts of the Universe. The basic objection is that light velocity sets stringent limits on classical communications. Second objection is that the communications require huge amount of energy unless they are precisely targeted. The third objection is that quantum coherence in very long, even astrophysical scales is required. In TGD framework this argument does not apply.

In Zero Energy Ontology (ZEO) communications in both directions of geometric time are possible and kind of time-like zig-zag curves make possible apparent superluminal velocities. Negentropic quantum entanglement provides second manner to share mental images, say sensory information remotely. The proposed model leads to a general idea that the attachment of information molecules such as neurotransmitters and psychedelics to a receptor as a manner to induce a remote connection involving transfer of dark potons signals in both directions of geometric time to arbitrarily long distances. The formation of magnetic flux tube contact is a prerequisite for the connection having interpretation as direct attention or sense of presence. One can see living organisms as systems continually trying to build this kind of connections created by a reconnection of U-shaped flux tubes serving as magnetic tentacles. Dark matter as a hierarchy of phases with arbitrary large value of Planck constants guarantees quantum coherence in arbitrary long scales.

The natural TGD inspired hypothesis about what happens at the level of brain to be discussed in sequel in detail goes as follows.

  1. Psychedelics bind to the same receptors as the neurotransmitters with similar aromatic rings (weaker assumption is that neurotransmitters in question possess aromatic rings). This is presumably consistent with the standard explanation of the effect of classical psychedelics as a modification of serotonin uptake. This binding replaces the flux tube connection via neurotransmitter to some part of the personal magnetic body with a connection via psychedelic to some other system, which might be even in outer space. A communication line is created making among other things possible remote sensory experiences.

    Magnetic fields extending to arbitrary large distances in Maxwell's theory are replaced with flux tubes in TGD framework. The magnetic bodies of psychedelics would carry very weak magnetic fields and would have very large heff - maybe serving as a kind of intelligence quotient.

  2. This would be like replacing the connection to the nearby computer server with a connection to a server at the other side of the globe. This would affect the usual function of transmitter and possibly induce negative side effects. Clearly, TGD inspired hypothesis gives for the psychedelics much more active role than standard hypothesis.
  3. Phychedelics can be classified into two groups depending on whether they contain derivative of amino-acid trp with two aromatic rings or phe with one aromatic ring. Also DNA nucleotide resp. its conjugate have 2 resp. 1 similar aromatic rings. This suggests that the coupling between information molecule and receptor is universal and same as the coupling between the two bases in DNA double strand and consists of hydrogen bonds. This hypothesis is testable since it requires that the trp:s/phe:s of the information molecule can be brought to same positions as phe:s/trp:s in the receptor. If also protein folding relies on this coupling, one might be able to predict the folding to a high degree.
  4. A highly suggestive idea is that molecules with aromatic rings are fundamental conscious entities at the level of molecular biology, and that more complex conscious entities are created from them by reconnection of flux tubes. DNA/RNA sequences and microtubules would be basic examples about this architecture of consciousness. If so, protein folding would be dictated by the formation trp-phe contacts giving rise to larger conscious entities.
See the chapter Meditation, Mind-Body Medicine and Placebo: TGD point of view or the revised article Psychedelic induced experiences as key to the understanding of the connection between magnetic body and information molecules?.

Direct evidence for dark DNA?!

This morning I learned in Sciencedaily about extremely interesting finding related to DNA. The finding is just what breakthrough discovery should be: it must be something impossible in the existing world view.

What has been found is that knock-out (removing parts of gene to prevent transcription to mRNA) and knock-down of gene (prevent protein translation) seem to have different consequences. Removing parts of gene need not have the expected effect at the level of proteins! Does this mean that somehow DNA as a whole can compensate the effects caused by knock-out but not those by knock-down?

Could this be explained by assuming that genome is a hologram as Gariaev et al have first suggested? Also TGD leads to a vision about living system as a conscious hologram. Small local changes of genes could be compensated. Somehow the entire genome would react like brain to a local brain damage: other regions of brain take the duties of the damaged region.

Could the idea about DNA double strand as nano-brain having left and right strands instead of hemispheres help here. Does DNA indeed act as a macroscopic quantum unit? The problem is that transcription is local rather than holistic process. Something very simple should lurk behind the compensation mechanism.

Could transcription transform dark DNA to dark mRNA?

Also the TGD based notion of dark DNA comes in mind (see this and this). Dark DNA consists of dark proton sequences for which states of single DNA proton correspond to those of DNA, mRNA, aminoacids, and tRNA. Dark DNA is one of the speculative ideas of TGD inspired quantum biology getting support from Pollack's findings . Ordinary biomolecules would only make their dark counterparts visible: dark biomolecules would serve as a template around which ordinary biomolecules such as DNA strands are formed in TGD Universe.

Although ordinary DNA is knocked out of ordinary gene, dark gene would still exist! If dark DNA actually serves as template for the transcription to mRNA, everything is still ok after knockout! Could it be that we do not understand even transcription correctly? Could it actually occur at the level of dark DNA and mRNA?! Dark mRNA would attach to dark DNA after which ordinary mRNA would attach to the dark mRNA. One step more!

Damaged DNA could still do its job! DNA transcription would would have very little to do with bio-chemistry! If this view about DNA transcription is correct, it would suggest a totally new manner to fix DNA damages. These damages could be actually at the level of dark DNA, and the challenge of dark genetic engineering would be to modify dark DNA to achieve a proper functioning.

Could dark genetics help to understand the non-uniqueness of the genetic code?

Also translation could be based on pairing of dark mRNA and dark tRNA. This suggests a fresh perspective to some strange and even ugly looking features of the genetic code. Are DNA and mRNA always paired with their dark variants? Do also amino-acids and anticodons of tRNA pair in this manner with their dark variants? Could the pairings at dark matter level be universal and determined by the pairing of dark amino-acids with the anticodons of dark RNA? Could the anomalies of the code be reduced to the non-uniqueness of the pairing of dark and ordinary variants of basic bio-molecules (pairings RNA--dark RNA, amino-acid-- dark amino-acid, and amino-acid--ordinary amino-acid in tRNA).

  1. There are several variants of the genetic code differing slightly from each other: correspondence between DNA/mRNA codons and amino-acids is not always the same. Could dark-dark pairings be universal? Could the variations in dark anticodon - anticodon pairing and dark amino-acid-amino-acid pairing in tRNA molecules explain the variations of the genetic code?
  2. For some variants of the genetic code a stop codon can code for amino-acid. The explanation at the level of tRNA seems to be the same as in standard framework. For the standard code the stop codons do not have tRNA representatives. If stop codon codes for amino-acids, the stop codon has tRNA representation. But how the mRNA knows that the stop codon is indeed stop codon if the tRNA associated with it is present in the same cell?

    Could it be that stop codon property is determined already at the level of DNA and mRNA? If the dark variant of genuine stop codon is missing in DNA and therefore also in mRNA the translation stops if it is induced from that at the level of dark mRNA. Could also the splicing of mRNA be due to the splitting of dark DNA and dark mRNA? If so genes would be separated from intronic portions of DNA in that they would pair with dark DNA. Could it be that the intronic regions do not pair with their dark counterparts. They would be specialized to topological quantum computations in the TGD inspired proposal.

    Start codon (usually AUG coding met) serves as a start codon defining the reading frame (there are 3 possible reading frames). Dark DNA would naturally begin from this codon.

  3. Also two additional amino-acids Pyl and Sec appear in Nature. Gariaev et al have proposed that the genetic code is context dependent so that the meaning of DNA codon is not always the same. This non-universality could be reduced to the non-uniqueness of dark amino-acid--amino-acid pairing in tRNA if genetic code is universal.

Could dark genetics help to understand wobble base pairing?

Wobble base pairing is second not-so-well understood phenomenon. In the standard variant of the code there are 61 mRNAs translated to amino-acids. The number of tRNA anticodons (formed by the pairs of amino-acid and RNA molecules) should be also 61 in order to have 1-1 pairing between tRNA and mRNA. The number of ordinary tRNAs is however smaller than 61 in the sense that the number of RNAs associated with them is smaller than 45. tRNA anticodons must be able to pair with several mRNA codons coding for given amino-acid. This is possible since tRNA anticodons can be chosen to be representative for the mRNA codons coding a given amino-acid in such that all mRNA codons coding for the same amino-acid pair with at least one tRNA anticodon.

  1. This looks somewhat confusing but is actually very simple: genetic code can be seen as a composite of two codes: first 64 DNAs/mRNAs to are coded to N<45 anticodons in tRNA, and then these N anticodons are coded to 20 amino-acids. One must select N anticodon representatives for the mRNAs in the 20 sets of mRNA codons coding for a given amino-acid such that each amino-acid has at least one anticodon representative. A large number of choices is possible and the wobble hypothesis of Crick pose reduce the number of options.
  2. The wobble hypothesis of Crick states that the nucleotide in the third codon position of RNA codon of tRNA has the needed non-unique base pairing: this is clear from the high symmetries of the third basis. There is exact U-C symmetry and approximate A-G symmetry with respect to the third basis of RNA codon (note that the conjugates of RNA codons are obtained by A↔U and C↔G permutations).
  3. The first two basis in the codon pair in 1-1 manner to the second and third basis of anticodon. The third basis of anticodon corresponds to the third letter of mRNA codon. If it is A or C the correspondence is assumed to be 1-to-1: this gives 32 tRNAs. If the first basis of anticodon is G or U the 2 mRNA basis can pair with it: they would be naturally A for G and C for U by symmetry. One would select A from A-G doublet and C from U-C double. This would give 16 anticodons: 48 anticodons altogether, which is however larger than 45. Furthermore, this would not give quite the correct code since A-G symmetry is not exact.

    Smaller number of tRNAs is however enough since the code has almost symmetry also with respect to A and C exchange not yet utilized. The trick is to replace in some cases the first basis of anticodon with Inosine I, which pairs with 3 mRNA basis. This replacement is possible only for those amino-acids for which the number of RNAs coding the amino-acid is 3 or larger (the amino-acids coded by 4 or 6 codons).

  4. It can be shown at least 32 different tRNAs are needed to realize genetic code by using wobble base pairing. Full A-C and G-U symmetry for the third basis of codon would give 16+16=32 codons. Could one think that tRNA somehow realizes this full symmetry?
How dark variants of could help to understand wobble base pairing? Suppose for a moment that the visible genetics be a shadow of the dark one and fails to represent it completely. Suppose the pairing of ordinary and dark variants of tRNA anticodons resp. amino-acids and that translation proceeds at the level of dark mRNA, dark anticodons, and dark amino-acids, and is made visible by its bio-chemical shadow. Could this allow to gain insights about wobble base pairing? Could the peculiarities of tRNA serve for some other - essentially bio-chemical - purposes?

The basic idea would be simple: chemistry does not determine the pairing but it occurs at the level of the dark mRNA codons and dark tRNA anticodons. There would be no need to reduce wobble phenomenon to biochemistry and the only assumption needed would be that chemistry does not prevent the natural dark pairing producing standard genetic code apart from the modifications implied by non-standard dark amino-acid--amino-acid pairing explaining for different codes and the possibility that stop codon can in some situation pair with dark mRNA.

One can consider two options.

  1. The number of dark tRNAs is 64 and the pairings between dark mRNA and dark anticodons and dark anticodons and dark amino-acids are 1-to-1 and only the pairing between dark RNA codons and anticodons in tRNA is many-to-1.
  2. The model of dark genetic code) suggests that there are 40 dark proton states, which could serve as dark analogs of tRNA. This number is larger than 32 needed to realize the genetic code as a composite code. I have cautiously suggested that the proposed universal code could map dark mRNA states of the same total spin (there is breaking of rotational symmetry to that around the axis of dark proton sequences) to dark tRNA/dark amino-acid states with the same total spin. The geometric realization would in terms of color flux tubes connecting the dark protons of corresponding dark proton sequences. Also in ordinary nuclei nucleons are proposed to be connected by color flux tubes so that they form nuclear strings and dark proton sequences would be essentially dark variants of nuclei.
One should understand the details of the dark mRNA--tRNA anticodon correspondence. One can also ask whether the dark genetic code and the code deduced from the geometric model for music harmony in terms of Platonic solids are mutually consistent. This model implies the decomposition of 60+4 DNA codons to 20+20+20+4 codons, where each "20" corresponds to one particular icosahedral Hamilton's cycle with characteristic icosahedral symmetries. "4" can be assigned to tetrahedron regarded either disjoint from icosahedron or glued to it along one of its faces. This allows to understand both the standard code and the code with two stop codons in which exotic amino-acids Pyl and Sec appear. One should understand the compositeness 64→ 40 →20 of the dark genetic code and and whether it relates to the icosatetrahedral realization of the code.

I have proposed that dark variants of transcription, translation, etc.. can occur and make possible kind of R&D laboratory so that organisms can test the consequences of variations of DNA. If ordinary translation and transcription are induced from their dark variants and if dark biomolecules could also appear as unpaired variants, these processes could occur as purely dark variants. Organisms could indeed do experimentation in the virtual world model of biology and pairing with ordinary bio-molecules would make things real.

For background see the new chapter Quantum Mind, Magnetic Body, and Biological Body or the article "Direct Evidence for Dark DNA?!".

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