Sunday, September 29, 2019

The mysterious dichloromethane droplet, which refuses to sink in water and begins to spin

I received from Resonance Foundation an interesting link to article "Chemists baffled by droplet spiraling to its doom" telling about the strange behavior of droplets of dichloromethane (DCM) at the surface of water. DCM is heavier than water and one would expect it to sink down but it doesn't: it floats and starts to spin emitting smaller droplets from its boundary so that it eventually decays compeltely. This is like evaporation process said to resemble the behavior of spiral galaxy.

I could understand why the droplet floats - by creating a film acting as a boat - and Marangoni effect causing the droplet to decay by emitting smaller droplets (being due to the reduction of string tension at droplet water interface causing radial outwards directed tangential force).

But I could not understand how droplet could start to rotate. Where is the opposite angular momentum. Does water below the droplet rotate in opposite direction?

One strategy in TGD framework is to proceed in general manner.

  1. Self-organization process is in question and the rotation could have interpretation as generation long length scale motion requiring long range correlations. Also the build-up of a "boat" as liquid layer coming from droplet allowing the rest of droplet to float instead of sinking to the water would be part of this process.

  2. Energy feed is always involved with all self-organization processes. In TGD Universe one can ask whether self-organizing systems are analogous to living systems: see this.

    For living systems in TGD Universe the metabolic energy feed is needed to keep the distribution of subsystems with Planck constant heff=nh0 larger than its standard value and responsible for long range quantum correlations. This because the larger the value of heff characterizing the phase of ordinary matter is, the larger the energy of the system is, and because heff tends to decrease spontaneouly. Phase of ordinary mattter with nonstandard value of heff has interpretation as dark matter.

    Quantum scales are typically proportional to heff and large value means long scale of quantum coherence at the level of magnetic body which serves as a "boss" of ordinary matter in master slave hierarchy. If so, dark matter in TGD Universe would be visible through self-organization processes: quantum coherence in long lengths cales would force self-organization and generation of long range correlations.

  3. This picture would suggest that also now magnetic body carrying dark matter phases is present. Could the angular momentum opposite to that of the rotating droplet be assigned with the rotating dark matter at magnetic body? I have proposed analogous explanation for the spontaneous accelerration rotation in rottatin magnetic systems reported by Godin and Roschin: see this .

    It should be easy to kill this hypothesis: the alternative standard physics option is that it is in the liquid below the droplet so that it would rotate in opposite direction.

  4. Where does the needed "metabolic" energy feed come from. The decay of the droplet means that its surface tension is reduced. Surface tension measures the surface energy density so that surface energy must be lost. Could part of this energy go to the self-organization as "metabolic" energy for magnetic body and for rotational. Part of energy would go to the radial motion of smaller droplets emanating from the droplet.

  5. Surface tension is thought to be due to cohesive forces. In case of water and some other liquids hydrogen bonds would be responsible for them. London forces would be attractive interactions between dipoles of polarizable molecules and would contribute for polar molecules. Surface tension characterizes surface energy density and thus energy could come from this as the the droplet decays to smaller ones. But does this make sense?

    One can argue that this decay to smaller droplets increases surface area so that the process would not liberate energy but require it. The droplet floats by reducing its density (Arhimedes law). This increases its volume. Couls the emitted droplets have the original original density so that their volume would be smaller and surface area too. Could this reduces to total surface energy in the process? The rest would go to rotation?

In FB Wes Johnson suggested that water droplet could act as a propeller. The droplet indeed looks like propeller. Probably you mean that propeller property causes lift so that buoynancy would not be needed? This looks like a good idea. There would be two models. Propellor model and buoynancy model.
  1. For the buoynancy model the expansion of the droplet could provide the needed buoyancy: the density of the droplet should become smaller than that of water. Droplet would generate a membrane serving as a boat. The droplet would expand and this expansion would store energy, which would be liberated. Where do the energy and angular momentum come from?

  2. Both options lead to the same question. Were do energy angular momentum come? Could the energy and angular momentum come from water or from the flux tubes/sheets of the magnetic body of water as h_eff decreases and liberates energy? Flux tubes in water accompany hydrogen bonds and even long flux tubes could correspond to hydrogen bonds. Magnetic body of water would save the droplet from drowning!

  3. This argument involves only energy. Entropy is also involved. I just wrote a little article about application of minimization of Gibbs energy G to water in TGD sense. One has Δ G=Δ H-T Δ S ≤ 0, H is enthalpy, the heat used or liberated. It is safest to have Δ S>0. If flux tubes in water shorten, long range order reduced to that in shorter length scale so that entropy is generated. This liberates also energy if long dark flux tubes behave like hydrogen bonds.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Saturday, September 28, 2019

Epigenesis, inherited memories and moods lasting over several generations

Nikolina Benedikovic had an interesting comment concerning multiverse interpretation. The comment was following.

"One can imagine an intelligent amoeba with a good memory. As time progresses, the amoeba is constantly splitting, each time the resulting amoebas having the same memories as the parent. Our amoeba hence does not have a life line, but a life tree." - Huge Everett

Nikolina: Dear Mr. Everett!
Before we find out what the true interpretation of quantum mechanics is, we will have to answer this question; why the amoeba possesses this "super power" of splitting and the electron and human being don't.

I agree with Nikolina. The following is my comment about what is involved.

1. What behaviors are?

The behavior of amoeba has nothing to do with parallel universes of Everett. The behavior as such is however highly interesting and challenges standard theories of biology and perhaps also of physics. Memories seem to replicate.

  1. What do we mean with memories now: do we mean behaviors, skills, conditionings? Or episodal, sensory memories. I think it is memories in the first sense of the word. Suppose that essentially conditionings are in question.

    In this respect a lot of progress happened as it was discovered that RNA somehow represents the memories: taking RNA of conditioned sea snail and scattering it over the neurons fo second snail in lab induces the conditons of the snail to these neurons.

  2. Epigenetic approach would suggest that the behaviours essentially the same but now one does not have any convincing model for the model of the epigenesis.

2. What TGD inspired quantum biology and neuro-science can tell?

2.1 Key questions

There are two key questions that one must answer.

  1. What replication is?

    In TGD Universe we are 4-D entities - quantum states are superpositions of space-time surfaces obeying deterministic dynamics. This solves the problem of free will and basic problem of quantum measurement theory. The superposition of space-time surface would be analogous to superposition of deterministic computer programs, behaviours, or biological functions in classical sense. Free will would select the program.

  2. What memories as learned behaviours are? One can imagine several models, which need not exclude each other.

    1. For instance, could it be that the replicas of ameba have geometric past that is partially shared: the part of the past as amoeba before the replication?

    2. Second TGD explanation would be based on what conditions are? They involve emotions in an essential manner. Emotions are induced and induce behaviors and conditionings involve long term moods. The mysterious epigenetic inheritance could be inheritance of moods affecting gene expression: moods could be inhereted and have time-span of several generations: this conforms with option a).

2.2 What moods are?

Suppose that conditions are due to long term moods in turn correlating with behavior and at basic level with genetic expression. Consider a TGD based model for moods, option b).

  1. Music - its harmony defined by allowed chords - represents emotions and generates them. The allowed 3-chords of bio-harmony, the set of which can vary, would define the mood.

  2. Genes are associated with information. Codon contains 6 bits of information. Magnetic body with large heff is the boss, the "wise guy", controlling biological body and biochemistry so that genetic code must have primary representation at the level of flux tubes. Dark proton sequences at flux tubes interpreted as dark nuclei indeed represent codons as 3-proton units. The states of 3- proton units turn out to correspond to DNA, RNA, tRNA, amino-acids and vertebrate genetic code is predicted.

    Chemical representation would be secondary representation only, mimicry, and often incomplete.

    Dark proton sequences also realizing vertebrate genetic code would also have positive charge neutralizing the negative charge of nucleotides and make DNA stable. Pollack effect would generate the dark flux tube and this would require metabolic energy and in absence of it DNA would not be stable.

  3. Dark proton sequences must also communicate by dark photons with large heff. The communications must rely on resonance, actually there must be resonance between similar 3-proton units, dark codons. Therefore 3-chords consisting 3 dark photons must represent the codons represented by 3 protons. Only identical codons have resonant coupling. This makes possible remote replication of DNA reported by HIV nobelist Montagnier (see this).

  4. Allowed 3-chords define the harmony and emotional state mood. In TGD representations of emotions in terms of bio-harmony would provide the representation of genetic codons defined by RNA as 3-chords of light, triplets of 3 dark photons. The icosatetrahedral model for harmony realizing bioharmony gives also rise to vertebrate genetic code: the 6-bit units defined by codons correspond to ordinary temporarily local intellect, and the harmony to the holistic emotional intellect.

  5. RNA and DNA, tRNA, amino-acids would naturally be represented by light 3-chords in communications. Given codon would only tell its name by the chord and resonate with codon having same name. The codons would couple by chords via triple resonance. Same DNA sequences could be in different mood defined by bioharmony and its expression would depend on this: this would give rise to epigenetics. Epigenetic inheritance would be emotions lasting for several generations.

    The bioharmony associated with RNA could represent the mood infecting also DNA and generating DNA expression giving rise to the behavior related to conditioning.

  6. If this were the case then the inheritance of memories (in this sense could be inheritatance of conditionings as long term moods. The replications of RNAs and DNAs and possible other biomolecules carrying the conditioning would give rise to replication of memories as behaviors induced by moods.

  7. These moods can be very long term moods and extend over generations. This would fit with the model in which replicated amoebas have the 4-D magnetic body amoeba of the geometric past as part of their 4-D magnetic body.

To sum up, behaviors as conditionings could be caused by moods, which can last for several generations. This would bring in magnetic body as active agent. The representation genetic code in terms dark proton sequences and by 3-chords of dark photons would give a realization of both the "bitty" and emotional aspects of intelligence. Also the notions of 4-D brain and organism having temporal span of several generations as space-time surfaces would be essential for the understanding the inheritance of emotions. We should be very careful for what we do since also our children can feel themselves proud of or guilty for what we did.

See the short article Epigenesis, inherited memories and moods lasting over several generations, the article Geometric theory of harmony or the chapter with the same title .

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Thursday, September 26, 2019

Minimization of Gibbs free energy as thermodynamical variational principle in TGD framework

Minimization of Gibbs free energy is applied routinely in bio-chemistry as a thermodynamical variational principle. I have however not applied thermodynamical variational principles systematically in TGD inspired quantum biology. My excuse could be that it is not clear whether dark matter as heff=n× h0 phases is in thermal equilibrium with the ordinary matter. Therefore the arguments have been based mostly on energy minimization and make sense thermodynamically at zero temperature limit.

This article was inspired by highly interesting findings related to the stability of DNA double strand. It has been thought that hydrogen bonds between the bases of the two strands are responsible for the stability. This explanation has been challenged (for a popular article see this). According to the article of Bobo Feng et al, the experimental findings support the proposal that hydrophobic forces are actually responsible for the stability. The function of hydrogen bonds would be to take care of correct base pairing rather than stabilization.

In passive state DNA strands would bind together by hydrophobic forces keeping water out of the interior of DNA double strand forming a kind of dry pocket. When DNA is active - say replication or transcription is occurring - an appropriate enzyme opens DNA by splitting the hydrogen bonds and the interior parts get in contact with water. This process requires energy provided by ATP. After than the process could proceed in TGD Universe as discussed here).

The attempt to gain an improved understanding of hydrophobic interactions led to the realization that I have not been considered the possibility that Gibbs free energy might provide a thermodynamical variational principle applicable also to dark matter as heff=n× h0 phases, in particular allowing to get a quantitative grasp on the model of water as a multi-phase system involving magnetic flux tubes with various values of heff(see this).

See the article Minimization of Gibbs free energy as thermodynamical variational principle in TGD framework or the chapter Dark Nuclear Physics and Condensed Matter of "Hyper-finite Factors, p-Adic Length Scale Hypothesis, and Dark Matter Hierarchy: Part II ".

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Monday, September 23, 2019

How could the representations of genetic code as dark 3-chords and nucleotide triplets relate?

One of the poorly understood aspects of the model is how the various representations of the code relate.

Frequency coding of nucleotides is not possible

Frequency coding of nucleotides would look natural but it is easy to see that it is in conflict with bio-harmony.

  1. The representations as dark proton triplets and dark photon triplets do not involve decomposition to ordered triplet of letters as the ordinary chemical representation does. Dark protons are entangled and one cannot order them and there is no obvious ordering of the frequencies of dark photons.

    This is not a problem for the correspondence between dark proton triplets and dark photon triplets and one can even imagine assignment of dark cyclotron photons with 3 parallel flux tubes acting as wave guides. This could mediate the interaction between dark variants of basic biomolecules with same value of heff as frequency resonance.

  2. The interaction between ordinary DNA/RNA/tRNA and its dark variant should involve the transformation of dark photon triplet associated with flux tube triplet emanating from dark bio-molecule to ordinary photons (possibly bio-photons) and energy resonance would be involved. Is the energy resonance involved with the formation of the dark-ordinary pairs or with the sustainment of these pairings? The example of benzene suggests sustainment.

  3. The assumption that energy resonance is involved with dark-ordinary pairing indeed leads to problems. The first guess would be that ordinary photon triplet somehow carries information about the position of nucleotide in the codon. The 4 nucleotides would correspond to 4 frequencies with frequency scale depending on the position inside the codon. There are indeed 12 frequencies in the 12-note scale so that 3 frequency scales with 4 frequencies associated with each of them would give 64 combinations of frequencies.

    Frequency coding of nucleotides however leads to a problem. The first two letters of the codon are known to determine the amino-acid coded by it to a high degree since the third letter typically distinguishes between 1 or 2 amino-acids only, and labels codons at the orbit of DNA codon defining amino-acid. Therefore for DNA codons coding same amino-acid the first two frequencies should be same. This is not the case for bio-harmony for the simple reason that the frequencies of 3-chords along the orbit defining amino-acids are different. Only the frequency ratios defining the type of the chord are same along the orbit.

    The frequency ratios determine the correspondence so that the correspondence can be only between entire dark and ordinary codons, and cannot be reduced to correspondence between frequencies and letters. Holism does not reduce to reductionism.

Does the impossibility of frequency coding of nucleotides lead to problems with the models of replication and transription?

This becomes a potential problem in the model for DNA replication and transcription to RNA.

  1. The basic picture about bio-catalysis in TGD framework is following. U-shaped magnetic flux tubes emanate from the reactants and can reconnect to form a pair of flux tubes connecting the reactants. The shortening of the flux tube pair by a reduction of heff brings the reactants together and liberates the energy needed to kick the reactants over the potential wall making the reaction rate extremely low otherwise.

    The U-shaped flux tubes or flux tube triplets would be associated with dark codons of dark DNA accompanying DNA strand, and would be formed as the flux tube pair(s) connecting the strands split by the reversal of reconnection. The heff associated with resulting U-shaped flux tubes associated with replicating strands would increase requiring metabolic energy. They would get longer and could act as tentacles scanning the environment to spot similar flux tubes assignable to nucleotides or codons by resonance.

  2. In the standard picture one assumes that nucleotides defining the letters of the codons appear as non-correlated molecules in the environment, and that each codon is built by a stepwise process in which letters attach to it. The letters can respond only to single frequency and cannot "know" which position to attach to. Thefrequency coding is not consistent with the idea that dark photon triplet assigned with the dark codon gives rise to energy resonance with the letters one by one.

    Could the triple resonance occur as single step and attach all 3 nucleotides in single step? Or could the triple resonance be a collective frequency resonance with dark codon already attached to the ordinary codon in the environment. Ordinary-dark pairing by energy resonance would sustain rather than generate DNA strand since otherwise the Coulomb repulsion due to the large negative charge of DNA does not allow stability.

  3. The problem is that it is nucleotides seem to appear in the environment rather than codons. Could the nucleotides of the environment actually form loose codons connected to dark codons by long flux tubes with large value of heff? Could the reduction of heff bringing nucleotides together induce the reduction of flux tube lengths giving rise to ordinary codon? If the reduction of heff for flux tubes occurs nucleotide-by nucleotide, one would have consistency with the standard picture. The simplest picture is following.

    Dark codons are paired with the loose variants ordinary codons. The opening of DNA double strand leads to the splitting of the flux tube pairs connecting the ordinary codons of strands to U-shaped flux tubes, which reconnect with U-shaped flux tubes coming dark codons paired with loose ordinary codons. The reduction of heff d pairs nucleotides of loose codons with those of ordinary codons.

  4. The pairs of dark codons and loose codons would be analogous to tRNA molecules. One can imagine even pre-tRNA molecules with loose coupling of RNA and amino-acid so that replication and transcription would be very similar topological processes. Also RNA transcription and translation of RNA to amino-acids would rely on similar mechanism. The only difference would be that only the second - active - strand would form U-shaped flux tubes connecting with dark RNA codons.

What about remote DNA replication?

This model could also explain remote replication of DNA for which Montagnier et al have reported evidence. Also remote transcription is predicted to be possible. I have already earlier considered a model of remote replication in an article written together with Peter Gariaev who has reported this kind phenomenon already earlier. I have also discussed the findings of Montagnier et al.

  1. The experiment involves two vessels, call them A and B. A contains genes and B only nucleotides - at least according to the standard picture. There is irradiation using 7 Hz frequency not far from the lowest Schumann frequency having a nominal value of 7.8 Hz. What happens is that the replicas of genes appear in B. It is also reported that the DNA generates em radiation possibly responsible for the information transfer.

  2. The proposed model for the ordinary DNA replication generalizes easily to describe also remote replication. The new element would be that the U-shaped flux tubes from A would extend to B - here 7 Hz radiation could be essential - , would be parallel to each other, and have same average length, which is natural if they have same value of heff. Also the experimental arrangement could favor parallel flux tubes. In B the dark codons paired with loose codons formed from ordinary nucleotides would be present, and their U-shaped flux tubes would reconnect with those coming from A. Remote replication could take place: here it is essential that the U-shaped flux tubes are parallel and have very nearly the same length.

    The TGD interpretation would be that the Earth's magnetic body is involved and generates quantum coherence in the length scale at least the size of the system studied. The reported em radiation would naturally relate to the dark photon triplets representing the codons.

Is ZEO needed to understand the replication?

In TGD one must give up thinking in terms of standard ontology of bio-chemistry in which the process is a kinetic process governed by differential equations for the populations of molecules and proceeding in step-wise manner nucleotide by nucleotide. ZEO suggests temporal holism - at least at the level of single dark codon, which cannot be built building brick by building brick.

  1. An open question is in which time scale this temporal quantum holism holds true: in the time scale of addition of single codon or in the time scale of replication of gene or something else? In the following the possibility that temporal holism holds in the time scale for the pairing of dark codons.

  2. In ZEO one could have state function reduction in which initial state corresponds to dark codon plus population of nucleotides and final state to dark codon paired with the ordinary codon formed from 3 nucleotides in energy resonance with the codon formed from nucleotides. What matters are only the initial and final states.

  3. If "big" state function reduction (BSFR) is in question, the final state would correspond to a superposition of deterministic time evolutions leading from the outcome of the reduction to geometric past, possibly but not necessary to a state in which nucleotides do not form codon paired with the dark codon.

  4. The process would create strong correlations between the position of nucleotides of the codon and between
    the positions of codon and its dark variant and therefore a generation of entanglement. Unitary evolutions followed by "small" state function reductions (SSFRs) would generate a state as a superposition of the states satisfying the criteria of the desired final state and other states and BSFR would select the desired final state. It could be followed by BSFR returning the original arrow of time but doing nothing for the state.

See the article An Overall View about Models of Genetic Code and Bio-harmony or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Friday, September 20, 2019

The details of the genetic code in the model based on bio-harmony

TGD suggests several realizations of music harmonies in terms of Hamiltonian cycles representing the notes of music scale, most naturally 12-note scale represented as vertices of the graph used. The most plausible realization of the harmony is as icosahedral harmony (see this and this).

  1. Icosahedron (see this) has 12 vertices and Hamiltonian cycle as a representation of 12-note scale would go through all vertices such that two nearest vertices along the cycle would differ by quint (frequency scaling by factor 3/2 modulo octave equivalene). Icosahedron allows a large number of inequivalent Hamiltonian cycles and thus harmonies characterized by the subgroup of icosahedral group leaving the cycle invariant. This group can be Z6, Z4, or Z2 which acts either as reflection group or corresponds to a rotation by π.

  2. The fusion of 3 icosahedral harmonies with symmetry groups Z6, Z4 and Z2 gives 20+20+20=60 3-chords and 3+1 + 5 + 10 =19 orbits of these under symmetry group and almost vertebrate genetic code when 3-chords are identified as analogs of DNA codons and their orbits as amino-acids. One obtains counterparts of 60 DNA codons and 3+1 + 5 + 10 =19 amino-acids so that 4 DNA codons and 1 amino-acid are missing.

  3. The problem disappears if one adds tetrahedral harmony with 4 codons as faces of tetrahedron and 1 amino-acid as the orbit of the face of tetrahedron. One obtains 64 analogs of DNA codons and 20 analogs of amino-acids. I call this harmony bio-harmony. The predicted number of DNA codons coding for given amino-acid is the number of triangles at the orbit of given triangle and the numbers are those for genetic code.

  4. How to realize the fusion of harmonies? Perhaps the simplest realization that I have found hitherto is based on union of tetrahedron of 3 icosahedrons obtained by gluing tetrahedron to icosahedron along its face which is triangle. The precise geometric interpretation of this realization has been however missing and I have considered several variants. I have proposed that the model could explain the two additional amino-acids Pyl and Sec appearing in Nature.

    There is also a slight breaking of symmetries: ile 4-plet breaks into ile triplet and met singlet and trp double breaks into stop and trp also leu 4-plet can break in leu triplet and ser singlet (see this). This symmetry breaking should be understood.

The following argument suggests a more detailed solution of these problems than proposed earlier.
  1. The copies of icosahedron would differ by a rotation by multiples of 2π/3 (Z3) around axis through the common triangular face. This face unlike the other faces remains un-affected. Also tetrahedron remains un-affected so that it is counted only once.

    If the 3 copies of the icosahedral common face are counted as separate (this is important!), one obtains 20+20+20 faces from icosahedron. If also tetrahedral shared faces is counted as separate, tetrahedron gives 4 faces: 64 codons altogether as required. One obtains 19 orbits from the 3 icosahedra and 1 orbit from tetrahedron: 20 orbits as counterparts of amino-acids altogether.

  2. But can one really counter the 4 common faces as separate? One must do so. Could these faces be interpreted as somehow special codons? Maybe as stop codons or start codons for the vertebrate genetic code which also corresponds to the realization of DNA, RNA ,tRNA, and amino-acids as dark proton triplets so that DNA sequences would correspond to dark proton sequences. Could the shared codons be assigned with various modifications of the vertebrate code involving also exotic amino-acids Pyl and Sec.

  3. Consider first the tetrahedral face. If the common face is removed from the 4-face orbit of tetrahedron, the orbit has only 3 faces and correspond to an amino-acid coded by 3 DNA codons. ile is the only such amino-acid and the interpretation could be that one ile corresponds to the 3 tetrahedral faces and met acting as start codon to the fourth shared face.

  4. Also 3 icosahedral amino-acids corresponding to orbits containing the shared face can lose 1 codon each. To nake this more concrete, one can look for the deviations from the vertebrate code.

    1. There are 10 doublets if the doublet UAA, UAG acting as stop codons is counted as doublet coding for stop regarded formally as amino-acid.

    2. The second member in the doublet UGA, UGG coding for tyr in code table could correspond to a common face and act as a stop codon.

    3. For the modifications of genetic code UAG coding for stop can code for Pyl and UGA coding for stop can also code for Sec. UGA can also code for trp so that there would not be any symmetry breaking in this case. Could UAG and UGA correspond to common faces for two icosahedra?

    4. There is also third icosahedral shared face. CUG coding for leu can also code for ser. Could this correspond to the third exceptional codon associated with the icosahedral part of the code?

  5. If the answers to the questions are affirmative, all basic deviations from the vertebrate code can be understood. The translation of the codons associated with shared face would be unstable for some reason.

    1. 3-chord representation is more fundamental than the chemical one. This could mean that the chords associated with the shared faces are very near to each other so that the correspondence between 3-chord representation and chemical representation of codons becomes unstable if based on triple resonance.

    2. The proposal has indeed been that the 13th vertex implied by tetrahedron corresponds to a note very near to one of the notes of 12-note scale - this note is necessary since the 12-note scale defined by quints gives 12th note slightly more than octave under octave equivalence as discovered already by Pythagoras.

      If this picture is correct, the symmetry breaking of the genetic code would be due to the presence of the face common to icosahedron and tetrahedron and reflect the problem discovered already by Pythagoras. The rational number based Pythagorean scale defined by quints is special: people with absolute pitch prefer it over the well-tempered scale involving powers of irrational number 21/12 requiring extension of rationals.

See the article An Overall View about Models of Genetic Code and Bio-harmony or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Monday, September 16, 2019

How the new view about solar fusion forces to change the ordinary views about nuclear physics?

First a general comment about nuclear physics, which applies with appropriate modifications also to the evolution of theoretical particle physics (or lack of it) after the emergence of standard model followed by GUTS and superstring models.

  1. One can see the standard nuclear physics as a tragic Odysseia due to the stubborn sticking to the naive length scale reductionism. All began with the modelling of nucleons as point like particles inspired by the successes of atomic physics. It turned out that the model for nucleons as point like particles failed and we still do not understand low energy nuclear physics. The wave-mechanical potential models and QFT models assuming the notion of point-like nucleon led to an inflation of nuclear models each of them explaining some aspects of nuclei but a real theory is still missing.

  2. Dark nuclear physics was originally suggested in TGD framework to explain "cold fusion" and later conjectured to allow the understanding of pre-stellar evolution as a step-wise process leading to the gradual heating of matter leading to nuclear fusion. The model relies on nuclear strings and their dark variants as dark nuclear matter. In this article it is argued that this picture leads to a realistic model of nuclear fusion and of stellar core and perhaps entire stellar interior as a dark spaghetti like structure. Ironically, "cold fusion" researchers regarded for decades as the pariahs of physics community, would show the path to follow.

The proposed model involves several new deep ideas inspired by the fusion of general TGD based visions about nuclear physics on one hand and about the formation of galaxies, stars, and planets on the other hand. Behind both visions is the notion about fractal hierarchy of flux tubes formed from cosmic strings by gradual thickening during the cosmic evolution. A further important piece is ZEO based view about quantum state and quantum measurement forcing to modify ordinary quantum mechanical description.
  1. The idea is that Sun and its Kähler magnetic field form a sub-tangle of the galactic tangle associated with a long cosmic string and extending outside Sun, and perhaps including also planets as sub-tangles. This can be made more precise by assuming that total mass of the straight cosmic string portion involved equals to the total mass of the system considered. The estimate from the diameter of Sun suggests that the total mass is few times the solar mass. This model connects closely with the problem of cosmological constant solved by the twistor lift of TGD and solar physics can be associated with one particular value of length scale dependent cosmological constant: also this idea forced by TGD is revolutionary.

  2. Quantum classical correspondence stating that quantum states are superpositions of Bohr orbit like preferred extremals challenges the idea about tunnelling as an essential element of nuclear physics. The first option is that BSFR - identified as ordinary → dark phase transition increasing the value of heff and involving time reversal followed by its reversal - allows wave-mechanical tunnelling as an approximate description. An alternative realization encouraged by M8-H duality would be as SSFR involving no time reversal but discontinuity at the level of space-time development involving TGD counterparts of branes. This option resonates with the idea about sequence of SRFFs as TGD counterpart of a unitary time evolution suggested by the wave mechanical model. In any case, both TGD view about dark matter and ZEO would become part of nuclear physics, and mean giving up standard ontology and standard wave mechanics as a description of nuclei.

    It would not be surprising if similar view about tunnelling could apply also to particle reactions and I have proposed that dark variants of nuclei of M89 hadron physics as scaled variant of ordinary M107 hadron physics have made themselves visible via the observed (but neglected) bumps with masses obtained by scaling up the masses of ordinary mesons by factor 512. Tunnelling would be now from ordinary hadron physics to dark M89 hadron physics.

  3. When one has paradox, one knows that something is wrong with the basic conceptualization. The presence of dark variants of nuclei makes itself directly visible via the conflict between metallicities deduced from spectroscopy and meteorite abundances and those derived from helio-seismology and solar neutrino physics. Besides ordinary nuclei also their dark variants would present and contribute to metallicity in the solar interior.

See the article Solar metallicity problem from TGD perspective or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

New predictions from the flux tube model of galaxies

The proposed solution of the abundance problem of solar models leads to a much more detailed view about
the formation of stars as flux tube tangles. The model allows to relate to radius of the Sun to its mass assuming that Sun has been produced by a thickening of a straight portion of a cosmic string. This
I have proposed that this general vision applies also to the formation of spiral galaxies. This can be tested in the case of Milky Way at order of magnitude level.

  1. The mass M(gal) of the Milky way is estimated to be in the range [.8,4.5]× 1012M(Sun). For a string with maximal string tension this would correspond to a direct string portion with length L(gal)= M(gal)/R(Sun)= M(gal)/M(Sun).
    In fact, this stringy mass formula is known to hold for quite a many astrophysical objects as I learned decades ago in a particle physics conference - in good old times times particle physics conferences allowed non-main-stream talks during the last conference day. This gives the estimate L(gal)∈ [.6,3.3]× 105 ly. The radius Rgal of galaxy is estimated to be in the range [.75,1.0]× 105 ly. The length of string within galactic radius would satisfy Lgal=[.8,3.3]Rgal. The estimate excludes the lower bound. For the upper bound the one has Lgal ∼ 3.3 × Rgal.

    The thickness of the Milky Way is about 2× 103 ly which suggests that the portion of long string making galaxy is soaked up to the galactic plane..

  2. The supermassive blackhole in the galactic center is estimated to have mass M(BH)=4× 106× M(Sun). By scaling this would correspond to a straight cosmic string portion with length LBH∼ .1 ly. The size of the galactic blackhole (see this) is RS,BH∼ 4.4× 10-5 ly giving RS,BH/Lgal∼ 4.4× 10-4. One has Tmax∼ 10-6/G and blackhole corresponds effectively to a string with tension TG∼ 1/2G and length RS,BH so that the ratio would be RS,BH/Lgal ∼ 2G/Tmax∼ 2× 10-6. The straight string with length LBH would have been compressed to a volume of Schwartchild radius RB,S∼ 2-11LBH.

  3. Could the spiral structure of spiral galaxies involving several spiral correspond to a rotating cosmic string thickened to a flux tube? The original model for the spiral structure as a cosmic string at rest in in Robertson-Walker coordinates and seemingly rotating in linear Minkowski coordinates failed since it predicted too weak spiralling. The observed spiral structure could however corresponds to a thickened dark flux tube with lower string tension and longer length.

    If so the length of the original spiral should be about Lgal=3.3× Rgal. Perhaps the primordial configuration of the dark flux tube could be modelled as a cosmic string solution at rest in Robertson-Walker coordinates, which then thickened and gained length becoming more spiral.

  4. For elliptic galaxies (see this) the sizes vary in the range [3× 103, 7× 105] ly (roughly 2 orders of magnitude) and masses in the range [105,1013] ly (8 orders of magnitude!) so that linear relationship between size and mass is excluded. The length L(gal) of the original straight string would be in the range [10-8,7.4× 105] ly giving Lgal∈ [.3× 10-6,1.0]× Rgal. Thus elliptical cannot correspond to cosmic strings. At the upper limit elliptic galaxy could correspond to straight cosmic string and the visible matter would not come from the decay of the cosmic string. This estimate conforms with the earlier proposal that only spiral galaxies correspond to cosmic strings.

See the article Solar metallicity problem from TGD perspective or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Friday, September 13, 2019

Solar metallicity problem from TGD perspective

For ten years ago it was thought that Sun is a well-understood system but more precise computations demonstrated a problem. The metallicities deduced from spectroscopic data deviate strongly from those deduced from helio-seismology and solar neutrino data as described in the Annual Review of Astronomy and Astrophysics by Martin Asplund et al, who were pioneers modelling solar surface as 3-D structure rather than idealizing it with 2-D structure.

The abundances used are determined from meteorites and these estimates are more accurate and are consistent with the values determined by Asplund et al and used also to extrapolate the metallicities in core.

  1. The metallicity of Sun deduced from spectroscopy by Asplund et al would be 1.3 per cent whereas the older model and also helio-seismology give 1.8 per cent metallicity. Is the metallicity indeed 1.3 per cent using standard model to extrapolate the spectroscopic data at surface? Or is it 1.8 per cent deeper in the interior in which case the extrapolation used to deduce metallicity in the interior would not be realistic.

  2. There are also other discrepancies. The height of convective zone at which radiative energy transfer is replaced with convection is given by RCZ= .724R. The predicted He abundance at surface is Ysurf=.231. These values are in conflict with RCZ= .713R and Ysurf=.248 deduced from helio-seismological data. Also density and sound velocity profiles deviate from those deduced from the helio-seismology. The earlier model approximating solar surface as 2-D structure is in excellent accordance with the helio-seismological data.

Dark matter identified as heff=nh0 phases has become key player in TGD inspired new physics being now a crucial element of TGD based view about living matter. Dark nuclear fusion is proposed to provide the new physics allowing to understand "cold fusion". In the following it will be found that dark matter in TGD associated with solar core could provide an elegant solution also to the solar metallicity problem.

In TGD classical physics is an exact part of quantum physics. The tunnelling phenomenon essential for nuclear physics based model of solar nuclear fusion would correspond in TGD to a state function reduction creating a phase consisting of dark nuclei which can fuse without tunnelling due to the reduction of the binding energy scale. State function reduction to ordinary phase leads to the final state of the reaction. In ZEO "big" (ordinary) state function reduction would reverse the arrow of time so that if tunnelling phenomenon is assignable to "big" state function reduction rather than TGD counterpart of "weak" measurement, ZEO would make possible nuclear fusion.

The missing nuclear matter inside core would be dark variants of nuclei associated with dark flux tubes. This would explain the conflict between the metallicities deduced from spectroscopic and meteoritic data on one hand and those deduced from helio-seismic data. The reason is that sound waves and photons in the core couple to both ordinary and dark matter so that helio-seismology gives metallicities as sums of ordinary and dark metallicities. Using the estimate for the thickness of the dark flux tube coming from the TGD based model of "cold fusion", one can estimate the length of dark flux tube inside solar core and it turns out to fill about 30 per cent of its volume.

One can relate the model also to the model for the formation of galaxies, stars, and planets as tangles assignable to cosmic strings thickened to flux tubes implying the decay of their Kähler magnetic energy to ordinary matter in analogy with the decay of inflaton field and nice quantitative estimates follow. Also a connection with twistor lift of TGD predicting hierarchy of cosmological constants emerges and the radius of solar core turns out to corresponds to the value of cosmological constant implied by the amount of missing matter identified as dark matter at flux tubes.

See the article Solar metallicity problem from TGD perspective or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Thursday, September 05, 2019

The problem with SUSY

SUSY is the basic problem of modern physics. Or rather its mis-interpretation forcing Majorana spinors and loss of fermion number conservation. Most importantly, there is no sign about SUSY in this sense at LHC but it seems that the message is still not received.

SUSY has been also a problem of TGD for decades. TGD forces a huge extension of super-conformal invariance by replacing 2-D surfaces with 3-D light-like surfaces. The extended super-conformal and super-symplectic symmetries characterize also the light-cone boundary of 4-D Minkowski space with points replaced with CP2 making the dimension of M4 unique. M4×CP2 is also forced by the existence of twistor lift of TGD.

TGD SUSY must conserve fermion number. How? TGD allows separate conservation of baryon and lepton number and the idea was that right-handed neutrino generates the least broken SUSY as N=2 supersymmetry. The idea was wrong.

The generalization of super-space geometry to a super-geometry of sub-manifolds led to a beatiful generalization of super-imbedding space in which coordinates are hermitian and their superparts are sums of monomials of quarks and antiquarks with vanishing quark number. Leptons are also possible but they are not necessary and actually excluded by SO(1,7) triality.

This also led to a generalization of second quantization of quark field implying SUSY as side product: in particular, theta parameters are replaced with oscillator operators for sparticles are created by local composites of quark oscillator operators. This is something totally new. Number theoretical vision plays crucial role in the picture.

Quark super spinors can have similar structure and the monomials in their expansion possess same electroweak quantum numbers as quarks. Leptons can be regarded as local composites of 3 antiquarks and thus spartners of quarks. SUSY would have been staring us directly to eyes for almost a century! Matter antimatter asymmetry is generated because small CP breaking predicted by TGD favors local composites of quarks as leptons over non-local composites for antibaryons. Standard model spectrum is predicted apart from pseudoscalar for which there exist indications from LHC at correct mass.

The outcome is an explicit proposal for S-matrix: S-matrix would be given by super-variant of the exponential of action defining the super-Kaehler function of "world of classical worlds" (WCW) generalized to super-Kaehler geometry. The construction of unitary S-matrix has been second challenge of TGD for decades. Rather precisely 41 years after the emergence of the basic idea of TGD I can say that it is done now!

Against this background it is somewhat frustrating to see colleagues busily planning new super-collider to test a wrong vision about SUSY already known to be excluded by LHC findings.

For details see the article Recent view about SUSY in TGD Universe .

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Tuesday, September 03, 2019

Do hydrogels learn in presence of irradiation and heating?

A research group in Aalto yliopisto led by professor Olli Ikkala has published an interesting article with title " Programmable responsive hydrogels inspired by classical conditioning algorithm". What is observed
that a system consisting of hydrogel and Gold nanoparticles can get conditioned when it is heated in the presence of irradiation at blue and red wavelengths. Conditioning means that the system melting under heating learns to melt in the presence of only irradiation. The experimenters assume that the Gold nanoparticles forming chains during heating serve as a memory element in the learning.

The TGD based quantum model for the conditioning of hydrogel system relies on TGD inspired general model of living systems extended recently to a model of quantum self-organization in which energy feed serving as metabolic energy feed induces generation of dark matter as heff=nh0 phases of ordinary matter at the magnetic body of the system. In number theoretic vision the presence of these phases correspond to higher algebraic complexity and higher "IQ".

The light signal would generate Pollack effect, which in TGD framework means transfer of protons from photo-acids to dark heff=nh0 protons at magnetic flux tubes parallel to nanoparticle chains. The "IQ" of the system or its magnetic body characterized by heff would increase and it would become able to self-organize. The energy from the heating would be stored to the nanoparticle chains taking the role of proteins as energy storage. Melting would be a self-organization process increasing complexity, and in absence of heating (and perhaps even in its presence) the gel phase would receive the energy needed from the nanoparticle chains. The conditioning in this sense would not be a passive mechanical response. The system would be macroscopic quantum system, and the energy feed would make possible for it to evolve to a higher level of complexity and conscious intelligence.

See the article Do hydrogels learn in presence of irradiation and heating? or the chapter Life-like properties observed in a very simple systems.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Monday, September 02, 2019

Has LIGO observed gravitational echoes in 21 minute time scale?

LIGO has observed for few days ago two gravitonal waves with a time lapse of 21 minutes in the same direction (see this). The events are christened as S190828j and S190828l. This suggests that the signals coule orginate from same event. Gravitational lense effect could be one explanation.

TGD suggests an alternative explanation based on the notion of gravitational flux tubes. Magnetic flux tubes, in particular gravitational flux ones, form loops. The later signal could have spent 21 minutes by rotating around this kind of loop. This rotation can occur several times but the intensity of signal is expected to diminish exponentially if only a constant fraction remains in loop at each turn.

This sticking of radiation inside magnetic loops predicting echo like phenomenon is a general prediction of TGD and I have considered the possible occurrence of this phenomenon for cosmic gamma rays arriving in solar solar system in a model for solar cycle.

This kind of repetition of the signal has been observed already earlier for gravitational waves and has been dubbed "blackhole echoes" (see this) but in a time scale of .1 seconds (fundamental bio-rhythm by the way). For possible TGD based explanations of blackhole echoes see this and this.

The two time scales differ by four orders of magnitude but one cannot exclude same explanation. With light velocity Earth sized loop would correspond to a time lapse of about .1 seconds. Light travels in 21 minutes over a distance of 378 million kilometers to be compared with astronomical unit AU = 150 million kilometers defining the distance of Earth from Sun. Therefore loops in the scale of Earth's orbit around Sun could be involved and perhaps associated with the magnetic body of the collapsed system. .1 seconds defining the time scale for the blackhole echoes in turn corresponds to a circumference of order Earth circumference.

See the article TGD View about Quasars or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.