Thursday, June 18, 2015

Aromatic rings as the lowest level in the molecular self hierarchy?

I had the opportunity to participate the conference Towards Science of Consciousness 2015 held in Helsinki June 8-13. Of special interest from TGD point of view were the talks of Hameroff and Bandyopadphyay, who talked about aromatic rings (ARs) (see this).

I have also wondered whether ARs might play key role with motivations coming from several observations.

  1. In photosynthesis ARs are a central element in the energy harvesting system , and it is now known that quantum effects in longer length and time scales than expected are involved. This suggests that the ARs involved fuse to form a larger quantum system connected by flux tubes, and that electron pair currents follow along the flux tubes as supra currents.

    DNA codons involve ARs with delocalized pi electrons, neurotransmitters and psychoactive drugs involve them, 4 amino-acids Phe, trp, tyr and his involve them and they are all hydrophobic and tend to be associated with hydrophobic pockets. Phe and trp appear in hydrophobic pockets of microtubules.

  2. The notion of self hierarchy suggests that at molecular level ARs represent the basic selves. ARs would integrate to larger conscious entities by a reconnection of the flux tubes of their magnetic bodies (directing attention to each other!). One would obtain also linear structures such as DNA sequence in this manner. In proteins the four aromatic amino-acids would represent subselves possibly connected by flux tubes. In this manner one would obtain a concrete molecular realization of self hierarchy allowing precise identification of the basic conscious entities as aromatic rings lurking in hydrophobic pockets.

  3. Given AR would be accompanied by a magnetic flux tube and the current around it would generate magnetic field. The direction of the current would represent a bit (or perhaps even qbit). In the case of microtubules the phe-trp dichotomy and direction of current would give rise to 4 states identifiable as a representation for four genetic letters A,T,C,G. The current pathways proposed by Hameroff et al consisting of sequences of current rings (see this) could define the counterparts of DNA sequences at microtubule level.

    For B type microtubules 13 tubulins, which correspond to single 2π rotation, would represent basic unit followed by a gap. This unit could represent a pair of helical strands formed by flux tubes and ARs along them completely analogous to DNA double strand. This longitudinal strand would be formed by a reconnection of magnetic flux tubes of the magnetic fields of ARs and reconnection occurring in two different manners at each step could give rise to braiding.

  4. The magnetic flux tubes associated with the magnetic fields of nearby aromatic rings could suffer reconnection and in this manner a longitudinal flux tubes pair carrying supra current could be generated by the mechanism of bio-superconductivity discussed (see this) and working also for the ordinary high Tc super conductivity. The interaction of microtubule with frequencies in the scales kHz, GHz, and THz scales would induce longitudinal superconductivity as a transition to phase A from phase B meaning generation of long super-conducting wires.

    This view suggests that also DNA is superconductor in longitudinal direction and that oscillating AC voltage induces the superconductivity also now. Bandyopadphyay indeed observed the 8 AC resonance frequencies first for DNA with frequency scales of GHz, THz, PHz, which suggests that dark photon signals or AC voltages at these frequencies induce DNA superconductivity. According to the model of DNA as topological quantum computer DNA is superconductor also in the transversal degrees of freedom meaning that there are flux tubes connecting DNA to a lipid layer of the nuclear or cell membrane (see this and this).

  5. Interestingly, the model of Hameroff et al for the helical pathway (see this) assumes that there are three aromatic rings per d=1 nm length along microtubule. This number is same as the number of DNA codons per unit length. It is however mentioned that the distance between aromatic rings trp and phe in MT is about d=2 nm. Does this refer to average distance or is d=1 nm just an assumption. In TGD framework the distance would scale as heff so that also scaling of DNA pathway by a factor 6 could be considered. In this case single tubulin could correspond to genetic codon.

    If d=1 nm is correct, these helical pathways might give rise to a representation of memetic codons representable as sequences of 21 genetic codons meaning that there are 2126 different memetic codons this. DNA would represent the lowest level of hierarchy of consciousness and microtubules the next level. Note that each analog of DNA sequences corresponds to different current pathway.

  6. What is especially interesting, that codon and its conjugate have always altogether 3 aromatic cycles. Also phe and trp appearing in MTs have this property as also tyr and his. Could these 3 cycles give rise to 3-braid? The braid group B3, which is covering of permutation group of 3 objects. Since B2 is Abelian group of integers, 3-braid is the smallest braid, which can give rise to interesting topological quantum computation.

    B3 is also the knot group of trefoil knot, and the universal central extension of the modular group PSL(2,Z) (a discrete subgroup of Lorentz group playing a key role in TGD since it defines part of the discrete moduli space for the CDs with other boundary fixed (see this). Quite generally, B(n) is the mapping class group of a disk with n punctures fundamental both in string model: in TGD where disk is replaced with partonic 2-surface.

For details see the chapter Quantum model for nerve pulse of "TGD and EEG" or the article Impressions created by TSC 2015 conference.

For a summary of earlier postings see Links to the latest progress in TGD.


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