## Wednesday, February 27, 2008

### DNA as topological quantum computer and ageing

The notion of anomalous em charge is one of the basic implications of the many-sheeted space-time concept. It can be assigned to wormhole contacts carrying fermion and antifermion quantum numbers at their throats. If the classical electromagnetic fields at the two space-time sheets are different, the wormhole contact couples to the difference of vector potentials and behaves like a particle with anomalous charge although the net charge is vanishing.

In the model of DNA as topological quantum computer the braid strands (whose braiding defines tqc program) emanate from DNA nucleotides and end up to the lipids of the nuclear and cellular membranes. They are colored in the sense that one can tell whether the strand arrives from A,T,C or G. This is achieved by representing the braid strand as a wormhole magnetic flux tube with CP conjugate wormhole throats at its ends. To A,T,C,G one assigns a wormhole contact with quark u,d or its antiquark at the "upper" throat and its CP conjugate at the "lower" throat.

There are also symmetries: A and T resp. G and C are mapped to quark and its antiquark so that DNA conjugation corresponds to CP conjugation. Chargaff's rules A≈ T and G≈ A for single DNA strand state that DNA as a whole is matter-antimatter symmetric. A and G are mapped to u,d or their antiquarks and correspond therefore to isospin doublet. This allows to interpret the almost exact A-G and T-C symmetries of the third nucleotide of codon in terms of strong isospin symmetry. Both symmetries can break down for short portions of DNA.

The anomalous em charge of DNA is due to the fact that DNA is negatively charged (2 units of charge per nucleotide due to phosphate) and generates classical em field at the "upper" sheet of wormhole magnetic flux tube. The nearly vanishing Qa for DNA is interpreted as a stability condition for DNA. For long DNA strands Chargaff's rules A≈ T and G≈ A indeed guarantee the vanishing of Qa since A and T resp. C and G correspond to quark and its antiquark. There are four options concerning nucleotide quark correspondence and therefore also the identification of Qa: for one of them one has Qa= [2(A-T)-(G-C)]/3. Integer valuedness allows color singletness for the many quark-antiquark state assignable to DNA strand via the mapping of A,T,C,G to quarks and antiquarks.

Telomeres are of special interests as far as anomalous em charge is considered. Chromosomes are not copied completely in cell replication, and one function of telomeres is to guarantee that the translated part of genome replicates completely for sufficiently many cell divisions. Telomeres consists of 3-20 kilobases long repetitions of TTAGGG, and there is a 100-300 kilobases long repeating sequence between telomere and the rest of the chromosome. Telomeres can form can also 4-stranded structures. Telemere end contains a hair-pin loop as a single stranded part, which prevents the action of DNA repair enzymes on the chromosome end.

Telomerase is a reverse transcriptase enzyme involved with the synthesis of telomeres using RNA strand as a template but since its expression is repressed in many types of human cells, telomere length shortens in each cell replication. In the case of germ cells, stem cells and white blood cells telomerase is expressed and telomere length preserved. Telomere shortening is known to relate to ageing related diseases. On the other hand, overactive telomere expression seems to correlate with cancer.

If telomeres possess braid strands, the compensation of Qa might provide an additional reason for their presence. If this the case and if telomeres are strict multiples of TTAGGG, the shortening of telomeres generates a non-vanishing Qa unless something happens for the active part of DNA too. Color singletness condition should however remain true: the disappearance of 3n multiples of TTAGGG in each replication is the simplest guess for what might happen. In any case, DNA strands would become unstable in cell replication. Qa could be reduced by a partial death of DNA in the sense that some portions of braiding disappear. Also this would induce ill functioning of tqc harware perhaps related to ageing related diseases. Perhaps evolution has purposefully developed this ageing mechanism since eternal life would stop evolution.

For a more detailed exposition and background see the chapter DNA as Topological Quantum Computer of "Genes and Memes".

## Tuesday, February 26, 2008

### Connection between laser induced healing, acupuncture, and association of DC currents with the healing of wounds

The findings of Robert Becker (the book "Electromagnetism and Life" by Becker and Marino can be found from web) meant a breakthrough in the development of bioelectromagnetics. One aspect of bioelectromagnetic phenomena was the discovery of Becker that DC currents and voltages play a pivotal role in various regeneration processes. Why this is the case is still poorly understood and Becker's book is a treasure trove for anyone ready to challenge existing dogmas. The general vision guiding Becker can be summarized by a citation from the introduction of the book.

Growth effects include the alteration of bone growth by electromagnetic energy, the restoration of partial limb regeneration in mammals by small direct currents, the inhibition of growth of implanted tumors by currents and fields, the effect upon cephalocaudal axis development in the regenerating flatworm in a polarity-dependent fashion by applied direct currents, and the production of morphological alterations in embryonic development by manipulation of the electrochemical species present in the environment. This partial list illustrates the great variety of known bioelectromagnetic phenomena.

The reported biological effects involve basic functions of living material that are under remarkably precise control by mechanisms which have, to date, escaped description in terms of solution biochemistry. This suggests that bioelectromagnetic phenomena are fundamental attributes of living things­ - ones that must have been present in the first living things. The traditional approach to biogenesis postulates that life began in an aqueous environment, with the development of complex molecules and their subsequent sequestration from the environment by membranous structures. The solid-state approach proposes an origin in complex crystalline structures that possess such properties as semiconductivity, photoconductivity, and piezoelectricity. All of the reported effects of electromagnetic forces seem to lend support to the latter hypothesis.

1. Observations relating to CNS

The following more quantitative findings, many of them due to Becker, are of special interest as one tries to understand the role of DC currents in TGD framework.

1. CNS and the rest of perineural tissue (tissue surrounding neurons including also glial cells) form a dipole like structure with neural system in positive potential and perineural tissue in negative potential. There is also an electric field along neuron in the direction of nerve pulse propagation (dendrites correspond to - and axon to +) (note that motor nerves and sensory nerves form a closed loop). Also microtubules within axon carry electric field and these fields are probably closely related by the many-sheeted variants of Gauss's and Faraday's laws implying that voltages along two different space-time sheets in contact at two points are same in a static situation.

2. A longitudinal potential along front to back in brain with frontal lobes in negative potential with respect to occipital lobes and with magnitude of few mV was discovered. The strength of the electric field correlates with the level of consciousness. As the potential becomes weaker and changes sign, consciousness is lost. Libet and Gerard observed traveling waves of potentials across the cortical layers (with speeds of about 6 m/s: TGD inspired model of nerve pulse predicts this kind of waves). Propagating potentials were discovered also in glial cells. The interpretation was in terms of electrical currents.

3. It was found that brain injury generated positive polarization so that the neurons ceased to function in an area much larger than the area of injury. Negative shifts of neuronal potentials were associated with incoming sensory stimuli and motor activity whereas sleep was associated with a positive shift. Very small voltages and currents could modulate the firing of neurons without affecting the resting potential. The "generating" potentials in sensory receptors inducing nerve pulse were found to be graded and non-propagating and the sign of the generating potential correlated with sensory input (say increase/reduction of pressure. Standard wisdom about cell membrane has difficulties in explaining these findings.

4. The natural hypothesis was that these electric fields are accompanied by DC currents. There are several experimental demonstrations for this. For instance, the deflection of assumed DC currents by external magnetic field (Hall effect) was shown to lead to a loss of consciousness.

2. Observations relating to regeneration

The second class of experiments used artificial electrical currents to enhance regeneration of body parts. These currents are nowadays used in clinical practice to induce healing or retard tumor growth. Note that tissue regeneration is a genuine regeneration of an entire part of organism rather than mere simple cell replication. Salamander limb generation is one of the most studied examples. Spontaneous regeneration becomes rare at higher evolutionary levels and for humans it occurs spontaneously only in the fractures of long bones.

2. Tissue regeneration occurs only if some minimum amount of neural tissue is present suggesting that CNS plays a role in the process although the usual neural activity is absent. The repeated needling of the stump had positive effect on regeneration and the DC current was found to be proportional to innervation. Hence needling seems to stimulate innervation or at least inducing formation of DC currents. Something like this might occur also in the case of acupuncture.

3. Regeneration involves de-differentiation of cells to form a blastema from which the regenerated tissue is formed. Quite early it was learned that carcinogens induce de-differentiation of cells because of their steric properties and by making electron transfer possible and that denervation induces tumor formation. From these findings Becker concluded that the formation of blastema could be a relatively simple process analogous to tumor growth whereas the regeneration proper is a complex self-organization process during which the control by signals from CNS are necessary and possibly realized in terms of potential waves.

4. Regeneration is possible in salamander but not in frog. This motivated Becker and collaborators to compare these situations. In an amputated leg of both salamander and frog the original negative potential of or order -1 mV went first positive value of order +10 mV. In frog it returned smoothly to its original value without regeneration. In salamander it returned during three days to the original base line and then went to a much higher negative value around -20 mV (resting potential is around -70 mV) followed by a return to the original value as regeneration had occurred. Thus the large negative potential is necessary for the regeneration and responsible for the formation of blastema. Furthermore, artificial electron current induced regeneration also in the case of frog and in even in the denervated situation. Thus the flow of electrons to the stump is necessary for the formation of blastema and the difference between salamander and frog is that frog is not able to provide the needed electronic current although positive potential is present.

5. It was also learned that a so called neural epidermic junction (NEJ) formed in the healing process of salamander stump was responsible for the regeneration in the presence of nervation. The conclusion was that the DC voltage and electronic current relevant for regeneration can be assigned the interface between CNS and tissue rather than with the entire nerve and regeneration seems to be a local process, perhaps a feed of metabolic energy driving self-organization. Furthermore, NEJ seems to make possible the flow of electrons from CNS to the stump.

6. The red blood cells of animals other than mammals are complete and possess thus nuclei. Becker and collaborators observed that also red blood cells dedifferentiated to form blastema. Being normally in a quiescent state, they are ideal for studying de-differentiation. It was found that electric current acted as a trigger at the level of cell membrane inducing de-differentiation reflected as an increased amount of mRNA serving as signal for gene expression. Also pulsed magnetic field was found to trigger the de-differentiation, perhaps via induced electric field. By the way, the role of the cell membrane fits nicely with the view about DNA-cell membrane system as topological quantum computer with magnetic flux tubes connecting DNA and cell membrane serving as braids.

7. The experiments of Becker and collaborators support the identification of the charge carriers of DC currents responsible for the formation of large negative potential of stump as electrons. The test was based on the different temperature dependence of electronic and protonic conductivities. Electronic conductivity increases with temperature and protonic conductivity decreases and an increase was observed. In TGD based model also super-conducting charge carriers are possible and this finding does not tell anything about them.

3. A TGD based model for the situation

On basis of these observations one can try to develop a unified view about the effects of laser light, acupuncture, and DC currents. It is perhaps appropriate to start with the following - somewhat leading - questions inspired by a strong background prejudice that the healing process - with control signals from CNS included - utilizes the loading of many-sheeted metabolic batteries by supra currents as a basic mechanism. In the case of control signals the energy would go to the "moving of the control knob".

1. Becker assigns to the system involved with DC currents an effective semiconductor property. Could the effective semiconductor property be due the fact that the transfer of charge carriers to a smaller space-time sheet by first accelerating them in electric field is analogous to the transfer of electrons between conduction bands in semiconductor junction? If so, semiconductor property would be a direct signature of the realization of the metabolic energy quanta as zero point kinetic energies.

2. Supra currents flowing along magnetic flux tubes would make possible dissipation free loading of metabolic energy batteries. This even when oscillating Josephson currents are in question since the transformation to ohmic currents in semiconductor junction makes possible energy transfer only during second half of oscillation period. Could this be a completely general mechanism applying in various states of regeneration process. This might be the case. In quantal situation the metabolic energy quanta have very precise values as indeed required. For ohmic currents at room temperature the thermal energies are considerably higher than those corresponding to the voltage involved so that they seem to be excluded. The temperature at magnetic flux tubes should be however lower than the physiological temperature by a factor of order 10-2 at least for the voltage of -1 mV. This would suggest high Tc super-conductivity is only effective at the magnetic flux tubes involved. The finding that nerve pulse involves a slight cooling of the axonal membrane proposed in the TGD based model of nerve pulse to be caused by a convective cooling due the return flow of ionic Josephson currents would conform with this picture.

3. What meridians are and what kind of currents flow along them? Could these currents be supra currents making possible dissipation-free energy transfer in the healthy situation? Does the negative potential of order -1 mV make possible flow of protonic supra currents and loading of metabolic batteries by kicking protons to smaller space-time sheets? Could electronic supra currents in opposite direct induce similar loading of metabolic batteries? Could these tow miniature metabolisms realize control signals (protons) and feedback (electrons)?

The model answering these questions relies on following picture. Consider first meridians.

1. The direct feed of metabolic energy as universal metabolic currencies realized as a transfer of charge carriers to smaller space-time sheets is assumed to underly all the phenomena involving healing aspect. Meridian system would make possible a lossless metabolic energy feed - transfer of "Chi" - besides the transfer of chemically stored energy via blood flow. The metabolic energy currencies involved are very small as compared to .5 eV and might be responsible only for "turning control knobs". The correlation of the level of consciousness with the overall strength of DC electric fields would reduce to the level of remote metabolic energy transfer.

2. The model should explain why meridians have not been observed. Dark currents along magnetic flux tubes are ideal for the energy transfer. If the length of the superconducting "wire" is long in the scale defined by the appropriate quantum scale proportional to hbar, classical picture makes sense and charge carriers can be said to accelerate and gain energy ZeV. For large values of hbar an oscillating Josephson current would be in question. The semiconductor like structure at the end of meridian -possibly realized in terms of pair of space-time sheets with different sizes- makes possible a net transfer of metabolic energy even in this case as pulses at each half period of oscillation. The transfer of energy with minimal dissipation would thus explain why semiconductor like property is needed and why acupuncture points have high value of conductivity. The identification of meridians as invisible magnetic flux tubes carrying dark matter would explain the failure to observe them: one further direct demonstration for the presence of dark matter in biological systems.

3. In the case of regeneration process NEJs would be accompanied by a scaled down version of meridian with magnetic flux tubes mediating the electronic Josephson current during blastema generation and protonic supra current during the regeneration proper. Space-time sheets of proton resp. electron correspond to kp and ke= kp+11. In a static situation many-sheeted Gauss law in static situation would guarantee that voltages over NJE are same.

4. One can of course worry about the smallness of electrostatic energies E=ZeV as compared to the thermal energy. Zero point kinetic energy could correspond also to the magnetic energy of the charged particle. For sufficiently large values of Planck constant magnetic energy scale is higher than the thermal energy and the function of voltage could be only to drive the charged particles along the flux tubes to the target, and perhaps act as a control knob with electrostatic energy compensating for the small lacking energy.

Suppose for definiteness magnetic field strength of B=.2 Gauss explaining the effects of ELF em fields on brain and appearing in the model of EEG. Assume that charged particle is in minimum energy state with cyclotron quantum number n=1 and spin direction giving negative interaction energy between spin and magnetic field so that the energy is (g-2)×hbar eB/2m. Assume that the favored values of hbar correspond to number theoretically simple ones expressible as a product of distinct Fermat primes and power of 2. In the case of proton with g ≈ 2.7927 the standard metabolic energy quantum E0≈ .5 eV would require roughly hbar/hbar0=17×234. For electron g-2≈ α/π≈ .002328 gives hbar/hbar0=5×17×230.

Consider next NEJs and semiconductor like behavior and charging of metabolic batteries.

1. Since NEJ seems resembles cell membrane in some respects, the wisdom gained from the model of cell membrane and DNA as tqc can be used. The model for nerve pulse and the model for DNA as topological quantum computer suggest that dark ionic currents flowing along magnetic flux tubes characterized by a large value of Planck constant are involved with both meridians and NJEs and might even dominate. Magnetic flux tubes act as Josephson junctions generating oscillatory supra currents of ions and electrons. For large values of hbar also meridians are short in the relevant dark length scale and act as Josephson junctions carrying oscillatory Josephson currents.

2. The findings of Becker suggest that acu points correspond to sensory receptors which are normally in a negative potential. The model for the effects of laser light favors (but only slightly) the assumption that in a healthy situation it is protons arriving along magnetic flux tubes which are kicked to the smaller space-time sheets and that negative charge density at acu point attracts protons to the acu point. Electrons could of course flow in reverse direction along their own magnetic flux tubes and be kicked to the smaller space-time sheets at the positive end of the circuit. In the case of brain, protonic end would correspond to the frontal lobes and electronic end to the occipital lobes. This kind of structure could appear as fractally scaled variants. For instance, glial cells and neurons could form this kind of pair with neurons in negative potential and glial cells in positive potential as suggested by the fact that neuronal damage generates positive local potential.

3. Classically the charge carriers would gain energy E=ZeV as they travel along the magnetic flux tube to NJE. If this energy is higher than the metabolic energy quantum involved, it allows the transfer of charge carrier to a smaller space-time sheet so that metabolic resources are regenerated. Several metabolic quanta could be involved and the value of V(t) would determine, which quantum is activated. The reduction of the V below critical value would lead to a starvation of the cell or at least to the failure of control signals to "turn the control knob". This should relate to various symptoms like pain at acupuncture points. In a situation requiring acupuncture the voltage along flux tubes would be so small that the transfer of protons to the smaller space-time sheets becomes impossible. As a consequence, the positive charge carriers would accumulate to the acu point and cause a further reduction of the voltage. Acupuncture needle would create a "wound" stimulating large positive potential and the situation would be very much like in regeneration process and de-differentiation induced by acupuncture could be understood.
Many questions remain to be answered.

1. What causes the dedifferentiation of the cells? The mere charging of metabolic energy batteries? If so then the amount of metabolic energy- "chi"- possessed by cell would serve as a measure for the biological age of cell and meridian system feeding "chi" identified as dark metabolic energy would serve as a rejuvenating agent also with respect to gene expression. Or does the electric field define an external energy feed to a self-organizing system and create an electromagnetic environment similar to that prevailing during morphogenesis inducing a transition of cells to a dedifferentiated state? Or could DNA as tqc allow to understand the modification of gene expression as being due to the necessity to use tqc programs appropriate for regeneration? Or should cells and wounded body part be seen as intentional agents doing their best to survive rather than as passive parts of biochemical system?

2. Acupuncture and DC current generation are known to induce generation of endorphins. Do endorphins contribute to welfare by reducing the pain or do they give a conscious expression for the fact that situation has improved as a result of recharging of the metabolic energy batteries?

For background see that chapter The New Physics Behind Qualia.

## Monday, February 25, 2008

### Direct support for universal metabolic energy quanta

There is direct support for the notion of universal energy quanta. The first support comes from the effect of low-power laser light on living matter. More than 30 years ago a method known with various names such as low-power laser therapy, bio-stimulation, or photo bio-modulation emerged [1] and has now a wide range of applications. The treatment can apply both non-coherent (light emitting diodes) or coherent (laser light). In the case of of non-coherent light the method applies thin structures with thickness smaller than coherence length of light so that there is no difference between non-coherent and laser light. Laser light applies to situation when both the thickness of the surface layer and structure itself in range 1 mm- 1 cm and shorter than coherence length. Often the irradiation is applied to wounds and sites of injuries, acupuncture points, and muscle trigger points. The method involves several parameters such as wavelength in the range 400-900 nm (IR and near IR light), output power (10-100 mW), continuous wave and pulsed operation modes, and pulse parameters.

1. What is known?

The article of Tiina Karu [1] gives a brief summary about what is known.

1. The action spectrum characterizes the maxima of the biological response as a function of wavelength. Action spectrum is essentially universal. For near IR and IR light the maxima of spectra are at 620, 680, 760, 820-830 nm. The spectrum continues also to visible light [1] but I do not have access these data.

2. The action can induce both physiological and morphological changes in non-pigmental cells via absorption in mitochondria. HeNe laser (λ=632.8 nm) can alter the firing pattern of nerves and can mimic the effect of peripheral stimulation of a behavioral reflex.

2. Biochemical approach

In [1] the biochemical approach to the situation is discussed.

1. In standard biochemistry based approach the natural hypothesis is that the maxima correspond to some molecular absorption lines and the task is to identify the photo acceptor. The primary acceptor in IR-to red spectral region is believed to be the terminal enzyme of the respiratory chain cytochrome c oxidase located in mitochondrion but this is just an assumption.In the violet-to-blue spectral region flavoproteins (e.g. NADHdehydrogenace in the beginning of respiratory chain) are among the photo acceptors as terminal oxidases. It is known that also non-mitochondrial enhancement of cellular metabolism exist, which does not fit well with the vision about mitochondria as power plants of cell. It is believed that electronic excitation occurs and somehow leads to the biological effect.

2. The natural assumption in biochemistry framework is that the stimulation increases the effectiveness of cellular metabolism by making the utilization of oxygen more effective. The effect of the light would occur at the control level and induce secondary reactions (cellular signaling cascades or photo signal transduction and amplification) affecting eventually the gene expression.

3. Three different regulation pathways have been suggested [1]. Since small changes in ATP level can alter cellular metabolism significantly, the obvious idea is that photoacceptor controls the level of intracellular ATP. In starving cells this looks especially attractive hypothesis. In many cases however the role of redox homeostasis is however believed to be more important than that of ATP. The second and third pathways would indeed affect cellular redox potential shifting it to more oxidized direction. The mechanism of regulation is however not understood. Hence one can say that there is no experimental proof or disproof for the standard approach.

3. TGD inspired approach

In TGD framework the first guess is that irradiation pumps directly metabolic energy to the system by kicking particles to smaller space-time sheets. This kind of direct energy feed would be natural when the cell is starving or injured so that its control mechanisms responsible for the utilization of oxygen are not working properly. For Bose-Einstein condensate of photons this effect would be especially strong being proportional to N2 rather than N, where N is photon number. The effect would also appear coherently in a region whose size is dictated by coherence length when the target is thick enough.

There is a simple killer test for the proposal. The predicted energies are universal in the approximation that the interactions of protons (or electrons) kicked to the smaller space-time sheets with other particles can be neglected. The precise scale of metabolic energy quanta can be fixed by using the nominal value of metabolic energy quantum .5 eV in case of proton. This predicts the following spectrum of universal energy quanta for proton

Δ Ek,n(p)= E0(k,p)× (1-2-n) ,

E0(k,p)= E0(137,p)2137-k≈ 2137-k× .5 eV .

and following for electron

Δ Ek,n(e)= E0(k,e)× (1-2-n) , E0(k,e) =\frac{mp}{211me} E0(137,p)2148-k≈ 2148-k× .4 eV .

k characterizes the p-adic length scale and the transition corresponds to the kicking of charged particle from space-time sheet having k1=k+n to k=n.

The shortest wavelength 630 nm is rather close to the wavelength of HeNe laser and corresponds to red light with E0= 2.00 eV. Thus one would have k=135 in the case of proton which corresponds to roughly one of atomic radius for ordinary value of \hbar. For electron one would have k=150 which corresponds to L(151)/21/2: L(151)=10 nm corresponds to cell membrane thickness. This table gives the energies of photons for action spectrum and predicted values in the case of proton, which provides a better fit to the data.

The largest error is 7 per cent and occurs for $n=3$ transition. Other errors are below 3 per cent. Note that also in experiments of Gariaev [2,3] laser light consisting of 2 eV photons was used: in this case the induced radio wave photons - possibly dark photons with energy 2 eV - were reported to have a positive effect on the growth of potatoes. Note that also in experiments of Gariaev [2,3] laser light consisting of 2 eV photons was used: in this case the induced radio wave photons - possibly dark photons with energy 2 eV - were reported to have a positive effect on the growth of potatoes.

4. Possible explanation for the effect of IR light on brain

The exposure of brain to IR light at wavelength of 1072 nm is known to improve learning performance and give kick start to cognitive function [4]. The simplest explanation is that this light reloads the metabolic energy batteries of neurons by kicking electrons or protons or their Cooper pairs to larger space-time sheets. The wavelength in question is roughly one half of the wavelength associated with metabolic energy quantum with average energy .5 eV (2480 μm) assignable to the dropping of proton to a very large space-time sheet from k=137 space-time sheet or of electron from k=137+11= 148 space-time sheet. This if the electron and proton are approximated to be free particles. Energy band is in question since both the particles can have additional interaction energy.

For the kicking of electron from very large space-time sheet to k=147 space-time sheet the wave length would be below 1240 nm which is more than 10 per cent longer than 1072 nm. This would suggest that the final state electron is in excited state. The surplus energy is consistent with the width about 100 nm for the UIBs. This identification - if correct - would support the view that metabolic energy quanta are universal and have preceded the evolution of the biochemical machinery associated with metabolism and that the loading of metabolic energy batteries at the fundamental level correspond to the kicking of charged particles to smaller space-time sheets.

For background see that chapter The New Physics Behind Qualia of "Quantum Harware for Living Matter".

References [1] T. I. Karu (1998), {\em The Science of Low-Power Laser Therapy}, Gordon and Breach, Sci. Publ., London.

[2] P. P. Gariaev et al (2002), The spectroscopy of bio-photons in non-local genetic regulation , Journal of Non-Locality and Remote Mental Interactions, Vol 1, Nr 3.

[3] P. Gariaev et al (2000), The DNA-wave-biocomputer, CASYS'2000, Fourth International Conference on Computing Anticipatory Systems, Liege, 2000. Abstract Book, Ed. M. Dubois.

## Saturday, February 23, 2008

### Giant ropes of dark matter

Giant ropes of dark matter found in new sky survey is the title of New Scientist article describing the finding that dark matter seems to concentrate along string like filaments at the sky. The lengths of filaments are up to 270 million light years at least. Note that the size scale of large voids containing galaxies at their boundaries and known for long time to concentrate along stringy structures is same.

The finding is interpreted as a victory for models assuming that dark matter was originally evenly distributed but then gradually concentrated to form blobs and filaments. I do not know how much the formation of filaments is an input assumption rather than genuine prediction of these models.

In TGD framework the course of events would be just the opposite. The cosmic strings - not those of GUTs, but identified as string like objects of form X2×Y2, where X2 is minimal surface in M4 and Y2 in the most general case is holomorphic surface of CP2 - dominated the primordial stage of TGD inspired cosmology after which ordinary space-time with 4-D M4 projection emerged. These string like objects carried extremely strong magnetic fields and also dark matter, which can be also ordinary matter but in large hbar phase.

The M4 projections of cosmic strings became 4-dimensional and begun to thicken with the cosmic expansion. The magnetic field within them weakened gradually. The model explains also the magnetic fields which fill the cosmos but whose origin is one of the mysteries of the standard cosmology. Note that in GUTs long cosmic strings would remain as such and this leads to problems since they have not been observed.

In TGD Universe this kind of magnetic flux tubes carrying dark matter appear even in living matter and are responsible for the quantum control of visible part of living system. The braids formed by magnetic flux tubes make DNA-cell membrane system topological quantum computer. The very strange findings about the behavior of cell membrane provide direct support for the prediction that a large fraction of biologically important ions are dark and possess large hbar. Note that in TGD framework also dark energy is dark matter and no cosmological constant is needed. The explanation for the periods of the accelerated cosmic expansion is in terms of phase transitions increasing the value of Planck constant.

Giant ropes of dark matter found in new sky survey is the title of New Scientist article describing the finding that dark matter seems to concentrate along string like filaments at the sky. The lengths of filaments are up to 270 million light years at least. Note that the size scale of large voids containing galaxies at their boundaries and known for long time to concentrate along stringy structures is same.

The finding is interpreted as a victory for models assuming that dark matter was originally evenly distributed but then gradually concentrated to form blobs and filaments. I do not know how much the formation of filaments is an input assumption rather than genuine prediction of these models.

In TGD framework the course of events would be just the opposite. The cosmic strings - not those of GUTs, but identified as string like objects of form X2×Y2, where X2 is minimal surface in M4 and Y2 in the most general case is holomorphic surface of CP2 - dominated the primordial stage of TGD inspired cosmology after which ordinary space-time with 4-D M4 projection emerged. These string like objects carried extremely strong magnetic fields and also dark matter, which can be also ordinary matter but in large hbar phase.

The M4 projections of cosmic strings became 4-dimensional and begun to thicken with the cosmic expansion. The magnetic field within them weakened gradually. The model explains also the magnetic fields which fill the cosmos but whose origin is one of the mysteries of the standard cosmology. Note that in GUTs long cosmic strings would remain as such and this leads to problems since they have not been observed.

In TGD Universe this kind of magnetic flux tubes carrying dark matter appear even in living matter and are responsible for the quantum control of visible part of living system. The braids formed by magnetic flux tubes make DNA-cell membrane system topological quantum computer. The very strange findings about the behavior of cell membrane provide direct support for the prediction that a large fraction of biologically important ions are dark and possess large hbar. Note that in TGD framework also dark energy is dark matter and no cosmological constant is needed. The explanation for the periods of the accelerated cosmic expansion is in terms of phase transitions increasing the value of Planck constant.

I add an excerpt from a New Scientist article about cosmic strings.

Discovering them would be really big news. String theory has often been criticised as a theorists’ plaything, a pretty piece of mathematics unable to make any testable predictions. That perception would change pretty fast if we were to find a host of giant superstrings crisscrossing the skies.

Just this has been now done. But not for superstrings. So they decide to forget it once again. I hope that reader could sense some of my despair. More than two decades of attempts to open the eyes of colleagues to see the reality which is staring directly to their empty eyes and doing all it can to gain their attention. All in vain. You know: "We-know".

A further comment added: In Cosmic Variance there are comments about the recent very stringent experimental limits on the properties of WIMPs (weakly interacting massive particles). Perhaps the time is becoming ripe for challening various routine assumptions about dark matter.

1. The first standard assumption is that dark matter has no classical long range interactions with the visible matter except gravitation. Experimental tests are however in astrophysical scales and do not tell anything about possible classical electromagnetic interactions.

2. The second implicit assumption is that if the interactions of dark and visible matter via classical fields are possible then both dark and visible particles can appear in the same vertex of Feynman diagram. In TGD framework the generalization of the motion of imbedding space however implies that particles in different sectors of imbedding space cannot appear in the same vertex of Feynman diagram. Interactions via all classical fields are however possible and also the exchange of quanta leaking between different sectors of the 8-D imbedding space (visible-dark phase transition for exchanged particles). This picture of course requires a considerable generalization of quantum theory by introducing the hierarchy of Planck constants and bringing in anyons at the level of fundamental physics.

## Friday, February 22, 2008

### On direct testing of quantum consciousness

Quantum entanglement and its reduction in "cognitive" quantum measurement could provide a direct test of quantum consciousness. Andrei Khrennikov [1] has proposed a mathematical formulation of "quantum like" behavior based on his proposal that so called context dependent probabilities could provide alternative description for quantum mechanical interference phenomenon. In quantum theory context would correspond to the choice of quantization axis. Khrennikov has also proposed a modification of Bell inequalities so that they apply on conditional probabilities: this would make it possible to avoid the task of preparing entangled state of brains. The hope is that one could forget completely the microscopic structure of quantum brain and test quantum like behavior by making simple experiments involving just questions to the subject persons and finding whether or not classical rules for conditional probabilities hold true or not.

1. First experiment

Bistable percepts induced by ambiguous figures are especially attractive from the point of view of experimentation. The question would be "Which of the two possible percepts?" and the outcome would be answer to this question. The first experiment reported in [2] was following.

1. Consider a group S of subject persons. Divide it into two groups U and V containing equally many subject persons. Represent for members of U the question A (bistable percept A). From this one can deduce the probalities p(A=+) and p(A=-). Represent for members of V the question B and and immediately after than the question A (bistable percept A) for those who answered B=-. This experiment gives the conditional probabilities p(A=x/B=y).

2. The quantity

cos(θx) = [p(A=x)- p(B=+)p(A=x/B=+) -p(B=-)p(A=x/B=-)]/[2(p(B=+)p(B=-)p(A=x/B=+)p(A=x/B=-)1/2], x=+/-.

measures the failure of the basic rule

p(A=x)=p(B=+)p(A=x/B=+) +p(B=-)p(A=x/B=-)

for classical conditional probability. Note that in quantum theory similar rules applies to transition amplitudes (conditional probability amplitudes) corresponding to the addition of a complete set of states in the inner product between two states (for instance, repeated application of this gives rise to path integral formulation).

3. One can describe the situation in terms of "quantum like state"

Ψ(A=x)= [p(B=+)p(A=x/B=+)]1/2 +e+/- [p(B=-)p(A=x/B=-)]1/2

satisfying p(A=+x) =|Ψ(A=x)|2. If cos(θx) is non-vanishing one can say that that the situation is quantum like. Conte and collaborators conclude that this is indeed the case [2].

2. Second experiment

Second experimental test is more complex and involves generalization of Bell's inequality so that it involves conditional probabilities [1] Let A,B,C=+/- be arbitrary dichotomous random variables satisfying Kolmogorov axioms characterizing classical probability. Then the following analog of Bell inequality can be shown to hold true:

P(A=+,B=+) + P(C=+,B=-)≥ P(A=+,C=+).

In terms of conditional probabilities one has

P(A=+/B=+)/P(B=+) + P(C=+/B=-)/P(C=+) ≥ P(A=+/C=+)/P(C=+).

If the random variables are symmetrically distributed so that one has P(X=+/-)=1/2, for X=A,B,C one obtains

P(A=+/B=+)+P(C=+/B=-)≥ P(A=+/C=+) .

Note that this form of equality is by no means necessary. The symmetric distributions for the random variables would however correspond to maximal entanglement in spin system given best hopes for the violation of the Bell inequality.

1. The test is following. Consider a group S of subject persons divided into subgroups U and V as above. Pose to the members of U question B and immediately after that question A for those who answered B=+ and question C for those who answered B=-1. For group V represent first the question C and for those who answer C=+ represent the question A. The failure of inequality could regarded as a direct proof for quantum like behavior. That failure does not occur does not of course mean that system is classical but only that the quantal effects are not large enough.

2. The analogy with Bell's inequality suggest that the questions are analogous to posing the spins of spin pair in spin singlet state to an external magnetic fields determining the quantization axis. The inequality tend to fail when the directions of the magnetic fields for the two spins differ enough. Thus the failure is expected if the questions, in other words ambiguous figures producing bistable percepts differ enough.

3. Criticism and possible improvement of the experiment

In the case of spin pairs the tests of quantum behavior are carried out for the members of spin pair by putting them to magnetic fields having different directions. Now the pair of experiments is made for a single subject person. Hence there is no need to prepare quantum entangled pair of conscious entities.

The use of ensemble is the problematic aspect of experiments. Human beings are extremely complex systems and one can argue that it is impossible to prepare an ensemble of identical systems in cognitive sense. A possible manner to avoid the problem would be the replacement of ensembles with a time series of experiments performed for a single subject person. In both experiments one could perform the two kinds of experiments many times to single subject person and deduce various probabilities and cos(θ) from the outcome of the experiments.

4. Interpretation in terms of zero energy ontology and DNA as tqc

The discussions with Elio Conte led to the realization that in zero energy ontology the experiments differ from the corresponding experiments for two-spin system only in that space-like entanglement is replaced with time like entanglement. The experiment would be essentially a measurement of probabilities defined by the matrix elements of M-matrix defining the generalization of S-matrix. Hence Bell's inequalities and their generalizations should apply in genuine quantum sense. By performing the experiments for a single subject person as time series one might be therefore able study whether quantum consciousness in the sense of TGD makes sense.

Quantum consciousness approach however requires that bistable percepts have genuine microscopic quantum states as their physical correlates. This is not assumed in the approach of Khrennikov.

1. If the vision about DNA as topological quantum computer makes sense, the question to the answer "Which of the two possible percepts?" can be regarded as a qubit which is some function of a large number of qubits and same function irrespective of the ambiguous figure used. This could hold quite generally, at least for a given sensory modality. The qubits appearing as arguments of this function are determined by the sensory input defined by the ambiguous figure. The ambiguous figure would take the role of magnetic field determining the directions of quantization axes for a large collection of qubits appearing as arguments of the Boolean function (one cannot exclude the possibility that neuronal synchrony forces all these axes to have same direction). Qubit could correspond to spin or some spin like variable. The quantization axes could correspond in this case to the direction of external magnetic field acting on 1-gate of tqc.

2. Qubit could be replaced with an n-state system: this would require a generalization of the Bell inequalities. The model of DNA as tqc suggests that qubit might be replaced with qutrit defined by a quark triplet (third quark with vanishing color isospin would correspond to ill-defined truth value. The inability of subject persons to identify the percept always indeed encourages to consider this option. Color group SU(3) (SO(3) subset SU(3)) defines the set of possible quantization axes as points of the flag manifold F= SU(3)/U(1)× U(1) (SO(3)/SO(2)= S2). Quantization axes would be determined by the direction of color magnetic field in color Lie algebra and sensory input would define a sequence of 1-gates at the lipids ends of the braid strands, and realized as color rotations of the flux tube defining braid strand. This hypothesis would conform with the proposal of Barbara Shipman that honeybee dance that quarks are in some mysterious manner involved with cognition [3].

For background see that chapter DNA as Topological Quantum Computer of "Genes and Memes".

References

[1] A. Khrennikov (2004), Bell's inequality for conditional probabilities as a test for quantum like behaviour of mind, arXiv:quant-ph/0402169.

[2] E. Conte, O. Todarello, A. Federici, J. P. Zbilut (2008), Minds States Follow Quantum Mechanics During Perception and Cognition of Ambigious Figures: A Final Experimental Confirmation, arXiv:0802.1835v1 [physics.gen-ph].

B. Shipman (1998), A symmetry of order two in the full Kostant-Toda lattice.

## Thursday, February 21, 2008

### Quantum model of nerve pulse VI: Deducing the presence and basic properties of dark matter from the strange behavior or cell membrane

The strange findings about the behavior of cell membrane [1,2,3,4,5,6] had strong impact on the evolution of TGD inspired model of biosystems. One would expect that when cell is posed to metabolic deprivation, it soon ceases to function since ionic pumps require a lot of metabolic energy. This did not happen. Second absolutely amazing finding was that ionic currents through cell membrane are obviously quantal and even more: remain essentially same when cell membrane is replaced with an artificial membrane.

TGD based model for nerve pulse in its recent form explains all these findings. One can however ask what is the role of ionic pumps and channels if oscillatory Josephson currents make pumps un-necessary. The vision about dark matter and the model of nerve pulse formulated in terms of Josephson currents brings an additional perspective to the role of pumps and channels and allows to achieve harmony with the standard views about their role.

1. In long length scales visible matter forms roughly 5 per cent of the total amount of matter. In TGD Universe the dark matter would correspond to matter with large Planck constant including dark variants of ordinary elementary particles. In living matter situation could be the same and visible matter could form only a small part of the living matter. Dark matter would be however visible in the sense that it would interact with visible matter via classical electromagnetic fields. Hence one can consider the possibility that most of the biologically important ions and perhaps even molecules reside at the magnetic flux quanta in large hbar phase.

2. The function of pumps and channels could be same as in standard model since also in TGD Universe homeostasis and its control at the level of visible matter requires them. The metabolic energy needed for this purpose would be however dramatically smaller and a reliable estimate for this would allow an estimate of the portion of dark matter in living systems. Pumps and channels could also serve the role of sensory receptors by allowing to take samples about chemical environment.

To sum up, the strange discoveries about the behavior of cell membrane provide direct experimental evidence for the presence of dark matter in living systems, for the prediction that it interacts with ordinary matter via classical electromagnetic fields, and for the assumption that it does not dissipate appreciably and could therefore have large value of hbar and form macroscopic quantum phases.

For background see the chapter Quantum Model of Nerve Pulse of "TGD and EEG".

References

[1] G. Pollack (2001), Cells, Gels and the Engines of Life, Ebner and Sons.

[2] G. N. Ling (1962) A physical theory of the living state: the association-induction hypothesis; with considerations of the mechanics involved in ionic specificity. New York: Blaisdell Pub. Co.

Ibid(1978):Maintenance of low sodium and high potassium levels in resting muscle cells. Journal of Physiology (Cambridge), July: 105-23.

Ibid(1992): A revolution in the physiology of the living cell. Malabar, FL: Krieger Pub. Co.

G.N. Ling et al(1978): Experimental confirmation, from model studies, of a key prediction of the polarized multilayer theory of cell water. Physiological Chemistry and Physics, 10:1, 1978: 87-8.

[3] B. Sakmann and B. Neher (1983): Single-channel recording. Plenum Press, New York and London.

[4] W. K. Purves and G. H. Orians (1987): Life: The Science of Biology. Sunderland, Massachusetts: Sinauer.

[5] F. Sachs, F. Qin (1993), Gated, ion-selective channels observed with patch pipettes in the absence of membranes: novel properties of a gigaseal. Biophysical Journal, September: 1101-7.

[6] A. A. Lev et al (1993), Rapid switching of ion current in narrow pores: implications for biological ion channels. Proceedings of the Royal Society of London. Series B: Biological Sciences, June, 187-92.

## Wednesday, February 20, 2008

### DNA as topological quantum computer: XII

In previous postings I, II, III, IV, V, VI, VII, VIII, IX, X, XI I have discussed various aspects of the idea that DNA could acts as a topological quantum computer using fundamental braiding operation as a universal 2-gate.

One of the challenges is the realization of single particle gates representing U(2) rotation of the qubit. The first thing to come mind was that U(2) corresponds to U(2) rotation induced by magnetic field and electric fields. Yesterday I realized much more elegant realization in terms of SU(3) rotation, where SU(3) is color group associated with strong interactions. Soon I remembered that there is direct evidence for the prediction that color SU(3) is associated with tqc and thus cognition: something that does not come first in mind! I have myself written text about the strange finding of topologist Barbara Shipman suggesting that quarks are in some mysterious manner involved with honeybee dance and proposed an interpretation.

1. The realization of 1-gate in terms of ordinary rotations

The realization of single particle gates as U(2) transformations leads naturally to the extension of the braid group by assigning to the strands sequences of group elements satisfying the group multiplication rules. The group elements associated with a nth strand commute with the generators of braid group which do not act on nth strand. G would be naturally subgroup of the covering group of rotation group acting in spin degrees of spin 1/2 object. Since U(1) transformations generate only an overall phase to the state, the presence of this factor might not be necessary. A possible candidate for U(1) factor is as a rotation induced by a time-like parallel translation defined by the electromagnetic scalar potential Φ=At.

A possible realization for single particle gate- characterized by s subset SU(2)- would be as SU(2) rotation induced by a magnetic pulse. This transformation is fixed by the rotation axis and rotation angle around this axes. This kind of transformation would result by applying to the strand a magnetic pulse with magnetic field in the direction of rotation axes. The duration of the pulse determines the rotation angle. Pulse could be created by bringing a magnetic flux tube to the system, letting it act for the required time, and moving it away. U(1) phase factor could result from the electromagnetic gauge potential as a non-integrable phase factor exp(ie∫ Atdt/hbar) coming from the presence of scale potential Φ=At in the Hamiltonian.

One can criticize this model. The introduction of magnetic pulses does not look an attractive idea and seems to require additional structures besides magnetic flux tubes (MEs?). It would be much nicer to assign the magnetic field with the flux tubes defining the braid strands. The rotation of magnetic field would however require changing the direction of braid strands. This does not look natural. Could one do without this rotation by identifying spin like degree of freedom in some other manner? This is indeed possible.

2. The realization of 1-gate in terms of color rotations

TGD predicts a hierarchy of copies of scaled up variants of both weak and color interactions and these play a key role in TGD inspired model of living matter. Both weak isospin and color isospin could be considered as alternatives for the ordinary spin as a realization of qubit in TGD framework. Below color isospin is discussed. Below color isospin is discussed but one could consider also a realization in terms of nuclei and their exotic counterparts differing only by the replacement of neutral color bond between nuclei of nuclear string with a charged one. Charge entanglement between nuclei would guarantee overall charge conservation.

1. Each space-time sheet of braid strands contains quark and antiquark at its ends. Color isospin and hypercharge label their states. Two of the quarks of the color triplet form doublet with respect to color isospin and the third is singlet and has different hyper charge Y. Hence qubit could be realized in terms of color isospin I3 instead of ordinary spin but third quark would be inert in the Boolean sense. Qubit could be also replaced with qutrit and isospin singlet could be identified as a statement with ill-defined truth value. Trits are used also in ordinary computers. In TGD framework finite measurement resolution implies fuzzy qubits and the third state might relate to this fuzziness.

2. Magnetic flux tubes are also color magnetic flux tubes carrying non-vanishing classical color gauge field in the case that they are non-vacuum extremals. The holonomy group of classical color field is an Abelian subgroup of the U(1)× U(1) Cartan subgroup of color group. Classical color magnetic field defines the choice of quantization axes for color quantum numbers. For instance, magnetic moment is replaced with color magnetic moment and this replacement is in key role in simple model for color magnetic spin spin splittings between spin 0 and 1 mesons as well as spin 1/2 and 3/2 baryons.

3. There is a symmetry breaking of color symmetry to subgroup U(1)I3× U(1)Y and color singletness is in TGD framework replaced by a weaker condition stating that physical states have vanishing net color quantum numbers. This makes possible the measurement of color quantum numbers in the manner similar to that for spin. For instance, color singlet formed by quark and antiquark with opposite color quantum numbers can in the measurement of color quantum numbers of quark reduce to a state in which quark has definite color quantum numbers. This state is a superposition of states with vanishing Y and I3 in color singlet and color octet representations. Strong form of color confinement would not allow this kind of measurement.

4. Color rotation in general changes the directions of quantization axis of I3 and Y and generates a new state basis. Since U(1)× U(1) leaves the state basis invariant, the space defined by the choices of quantization axes is 6-dimensional flag manifold F=SU(3)/U(1)×U(1). In contrast to standard model, color rotations in general do not leave classical electromagnetic field invariant since classical em field is a superposition of color invariant induced Kähler from and color non-invariant part proportional classical Z0 field. Hence, although the magnetic flux tube retains its direction and shape in M4 degrees of freedom, its electromagnetic properties are affected and this is visible at the level of classical electromagnetic interactions.

5. If color isospin defines the qubit or qutrit in topological quantum computation, color quantum numbers and the flag manifold F should have direct relevance for cognition. Amazingly, there is a direct experimental support for this! Years ago topologist Barbara Shipman made the intriguing observation that honeybee dance can be understood in terms of a model involving the flag manifold F (see this, this, and this). This led her to propose that quarks are in some mysterious manner involved with the honeybee dance. My proposal was that color rotations of the space-time sheets associated with neurons represent geometric information: sensory input would be coded to color rotations defining the directions of quantization axes for I3 and Y. Subsequent state function reduction would provide conscious representations in terms of trits characterizing for instance sensory input symbolically.

I introduced also the notions of geometric and sensory qualia corresponding to the two choices involved with the quantum measurement: the choice of quantization axes performed by the measurer and the "choice" of final state quantum numbers in state function reduction. In the case of honeybee dance geometric qualia could code information about the position of the food source. The changes of color quantum numbers in quantum jump were identified as visual colors. In state function reduction one cannot speak about change of quantum numbers but about their emergence. Therefore one must distinguish between color qualia and the conscious experience defined by the emergence of color quantum numbers: the latter would have interpretation as qutrit.

To sum up, this picture suggests that 1-gates of DNA tqc (understood as "dance of lipids") are defined by color rotations of the ends of space-like braid strands and at lipids. The color rotations would be induced by sensory and other inputs to the system. Topological quantum computation would be directly related to conscious experience and sensory and other inputs would fix the directions of the color magnetic fields.

For details see the chapter DNA as Topological Quantum Computer of "Genes and Memes".

## Tuesday, February 19, 2008

### We know!

TGD was born 4 years before superstring model. Around 1994 I performed first version of p-adic mass calculations of elementary particle masses. Now I am now applying TGD at precise quantitative level to model bio-systems as macroscopic quantum systems. At this moment M-theorist's most notable attempts to build connection to observed reality are speculations about the possibility of blackholes and time machines in LHC.

In today's Cosmic Variance, only five centuries after Newton, Sean Carroll - after stating clearly that we cannot know anything for sure- told us that - after all- "we know" that there is definitely no new physics involved with living cell or brain. To induce the desired associations the title of posting referred to telekinesis but the message was "No New Physics-Period". Lubos echoed Sean Carroll's "we-know"'s (the title referred now to spoon bending).

Neither Sean nor Lubos bothered to mention dark matter- roughly 95 percent of all matter that exists- and its possible relevance for biology since they "we-know" that it has only cosmological relevance. Lubos also emphasized that quantum theory in the realm acceccible to experimentation has reached its final form. In particular, "we-know" that Planck constant has only single value. Message taken.

The grateful audience joined to stormy applauds for these "we-knower"'s but there was also an exception. Someone not-so-well-informed mentioned that DNA double strands have "telepathic abilities". DNA double strands are able to gather together in solution: the same ability of single strand and conjugate has been known for a long time.

In the case of single DNA strands TGD explains this in terms magnetic flux tubes connecting DNA and conjugate DNA strands: also attraction of double strands could be explained by this mechanism. These magnetic flux tubes carrying particles in large Planck constant phase and defining braids could make DNA topological quantum computer. The phase transitions changing hbar and inducing shortening (or lengthening) of the braid strands would allow biomolecules to find each other and play key role in bio-catalysis: consider only DNA replication, transcription of DNA to mRNA, and translation of mRNA to aminoacid sequences.

The reaction of Lubos Motl was what one might have expected: "The full article is here, http://pubs.acs.org/cgi-bin/abst.../jp7112297.html - it is really amazing or, more likely, complete rubbish" (note that the ability of single strands to find each other is known for decades!).

So many theoreticians in this state of "we-knowing" see only what their theory allows them to see. Brings in my mind similar situation more than century ago before quantum mechanics: also then "we-know"'ed that classical mechanics is all that is needed to describe every imaginable observation. History does not seem to be a good teacher but also its students seem to be often rather silly.

### Quantum model of nerve pulse V: Summary

Quite recently I learned [1,2,3,4,5] (thanks to Ulla Mattfolk) that nerve pulse propagation seems to be an adiabatic process and thus does not dissipate: the authors propose that 2-D acoustic soliton is in question. Adiabaticity is what one expects if the ionic currents are dark currents (large hbar and low dissipation) or even supra currents. Furthermore, Josephson currents are oscillatory so that no pumping is needed. Combining this input with the model of DNA as topological quantum computer (tqc) [8] leads to a rather precise model for the generation of nerve pulse. The following gives a brief summary of main points of the model in its recent form.

1. The system would consist of two superconductors- microtubule space-time sheet and the space-time sheet in cell exterior- connected by Josephson junctions represented by magnetic flux tubes defining also braiding in the model of tqc. The phase difference between two super-conductors would obey Sine-Gordon equation allowing both standing and propagating solitonic solutions. A sequence of rotating gravitational penduli coupled to each other would be the mechanical analog for the system. Soliton sequences having as a mechanical analog penduli rotating with constant velocity but with a constant phase difference between them would generate moving kHz synchronous oscillation. Periodic boundary conditions at the ends of the axon rather than chemistry determine the propagation velocities of kHz waves and kHz synchrony is an automatic consequence since the times taken by the pulses to travel along the axon are multiples of same time unit. Also moving oscillations in EEG range can be considered and would require larger value of Planck constant in accordance with vision about evolution as gradual increase of Planck constant.

2. During nerve pulse one pendulum would be kicked so that it would start to oscillate instead of rotating and this oscillation pattern would move with the velocity of kHz soliton sequence. The velocity of kHz wave and nerve pulse is fixed by periodic boundary conditions at the ends of the axon implying that the time spent by the nerve pulse in traveling along axon is always a multiple of the same unit: this implies kHz synchrony. The model predicts the value of Planck constant for the magnetic flux tubes associated with Josephson junctions and the predicted force caused by the ionic Josephson currents is of correct order of magnitude for reasonable values of the densities of ions. The model predicts kHz em radiation as Josephson radiation generated by moving soliton sequences. EEG would also correspond to Josephson radiation: it could be generated either by moving or standing soliton sequences (latter are naturally assignable to neuronal cell bodies for which hbar should be correspondingly larger): synchrony is predicted also now.

3. The previous view about microtubules in nerve pulse conduction can be sharpened. Microtubular electric field (always in the same direction) could explain why kHz and EEG waves and nerve pulse propagate always in same direction and might also feed energy to system so that solitonic velocity could be interpreted as drift velocity. This also inspires a generalization of the model of DNA as topological quantum computer [7] since also microtubule-cell membrane systems are good candidates for performers of tqc. Cell replication during which DNA is out of game seems to require this and microtubule-cell membrane tqc would represent higher level tqc distinguishing between multi-cellulars and mono-cellulars.

4. New physics would enter in several manners. Ions should form Bose-Einstein cyclotron condensates. The new nuclear physics predicted by TGD [8] predicts that ordinary fermionic ions (such as K+, Na+, Cl-) have bosonic chemical equivalents with slightly differing mass number. Anomalies of nuclear physics and cold fusion provide experimental support for the predicted new nuclear physics. Electronic supra current pulse from microtubules could induce the kick of pendulum inducing nerve pulse and induce a small heating and expansion of the axon. The return flux of ionic Josephson currents would induce convective cooling of the axonal membrane. A small transfer of small positive charge into the inner lipid layer could induce electronic supra current by attractive Coulomb interaction. The exchange of exotic W bosons which are scaled up variants of ordinary W+/- bosons is a natural manner to achieve this if new nuclear physics is indeed present. There are a lot of support for this new physics: cold fusion and nuclear transmutations in living matter [8] ( these I have discussed in previous postings).

For background see that chapter Quantum Model of Nerve Pulse of "TGD and EEG".

References

[1] Soliton model.

[2] T. Heimburg and A. D. Jackson (2005), On soliton propagation in biomembranes and nerves, PNAS vol. 102, no. 28, p.9790-9795.

[3] T. Heimburg and A. D. Jackson (2005), On the action potential as a propagating density pulse and the role of anesthetics, arXiv : physics/0610117 [physics.bio-ph].

[4] K. Graesboll (2006), Function of Nerves-Action of Anesthetics, Gamma 143, An elementary Introduction.

[6] Saltation.

[7] The chapter DNA as Topological Quantum Computer of "Genes and Memes".

[8] The chapter Nuclear String Physics of "p-Adic Length Scale Hypothesis and Dark Matter Hierarchy".

## Sunday, February 17, 2008

### TGD assigns 10 Hz biorhythm to electron as an intrinsic frequency scale

p-Adic coupling constant evolution and origins of p-adic length scale hypothesis have remained for a long time poorly understood. The progress made in the understanding of the S-matrix of the theory (or rather, its generalization M-matrix) (see this) has however changed the situation. The unexpected prediction is that zero energy ontology assigns to elementary particles macroscopic times scales. In particular, the time scale assignable to electron correspond to the fundamental biorhythm of 10 Hz.

1. M-matrix and coupling constant evolution

The final breakthrough in the understanding of p-adic coupling constant evolution came through the understanding of S-matrix, or actually M-matrix defining entanglement coefficients between positive and negative energy parts of zero energy states in zero energy ontology (see this). M-matrix has interpretation as a "complex square root" of density matrix and thus provides a unification of thermodynamics and quantum theory. S-matrix is analogous to the phase of Schrödinger amplitude multiplying positive and real square root of density matrix analogous to modulus of Schrödinger amplitude.

The notion of finite measurement resolution realized in terms of inclusions of von Neumann algebras allows to demonstrate that the irreducible components of M-matrix are unique and possesses huge symmetries in the sense that the hermitian elements of included factor N subset M} defining the measurement resolution act as symmetries of M-matrix, which suggests a connection with integrable quantum field theories.

It is also possible to understand coupling constant evolution as a discretized evolution associated with time scales Tn, which come as octaves of a fundamental time scale: Tn=2iT0. Number theoretic universality requires that renormalized coupling constants are rational or at most algebraic numbers and this is achieved by this discretization since the logarithms of discretized mass scale appearing in the expressions of renormalized coupling constants reduce to the form log(2i)=nlog(2) and with a proper choice of the coefficient of logarithm log(2) dependence disappears so that rational number results.

2. p-Adic coupling constant evolution

Could the time scale hierarchy Tn= 2iT0 defining hierarchy of measurement resolutions in time variable induce p-adic coupling constant evolution and explain why p-adic length scales correspond to Lp propto p1/2R, p≈ 2k, R CP2 length scale? This looks attractive but there is a problem. p-Adic length scales come as powers of 21/2 rather than 2 and the strongly favored values of k are primes and thus odd so that n=k/2 would be half odd integer. This problem can be solved.

1. The observation that the distance traveled by a Brownian particle during time t satisfies r2= Dt suggests a solution to the problem. p-Adic thermodynamics applies because the partonic 3-surfaces X2 are as 2-D dynamical systems random apart from light-likeness of their orbit. For CP2 type vacuum extremals the situation reduces to that for a one-dimensional random light-like curve in M4. The orbits of Brownian particle would now correspond to light-like geodesics \gamma3 at X3. The projection of γ3 to a time=constant section X2 subset X3 would define the 2-D path γ2 of the Brownian particle. The M4 distance r between the end points of γ2 would be given r2=Dt. The favored values of t would correspond to Tn=2iT0 (the full light-like geodesic). p-Adic length scales would result as L2(k)= D T(k)= D2kT0 for D=R2/T0. Since only CP2 scale is available as a fundamental scale, one would have T0= R and D=R and L2(k)= T(k)R.

2. p-Adic primes near powers of 2 would be in preferred position. p-Adic time scale would not relate to the p-adic length scale via Tp= Lp/c as assumed implicitly earlier but via Tp= Lp2/R0= p1/2Lp, which corresponds to secondary p-adic length scale. For instance, in the case of electron with p=M127 one would have T127=.1 second which defines a fundamental biological rhythm. Neutrinos with mass around .1 eV would correspond to L(169)≈ 5 μm (size of a small cell) and T(169)≈ 1.× 104 years. A deep connection between elementary particle physics and biology becomes highly suggestive.

3. In the proposed picture the p-adic prime p≈ 2k would characterize the thermodynamics of the random motion of light-like geodesics of X3 so that p-adic prime p would indeed be an inherent property of X3.

4. The fundamental role of 2-adicity suggests that the fundamental coupling constant evolution and p-adic mass calculations could be formulated also in terms of 2-adic thermodynamics. With a suitable definition of the canonical identification used to map 2-adic mass squared values to real numbers this is possible, and the differences between 2-adic and p-adic thermodynamics are extremely small for large values of for p≈ 2k. 2-adic temperature must be chosen to be T2=1/k whereas p-adic temperature is Tp= 1 for fermions. If the canonical identification is defined as

n≥0 bn 2n→ ∑m≥12-km0≤ n< m bkm+n2n.

It maps all 2-adic integers n<2k to themselves and the predictions are essentially same as for p-adic thermodynamics. For large values of p≈ 2k 2-adic real thermodynamics with TR=1/k gives essentially the same results as the 2-adic one in the lowest order so that the interpretation in terms of effective 2-adic/p-adic topology is possible.

3. p-Adic length scale hypothesis and biology

The basic implication of zero energy ontology is the formula T(k)≈ 2k/2L(k)/c= L(2,k)/c. This would be the analog of E=hf in quantum mechanics and together hierarchy of Planck constants would imply direct connection between elementary particle physics and macroscopic physics. Especially important this connection would be in macroscopic quantum systems, say for Bose Einstein condensates of Cooper pairs, whose signature the rhythms with T(k) as period would be. The presence of this kind of rhythms might even allow to deduce the existence of Bose-Einstein condensates of hitherto unknown particles.

1. For electron one has T(k)=.1 seconds which defines the fundamental fe=10 Hz bio-rhythm appearing as a peak frequency in alpha band. This could be seen as a direct evidence for a Bose-Einstein condensate of Cooper pairs of high Tc super-conductivity. That transition to "creative" states of mind involving transition to resonance in alpha band might be seen as evidence for formation of large BE condensates of electron Cooper pairs.

2. TGD based model for atomic nucleus (see this) predicts that nucleons are connected by flux tubes having at their ends light quarks and anti-quarks with masses not too far from electron mass. The corresponding p-adic frequencies fq= 2kfe could serve as a biological signature of exotic quarks connecting nucleons to nuclear strings . kq=118 suggested by nuclear string model would give fq= 218fe=26.2 Hz. Schumann resonances are around 7.8, 14.3, 20.8, 27.3 and 33.8 Hz and fq is not too far from 27.3 Hz Schumann resonance and the cyclotron frequency fc(11B+)=27.3 Hz for B=.2 Gauss explaining the effects of ELF em fields on vertebrate brain.

3. For a given T(k) the harmonics of the fundamental frequency f=1/T(k) are predicted as special time scales. Also resonance like phenomena might present. In the case of cyclotron frequencies they would favor values of magnetic field for which the resonance condition is achieved. The magnetic field which in case of electron gives cyclotron frequency equal to 10 Hz is Be≈ 3.03 nT. For ion with charge Z and mass number A the magnetic field would be BI= (A/Z)× (mp/me)×Be. The B=.2 Gauss magnetic field explaining the findings about effects of ELF em fields on vertebrate brain is near to BI for ions with fc alpha band. Hence the value of B could be understood in terms of resonance with electronic B-E condensate.

4. The hierarchy of Planck constants predicts additional time scales T(k). The prediction depends on the strength of the additional assumptions made. One could have scales of form nT(k)/m with m labeling the levels of hierarchy. m=1 would give integers multiples of T(k). Integers n could correspond to ruler and compass integers expressible as products of first powers of Fermat primes and power of 2. There are only four known Fermat primes so that one has n=2ii Fi, Fi in {3,5,17,257, 216+1}. In the first approximation only 3- and 5- and 17-multiples of 2-adic length scales would result besides 2-adic length scales. In more general case products m1m2 and ratios m1/m2 of ruler and compass integers and their inverses 1/m1m2 and m2m1 are possible.

5. Mersenne primes are expected to define the most important fundamental p-adic time scales. The list of real and Gaussian (complex) Mersennes Mn possibly relevant for biology is given by n=89, 107, 113*, 127, 151*,157*, 163*, 167* ('*' tells that Gaussian Mersenne is in question). See the table.

For background see that chapter New Physics and Qualia of "Quantum Hardware of Living Matter".

## Thursday, February 14, 2008

### Quantum model of nerve pulse IV: Could microtubule-axon system perform topological quantum computation?

The proposed picture is consistent with the model of DNA as a topological quantum computer [7] and with the idea that also microtubuli could be involved with tqc. The model of DNA as tqc in its basic form assumes that DNA is connected to the nuclear membrane and cell membranes associated with the cell body by magnetic flux tubes such that each nucleotide is connected to single lipid. Tqc programs are coded to the temporal braiding patters of lipids. This requires that lipid layer is liquid crystal and thus below the critical temperature. The flux tube connecting DNA to inner lipid layer and that beginning from outer lipid layer can form single flux tube or be split. If they form single flux tube braiding and tqc are not possible. During tqc the braid strands going through cell membrane are split and the dance of lipids induced by water flow defining time like braiding (hydrophilic lipid ends are anchored to the cellular water) induces braiding of the magnetic flux tubes which write the tqc program to memory. Furthermore, the lifetimes of flux tubes in the connected state must be short enough to prevent the generation of a nerve pulse. This is the case if the temperature is sufficiently below the critical temperature. The ionic supra currents are identifiable as the observed quantal non-dissipative currents flowing through the cell membrane when tqc is not on.

Centrioles have their own genetic code realized in terms of RNA and they play key role during gene replication when DNA is out of the game. This encourages to think that microtubuli make possible an independent tqc like process. How microtubule-axon system could then perform tqc? One can consider two options and also their hybrid in the proposed model for nerve pulse.

1. Option I: Magnetic flux tubes connect microtubules to the space-time sheet of cell exterior. In the model of DNA as tqc these flux tubes continue back to the nucleus or another nucleus: the flux tubes must be split at cell membrane during tqc and this splitting induces the required isolation from the external world during tqc. During nerve pulse the situation would be different and the flow of lipids in liquid phase could induce braiding: the isolation would however fail now. Tqc would explain why the axon melts during nerve pulse.

One can become critical and ask why also the magnetic flux tubes from DNA could not end to the space-time sheet of the cell exterior. The justification for 'No' (besides isolation) could be that also cell soma would possess standing soliton sequence like waves and standing nerve pulses.

Could one then see this tqc as a special variant of DNA-membrane tqc? The idea about magnetic flux tubes emanating from DNA and flowing along microtubuli interiors and radiating to the axonal membrane looks ugly: in any case, this would not affect tqc and nerve pulse could be seen as a direct gene expression.

2. Option II: For some years ago I considered the possibility of a gel-sol-gel phase transition proceeding along the surface surface of the micro-tubuli, accompanying nerve pulse, perhaps inducing nerve pulse, and coding for long term sensory memories in terms of 13 13-bit sequences defined by the tubulin helices with bit represented as a conformation of microtubule. This hypothesis might be easily shown to be wrong on basis of the available experimental facts already now. Suppose however that this phase transition happens and that the braid strands do not continue from the microtubular surface to the cell nucleus. In this case the braiding could be induced by a gel-sol-gel transition accompanying and perhaps generating the nerve pulse at the microtubular level and inducing the disassembly of the tubulins followed by re-assembly inducing the braiding. Also this braiding would contribute to tqc like process or at least memory storage by braiding.

The following considerations do not depend on the option used.

1. What comes first in mind is that the braiding codes memories, with memories understood in TGD sense using the notion of 4-D brain: that is in terms of communications between brain geometrically now and brain in the geometric past. In standard neuroscience framework braiding of course cannot code for memories since it changes continually. Nerve pulse sequences would code for long term sensory memories in a time scale longer than millisecond and microtubular phase transition could have a fine structure coding for sensory data in time scales shorter than nerve pulse duration. The fact is that we are able to distinguish from each other stimuli whose temporal distance is much shorter than millisecond and this kind of coding could make this possible. Also the direct communication of the auditory (sensory) input using photons propagating along MEs parallel to axon could also explain this.

2. In the model of DNA as tqc nucleotides A,T,C,G are coded into a 4-color of braid strand represented in terms of quarks u,d and their antiquarks. An analogous coding could be present also now. The coding would result if DNA is connected to microtubuli but this option does not look attractive. If each aminoacid can be accompanied by 3-braid with colors of any of DNA codons coding each aminoacid of tubulin would be connected to 3 lipids. As a matter fact, 3-braids can be regarded as fundamental sub-modules of tqc programs since 3-braid is the smallest N-braid which can do non-trivial tqc. Tubulins could be seen as higher level modules consisting of order hundred 500 amino-acids. This corresponds to a DNA strand with length of about .5 μm corresponding to p-adic length scale L(163) which is one of the four magic p-adic length scales (k=151,157,163,167) which correspond to Gaussian Mersennes. This higher level language character of microtubular tqc programs would conform with the fact that only eukaryotes possess them.

3. Cellular cytoskeleton consists of microtubuli. Could microtubular tqc -in either of the proposed forms- take place also at the cell soma level? Could DNA-nuclear membrane system define the primordial tqc and microtubular cytoskeleton-cell membrane system a higher level tqc that emerged together with the advent of the multicellulars? Is only the latter tqc performed at the multicellular level? The notions of super- and hypergenome encourage to think that both tqcs are performed in all length scales. One can imagine that ordinary cell membrane decomposes into regions above and below the critical point (the value of the critical temperature can be controlled. Those below it would be connected to DNA by flux tube bundles flowing inside the microtubular cylinders. Microtubular surfaces would in turn be connected to the regions above the critical point. One should also understand the role of M13=213-1 12-bit higher level "genetic code" assignable naturally to microtubuli. For instance, could the bit of this code tell whether the module defined by the tubulin dimer strand bundle participates tqc or not?

For background see that chapter Quantum Model of Nerve Pulse of "TGD and EEG".

References

[1] Soliton model.

[2] T. Heimburg and A. D. Jackson (2005), On soliton propagation in biomembranes and nerves, PNAS vol. 102, no. 28, p.9790-9795.

[3] T. Heimburg and A. D. Jackson (2005), On the action potential as a propagating density pulse and the role of anesthetics, arXiv : physics/0610117 [physics.bio-ph].

[4] K. Graesboll (2006), Function of Nerves-Action of Anesthetics, Gamma 143, An elementary Introduction.

[6] Saltation.

[7] The chapter DNA as Topological Quantum Computer of "Genes and Memes".

### Quantum model of nerve pulse III: Relation to Hodgkin-Huxley model

Before the replacement of Hodgkin-Huxley model with a genuinely quantal model can be taken seriously, one must answer many difficult questions which also Hodgkin and Huxley must have faced as they developed their own model. In the following I will go through the basic questions and quantum answers to them.

1. Questions and answers

Q: In the resting state membrane potential is negative and cell has a negative net charge. What stabilizes the cell against the leakage of the negative charge if pumps and channels are not responsible for this?

A: The findings about the strange behavior of cell membrane inspire TGD based answer. Cell membrane space-time sheet is its own quantum world and the flow of ions occurs only in the presence of magnetic flux tubes connecting it to the external world. These currents a however oscillatory Josephson currents if dissipation is absent. Hence there is no need to cut completely the connections to the external world.

Q: How the resting state can result spontaneously if pumps are absent?

A: If ionic currents are Josephson currents, they are automatically oscillating and the return to the original state is guaranteed. The flux tubes carrying the ionic currents will be assumed to connect axonal microtubules to the space-time sheet of the cell interior. Consider first the most obvious objections.

1. Dark ions could not transform to ordinary ones in the exterior of the cell membrane. This might indeed kill the model.

2. If ionic currents are Josephson currents, they are automatically oscillating and the return to the original state is guaranteed. The objection is that all biologically important ions are not bosons and the model for high Tc super-conductor in its recent form allows only electronic and protonic Cooper pairs at room temperature [8]. TGD based nuclear physics however predicts the possibility of exotic nuclei for which one or more color bonds connecting nucleons to the nuclear string are charged. These exotic nuclei with electronic states identical to those of genuine ions could save the situation. The table below describes how cyclotron frequencies for B=.2 Gauss of the most important ions are modified in the simplest replacements with exotic ions. For instance, the notation Mg++- tells that there is double electronic ionization and electron shell of Argon as usual but that one color bond is negatively charged.

23Na+19Ne+: 13.1 Hz → 15.7 Hz

23Na+24→ Mg++-: 13.1 Hz→ 12.5 Hz

39K+40→ A+: 7.7 Hz→ 7.5 Hz

39K+40Ca++-: 7.7 Hz→ 7.5 Hz

35Cl-40A-: 8.6 Hz →7.5 Hz

fc(K+) and fc(Cl-) are replaced with the frequency 7.5 Hz and one can do only using the cyclotron frequencies fc(Ca++)/2=7.5 Hz, fc(Mg++)=12.5 Hz, and fc(Ca++)=15 Hz. The nominal values of the lowest Schumann frequencies are 7.8 Hz and 14.3 Hz. All ions with relevance for nerve pulse and EEG could be bosonic ions or bosonic pseudo-ions. I do not know how well the needed ionization mechanisms are understood in the standard framework.

For small oscillations the maximal charge transfer ΔQ generated by an oscillating ionic Josephson current during the cycle is proportional to hbar /fJ propto hbar2 and hbar /Ω propto hbar for solitonic situation. ΔQ is very small for the ordinary value of hbar : also the oscillation period is very small. For large values of hbar situation changes and large maximal ion transfers are possible.

An hbar increasing phase transition could be involved with the generation of the nerve pulse. Quantum criticality during nerve pulse generation indeed suggest the presence of flux tubes with varying values of hbar . The lifetimes of the connected flux tubes could be proportional to hbar at criticality. A fractal hierarchy of pulses and EEG like oscillations of the membrane potential corresponding to various values of hbar is suggestive.

Q: Can one make this more quantitative?

A: One can construct a model based on Sine-Gordon wave equation [7] for the phase different Φ between the superconductors connected by Josephson junction sequences defined by magnetic flux tubes and idealizable as a continuous Josephson junction.

1. For a Josephson junction idealizable as a hollow cylinder with radius R and thickness d the expression of the Josephson current reads as

J= J0sin(Ze∫ Vdt/hbar)

J0 is in case of cell membrane given by

J0= (Ze2π dR/Λ2) ×(hbar/m) ,

where R and d would be now the radius and thickness of the axon, Λ is the magnetic peneration length, and m is the mass of the charge carrier. Although this expression does not hold true as such when Josephson junctions are replaced by magnetic flux tubes connecting microtubuli and axon, one can can safely make some qualitative conclusions. The amplitude of the Josephson current increases with hbar . For electron the value of the amplitude is by a factor x≈ Amp/me≈ 211A larger than for ion with a mass number A. This gives for electron Cooper pairs a unique role as an initiator of the nerve pulse. Note that the amplitudes of the Josephson currents of electron and ions are quite near to each other if one has hbar (ion)= 211A×hbar: this might explain why the powers of 211 for hbar seem to be favored.

2. Electronic Josephson current dominates and makes it ideal for the generation of nerve pulse (kick to gravitational pendulum). This is possible if the net amount of electronic charge is so small that it flows out during the generation of flux tubes. For ions this need not occur even if ion densities are of same order of magnitude. Constant voltage V creates an oscillating current and no catastrophic leakage takes place and the resting state results automatically. The ionic Josephson currents assignable to the magnetic flux tubes connecting microtubules through the cell membrane to the external world could be responsible for the nerve pulse.

3. The mechanical analog for Sine-Gordon system [8] assignable to Josephson junction is rotating pendulum but one must be cautious in applying this analogy. There are two options concerning the modeling of the situation.
1. Membrane potential represents an external voltage V(t) and one has Φi= Zie∫ Vdt/hbar, where Φi is the phase difference between Bose-Einstein condensates.
2. System is autonomous and membrane potential V(t)=hbar (dΦi/dt)/Zie is completely determined by the dynamics of any phase Φi. This option is highly predictive and discussed in the sequel.

4. The analogy with gravitational pendulum allows to identify the phase angle Φ as the counterpart of angle Θ characterizing angular position of mathematical pendulum (note that this analogy can be misleading since it implicitly brings in 3-D thinking).
1. In this picture rotating pendulum corresponds to a soliton sequence containing infinite number of solitons: both stationary and moving soliton sequences are obtained. The sign of Ω=dΦ/dt is fixed and approximately constant for large values of Ω. Resting potential could correspond to this kind of situation and Ω ≈ 2π kHz is suggested by kHz synchrony. A mechanism of this synchrony will be discussed below. For large values of hbar even values of Ω in EEG range could correspond to membrane potential. For large values of Ω one as V≈ hbarΩi/Zie. If also EEG rhythms correspond to Ω they must correspond to different values of hbar and f propto 1/hbar would hold true. Changes in the dominating EEG rhythm (40 Hz, 10 Hz, 5 Hz,..) could correspond to phase transitions changing hbar to given value for a large number of axons. The maximal charge transfer during single period is proportional to Δ Q propto 1/Ω.
2. Hyperpolarization/polarization would mean fastening/slowing down of the pendulum rotation and slowing down would make the system unstable. Near criticality against the generation of nerve pulse would mean that pendulum is rotating rather slowly (Ω<< fJ ) so that a small kick can transform rotation to oscillation. The sign of V propto dΦ/dt would change and large amplitude oscillatory motion would result for single period only after which a kick in opposite direction would lead back to the resting state. Membrane potential varies between the resting potential V0=-75 V and V1=+40 V during nerve pulse: V1>|V0| would have killed the model. Note that V1=40 V is rather near to the critical potential about V1=50 V: ideally these potentials should be identical.
3. The so called breathers -both stationary and moving- correspond to soliton-antisoliton bound state (see the visualization here). Breathers could be identified as large amplitude oscillations around Φ=0 ground state. Physical intuition suggests that breathers are possible also for a ground state corresponding to a rotating pendulum (representing moving or stationary waves). They would correspond to kicking of one pendulum in a sequence of penduli along z-axis rotating in phase at the initial moment. The kick could correspond to a genuine external perturbation generated by a pair electronic supra current pulses of opposite sign giving constant velocity increments ΔΩ initiating and halting the nerve pulse just like they would do in the case of tqc but in opposite time order. If the background corresponds to a propagating EEG wave, also nerve pulse is expected to propagate with same velocity. The propagation direction of EEG wave would also explain why nerve pulses propagate only in single direction.

5. For the ordinary value of hbar , the frequency of the Josephson current corresponds to that assignable to energy .07 eV being around 1.6×1013 Hz and quite high. For x==hbar /hbar0=244 the frequency would be near to cyclotron frequency of about 1 Hz assignable to DNA strands. For x=3× 23× 13 the frequency would be near to the fundamental 10 Hz frequency which is secondary p-adic time scale associated with electron and correspond to the temporal duration of negative energy space-time sheet assignable to electron. For x=3× 23× 11 one would obtain a 640 Hz frequency which corresponds to the time scale of nerve pulse. It seems clear that the original hypothesis that only powers of 211 define the spectrum of Planck constant is too restrictive. The requirement that cyclotron frequencies and Josephson frequencies are proportional to each other for small oscillations would guarantee resonant behavior for common strength of the magnetic field would give hbar propto A. This would require that each ion species lives at its own flux tubes.

Q: What instabilizes the axon? Why the reduction rather than increase of the magnitude of the membrane potential induces the instability? Why the reduction of the resting potential below the critical value induces nerve pulse?

A: Large enough voltage pulse between microtubules and membrane could generate electronic DC supra current. The introduction of a small amount of positive charge to the inner lipid layer and staying there for some time would generate the voltage pulse between microtubules and lipid layer so that DC electronic supra current would be induced, and induce the reduction Δ V≈ .02 eV of the magnitude of the membrane potential. A similar introduction of negative charge would induce hyperpolarization and the direction of the current would be opposite if it is generated at all. The mechanism generating the small positive charge to the inner lipid layer could be based on the exchange of exotic W bosons between pairs of exotic nuclei at opposite sides of the cell membrane so that the negative charge of the inner lipid layer would be reduced.

Q: Can one understand the observed radial force, the increase of the radius of axons and the reduction of its thickness, and heating followed by cooling?

A: The observed outward force acting on a test system might be due to the ionic Josephson currents to which the test system responds. During the second half of the pulse the sign of the ionic force is predicted to change. The pressure caused by the electronic Josephson current pulse before the connection of flux tubes to single flux tube might relate to the increase of the radius of the axonal membrane and with the reduction of its thickness as well as the slight increase of its temperature as being due to the electrons which heat the lipid layer as they collide with it. The ions return at the second half of the pulse and could transfer the heat away by convection.

1. This hypothesis gives the estimate for the force f per unit area as

f2e(t)= (dn(lipid)/da) ×(J(t)/2e)× hbar k

= (dn(lipid)/da) × U× (hbar2 k/2me)× sin(ωJ(2t)) ,

U= (2π A/Λ2) .

The parameter A corresponds to the parameter dR in the case that Josephson junctions have the thickness of axonal membrane, and is not relevant for order of magnitude estimate. R corresponds to the distance between microtubules and cell exterior space-time sheet to which flux tubes end. dn(lipid)/da is the 2-D density Josephson junctions equal to the density of lipids.

k≈ 1/R is the wave vector of electron Cooper pair at the magnetic flux tube. The 3-momentum of electron is enormous for the proposed value of hbar , and the only possible interpretation is that the four-momentum of electron is virtual and space-like and corresponds to exchange of space-like virtual photon describing Coulomb interaction with lipid layer.

Λ2 satisfies in the first approximation the formula

Λ-2 = (4π e2ne/me)+ ∑I (4π e2nI/AmI)= αem16π2 ×hbar0[(ne/me)+ ∑I (nI/AImI)].

Note that there is no real dependence on hbar . Above critical voltage electrons could dominate in the expression but during nerve pulse ions should give the dominating contributions. U cannot be too far from unity.

2. From this one can integrate the total momentum of Cooper pairs transferred to the lipid layer before the flux tubes fuse together if one knows the value of time t when this happens. F propto hbar2/me2 proportionality implies that for the required large value of hbar /hbar0 ≈ 3× 233 the force is by a factor 6× 1020 stronger than for hbar0.

3. The force caused by ionic Josephson currents on piston is given by

f(t)= ∑I (2me/mI) (2/ZI) × f2e (τ)

τ=(ZI/2)×(Ω/ωJ)× t .

4. The comparison with the observed force gives estimate for the value of magnetic penetration length and thus density of electrons at the flux tube.

According to [3] in one particular experiment the force on piston of area S= .01 cm2 at the maximum of voltage (t= 2π/Ω) is F= 2 nN. This gives a killer test for the model. One obtains an estimate for the parameter U=(Λ2/2π A) as

U=Λ2/2πA= (dn(lipid)/da) × (hbar2 k/mpcF)× ∑I (2/AIZI) .

The value of U should not deviate too much from unity. One can use the estimates

hbar/hbar0=3×233 , k=2π/R.

Note that the experimental arrangement forces to use this value of k. The actual value in normal situation would be smaller and depends on the distance of the boundary of the cell exterior space-time sheet on microtubules. Using the values d=10 nm and R=5 μm this gives

U≈ ∑I (2/AIZI)× X ,

X= 9× 266× (hbar02 2π/mpcFR)×(S/S(lipid)).

The factor X=.9267 is of order unity! Taking into account that hbar/hbar0 is enormously large number it is difficult to believe that the result could be mere accident. Hence U does not deviate too much from unity and there are good hopes that the model works.

For nI= xI/a3, a=10-10 m, and A= dR one obtains a direct estimate which combined with above estimate gives two conditions which should be consistent with each other:

U= 76.1×∑I(xI/AI) ,

U= .93×∑I(2/AIZI) .

These estimates are consistent for xI≈ 10-2, which makes sense.

Q: Where the primary wave propagates: along axon or along microtubules?

A: This question need not make sense if microtubules and axon are connected by magnetic flux tubes to form single quantum coherent system. That axonal microtubules have constant electric field which is always in same direction could explain why the background soliton sequences and nerve pulses propagate always in the same direction and suggests that the primary wave propagates along microtubules. On the other hand, if W exchange between cell exterior and exterior reduces the negative charge of the inner lipid layer then axon could be seen as initiator. This could induce conformational or gel-sol phase transition propagating along microtubule and inducing the pair of voltage pulses in turn inducing the fusion of flux tubes at cell membrane which in turn would induce criticality of the axonal membrane. For this option axonal soliton would be a shadow of the microtubular soliton rather than completely independent dynamical process.

Q: How nerve pulse velocities are determined?

A: At first glance it seems v could be determined by boundary conditions guaranteing synchronization of neuronal activity rather than by dissipation as in Hodkin-Huxley model. As a matter fact, dissipation turns out to affect also v just because it is determined by boundary conditions!

1. Hodkin-Huxley model would suggest that nerve pulse velocity v is dictated by frictional effects as an analog of a drift velocity. The rough order of magnitude estimates for the velocities of conformational waves along micro-tubuli are consistent with the velocities of nerve pulses. The proportionality v propto d of nerve pulse velocity to nerve axonal radius might be understood as resulting on the dependence on the length of flux tubes connecting axon and microtubules and mediating a frictional feedback interaction from axon. Feedback would be naturally reduced as d increases. Feedback interaction could explain also the sensitivity of the thermal parameters of the axonal membrane to the proteins in its vicinity. If the frictional feedback is due to the environmental noise at the axon amplified at quantum criticality this is what one expects. Quite generally, quantum criticality would explain the high sensitivity of the thermal parameters on noise. Saltation cannot be responsible for the higher conduction velocity in myelin sheathed portions of axon. The insulation would reduce the environmental noise at the level of axons and thus reduce the frictional feedback from axon to the microtubules.

2. The introduction of friction is however problematic in the recent situation. In absence of boundary conditions Sine-Gordon equation predicts for the propagating soliton sequences a continuous velocity spectrum and friction should affect Ω and V but it is not clear whether it can affect v.
1. In this framework the boundary boundary conditions at the ends of the axon or some subunit of axon would dictate the values of v: γΩ L/v=n2π corresponds to periodic boundary conditions (note that γ=(1-(v/c)2)1/2≈ 1 holds true). v=ΩL/n2π implies that friction indeed affects also v.
2. This relationship states that the time taken by the nerve pulse propagate through the axon is always T= L/v =n2π/Ω: this would synchronize neurons and Ω≈ 2π kHz is suggested by the well-known 1 kHz synchrony difficult to understand in the standard framework where v would be determined by chemistry rather than geometry. Myelin shielding could in this picture guarantee that coherent wave propagation is possible over the entire axon so that boundary conditions can be applied.
3. This would give v≈ ΩL/n2π≤ ΩL/2π. Ω= 2π kHz and n=1 would give for L in the range 1 cm -10 cm v in the range 10 m/s-100 m/s corresponding roughly to the observed range of values. For short axons velocity would be lower: for L=10 μm one would have v= .01 m/s. For longer axons the value of n could be higher or the axon would decompose into structural units for which periodic boundary conditions are satisfied. The sections between Ranvier nodes have length measured in millimeters as are also the lengths of axonal microtubules and 1 mm would correspond to a velocity of 1 m/s. The actual velocity for the myelinated sections varies between 18-100 m/s so that basic structural units should be longer.
4. The proportionality of v to the radius of axon would follow from the proportionality of the length of the axon or its basic sub-unit (not longer than ≈ 10 cm) to its radius: the simplest geometric explanation for this would be in terms of scaling invariance of the axonal geometry consistent with fractality of TGD Universe. In the standard framework this proportionality would be explained by the minimization of dissipative losses in the case of long axons: one cannot exclude some variant of this explanation also now since friction indeed reduces v.
5. There is an electric field associated with microtubules (always in same direction). Could this electric field play the role of external force feeding energy and momentum to the moving soliton sequence to compensate dissipation so that v would have interpretation as a drift velocity?

Q: Can one understand EEG in this framework?

A: Just like kHz waves also EEG generating waves could correspond to propagating soliton sequences. Since V is not affected, the value of hbar must be much larger and one must have hbar propto f, where f defines the EEG rhythm. It is known that EEG amplitudes associated with EEG rhythms behave roughly like 1/f. This can be understood. By Maxwell's equation the divergence of electromagnetic field tensor is proportional to 4-current implying the amplitude of EEG identified as Josephson radiation is proportional J0/Ω and therefore to hbar. The propagation velocity v= ΩL/2πn of EEG generating waves is rather slow as compared to kHz waves: for f=10 Hz one would have 10 cm long axon v=1 m /s. Synchronization results automatically from periodic boundary conditions at the ends of the axons.

Nerve pulses during EEG rhythms would have much slower velocity of propagation and the duration of nerve pulse would be much longer. The maximal charge transfer would be proportional to 1/hbar. It would thus seem that EEG and nerve pulse activity should exclude each other for a given axon. Ω is however smaller so that the generation of nerve pulse is easier unless also ion densities are lower so that J0 (analogous to gravitational acceleration g in pendulum analogy) is reduced. Perhaps this takes place. The consistency with the propagation velocity of microtubular conformational (or even gel-sol-gel) waves might pose additional constraints on v and thus on frequencies Ω for which nerve pulses are possible. That ordinary EEG is not associated with ordinary cells might be due to the fact that hbar is much smaller: the fractal analog of EEG generating waves could be present but these EEG waves would correspond to faster oscillations in accordance with the view about evolution as an increase of hbar.

For background see that chapter Quantum Model of Nerve Pulse of "TGD and EEG".

References

[1] Soliton model.

[2] T. Heimburg and A. D. Jackson (2005), On soliton propagation in biomembranes and nerves, PNAS vol. 102, no. 28, p.9790-9795.

[3] T. Heimburg and A. D. Jackson (2005), On the action potential as a propagating density pulse and the role of anesthetics, arXiv : physics/0610117 [physics.bio-ph].

[4] K. Graesboll (2006), Function of Nerves-Action of Anesthetics, Gamma 143, An elementary Introduction.

[6] Saltation.

[7] Sine-Gordon

[8] The chapter Bio-Systems as Super-Conductors: part I of "The Quantum Hardware of Living Matter".