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.