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