Sunday, June 17, 2018

Expanding Earth hypothesis, Platonic solids, and plate tectonics as symplectic flow

An FB discussion inspired by the recent findings of NASA suggesting the presence of life under the surface of Mars raised the question whether the TGD based Expanding Earth model is consistent with plate tectonics and with the motivating claim of Adams that the continents fit together nicely to cover the entire surface of Earth if its radius were one half of the recent radius. The outcome was what one might call Platonic plate tectonics.

  1. The expansion would have started from or generated decomposition of the Earth's crust to an icosahedral lattice with 20 faces, which contain analogs of what is known as cratons and having a total area equal to that of Earth before expansion. The prediction for the recent land area fraction is 25 per cent is 4.1 per cent too low. The simplest explanation is that expansion still continues but very slowly.

  2. The craton like objects (hereafter cratons) would move like 2-D rigid bodies and would fuse to form continents.

  3. The memory about the initial state should be preserved: otherwise there would exist no simple manner to reproduce the observation of Adams by simple motions of continents combined with downwards scaling. This might be achieved if cratons are connected by flux tubes to form a network. For maximal connectivity given triangular face is connected by flux tube to to all 3 nearest neighbour faces. Minimal connectivity corresponds to an essentially unique dodecahedral Hamiltonian cycle connecting cratons to single closed string. At least for maximal connectivity this memory would allow to understand the claim of Adams stating that the reduction of radius by factor 1/2 plus simple motions for the continents allow to transform the continents to single continent covering the entire surface of the scaled down Earth.

  4. The dynamics in scales longer than that of craton would be naturally a generalization of an incompressible liquid flow to area preserving dynamics defined by symplectic flow. The assumption that Hamilton satisfies Laplace equation and is thus a real or imaginary part of analytic function implies additional symmetry: the area preserving flow has dual.

For details and links see the article Expanding Earth hypothesis, Platonic solids, and plate tectonics as a symplectic flow or the longer article Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life.

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

Articles and other material related to TGD.

Monday, June 11, 2018

New results in the geometric model of bio-harmony

For some years ago I developed a model of music harmony. As a surprising side product a model of genetic code predicting correctly the number of codons coding given amino-acid emerged. Since music expresses and creates emotions, one can ask whether genes could have "moods" characterized by these bio-harmonies. The fundamental realization could be in terms of dark photon triplets replacing phonon triplets for ordinary music.

  1. The model relies on the geometries of icosahedron and tetrahedron and representation of 12-note scale as so called Hamiltonian cycle at icosahedron going through all 12 vertices of icosahedron. The 20 faces correspond to allowed 3-chords for harmony defined by given Hamiltonian cycle. This brings in mind 20 amino-acids (AAs).

  2. One has three basic types of harmonies depending on whether the symmetries of icosahedron leaving the shape of the Hamiltonian cycle is Z6, Z4 or Z2. For Z2 there are two options: Z2,rot is generated by rotation of π and Z2,refl by reflection with respect to a median of equilateral triangle.

  3. Combining together one harmony from each type one obtains union of 3 harmonies and if there are no common chords between the harmonies, one has 20+20+20 3-chords and a strong resemblance with the code table. To given AA one assigns the orbit of given face under icosahedral isometries so that codons correspond to the points of the orbit and orbit to the corresponding AA. 4 chords are however missing from 64. These one obtains by adding tetrahedron. One can glue it to icosahedron along chosen face or keep is disjoint.

  4. The model in its original form predicts 256 different harmonies with 64 3-chords defining the harmony. DNA codon sequences would be analogous to sequences of chords, pieces of music. Same applies to mRNA. Music expresses and creates emotions and the natural proposal is that these bio-harmonies correlate with moods that would appear already at molecular level. They could be realized in terms of dark photon triplets realized in terms of light and perhaps even music (living matter is full of piezo-electrets). In fact, also the emotions generated by other art forms could be realized using music of dark light.

The model of music harmony is separate from the model of genetic code based on dark proton triplets and one of the challenges has been to demonstrate that they are equivalent. This inspires several questions.
  1. Could the number of harmonies be actually larger than 256 as the original model predicts? One could rotate the 3 fused Hamilton's cycles with respect to each by icosahedral rotations other leaving the face shared by icosahedron and tetrahedron invariant. There are however conditions to be satisfied.

    1. There is a purely mathematical restriction. If the fused 3 harmonies have no common 3-chords the number of coded AAs is 20. Can one give up the condition of having no common 3-chords and only require that the number of coded AAs is 20?

    2. There is also the question about the chemical realizability of the harmony. Is it possible to have DNA and RNA molecules to which the 3-chords of several harmonies couple resonantly? This could leave only very few realizable harmonies.

  2. The model predicts the representation of DNA and RNA codons as 3-chords. Melody is also an important aspect of music. Could AAs couple resonantly to the sums of the frequencies (modulo octave equivalence) of the 3-chords for codons coding for given AA? Could coding by the sum of frequencies appear in the coupling of tRNA with mRNA by codewords and coding by separate frequencies to the letterwise coupling of DNA and RNA nucleotides to DNA during replication and transcription?

  3. What about tRNA. Could tRNA correspond to pairs of harmonies with 20+20+444 codons? What about single 20+4=24 codon representation as kind of pre-tRNA?

  4. What is the origin of 12-note scale? Does genetic code force it? The affirmative answer to this question relies on the observation that 1-1 correspondence between codons and triplets of photons requires that the frequency assignable to the letter must depend on its position. This gives just 12 notes altogether. Simple symmetry arguments fix the correspondence between codons and 3-chords highly uniquely: only 4 alternatives are possible so that it would be possible to listen what DNA sequences sounds in given mood characterized by the harmony.

  5. What disharmony could mean? A possible answer comes from 6 Hamiltonian cycles having no symmetries. These disharmonies could express "negative" emotions.

See the article New results in the model of bio-harmony or the new chapter Geometric theory of bio-harmony

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

Articles and other material related to TGD.

Friday, June 08, 2018

Your eyes are the mirrors of my soul!

A fascinating finding again: neuroscientist Giovanni Caputo reports that staring into someone's eyes for 10 minutes induces an altered state of consciousness.

This findings seems to provide direct support for one of the most radical predictions of TGD based quantum view about brain (see this). Neuroscientists assume that nerve pulse pattern generate in brain sensory mental images, in particular visual mental images. In TGD framework brain would build cognitive representations and decompose perceptive field into standard objects in this manner but would not produce sensory qualia. The sensory mental images would be realized at the level of sensory organs. This would involve repeated feedback by using virtual sensory input from brain (or even magnetic body of brain) to build standardized sensory mental images giving rise to pattern cognition. During REM sleep the virtual sensory input would form the entire sensory input. Nerve pulses are quite two slow to achieve this and they would only generate sensory patways, kind of wave guides, along which dark photons with non-standard value hefff=n×h0 of Planck constant would propagate forth and back.

This view allows to avoid the problem due to the fact that neuronal networks in various sensory areas look very much the same so that it is difficult to understand why they give rise to so different sensory qualia. The obvious objection is phantom limb phenomenon, which could be however understood is the pain in phantom limb is sensory memory of pain. It is indeed possible to produce sensory memories by an electrical stimulation of brain. In TGD the perceptive field would be 4-D and only sensory percepts would be localized to approximate time=constant snapshot having actually a finite duration of about .1 seconds. Memories (as distinguished from learned skills and conditionings) would correspond to contributions to memories from the geometric past.

Staring into eyes experience provides an opportunity to test the idea about virtual sensory input. A fusion of two conscious entities, call them A and B, at some level of self hierarchy might occur. This would involve entanglement, which in TGD framework would accompany the generation of magnetic flux tubes or actually flux tube pairs (by reconnection of flux loops) connecting the eyes of the experiencers and the propagation of the dark photons along flux tubes between the brains of A and B so that visual consciousness would be shared. For instance, A could see the virtual sensory input representing her own face at the face of B. This indeed happened! Volunteers had also out of body experiences (OBEs), had hallucinations of monsters, and saw besides themselves their relatives.

One particular fascinating question is what seeing one's own relatives could mean. The answer depends on whether the subject persons knew each other or not. If not, then the information about relatives of say A would have been transferred from A to B and then returned as virtual sensory input via eyes of B to eyes of A. This is of course possible also when the persons know each other. A would be looking into consciousness mirror defined by B! This experiment would be the first direct realization of fusion of two selves by quantum entanglement. The revolution in neuroscience is now in full swing!

See the article DMT, pineal gland, and the new view about sensory perception or the chapter Quantum Model for Nerve Pulse.

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

Articles and other material related to TGD.

Tuesday, June 05, 2018

When big dream changes to its diametric opposite

In Quanta Magazine there was an article by Robbert Dijkgraaf with title "There Are No Laws of Physics. There's Only the Landscape". Lubos Motl's aggressive rant reflects the deep frustration of superstring fanatics in the situation in which superstring theories are for all practical purposes dead.

The title of the article tells the message. The article repeats the same old wisdom: string model is the only viable model to describe physics. The problem is of course that string model fails to predict anything - as the title indeed tells. The natural reaction would be a simple question: "What went wrong?" but this question is not made. Instead one just gives up the very idea behind physics - that of finding principles that predict the universe as we observe it. Of course, it will predict also many other things but this universe inhabited by us must come out naturally.

In order to understand this it is good to notice that there are two views about mathematics and also physics.

  1. In the first view one tries to identify fundamental structures: classical number fields represent excellent example in this aspect. There are only 4 continuous number fields with real topology: reals, complex numbers, quaternions, and octonions. There is infinite number of p-adic number fields plus finite fields.

  2. In second view one tries to be as generic as possible and allows all imaginable structures.

The first view has traditionally dominated in physics and the very idea about unified theory crystallizes this view. Indeed, in the beginning the Big Good News in superstring theory was that we might have finally found the unique Theory Of Everything! It however turned out to be a hype. Now we are told that the Big Good News is that there is no such theory, only infinite landscape! The view about what is desirable has changed completely! This is actually familiar for psychologists: left brain builds the narrative which best suits to the situation and if all went wrong the new narrative represents the catastrophe as the initial goal!

I must admit being old-fashioned. By taking a sharper look, one begins to realize that this turning of coat is basically about the infinite vanity of human egos. Around 1984 when superstring mania began there was a horrible hurry to write epoch changing papers in the hope of even receiving a Nobel. No-one had time to think whether the basic idea that 2-D string world sheets are fundamental, is realistic. This idea would be realistic, if we lived in 2-D space-time. We however live in 4-D space-time and it would be natural to take 3-D surfaces to be the basic objects: they would represent either particle and 3-space depending on the the size scale of observer.

The idea was that spontaneous compactification would give 4-D space-time effectively. Soon it began to become clear that string model does not work as expected but it was quite too embarrassing to admit this: when too many people are wrong they decide collectively that they are right. Branes were introduced in the hope that 4-D space-time could correspond to brane. Around 1993 or so M-theory emerged as the last desperate attempt to make something out of superstring models. The outcome was landscape and almost a complete loss of predictivity. There were however some general predictions: SUSY at LHC energies, which was not found and the wrong sign of cosmological constant. This led eventually complete re-evaluation of what the great dream should have been: it was the landscape rather than unification of fundamental interactions and quantum theory of gravity!

I was lucky and managed to avoid of dropping to this collective trap. I had started towards the end of 1977 with the basic idea of TGD about space-time as 4-D surface in higher-dimensional space-time of form H=M4×S. This to solve the energy problem of general relativity due to the loss of Poincare symmetries: now they were lifted to H. It soon turned out that TGD can be also seen as a generalization of hadronic string model obtained by replacing string with 3-surface. I published my thesis 1982, 2 years before the first superstring revolution.

In the middle of superstring hysteria the obvious idea about the replacement of strings with 3-surfaces was missed despite that even the fundamental conformal invariance of 2-D string world sheets generalizes for 3-D light-like surfaces by their metric 2-dimensionality. Particles would have as basic building bricks 3-D light-like 3-surfaces at which the signature of the induced metric changes from Minkowskian to Euclidian. This makes 4-D space-time and the decomposition of higher-D imbedding space as H=M4×S unique.

S must be chosen so that H is completely unique both physically and mathematically. S= CP2 provides a geometrization of standard model symmetries, quantum numbers, and classical gauge fields plus gravitation. S= CP2 is also unique also mathematically: only CP2 and S4, E4 (and M4 in generalized sense) allow twistor spaces with Kähler structure. For this choice of H one has also so called M8-H duality . M8 provides number theoretical description using classical number fields part as a dual for the geometric description in terms of H (one could speak of number theoretical compactification which is not dynamical compactification which was hoped to give 4-D space-time in superstring models).

I am proud to confess that TGD view represents the old-fashioned view about unification: extreme local simplicity of dynamics at the fundamental level but topological complexity in all scales for many-sheeted space-time. At QFT limit (standard model plus GRT) the many-sheeted space-time is replaced with single sheeted one in long length scales. Topological information is lost and local dynamics becomes complex. TGD also changes the world view: length scale reductionism is replaced with fractal hierarchies, p-adic physics for various p-adic number fields and real numbers fused to adelic physics brings cognition to the realm of physics, quantum theory of consciousness baed on zero energy ontology and quantum biology emerge as applications or rather essential parts of fundamental physics.

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

Articles and other material related to TGD.

Monday, June 04, 2018

Did animals emerge only 100,000-200,000 y ago or did the mitochondrial mutation rate increase dramatically at that time?

I encountered an interesting popular article telling about findings challenging Darwin's evolutionary theory. The original article of Stoeckle and Thaler is here.

The conclusion of the article is that almost all animals, 9 out of 10 animal species on Earth today, including humans, would have emerged about 100,000 200,000 years ago. According to Wikipedia all animals are assumed to have emerged about 650 million years ago from a common ancestor. Cambrian explosion began around 542 million years ago. According to Wikipedia Homo Sapiens would have emerged 300,000-800,000 years ago.

On basis of Darwin's theory based on survival of the fittest and adaptation to a new environment, one would expect that the species such as ants and humans with large populations distributed around the globe become genetically more diverse over time than the species living in the same environment. The study of so called neutral mutations not relevant for survival and assumed to occur with some constant rate however finds that this is not the case. The study of so called mitochondrial DNA barcodes across 100,000 species showed that the variation of neutral mutations became very small about 100,000-200,00 years ago. One could say that the evolution differentiating between them began (or effectively began) after this time. As if mitochondrial clocks for these species would have been reset to zero at that time as the article states it This is taken as a support for the conclusion that all animals emerged about the same time as humans.

The proposal of (at least ) the writer of popular article is that the life was almost wiped out by a great catastrophe and extraterrestrials could have helped to start the new beginning. This brings in mind Noah's Ark scenario. But can one argue that humans and the other animals emerged at that time: were they only survivors from a catastrophe. One can also argue that the rate of mitochondrial mutations increased dramatically for some reason at that time.

Could one think that great evolutionary leap initiating the differentiation of mitochondrial genomes at that time and that before it the differentiation was very slow for some reason? Why this change would have occurred simultaneously in almost all animals? Something should have happened to the mitochondria and what kind of external evolutionary pressure could have caused it?

  1. To me the idea about ETs performing large scale genetic engineering does not sound very convincing. That only a small fraction of animals survived the catastrophe sounds more plausible idea. Was it great flood? One can argue that animals living in water would have survived in this case. Could some cosmic event such as nearby supernova have produced radiation killing most animals? But is mass extinction really necessary? Could some evolutionary pressure without extinction caused the apparent resetting of mitochondrial clock?

  2. In TGD based quantum biology the great leaps could be caused by quantum criticality perhaps induced by some evolutionary pressure due to some kind of catastrophe. The value of heff=nh0 (h0 is the minimal value of Planck constant) - kind of IQ in very general sense - in some part of mitochondria could have increased and also its value would have fluctuated. Did a new longer length scale relevant to the functioning of mitochondrias emerge? Did the mitochondrial size increase? Here I meet the boundaries of my knowledge about evolutionary biology!

  3. Forget for a moment the possibility of mass extinction. Could the rate of mutations, in particular the rate of neutral mutations, have increased as a response to evolutionary pressure? Just the increased ability to change helps to survive. This rate would become high at quantum criticality due to the presence of large quantum fluctuations (variations of heff). If the mitochondria were far from quantum quantum criticality before the catastrophe, the rate of mutations would have been very slow. Animal kingdom would have lived a period of stagnation. The emerging quantum criticality - forced by a catastrophe but not involving an extinction - could have increased the rate dramatically.

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

Articles and other material related to TGD.

Saturday, June 02, 2018

Replication of sequences of RNA codons is possible also in presence of folding!

There was a very interesting popular article in Spacedaily with title "Scientists crack how primordial life on Earth might have replicated itself" (see this). The research paper "Ribozyme-catalysed RNA synthesis using triplet building blocks" is here.

It is possible to replicate unfolded RNA strands in Lab by using enzymes known as ribozymes, which are RNA counterparts of enzymes, which are amino-adic sequences. In the presence of folding the replication is however impossible. Since ribozymes are in general folded, they cannot catalyze their own replication in this manner. The researchers however discovered that the replication using RNA triplets - genetic codons - as basic unit can be carried out in laboratory even for the folded RNA strands and with rather low error rate. Also the ribozyme involved can thus replicate. For units longer than 3 nucleotides the replication becomes prone to errors.

These findings are highly interesting in TGD framework. In TGD chemical realization of genetic code is not fundamental. Rather, dark matter level would provide the fundamental realizations of analogs of DNA, RNA, tRNA, and amino-acids as dark proton sequences giving rise to dark nuclei at magnetic flux tubes. Also ordinary nuclei correspond in TGD Universe to sequences of protons and neutrons forming string like entities assignable to magnetic flux tubes.

The basic unit representing DNA, RNA and tRNA codon and amino-acid would consist of 3 entangled dark protons. The essential aspect is that by entanglement the dark codons do not decompose to products of letters. This is like words of some languages, which do not allow decomposition to letters. This representation is holistic. As we learn to read and write, we learn the more analytic western view about words as letter sequences. Could the same hold true in evolution so that RNA triplets would have come first as entities pairing with dark RNA codons from from dark proton triplets as a whole? Later DNA codons would have emerged and paired with dark DNA codons. Now the coupling would have have been letter by letter in DNA replication and transcription to mRNA.

It is intriguing that tRNA consists of RNA triplets combined from amino-acids and analogs of mRNA triplets! The translation of mRNA to amino-acids having no 3-letter decomposition of course forces the holistic view but one can ask whether something deeper is involved. This might be the case. I have been wondering whether during RNA era RNA replicated using a prebiotic form of translational machinery, which replicated mRNA rather than translated RNA to protein formed from amino-acids (AAs).

  1. During RNA era amino-acids associated with pre-tRNA molecules would served as catalysts for replication of RNA codons. The linguistic mode would have been "holistic" during RNA er in accordance with the findings of the above experiments. RNA codon would have been the basic unit.

  2. This would have led to a smaller number of RNAs since RNA and RNA like molecules in tRNA are not in 1-1 correspondence. A more realistic option could have been replication of subset of RNA molecules appearing in tRNA in this manner.

  3. Then a great evolutionary leap leading from RNA era to DNA era would have occurred. AA catalyzed replication of RNA would have transformed to a translation of RNA to proteins and the roles of RNA and AA in tRNA would have changed. [Perhaps the increase of heff in some relevant structure as quantum criticality was reached led to the revolution?]

  4. At this step also (subset of) DNA and its transcription to (a subset of) mRNA corresponding to tRNA had to emerge to produce mRNA in transcription. In the recent biology DNA replicates and is transcribed nucleotide by nucleotide rather than using codon as a unit so that DNA and RNA polymerases catalyzing replication and transcription should have emerged at this step. An alternative option would involve the "tDNA" as the analog of "tRNA" and the emergence of polymerases later: this does not however look attractive if one accepts the idea about the transition from holistic to analytic mood.

    The ability of DNA to unwind is essential for the emergence of the "analytic linguistic mode" as an analog of written language (DNA) decomposing codons to triplets of letters. This must have been a crucial step in evolution comparable to the emergence of written language based on letters. Also the counterpart of RNA polymerase and separate RNA nucleotides for transcription should have emerged if not already present.

    The minimal picture would be emergence of a subset of DNA codons corresponding to RNAs associated with pre-tRNA and the emergence of the analogs of DNA and RNA polymerases as the roles of amino-acid and RNA codon in tRNA were changed.

  5. How DNA could have emerged from RNA? The chemical change would have been essentially the replacement of ribose with de-oxiribose to get DNA from RNA and U→ T. Single O-H in ribose was replaced with H. O forms hydrogen bonds with water and this had to change the hydrogen bonding characteristics of RNA.

    If the change of heff =n×h0 (one has h= 6× h0 in the most plausible scenario, see this and this) was involved, could it have led to stabilization of DNA. Did cell membrane emerge and allow to achieve this? I have proposed (see this) that the emergence of cell membrane meant the emergence of new representation of dark genetic code based on dark nuclei with larger value of heff.

The communication between dark and ordinary variants of biomolecules involves resonance mechanism and would also involve genetic code represented as 3-chords, music of light, and it is interesting to see whether this model provides additional insights.
  1. The proposal is that 3-chords assignable to nucleotides as music of light with allowed 64 chords defining what I have called bio-harmony is essential for the resonance (see this, this, and this). The 3 frequencies must be identical in the resonance: this is like turning 3 knobs in radio. This 3-fold resonance would correspond to the analytic mode. The second mode could be holistic in the sense that it would involve only the sum only the sum of the 3 frequencies modulo octave equivalence assigning a melody to a sequence of 3-chords.

  2. The proposal is that amino-acids having not triplet decomposition are holistic and couple to the sum of 3 frequencies assignable to tRNA and mRNA in this manner. Also the RNAs in tRNA could couple to mRNA in this manner. One could perhaps say that tRNA, mRNA and amino-acids codons sing whereas DNA provides the accompaniment proceeding as 3-chords. The couplings of DNA nucleotides to RNA nucleotides would realy on the frequencies assignable to nucleotides.

  3. If the sum of any 3 frequencies associated with mRNA codons is not the same except when the codons code for the same amino-acids, the representation of 3-chords with the sum of the notes is faithful. The frequencies to DNA and RNA nucleotides cannot be however independent of codons since the codons differing only by a permutation of letters would correspond to the same frequency and therefore code for the same amino-acid. Hence the information about the entire codon would be needed also in transcription and translation and could be provided either by dark DNA strand associated with DNA strand or by the interactions between the nucleotides of the DNA codon.

  4. The DNA codon itself would know that if is associated with dark codon and the frequencies assignable to nucleotides are determined by the dark DNA codon. It would be enough that the frequency of the letter depends on its position in the codon so that there would be 3 frequencies for every letter: 12 frequencies altogether.

    What puts bells ringing is that this the number of notes in 12-note scale for which the model of bio-harmony (see this and this) based on the fusion of icosahedral (12 vertices and 20 triangular faces) and tetrahedral geometries by gluing icosahedron and tetrahedron along one face, provides a model as Hamiltonian cycle and produces genetic code as a by-product. Different Hamiltonian cycles define different harmonies identified as correlates for molecular moods.

    Does each DNA nucleotide respond to 3 different frequencies coding for its position in the codon and do the 4 nucleotides give rise to the 12 notes of 12-note scale? There are many choices for the triplets but a good guess is that the intervals between the notes of triplet are same and that fourth note added to the triplet would be the first one to realize octave equivalence. This gives uniquely CEG #, C#FA,DF#/B b, and DG#B as the triplets assignable to the nucleotides. The emergence of 12-note scale in this manner would be a new element in the model of bio-harmony.

    There are 4!=24 options for the correspondence between {A, T, C, G} as the first letter and {C,C#,D,D#}. One can reduce this number by a simple argument.

    1. Letters and their conjugates form pyrimidine-purine pairs T, A and C,G. The square of conjugation is identity transformation. The replacement of note with note defining at distance of half-octave satisfies this condition (half-octave - tritonus - was a cursed interval in ancient music and the sound of ambulance realizes it).
      Conjugation could correspond to a transformation of 3-chords defined as

      CEG# ↔ DF#Bb , C#FA↔ D#GB .

    2. One could have

      {T, C} ↔ {CEG #, C#FA} , {A,G}↔ {DF#Bb,D#GB}

      or

      {T, C} ↔ {DF#Bb,D#GB} , {A,G}↔ {CEG#, C#FA} .

    3. One can permute T and C and A and G in these correspondences. This leaves 8 alternative options. Fixing the order of the image of (T, C) to say (C,C#) fixes the order of the image of (A, G) to (D,D#) by the half-octave conjugation. This leaves 4 choices. Given the bio-harmony and having chosen one of these 4 options one could therefore check what given DNA sequence sounds as a sequence of 3-chords (see this).

      Anyone willing to do this kind of experimentation obtains from me the program modules used the Garage band programs to produce a sequence of chords. A further interesting experiment would be check what kind of melodies come out if one assigns to a chord a note as the sum of frequencies of the chord reduced by octave equivalence to basic octave.

    That the position the frequency associated with the nucleotide depends on its position in the codon would also reflect the biochemistry of the codon and this kind of dependence would be natural. In particular, different frequencies associated with the first and third codon would reflect the parity breaking defining orientation for DNA.

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

Articles and other material related to TGD.

LSND anomaly is here again!

Sabine Hossenfelder told about the finding of MinibooNe collaboration described in arXiv.org preprint Observation of a Significant Excess of Electron-Like Events in the MiniBooNE Short-Baseline Neutrino Experiment.

The findings give strong support for old and forgotten LSND anomaly - forgotten because it is in so blatant conflict with the standard model wisdom. The significance level of the anomaly is 6.1 sigmas in the new experiment. 5 sigma is regarded as the threshold for a discovery. It is nice to see this fellow again: anomalies are the theoreticians best friends.

To me this seems like a very important event from the point of view of standard model and even theoretical particle physics: this anomaly with other anomalies raises hopes that the patient could leave the sickbed after illness that has lasted for more than four decades after it became a victim of the GUT infection.

LSND as also other experiments are consistent with neutrino mixing model. LSND however produces electron excess as compared to other neutrino experiments. Anomaly means that the parameters of the neutrino mixing matrix (masses, mixing angles, phases) are not enough to explain all experiments.

One manner to explain the anomaly would be fourth "inert" neutrino having no couplings to electroweak bosons. TGD predicts both right and left-handed neutrinos and right-handed ones would not couple electroweakly. In massivation they would however combine to single massive neutrino just like in Higgs massivation Higgs gives components for massive gauge bosons and only neutral Higgs having no coupling to photon remains. Therefore this line of thought does not seem terribly promising in TGD framework.

For many years ago I explained the LSND neutrino anomaly in TGD framework as being due to the fact that neutrinos can correspond to several p-adic mass scales. p-Adic mass scale coming as power of 21/2 would bring in the needed additional parameter. The new particles could be ordinary neutrinos with different p-adic mass scales. The neutrinos used in experiment would have p-adic length scale depending on their origin. Lab, Earth's atmosphere, Sun, ... It is possible that the neutrinos transform during their travel to less massive neutrinos.

What is intriguing that the p-adic length scale range that can be considered as candidates for neutrino Compton lengths is biologically extremely interesting. This range could correspond to the p-adic length scales L(k)∼ 2(k-151)/2L(151), k= 151,157, 163, 167, varying from cell membrane thickness 10 nm to 2.5 μm. These length scales correspond to Gaussian Mersennes MG,k=(1+i)k-1. The appearance of four of 4 Gaussian Mersennes in such a short length scale interval is a number theoretic miracle. Could neutrinos or their dark variants with heff= n× h0 (h= 6× h0 is the most plausible option at this moment, see this and this) together with dark variants weak bosons effectively massless below their Compton length have a fundamental role in quantum biology?

For the TGD based new physics and also for LSND anomaly see chapter New Particle Physics Predicted by TGD: Part I of "p-Adic physics".

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

Articles and other material related to TGD.

Thursday, May 24, 2018

Dark valence electrons and color vision

By its large orbital radius dark valence electron (dark in TGD sense, heff=n× h) sees atomic nucleus and other electrons, which are ordinary, effectively as an object of charge Zeff=1. Dark valence electron has reduced mass which in excellent approximation equals to that of electron so that the spectrum of bound state energies and transition energies is scaled down by the factor (h/heff)2. This irrespective of what the atom is. The only condition is that there is single unpaired valence electron guaranteed if Z for the atom is odd. For even Z an odd number of valence electrons must be associated with valence bonds: this would be the case for OH radical for instance.

The dynamics of dark valence electrons is universal with universal transition energy spectrum. One obtains a fractal hierarchy of dynamics labelled by the value of (h/heff)2, where heff=n× h0, h0 the minimal value of Planck constant, not necessary equal to h so that one has h=n0× h0. The quantum critical dynamics characterizing living matter in TGD Universe is indeed universal.

The dark photon communications in living matter could utilize these universal energy spectra besides cyclotron energy spectrum and Larmor spectrum assignable to dark particles at flux tubes and the spectrum of generalized Josephson frequencies assignable to cell membrane. In particular, vision and even other sensory modalities could rely on the transitions induced by the absorption of dark valence electron. In TGD also other sensory percepts are communicated from sensory receptors to the sensory areas of cortex (see this) and also here same universal transition energies of dark valence electrons might be involved.

This hypothesis when combined with the earlier ideas about color qualia leads to a highly predictive and testable model for the perception of colors. In particular the condition h=n0× h0, n0>1, is necessary for the model to work. n0=4 and n0=6 look the most realistic options. For n0=4 the number of values of n=8,9,10 and correspond to the number 3 of color sensitive receptors whereas n0=6 the number of values n=12,13,14,15 suggests the existence of a fourth color receptor sensitive to red light.

The statistical aspects of color summation can be understood from TGD inspired theory of consciousness in terms of the hypothesis that self experiences the mental images of sub-self as kind of statistical averages. The identification of quark colors as fundamental color qualia, the entanglement of quarks and antiquarks to form states in one-one correspondence with charged gluons, and the twistor space of CP2 play key roles in the model of color summation.

Remark: There is experimental evidence for the notion of dark valence electron coming from the decades old anomaly related to rare Earth metals (see this). For TGD based model see this). This finding led to a proposal that valence bonds could also involve non-standard values of Planck constant (see this).

See the article Dark valence electrons and color vision or chapter of "TGD based view about living matter and remote mental interactions" with the same title.