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Quantum Hardware of Living Matter

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Year 2018



About Comorosan effect in the clustering of RNA II polymerase proteins

The time scales τ equal 5, 10, and 20 seconds appear in the clustering of RNA II polymerase proteins and Mediator proteins (see this and the previous posting). What is intriguing that so called Comorosan effect involves time scale of 5 seconds and its multiples claimed by Comorosan long time ago to be universal time scales in biology. The origin of these time scales has remained more or less a mystery although I have considered several TGD inspired explanations for this time scale is based on the notion of gravitational Planck constant (see this).

One can consider several starting point ideas, which need not be mutually exclusive.

  1. The time scales τ associated with RNA II polymerase and perhaps more general bio-catalytic systems could correspond to the durations of processes ending with "big" state function reduction. In zero energy ontology (ZEO) there are two kinds of state function reductions. "Small" reductions - analogs of weak measurements - leave passive boundary of causal diamond (CD) unaffected and thus give rise to self as generalized Zeno effect. The states at the active boundary change by a sequence of unitary time evolutions followed by measurements inducing also time localization of the active boundary of CD. The size of CD increases and gives rise to flow of time defined as the temporal distance between the tips of CD. Large reductions change the roles of the passive and active boundaries and mean death of self. The process with duration of τ could correspond to a life-time of self assignable to CD.

    Remark: It is not quite clear whether CD can disappear and generated from vacuum. In principle this is possible and the generation of mental images as sub-selves and sub-CDs could correspond to this kind of process.

  2. I have proposed (see this) that Josephson junctions are formed between reacting molecules in bio-catalysis. These could correspond to the shortened flux tubes . The difference EJ=ZeV of Coulomb energy of Cooper pair over flux tube defining Josephson junction between molecules would correspond to Josephson frequency fJ= 2eV/heff. If this frequency corresponds to τJ= 5 seconds, heff should be rather large since EJ is expected to be above thermal energy at physiological temperatures.

    Could Josephson radiation serve as a kind of of synchronizing clock for the state function reductions so that its role would be analogous to that of EEG in case of brain? A more plausible option is that Josephson radiation is a reaction to the presence of cyclotron radiation generated at MB and performing control actions at the biological body (BB) defined in very general sense. In the case of brain dark cyclotron radiation would generate EEG rhythms responsible for control via genome and dark generalized Josephson radiation modulated by nerve pulse patterns would mediate sensory input to the MB at EEG frequencies.

    A good guess is that the energy in question corresponds to Josephson energy for protein through cell membrane acting as Josephson junction and giving to ionic channel or pump. This energy could be universal as therefore same also in the molecular reactions. The flux tubes themselves have universal properties.

  3. The hypothesis ℏeff= ℏgr= GMm/β0c of Nottale for the value of gravitational Planck constant gives large ℏ. Here v00c has dimensions of velocity. For dark cyclotron photons this gives large energy Ec∝ ℏgr and for dark Josephson photons small frequency fJ∝ 1/hgr. Josephson time scale τf would be proportional to the mass m of the charged particle and therefore to mass number of ion involved. Cyclotron time scale does not depend on the mass of the charged particle at all and now sub-harmonics of τc are natural.
The time scales assignable to CD or the lifetime-time of self in question could correspond to either cyclotron of Josephson time scale τ.
  1. If one requires that the multiplies of the time scale 5 seconds are possible, Josephson radiation is favoured since the Josephson time scale proportional to hgr ∝ m ∝ A, A mass number of ion.

    The problem is that the values A= 2,3,4,5 are not plausible for ordinary nuclei in living matter. Dark nuclei at magnetic flux tubes consisting of dark proton sequences could however have arbitrary number of dark protons and if dark nuclei appear at flux tubes defining Josephson junctions, one would have the desired hierarchy.

  2. Although cyclotron frequencies do not have sub-harmonics naturally, MB could adapt to the situation by changing the thickness of its flux tubes and by flux conservation the magnetic field strength to which fc is proportional to. This would allow MB to produce cyclotron radiation with the same frequency as Josephson radiation and MB and BB would be in resonant coupling.
Consider now the model quantitatively.
  1. For ℏeff= ℏgr one has

    r= ℏgr/ℏ= GMDm/cβ0= 4.5 × 1014× (m/mp) (y/β0) .

    Here y=MD/ME gives the ratio of dark mass MD to the Earth mass ME. One can consider 2 favoured values for m corresponding to proton mass mp and electron mass me.

  2. E= hefff gives the concrete relationship f =(E/eV) × 2.4 × 1014× (h/heff) Hz between frequencies and energies. This gives

    x=E/eV = 0.4× r × (f/1014 Hz) .

  3. If the cyclotron frequency fc=300 Hz of proton for Bend=.2 Gauss corresponds to bio-photon energy of x eV, one obtains the condition

    r=GMDmp/ ℏ β0≈ .83 × 1012x .

    Note that the cyclotron energy does not depend on the mass of the charged particle. One obtains for the relation between Josephson energy and Josephson frequency the condition

    x=EJ/eV = 0.4× .83 × 10-2× (m/mp)× (xfJ/Hz) , EJ= ZeV .

    One should not confuse eV in ZeV with unit of energy. Note also that the value of Josephson energy does not depend on heff so that there is no actual mass dependence involved.

For proton one would give a hierarchy of time scales as A-multiples ofτ(p) and is therefore more natural so that it is natural to consider this case first.
  1. For fJ=.2 Hz corresponding to the Comorosan time scale of τ= 5 seconds this would give ZeV= .66x meV. This is above thermal energy Eth= T=27.5 meV at T=25 Celsius for x> 42. For ordinary photon (heff= h) proton cyclotron frequency fc(p) would correspond for x>42 to EUV energy E>42 eV and to wavelength of λ<31 nm.

    The energy scale of Josephson junctions formed by proteins through cell membrane of thickness L(151)=10 nm is slightly above thermal energy, which suggests x≈ 120 allowing to identify L(151)=10 nm as the length scale of the flux tube portion connecting the reactants. This would give E≈ 120 eV - the upper bound of EUV range. For x=120 one would have GMEmp y/v0≈ 1014 requiring β0/y≈ 2.2. The earlier estimates (see this) give for the mass MD the estimate y∼ 2× 10-4 giving β0∼ 4.4× 10-4. This is rather near to β0= 2-11∼ me/mp obtained also in the model for the orbits of inner planets as Bohr orbits.

  2. For ion with mass number A this would predict τA= A× τp= A× 5 seconds so that also multiples of the 5 second time scale would appear. These multiples were indeed found by Comoran and appear also in the case of RNA II polymerase.
  3. For proton one would thus have 2 biological extremes - EUV energy scale associated with cyclotron radiation and thermal energy scale assignable to Josephson radiation. Both would be assignable to dark photons with heff=hgr with very long wavelength. Dark and ordinary photons of both kind would be able to transform to each other meaning a coupling between very long lengths scales assignable to MB and short wavelengths/time scales assignable to BB.

    The energy scale of dark Josephson photons would be that assignable with junctions of length 10 nm with long wavelengths and energies slightly above Eth at physiological temperature. The EUV energy scale would be 120 eV for dark cyclotron photons of highest energy.

    For lower cyclotron energies suggested by the presence of bio-photons in the range containing visible and UV and obtained for Bend below .2 Gauss, the Josephson photons would have energies ≤ Eth. That the possible values of Bend are below the nominal value Bend=.2 Gauss deduced from the experiments of Blackman does not conform with the earlier ad hoc assumption that Bend represents lower bound. This does not change the earlier conclusions.

    Could the 120 eV energy scale have some physical meaning in TGD framework? The corresponding wavelength for ordinary photons corresponds to the scale L(151)=10 nm which correspond to the thickness of DNA double strand. Dark DNA having dark proton triplets as codons could correspond to either k=149 or k=151. The energetics of Pollack effect suggests that k=149 is realized in water even during prebiotic period (see this).. In the effect discovered by Blackman the ELF photons would transform dark cyclotron photons having heff=hgr and energy about .12 keV. They would induce cyclotron transitions at flux tubes of Bend with thickness of order cell size scale. These states would decay back to previous states and the dark photons transformed to ordinary photons absorbed by ordinary DNA with coil structure with thickness of 10 nm. Kind of standing waves would be formed. These waves could transform to acoustic waves and induce the observed effects. Quite generally, dark cyclotron photons would control the dynamics of ordinary DNA by this mechanism.

    It is indeed natural to assume that Bend corresponds to upper bound since the values of magnetic field are expected to weaken farther from Earth's surface: weakening could correspond to thickening of flux tubes reducing the field intensity by flux conservation. The model for hearing (see this ) requires cyclotron frequencies considerably above proton's cyclotron frequency in Bend=.2 Gauss. This requires that audible frequencies are mapped to electron's cyclotron frequency having upper bound fc(e) = (mp/me) fc(p)≈ 6× 105 Hz. This frequency is indeed above the range of audible frequencies even for bats.

For electron one has hgr(e)= (me/mp)hgr(p) ≈ 5.3 × 10-4 hgr(p), ℏgr(p)=4.5× 1014/ (β0. Since Josephson energy remains invariant, the Josephson time scales up from τ(p)=5 seconds to τ(e)=(me/mP) τ(p)≈ 2.5 milliseconds, which is the time scale assignable to nerve pulses (see this).

To sum up, the model suggests that the idealization of flux tubes as kind of universal Josephson junctions. The model is consistent with bio-photon hypothesis. The constraints on hgr= GMDm/v0 are consistent with the earlier views and allows to assign Comorosan time scale 5 seconds to proton and nerve pulse time scale to electron as Josephson time scales. This inspires the question whether the dynamics of bio-catalysis and nerve pulse generation be seen as scaled variants of each other at quantum level? This would not be surprising if MB controls the dynamics. The earlier assumption that Bend=0.2 Gauss is minimal value for Bend must be replaced with the assumption that it is maximal value of Bend.

See the chapter Wormhole magnetic fields or the article Clustering of RNA polymerase molecules and Comorosan effect.



Why do RNA polymerase molecules cluster?

I received a link to a highly interesting popular article telling about the work of Ibrahim Cisse at MIT and colleagues (see this): at this time about clustering of proteins in the transcription of RNA. Similar clustering has been observed already earlier and interpreted as a phase separation Similar clustering has been observed already earlier and interpreted as a phase separation (see this). Now this interpretation is not proposed by experiments but experimenters say that it is quite possible but they cannot prove it.

I have already earlier discussed the coalescence of proteins into droplets as this kind of process in TGD framework. The basic TGD based ideas is that proteins - and biomolecules in general - are connected by flux tubes characterized by the value of Planck constant heff=n× h0 for the dark particles at the flux tube. The higher the value of n is the larger the energy of given state. For instance, the binding energies of atoms decrease like 1/n2. Therefore the formation of the molecular cluster liberates energy usable as metabolic energy.

Remark: h0 is the minimal value of heff. The best guess is that ordinary Planck constant equals to h=6h0 (see this and this).

TGD view about the findings

Gene control switches - such as RNA II polymerases in the DNA transcription to RNA - are found to form clusters called super-enhancers. Also so called Mediator proteins form clusters. In both cases the number of members is in the range 200-400. The clusters are stable but individual molecules spend very brief time in them. Clusers have average lifetime of 5.1±.4 seconds.

Why the clustering should take place? Why large number of these proteins are present although single one would be enough in the standard picture. In TGD framework one can imagine several explanations. One can imagine at least following reasons.

  1. One explanation could relate to non-determinism of state function reduction. The transcription and its initiation should be a deterministic process at the level of single gene. Suppose that the initiation of transcription is one particular outcome of state function reduction. If there is only single RNA II polymerase, which can make only single trial, the changes to initiate the transcription are low. This would be the case if the molecule provides metabolic energy to initiate the process and becomes too "tired" to try again. In nerve pulse transmission there is analogous situation: after the passing of the nerve pulse generation the neuron has dead time period. As a matter of fact, it turns out that the analogy could be much deeper.

    How to achieve the initiation with certainty in this kind of situation? Suppose that the other outcomes do not affect the situation appreciabley. If one particular RNA polymerase fails to initiate it, the others can try. If the number of RNA transcriptase molecule is large enough, the transcription is bound to begin eventually! This is much like in fairy tales about princess and suitors trying to kill the dragon to get the hand of princess. Eventually the penniless swineherd enters the stage.

  2. If the initiation of transcription requires large amount of metabolic energy then only some minimal number of N of RNA II polymerase molecules might be able to provide it collectively. The collective formed by N molecules could correspond to a formation of magnetic body with a large value of heff=n×h. The molecules would be connected by magnetic flux tubes.
  3. If the rate for occurrence is determined by amplitude which is superposition of amplitudes assignable to individual proteins the the rate is proportional to N2, N the number of RNA transcriptase molecules.

    The process in the case of cluster is indeed reported to to be suprisingly fast as compared to the expectations - something like 20 seconds. The earlier studies have suggests that single RNA polymerase stays at the DNA for minutes to hours. This would be a possible mechanism allowing to speed up bio-catalysis besides the mechanism allowing to find molecules to find by a reduction of heff/h= n for the bonds connecting the reactants and the associated liberation of metabolic energy allowing to kick the reactants over the potential wall hindering the reaction.

Concerning the situation before clustering there are two alternative options both relying on the model of liquid phase explaining Maxwell's rule assuming the presence of flux tube bonds in liquid and of water explaining its numerous anomalies in terms of flux tubes which can be also dark (see this).
  1. Option I: Molecules could be in a phase analogous to vapour phase and there would be very few flux tube bonds between them. The phase transition would create liquid phase as flux tube loops assignable to molecules would reconnect form flux tube pairs connecting the molecules to a tensor network giving rise to quantum liquid phase. The larger then value of n, the longer the bonds between molecules would be.
  2. Option I: The molecules are in the initial state connected by flux tubes and form a kind of liquid phase and the clustering reduces the value of n and therefore the lengths of flux tubes. This would liberate dark energy as metabolic energy going to the initiation of the transcription. One could indeed argue that connectedness in the initial state with large enough value of n is necessary since the protein cluster must have high enough "IQ" to perform intelligent intentional actions.
Protein blobs are said to be drawn together by the "floppy" bits (pieces) of intrinsically disorder proteins. What could this mean in the proposed picture? Disorder suggests absence of correlations between building bricks of floppy parts of the proteins.
  1. Could floppiness correspond to low string tension assignable to long flux loops with large heff/h=n assignable to the building bricks of "floppy" pieces? Could reconnection for these loops give rise to pairs of flux tubes connecting the proteins in the transition to liquid phase? Floppiness could also make possible to scan the enviroment by flux loops for flux loops of other molecules and in case of hit (cyclotron resonance) induce reconnection.
  2. In spite of floppiness in this sense, one could have quantum correlations between the internal quantum numbers of the building bricks of the floppy pieces. This would also increase the value of n serving as molecular IQ and provide molecule with higher metabolic energy liberated in the catalysis.
What about the interpretation of the time scales 5, 10, and 20 seconds? What is intriguing that so called Comorosan effect involves time scale of 5 seconds and its multiplest claimed by Comorosan long time ago to be universal time scales in bio-catalysis.

See the chapter Wormhole magnetic fields or the article Clustering of RNA polymerase molecules and Comorosan effect.



The experiments of Masaru Emoto with emotional imprinting of water

Sini Kunnas sent a link to a video telling about experiments of Masaru Emoto (see this) with water, which is at criticality with respect to freezing and then frozen. Emoto reports is that words expressing emotions are transmitted to water: positive emotions tend to generate beautiful crystal structures and negative emotions ugly ones. Also music and even pictures are claimed to have similar effects. Emoto has also carried out similar experiments with rice in water. Rice subjected to words began to ferment and water subject to words expressing negative emotions began to rotten.

Remark: Fermentation is a metabolic process consuming sugar in absence of oxygen. Metabolism is a basic signature of life so that at least in this aspect the water+rice system would become alive. The words expressing positive emotions or even music would serve as a signal "waking up" the system.

One could define genuine skeptic as a person who challenges existing beliefs and pseudo-skeptic (PS in the sequel) as a person challenging - usually denying - everything challenging the mainstream beliefs. The reception of the claims of Emoto is a representative example about the extremely hostile reactions of PSs as aggressive watchdogs of materialistic science towards anything that challenges their belief system. The psychology behind this attitude is same as behind religious and political fanatism.

I must emphasize that I see myself as a thinker and regard myself as a skeptic in the old-fashioned sense of the word challenging the prevailing world view rather than phenomena challenging the prevailing world view. I do not want to be classified as believer or non-believer. The fact is that if TGD inspired theory of consciousness and quantum biology describes reality, a revolution in the world view is unavoidable. Therefore it is natural to consider the working hypothesis that the effects are real and see what the TGD based explanation for them could be.

The Wikipedia article about Masaru Emoto (see this) provides a good summary of the experiments of Emoto and provides a lot of links so that I will give here only a brief sketch. According to the article Emoto believed that water was a "blueprint for our reality" and that emotional "energies" and "vibrations" could change the physical structure of water. The water crystallization experiments of Emoto consisted of exposing water in glasses to different words, pictures or music, and then freezing and examining the aesthetic properties of the resulting crystals with microscopic photography. Emoto made the claim that water exposed to positive speech and thoughts would result in visually "pleasing" crystals being formed when that water was frozen, and that negative intention would yield "ugly" crystal formations.

In 2008, Emoto and collaborators published and article titled "Double-Blind Test of the Effects of Distant Intention on Water Crystal Formation" about his about experiments with water in the Journal of Scientific Exploration, a peer reviewed scientific journal of the Society for Scientific Explorations (see this). The work was performed by Masaru Emoto and Takashige Kizu of Emoto’s own IHM General Institute, along with Dean Radin and Nancy Lund of the Institute of Noetic Sciences, which is on Stephen Barrett's Quackwatch (see this) blacklist of questionable organizations. PSs are the modern jesuits and for jesuits the end justifies the means.

Emoto has also carried experiments with rice samples in water. There are 3 samples. First sample "hears" words with positive emotional meaning, second sample words with negative emotional meaning, and the third sample serving as a control sample. Emoto reports (see this) that the rice subjected to words with positive emotional content began to ferment whereas water subject to words expressing negative emotions began to rotten. The control sample also began to rotten but not so fast.

In the article The experiments of Masaru Emoto with emotional imprinting of water I will consider the working hypothesis that the effects are real, and develop an explanation based on TGD inspired quantum biology. The basic ingredients of the model are following: magnetic body (MB) carrying dark matter as heff/h=n phases of ordinary matter; communications between MB and biological body (BB) using dark photons able to transform to ordinary photons identifiable as bio-photons; the special properties of water explained in TGD framework by assuming dark component of water implying that criticality for freezing involves also quantum criticality, and the realization of genetic code and counterparts of the basic bio-molecules as dark proton sequences and as 3-chords consisting of light or sound providing a universal language allowing universal manner to express emotions in terms of bio-harmony realized as music of light or sound. The entanglement of water sample and the subject person (with MBs included) realized as flux tube connections would give rise to a larger conscious entity expressing emotions via language realized in terms of basic biomolecules in a universal manner by utilizing genetic code realized in terms of both dark proton sequences and music of light of light and sound.

See the chapter Dark Nuclear Physics and Condensed Matter or the article The experiments of Masaru Emoto with emotional imprinting of water.



How the transition to superconductive state could be induced by classical radiation?

A popular article published in Science Alert tells about the finding that light can be squeezed to much smaller volume than the wave length using single sheet of graphene. The original article by David Alcaraz Aronzo et al is published in Science. A naive application of Uncertainty Principle suggests that this is impossible since this would mean a very large expectation value of momentum squared in transverse momentum degrees of freedom.

The finding is interesting from the point of view of classical limit of TGD. So called massless extremals (MEs) or topological light rays are extremely general solutions of field equations (practically independently of the details of the action principle: it is enough that it is general coordinate invariant). The counterparts of MEs are not possible in Maxwellian electrodynamics but TGD allows them because of the extreme non-linearity of the underlying geometric variational principle for which the topological pair of Maxwell's equations involving no currents is identically satisfied.

What MEs are?

MEs are 4- surfaces describing the propagation of massless topological field quanta of induced classical fields characterized by light-like propagation direction and polarization orthogonal to it. Classical 4-momentum is light-like. The propagation occurs with maximal signal velocity, and there is no dispersion so that pulse shape is preserved. If there are several pulses they must propagate in the same direction. The analogy is propagation of laser beam in waveguide. MEs are be ideal for targeted communications and MEs associaged with magnetic flux tubes and carrying dark photons assignable with wormohole contacts play a key role in TGD inspired quantum biology. A possible interpretation is as space-time correlates Bose-Einstein condensate of photons. Photons themselves would correspond to wormhole contacts (actually pairs of them) connecting ME to another space-time sheet, which could be magnetic flux tube or even ME.

MEs have finite size scale in directions orthogonal to the direction of propagation and MEs can be arbitrary thin. I do not see any reason why they could not be thinner than wavelength. The graphene seems to provide a situation in which classical modelling by MEs makes sense.

The QFT limit is obtained from many-sheeted space-time by replacing many-sheeted structure with a region of Minkowski space made slightly curved. Gauge potentials and gravitational fields are sums of the corresponding induced fields at space-time sheets so that the effects of these fields on a test particle sum up although fields themselves are at different space-time sheets. The linear superposition of Maxwell's theory is replaced with a set theoretic union of the space-time sheets in M4×CP2. The effects of the fields of space-time sheets on the test particle sum up just like in superposition of fields in Maxwell's theory.

For instance, this allows a situation in which one has two MEs describing propagation of signals in opposite directions as far effects on test particles are considered. This gives rise to standing waves not possible in TGD as single sheeted extremals. Lorentz transforms give analogs of em signals propagating with arbitrary velocity smaller than light velocity. Even field patterns for which the QFT limit corresponds to vanishing fields because the effects on test particles are trivial are possible: both sheets however carry non-vanishing fields with non-vanishing energy-momentum density.

Why the apparent breaking of Uncertainty Principle?

Why the apparent breaking of Uncertainty Principle is then possible in TGD? The point is that in TGD particles do not correspond to wavefunctions in a fixed space-time - this is true only at quantum field theory limit of TGD. Instead, they correspond to wave functions in what I call "world of classical worlds" (WCW). 3-space as "world" is in TGD replaced with 3-D surface defining the "world". In zero energy ontology (ZEO) one can identify space-time surfaces as preferred extremals of an action, which in a well-defined sense generalizes the Maxwell action for a point like charged particle. Thanks to holography, the space-time surface is characterized by 2 3-surfaces at its opposite ends - loci for initial and final states - located at the opposite boundaries of causal diamond (CD), whose M4 projection is intersection of future and past directed light-cones and would look like diamond if it were 2-D.

The world as 3-D surface or equivalently 4-D surface is the quantum dynamical object and space-time ceases to be a passive arena of dynamics. Uncertainty Principle holds true for wave functions in WCW rather than for induced fields at space-time surfaces. Therefore the apparent breaking of Uncertainty Principle is possible.

For background see the chapter Quantum antenna hypothesis .



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