Wednesday, January 11, 2012

Quantum view about metabolism

After the writing of the first version of the chapter discussing quantum view about metabolism for about decade ago several new ideas have emerged. Since 2007 the evidence that photosynthesis involves quantum coherence in electronic degrees of freedom in the cell scale has been accumulating: this discovery is in blatant conflict with the predictions of standard quantum theory but conforms nicely with one of the oldest TGD based proposal that living matter is high Tc electronic super-conductor and with the identification of dark matter as phases with large value of Planck constant.

Both the new ideas and the new experimental results motivated rewriting of the chapter. Below is a brief summary about the new ideas that have emerged during last years, and questions raised by them, and how they affect the quantum model of metabolism at the basic level. Especially interesting new result is a concrete and testable proposal for how living matter acts as a high T superconductor bound to have practical implications. This proposal allows also to understand the basic aspects of bio-chemistry (why the number of valence bonds per molecule is maximized). Also a unification of three different views about high living matter manages to be macroscopic quantum system emerges. This unification is only one example of amazing convergence of the basic ideas of TGD that has taken place during the last years.

1. Three different views about living matter as a macroscopic quantum system

There are three different views about how living system manages to be a macroscopic quantum system.

  1. The first vision is based on various kinds of super-conductivities. Electronic super-conductivity is assigned with the cell membrane and plays a key role in the model of cell membrane as a Josephson junction. Furthermore, the effects of ELF em fields on vertebrate brain (see this) suggest that biologically important ions form macroscopic quantum states and cyclotron Bose-Einstein condensates of bosonic ions have been suggested. The TGD based view about atomic nuclei (see this) predicts exotic nuclei chemically equivalent with ordinary ones but being bosons rather than fermions. Also these exotic ions could also form cyclotron Bose-Einstein condensates. Large value of Planck constant would guarantee that cycloctron energies proportional to hbar are above thermal energy.

  2. A more precise view about hierarchy of Planck constants as an implication of the enormous vacuum degeneracy of Kähler action has emerged (see this). According to this view non-standard values of Planck constant are only effective.

    As the idea about the hierarchy of Planck constants emerged, I proposed that favored values of Planck constant could comes are powers of 211. This was just a first guess inspired partially by the observation that the mass ratio of proton and electron is 940/.5= 1880 ∼ 211. I managed to find indications supporting this hierarchy and also this chapter contains traces of this idea. I became later skeptic but one could actually imagine a mechanism implying this kind of hierarchy. Dark protons with say r=hbar/hbar0= 1836=4× 33× × 17 would correspond to approximately same Compton length as ordinary electrons. It is natural to assign this value of hbar also to electrons and this gives Compton length 44.6 Angstroms not far from the p-adic length scale L(149)≈ 50 Angstroms assigned with the lipid layer of cell membrane. The condition that dark proton corresponds to this Compton length gives r= 18362: the electron Compton length comes now 8.1 μm, which corresponds to cell size scale. One could continue the resulting hierarchy of Planck constants indefinitely.

  3. The notion of negentropic entanglement making sense for rational and even algebraic entanglement probabilities has emerged as a possible characterizer of living matter emerged (see this). Quantum arithmetics allows to generalize the notion of rational so that p-adic real correspondence mediated by canonical identification is fixed uniquely and is both continuous and respects symmetries. One implication is an explanation for Shnoll effect , which could be important also in living matter.

This raises several questions.

  1. How high Tc super conductivity based on dark electron pairs and negentropic entanglement relate?

  2. Could it be that electron pairs in valence bonds are the carriers of negentropic entanglement and that they generate the magnetic flux tubes as parts of their magnetic bodies and in this manner space-time correlates for macroscopic quantum coherence? This makes sense only if the valence electron pairs in living matter have spin 1. The Cooper pairs of high Tc super-conductors are ineed known to have spin 1 (see this). If this view is correct, biological evolution would favor the maximization of covalent electron pairs and this indeed seems to be the case (carbohydrates, fundamental biomolecules, phosphates having as many as 8 valence bonds!) .

  3. Why large hbar would make possible negentropic entanglement or even force it? Is there some purely number theoretic reason for this? For instance, could the p-adic prime p characterizing quantum arithmetics divide the integer n characterizing the Planck constant or could prime valued integers n be favored?

2. Genetic code and dark nucleon states

New realization of the genetic code in terms of dark proton sequences identified as dark nucleons was discovered (see this and this).

  1. The states of dark proton are in natural one-one correspondence with DNA, RNA, tRNA, and amino-acids and vertebrate genetic code is realized in a natural manner. Dark nucleons realized DNA codons as entangled quark triplets. The effective chemical formula H1.5O for water in atto-second time scale supports this view (see this). How the notion of dark nucleon relates to negentropic entanglement of electrons? Could dark electron pairs and dark nucleons correspond to the same value of Planck constant? Could both dark protons and dark electrons play a key role in metabolism.

  2. The simplest guess is that DNA strands are accompanied by dark nuclei with one dark proton per DNA nucleotide. The resulting positive charged would stabilize the system by partially neutralizing the negative charge density due to the phosphorylation (2 negative charges per nucleotide). Dark proton sequences could be associated also with other important bio-polymers. If the spins of the dark protons are parallel the dipole magnetic fields give rise to flux tubes connecting the protons and one can assign to the large hbar protons a macroscopically quantum coherent phase.

  3. The natural guess would be that dark nucleus realization of the genetic code induces the biological realization as evolution assigns to dark nucleon sequences DNA, RNA, and aminoacid sequences with 1-1 correlation between dark nucleon state and basic unit of the sequence. The dark realization of genetic code suggest a totally new view about biological evolution as a process, which is analogous to R&D in high tech industry rather than being completely random (see this). The candidates for new genes could be tested at dark matter level and in the case that they work they would be transcribed to their chemical equivalents.

3. New ideas related to metabolism

Also new ideas related to metabolism have emerged at the same time when evidence for quantal aspects of photosynthesis has been emerging (see this, this, this, and this).

  1. Negentropic entanglement leads also to the idea about energy metabolism and negentropy transfer as different sides of the same coin. The model for DNA as topological in turn suggest that ADP → ATP and its reverse can be interpreted as a standardized reconnection process re-organizing connections between distant molecules connected by magnetic flux tubes by the relay defined by ATP molecule. Metabolic energy would - or at least could - go to the re-organization of the flux tube connections and therefore of the negentropic quantum entanglement. The question is how to fuse this vision with the hypothesis about metabolic currencies as differences of zero point kinetic energies for space-time sheets.

  2. The radiation from Sun defines the fundamental metabolic currency. Solar radiation cannot be said to negentropic since negentropic entanglement is a 2-particle property. Solar photons could possess a large value of hbar or - more plausibly - suffer at the magnetic body of the living system a phase transition increasing the value of hbar. Could the absorption of large hbar photons arriving from Sun or from magnetic body by electrons generate spin 1 valence electron pairs pairs or provide the metabolic energy needed to re-arrange the flux tube connections between distant molecules by ADP+Pi → ATP process?

4. DNA as a topological quantum computer vision

The vision about DNA as topological quantum computer (see this) has turned out to be very general allowing to imagine several concrete realizations. The essential element is the coding of DNA nucleotides and one can imagine several options.

  1. The original proposal for the realization of DNA as topological quantum computer is based on the representation of DNA nucleotides A, T, C, G as quarks u, d and their antiquarks and requires scaled up version of QCD (see this). This idea looks rather outlandish but could be justified by the strange findings of mathematician Barbara Shipman about honeybee dance (see this) and also by the p-adic length scale hierarchy and the hierarchy of Planck constants suggesting scaled variants of QCD like physics also in the length scale range relevant to the living cell.

  2. The question whether one could one use spin 1 triplet and spin 0 singlet of dark electron pair instead of quarks and their antiquarks to represent codons, is rather obvious. The problem is that S= 0 state for electron pair however gives rise to vanishing dipole field so that flux tube structure would not be possible. The generation of flux tube structure along which supra currents can flow is however an essential element of the proposed mechanism of super-conductivity.

  3. DNA as topological quantum computer hypothesis lead to the hypothesis that it is O= :s to which one must assign the flux tube pair responsible for the representation of the genetic code. Why O= would be in special role? And why should one have a pair of flux tubes? Could this relate to the coding of nucleotides by electron pairs? If there are two parallel flux tubes, one obtains tensor product 3× 3= 5+3+1 of electron triplets at the ends of the flux tubes. Could it be that A,T,C, and G are represented in terms of 3 and 1 and that the breaking of rotational invariance implies mixing of singlet and Sz=0 state of triplet so that nucleotides and their conjugates could correspond to the resulting two pairs related by reflection.

  4. ATP→ ADP+Pi would correspond to the reconnection of the flux tubes of the flux tube pair with hydrogen bonds associated with two water molecules. The flux tubes would split and end to water molecules containing valence electron pair so the negentropic entanglement might not be totally lost. The reverse process would create flux tube connection labelled by the spin state equivalent of A,T,C, or G.

5. Pessimistic generalization of the second law of thermodynamics

The possibility of negentropic entanglement raises the question about the fate of the second law of thermodynamics. The proposal for a generalization of the second law of thermodynamics (see this) based on the most pessimistic vision is that entropy indeed increases also when negentropic entanglement is generated in state function reduction. If the generation of negentropic entanglement is accompanied by a compensating entropic entanglement, how it is generated? Or is the maximally pessimistic generalization really necessary? Is it implied automatically in time scales longer than the characteristic time scale associated with the causal diamonds serving as the basic correlates for conscious selves. One must apply ensemble description in these time scales: does the non-determinism of quantum jump imply second law at the level of ensemble automatically. If this argument is correct, second law would cease to hold in time scales than that characterizing the relevant CD. One might be able to anwer these quesetion by trying to understand the situation in the case of metabolism.

During writing I realized that the old chapter must be split to two pieces. The chapter of "Biosystems as Conscious Holograms" contains the updated material.


At 10:53 PM, Blogger Ulla said...

Nice, also homeostasy related to entropy. Note allostasy has a higher level of entropy (more negentropic).

Eddington also looked at the ratio electron/proton and related it to the E-groups. Can you tell something about that? E-groups and helix-rotations?

Poincare is easier to relate to knots?

I am struck with Poincare now. What exactly is the difference to Einstein? Do you have a good reading for it?

Planck created his energy laws at the same time. Hbar is both length and energy. So hbar express a tension?

At 11:59 PM, Blogger Ulla said...

The radiation from Sun defines the fundamental metabolic currency. Solar radiation cannot be said to negentropic since negentropic entanglement is a 2-particle property. Solar photons could possess a large value of hbar or - more plausibly - suffer at the magnetic body of the living system a phase transition increasing the value of hbar. Could the absorption of large hbar photons arriving from Sun or from magnetic body by electrons generate spin 1 valence electron pairs pairs or provide the metabolic energy needed to re-arrange the flux tube connections between distant molecules by ADP+Pi → ATP process?

Must entanglement be between particles?

The photonic wave ('particle') is created by two parts, electric and magnetic fields, and creates magnetic and electric fields. No magneton is needed. Electrons are transferred from sun, as neutrons are? What happen with all those electrons at Earth? They create spin, vibrations, oscillations, SIZE (=length?). Hbar? Excitations comes from photons (quanta) is it said. Energy that comes from a boson (='negative' or 'shadow' particle, not antimatter) and sprouts forth as em-radiation (=tension, imbeddings), creating time, oscillations, vibrations, spin etc.

Antimatter also creates gammarays and gravity in the same way as ordinary matter.

The globe is shining? The space not.

Mostly em-radiation has no electron at all. What would be the particles then? Pions?

Photons are mostly/always entangled in pairs?

What is at the center of the ray? Only tension?

At 12:13 AM, Blogger Ulla said...

At 12:33 AM, Blogger Ulla said...

Photons and electrons are at two places at the same time =entangled?

At 10:16 AM, Blogger Ulla said...

Maybe I should delete my comments? I must learn so much. Photon is its own antiparticle too. Of course quanta is tension, as energy. Light that transport hbar? Wau! Enlightment?

I have an idea that entropy and negentropy oscillate, entropy creates negentropy that degenerate, again and again. Decoherence (surfaces for flux tubes) are created like waves on the ocean. So the organism is in fact oscillating between wave and particle state. This creates the window-effect of interference and homeostasy (ground level) - allostasy (higher coherent levels) of stability?

At 10:18 AM, Blogger Ulla said...

Look here, entanglement between fields or waves?

At 1:29 PM, Blogger Ulla said...
In a Minkowski spacetime, one may transform the Dirac wave function under the spin group, as one transforms coordinates under the Poincar\'e group. This is not an option in a curved spacetime. Therefore, in the equation proposed independently by Fock and Weyl, the four complex components of the Dirac wave function transform as scalars under a general coordinate transformation.

At 2:40 PM, Blogger hamed said...

Dear Matti,
Order of CP2 radius is 10^4 Planck lengths but ranges of the variable r in coordinates of cp2 is between 0…infinite. I can’t combine these views together? And on the other hand I remember somewhere in your posts that cp2 can have arbitrary size.
When I touch a keyboard by finger, join along boundaries bond take place at each scale at the same time. At scale of atoms and at scale of molecule and even at scale of my finger.(is it true?) For example at scale of my finger, if it is a new kind of force then what is the force? Something like long range forces?

What does vacuum means in TGD? And what does vacuum 3-surfaces means?

Yesterday, examinations of my university at this term finished and I got higher time to study about TGD (living with TGD all day long ;-)) I started from phenomenological aspects of TGD at the book “General View about Physics in Many-Sheeted Space-Time Part I and after that part2 “
With best Regards

At 7:31 PM, Anonymous said...

Dear Hamed,

this is a good question since it gives me a possibility to talk about the notion of coordinate distance and real distance defined by the Riemann/Kahler metric. The basic point is that coordinate distance is not a general coordinate invariant notion since one can introduce infinity of different coordinates and every choice would give different distance.

Let us consider CP_1 - two-sphere - as an example.

One must introduce coordinate patches which over lap. The minimum number is two. They cover North resp. South pole. If one tries to cover the entire 2-sphere by single patch one obtains a coordinate singularity which spherical coordinates indeed show: at poles all values of phi correspond to the same point.

With Kahler structure in mind one could interpret patches as complex planes and North/South pole for South/North patch would correspond to circle at infinity geometrically.

Complex coordinate distance would be infinite between poles but the metric distance defined by the induced metric would be just pi*R, R the radius. The metric distance is of course the correct distance.

Riemann geometry is the general coordinate invariant formulation for the notion of distance.

*One introduces line element ds^2=g_{ij}dx^idx^j and one can integrate distance s(A,B) as Int_A^B ds for any parametrized curve.

*One can also define angles in coordinate invariant manner, and the additional bonus is that one obtains the notion of curvature distinguishing sphere from flat plane. Curvature tensor, Ricci tensor, curvature scalar are the outcomes and one has all tools for formulating General Relativity!

*Kahler structure is additional refinement: metric tensor represents real unit and imaginary unit is represented by Kaehler form. i^2=-1 is represented by the tensor square J^2=-g.

Your question was about CP_2. Radial coordinate r is associated with one particular convenient choice of coordinates (U(2) subgroup of SU(3) is represented linearly and CP_2= SU(3)/U(2) holds true). One can also introduce 4 coordinates that are like angles in analogy with theta,phi for CP_1=S^2.

The actual distance is defined by CP_2 metric. For details related to the definition of metric see

By the way, CP_2 requires 3 coordinate patches diffeomorphic with R^4 or actually C^2 since one has complex structure and Kahler geometry. From the representation as complex projective space one can has coordinatization (z_1,z_2,z_3) with all points differing by complex scaling identified so that 4-D space results. One can choose coordinates for one of the patches to be (U=z_1/z_3,V= z_2/z_3,1). You can guess what the coordinates are for other two patches;-).

CP_2 radius could be defined in terms of a length of CP_2 geodesic L=2*pi*R. The length is same for all geodesics related by SU(3) isometries. One can imagine that one restricts consideration to geodesic sphere (two non-equivalent ones) and then takes the great circle to get geodesic circle.

At 8:17 PM, Anonymous said...

To Ulla:

The physical problem of general relativity is the lack of Poincare invariance. One can argue that it is obtained by approximation metric with flat metric locally but personally I am skeptic and believe that here lies the basic reason for the failure to quantized general relativity. For some reason, people refuse to take seriously the loss of Poincare and Lorentz symmetries.

In TGD framework imbedding space provides the Poincare invariance and it has turned out that this dramatically simplifies the interpretation and application of the theory.

Concerning you question. The treatment of spinor components as scalars is certainly wrong.
It is certainly true that in curved space-time the action of Lorentz group on spinors is not straight-forward since Lorentz symmetry as isometries is lost. One can however ask how general coordinate transformation affects spinors.

The introduction of spinor connection makes it possible to define the action of general coordinate transformation as a gauge transformation on spinor field. Spinor components would *not* be scalars but behave like spin 1/2 objects as one might indeed expect. One might perhaps say that Lorentz group would become gauge group.

The fact is however that it is not gauge symmetry but genuine symmetry and again TGD raises its head;-).

General Relativity has also other difficulties. For a generic space-time manifolds there exists no spinor structure! CP_2 is one example: in this case however there is very natural manner to generalize spinor structure and this leads to a correct prediction for standard model symmetries.

As a matter fact, Hawking was one of the colleagues who showed interest to CP_2 at the period when everyone talked about instantons and they discovered the generalization of spinor structure but never the fact that CP_2 codes for standard model symmetries!

Spinor structure makes itself visible also in a relative mundane conceptual problem of lattice QCD. The treatment of quark spinors in lattice QCD is very difficult and the reason is that the replacement of space-time with 4-D torus implies 16 different spinor structures. This causes the problems. In TGD one has induced spinor structure instead of the ordinary one, and the problem disappears.

At 10:22 PM, Blogger hamed said...

Dear Matti,
Thank you very much, I read the comments carefully; they are very useful for me.

At 12:39 AM, Blogger Ulla said...

Then there are only lightlike conditions left. Radiation? Note em-force is spacelike.

Once you said that the event horizon was non-Euclidean but the throut inside was Euclidean. Can you explain that better? Dark matter?

Also BH can be rotating or not.

I have seen the light :) Finally, after so many years.


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