Some applications of TGD inspired quantum biology: bio-catalysis, selection of bio-molecules, and remote metabolism

I wrote a new chapter "Getting philosophical: some comments about the problems of physics, neuroscience, and biology" to the book "TGD based view about consciousness, living matter, and remote mental interactions" as a re-organized and extended version of the original text written 2018 as an article and a section of a chapter of the book.

I added several detailed examples about the application of TGD inspired theory of quantum biology so solve basic problems of quantum biology. The details of the solutions discussed below have emerged during the last year. I have not discussed all problems. For instance, I have not excluded the vision about pre-biotic evolution in TGD Universe for which the recent findings from Mars challenging the Maxwellian view about magnetic fields and characterized as "magnetic madness" provide support (see this).

I have picked up the following examples discussed in the chapter representing the new results related to biocatalysis with application to DNA replication, to the selection of bio-molecules, and genetic code. Second topic is metabolism: I have included also a universal purely thermodynamical model of remote metabolism relying on zero energy ontology. Also a discussion of replication is included.

1. Questions related to bio-chemistry

1.1 Biocatalysis

Bio-catalysis remains a total mystery in bio-chemical approach. Magnetic body carrying dark matter could provide the needed mechanisms. Actually these mechanism would be also basic mechanisms behind water memory and - dare I say it aloud? - homeopathy (see this).

According to TGD view about catalysis, reactants find each other by cyclotron resonance for dark cyclotron radiation assignable to massless extremals (MEs) possibly associated with U-shaped flux tubes. The U-shaped flux tubes of the molecules reconnect to a pair of flux tubes connecting the molecules. This occurs only if the flux tubes have same strength of magnetic field and therefore same thickness by flux quantization. The same value of h_eff guarantees resonance. The next step is the shortening of the flux tubes by a reduction of h_eff and liberating the energy kicking the reactants over the potential wall making the process extremely slow otherwise.

DNA replication, transcription to RNA, and translation of RNA to amino-acids are the fundamental processes in biology and TGD should provide a general model for them. Consider DNA replication as an example.

1. The standard model assumes that DNA opens and nucleotides build up the DNA codons in ordered manner. Nucleotides would be caught one-by-one from the environment by U-shaped flux tubes from DNA reconnecting with similar flux tubes from nucleotides. In the proposed model however dark codons are the fundamental units and expected to induce the process at the level of chemistry. Dark codons do not allow a decomposition to letters. Therefore ordinary codons rather than nucleotides should serve as basic units in energy resonance binding them to dark codons (triple resonance or ordinary resonance with respect to the sum of resonance energies). This looks like a problem for both replication and transcription. Translation in which RNA codons are paired with amino-acids suggests a solution of the problem.
   
   
2. Suppose that dark codons are the basic units also in the environment, and are connected by long flux tubes with rather large h_eff to ordinary nucleotides forming thus loose but actually strongly correlated triplets. Nucleotides would serve as basic units only apparently: the entities in question would be analogous to tRNA codons. In the replication and transcription the dark codons of opening DNA sequences would form flux tube contacts with dark codons in the environment coupled to ordinary loose codons by dark triple resonance.
   

   After that the Planck constant h_eff associated with the connecting flux tubes would be reduced, the flux tubes would shorten and the complementary dark codon would be drawn near the the dark codon associated with DNA. Also the flux tubes connecting the dark codon to the nucleotides would shorten and the codon and complementary codon would form 3 base pairs. Shortening by a reduction of h_eff would provide the energy making the process fast enough. The loose codon property would allow to store the energy needed to make the reaction fast.
   
   

3. This model can explain also the claim of Montagnier et al about remote DNA replication (see this and this). Gariaev et al have reported the same process much earlier and together with Peter Gariaev we have developed a model for the process (see this).
   

   The situation is as follows. One has two vessels A and B: A contains genes and B only nucleotides. The vessels are connected by channels so narrow that the genes cannot leak through them. The system is irradiated at 7 Hz frequency, which is near the lowest Schumann frequency. The generation of the copies of genes in B is reported.
   

   The proposed model suggest that the flux tubes emanating from the dark DNA codons associated with the opening DNA extend to the other side - possibly through the channels so that there is a strong correlation between the directions of flux tubes and their endpoints are close to each other. If they have same value of h_eff they would have same length. They would reconnect with dark codons at the other side connected to nucleotide triplets by long flux tubes and the process would continue in the same manner as in the ordinary replication.
   
   

1.2 What selected the biomolecules?

Now philosopher is asking why only very few candidates for relevant biomolecules are actually selected. Who/what selected and how? This leads to very unpleasant questions circumvented by deciding that the emergence of life was nothing but a thermodynamical fluctuation. It has however become clear that complex organic molecules are present even in interstellar and intergalactic space. The miraculous thermodynamical fluctuation explaining evolution without real evolution would have been really huge.

Philosopher tends to conclude that we simply have no clue about what selection at the bio-molecular level really is and continue that some new physics is involved so that it is time to think giving up the reductionistic narrative.

The selection problem appears also at the level of biochemical reaction pathways. One can imagine endless variety of "reaction vertices". If one assumes that only very few basic "reaction vertices" are allowed but the rest not, one can construct a limited number of reaction pathways. But this is an ad hoc assumption: this selection of allowed reaction pathways certainly occurs but we do not have a slightest idea about the physics behind it.

There is also an analogy with computer science. One can construct endless variety of linguistically correct computer programs: why only very few of them would be selected. And with neuroscience: from a huge array of behavioral patters only some are selected.

Here one can of course try a loophole: Darwinian selection. But there is no selection in the Universe of physicalist. This would require free will and intentionality. The trick does not work.

But what about this network in which biomolecules are connected by this something already mentioned?, asks philosopher. Could this something connect only biomolecules if they are in the same relationship as sender and receiver of radio signal. Could these somethings connect stably only systems possessing common resonance frequencies? Could this criterion could select both the preferred biomolecules and the "reaction vertices" and thus also reaction pathways.

One can develop this idea further.

1. The resonance between systems with the same value of h_eff would be both frequency - and energy resonance. The resonance between systems with different values of h_eff requires change of h_eff of either system so that h_eff is same for the systems. Energy is conserved, which means that the frequency of the photon would change to satisfy E= h_eff,1f₁=h_eff,2f₂ . One would have only energy resonance.
   

   The resonance of dark matter states with bio-molecules would be energy resonance and make it possible for long scales to control short scales by inducing molecular transitions. The transformed photons could have interpretation as bio-photons (see this and this).
   
   

2. One can however argue that mere resonance is not enough to select bio-molecules. Magnetic flux tubes containing dark particles can vary their thickness and by the conservation of the monopole flux also magnetic field and cyclotron frequency so that they can get in resonance with any bio-molecule. A stronger condition is required.
   

   The obvious idea is that also biomolecules can be in resonance and surviving bio-molecules are able to build networks. Selection would not be selection of mere individuals but that of networks able to co-operate. There would be a choir singing resonantly in unisono rather than only resonating pairs. The biomolecules involved would have common transition energies which would poses extremely strong conditions on survivors.
   
   

1.3 Genetic code

Genetic code definitely represents information. Is it really an outcome of thermodynamical fluctuation? Is there some deep mathematics associated with the genetic code?, asks the philosopher now. Be patient!

Genome contains also intronic portion: most of it consists of introns and the intronic portion is the larger the higher the evolutionary level is. The prevailing interpretation has been as "junk". Is it really junk?, wonders philosopher. Luckily, the attitude that trash bin represents the highest level of evolution has begun to slowly change to more rational one.

Could there be a beautiful mathematics behind genetic code? Could it be something similar to codes in computer science and have not only one representation - the chemical one - but numerous representations? If computer science would have developed before genetics - this question would have been completely natural and we would probably know a lot about these representations. Could this dark matter with large Planck constant at these mysterious somethings identified by our philosopher tentatively as magnetic flux tubes realize the really fundamental representation of the genetic code and also of of DNA, RNA, tRNA, and amino-acids (AAs) in information theoretic sense? And could also radiation provide realization of genetic code necessary for communications? This is what the philosopher claims (see this, this, this, and this).

The most plausible vision at this moment is that since magnetic body is the boss, chemical code should be incomplete secondary representation of more fundamental genetic code realized at the level of magnetic body controlling bio-matter. The realizations based on 3-proton triplets and dark light 3-chords defining icosa-tetrahedral representation of the genetic code in terms of Hamiltonian cycles (see this) would be the deeper realizations. There would be several Hamiltonian cycles distinguishing assignable to the same chemical representation of the genetic code. The analogy with music suggests that the realization in terms of 3-chords defining bio-harmony gives rise to quantum correlates of emotions assignable to magnetic body as kind of higher level sensory perceptions. Genetic codon as 6-bit unit would correspond to the "bitty" aspects of intelligence and harmony would correspond to emotional intelligence as the holistic aspect of intelligence (see this). Emotions would be realized already at the level of magnetic body (see this, this, and this) .

The recent findings that the RNA of a conditioned sea snail scattered over neurons of second sea snail in Petri dish generate neuronal correlates of conditioning supports the view that the magnetic body of the RNA of sea snail infects the emotion/mood related to the conditioning. The emotional state, mood, of DNA and RNA would affect gene expression. Epigenesis is a poorly understood in standard biology and could be based on emotional states lasting for several generations. This is natural in ZEO (see this and this).

How different representations of the genetic code relate to each other?

1. The natural hypothesis is that given dark codon generates corresponding light 3-chord in communications and control. Alike likes alike rule of homeopathy suggests that triple resonance between identical codons is the basic mechanism of communications between various representations. Similar codons of DNA sequences would be in resonance if the mood defined by bio-harmony is same for them. For the same value of h_eff one would have both energy and frequency resonance for different values only energy resonance.
   
   
2. The condition that all possible - or at least some - moods coded by Hamiltonian cycles are realized, poses additional conditions on ordinary DNA codons since given codon should be able to respond to several 3-chords resonantly. An open question is whether ordinary codons responds via triple resonance or to the energy associated with the sum of the three frequencies in which case one can consider the possibility that the sum of frequencies does not depend of bio-harmony.
   
   
3. Since dark protons are entangled and do not allow a decomposition to letters, it is not possible to realize the correspondence with ordinary codons by assigning a frequency separately to each nucleotide: the chemical codon reacts as a holistic entity (see this). This gives highly non-trivial conditions on transcription and DNA replication: DNA and RNA nucleotides must form loose codons connected to dark codon by long flux tubes and in transcription/replication these flux tubes shorten. This allows to understand (see this) also the remote replication of DNA reported by Montagnier et al. The loose codons formed by nucleotides and dark codons would be very similar to tRNA codons except that the flux tubes connecting dark codon to nucleotide would be long.
   
   

2. Metabolism

Metabolism is one of the key aspects of biology. We must eat and plants must busily photosynthesize in order to survive. But why metabolic energy feed is needed? Again a mystery.

2.1 Non-equilibrium thermodynamics

Non-equilibrium thermodynamics is one attempt to answer this question. Thermodynamical equilibrium is completely uninteresting, entropy is maximal and in the case of local dynamics the state of system is completely determined by a small sample of it. However, if one has energy feed, situation changes since equilibrium becomes flow equilibrium. The energy feed guarantees that there is macroscopic dynamics rather than mere thermal motion at microscopic level.

Also in this case one has essentially the same situation everywhere unless one introduces macroscopic parameters - also energy flow - depending on time and position to get something more interesting. Simple reaction kinematics determined by differential equations can be replaced with that determined by partial differential equations obtained by allowing diffusion. Also temperature, pressure and other thermodynamical parameters can be allowed to depend on position and time. Turing proposed a model for the coloring of Zebra as outcome of this kind of dynamics. The model for neuronal membrane and nerve pulse generation is also a rough model trying to reproduce basic facts about nerve pulse generation using thermodynamics for neuronal membrane regarded as a capacitor. This is of course a mere parameterization of the situation. TGD leads to a quantum model for the situation (see this). Also the interpretation about the role of nerve pulse patterns at neuronal level changes dramatically (see this and this).

In non-equilibrium thermodynamics one speaks of self-organization. One can generalize this notion to quantum self-organization and the crucial criticality associated to the transitions between different self-organization patterns generalizes to quantum criticality (see this). Could these transitions correspond to spatio-temporal self organization patterns, behaviors, functions, programs. This in turn leads to deep connections with conformal symmetry (even its generalization in TGD), fractality, and universality of the dynamics. It is a pity that biologists do not seem to know much about these possibilities.

Now the philosopher starts to talk about ontology. Try to be patient. In standard physics the 3-D time= constant snapshot defines the state. This belief has led to weird proposals: in quantized general relativity one ends up with a proposal that there is no time at all.

2.2 ZEO based view about quantum self-organization

Could it be that 4-D deterministic time evolution between initial and final states could be more fundamental than the 3-D snapshot? Could superpositions of these 4-D evolutions define quantum states. If so, the state function reductions would occur between these superpositions and their non-determinism would be consistent with the determinism of field equations. Free will would not break laws of physics. It would be like starting new deterministic computer program. Our philosopher calls this ontology Zero Energy Ontology (ZEO) and claims that it leads to a theory of consciousness as a generalization of quantum measurement theory (see this). Irritating.

ZEO based quantum measurement theory predicts that in ordinary state function predicts that the arrow of time changes in ordinary state function reductions but is preserved in "small" state function reductions identifiable as analogs of so called weak measurements. The recent strange findings of Minev et al provide direct evidence for the change of the arrow of time in state function reductions of atomic systems (see this).

ZEO predicts also the possibility of signals propagating backwards in time. This led to the vision that episodal memories involve communications with the brain of geometric past (see this), to the idea that motor actions and sensory perception are time reversals of each other (see this): motor action would involve sending of negative energy control signals to the geometric past, and to the notion of remote metabolism based on quantum credit card mechanism. One can say that the system sends negative energy to a system able to receive it rather than receiving positive energy.

The energy of system as a function of h_eff increases when other parameters are kept constant. It costs energy build intelligence. h_eff for a given sub-system tends also to reduce spontaneously. Hence there must be continual energy feed to keep the level of conscious intelligence. A highly interesting possibility that this condition applies to all self-organizing systems. Self-organization generates long range coherence and requires energy feed. Could it be that dark matter makes itself visible by giving rise to long range correlations and coherence induced by dark matter at the magnetic body of the system (see this)?

Just as life also self-organization involves generation of coherence in long scales and requires energy feed. In the model for living system relying on dark matter as h_eff=n× h₀ phases at magnetic body of the system coherence is induced by quantum coherence of the dark matter, and metabolic energy feed is required to increase h_eff tending to reduce spontaneously. Could self-organization be quite generally modelled in the same manner so that dark matter would make itself visible in everyday physics? Could the realizations of the genetic code in terms of dark nuclei and dark photon 3-chords be involved with the self-organization of water and be involved with morphogenesis?

2.3 Does metabolic energy feed generate conscious information?

The basic question about the role of metabolic energy remains, says the philosopher. What is its real role? Energy feed generates structures and structural complexity means information. It seems that metabolic energy feed involves also a feed of information or generation of information. And because living systems are in question, philosopher cannot avoid the question whether this information is actually conscious information. Is there any other kind of information than conscious information?!

To this question standard physics has no answer: it can only describe entropy mathematically and identification of information as lack of entropy is the easy answer suggested in lack of anything better. The question about a possible measure for conscious information analogous to Shannon entropy is one manner to end up with p-adic physics as a correlate of cognition and the necessary fusion of real and various p-adic physics leads to adelic physics (see this). Adelic physics in turn predicts - surprise- surprise - a hierarchy of phases of matter labelled by the value of Planck constant h_eff/h₀=n defining the dimension of the extension of rationals defining the adele. These phases residing at these somethings defining the networks - magnetic flux tubes - make possible macroscopic quantum coherence inducing the coherence of living matter.

Quite generally, the energies of states as function of h_eff increase. For instance, atomic binding energy scales decreases like h_eff² and cyclotron energies scale like h_eff. In order to generate phases with non-standard value of h_eff energy feed is needed. This energy is identifiable as metabolic energy.

In adelic physics h_eff serves as a measure for the IQ of the living system in well-defined system. The higher its value, the better changes the system has for generating conscious information - and also for destroying it. This leads to a rather concrete view about the origin of good and evil. The ethics and moral are simple: good deed increases the conscious information of the universe. Conscious entity can choose whether to increase the conscious information of the universe or reduce it. Evil deeds indeed lead to a reduction of conscious information of the universe since the doer cannot confess others or even himself what he did. Also the members of community become secretive - complex encryption schemes develop. The self-knowledge of the universe knows is reduced. Luckily, evolution unavoidably occurs in statistical sense and resources of conscious information increase in long enough time scale.

2.4 Remote metabolism as a purely thermodynamical universal mechanism in ZEO

Quite recently (towards end of 2019) I found a more precice formulation for the intuitive notion of remote metabolism, which strongly suggests that energy is conserved in ZEO. There is a decomposition to system and the energy energy source: call them A and B. Intuitively, A receives energy from B by sending negative energy to B. What does this really mean?

1. A "big" (ordinary) state function reduction reversing arrow of time takes place: this would correspond to sending negative energy signal to past. The energy of A+B in the final time reversed state at new passive boundary of CD would be shared in new manner such that one can say that A has received from B the metabolic energy.
   
   
2. Energy would be conserved. I have also considered the interpretation that the total energy of the system associated with CD increases (see this and this): since CD itself breaks Poincare invariance, it seems that one cannot exclude this. However, the Poincare invariance is realized at the level of moduli space for the positions of the either boundary of CD, and one can assume energy conservation. Even the wave functions at the boundary of CD can be taken to be in the representations of Lorentz group acting as its isometries. Plane waves correspond to wave functions in the moduli space for the boundary of CD keeping second boundary fixed.
   
   
3. To make this more precise one must define metabolic energy more precisely by introducing the hierarchy of Planck constants and the fact that the increase of h_eff of sub-system keeping other parameters constant increases it energy. Second law means that A tends to loose energy due to the decrease of h_eff for its sub-systems. This is true also for the time-reversed state but in opposite direction of geometric time so that with respect to standard direction of time the energy increases. This would provide extremely general purely thermodynamical mechanism of remote metabolism.
   
   

See the updated article Getting philosophical: some comments about the problems of physics, neuroscience, and biology 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.

Could Mars have intramartial life?

A popular article in National Geographic (see this) tells about unexpected findings made by the first robotic geophysicist, the Insight lander revealed in the European Planetary Science Congress and the American Astronomical Society. There are odd magnetic pulsations with frequency around 10 mHz (see this) occurring at Martian night-time: for Earth these pulsations occur in frequency range 1 mHz to 1 Hz. Mars has much stronger magnetic field than expected. The magnetic field was detected at heights 96-400 km.

Besides this there is evidence for the existence for a global electrically conductive layer about 6 km below the surface, which suggest an underground reservoir of water. This has enormous implications for potential existence of life in Mars. There is also earlier evidence for the existence of salty, liquid water measuring about 19 km across (see this).

These findings bring in mind TGD based model for expanding Earth (see this, this, and this).

1. The observation is that if Earth has radius one half of itse recent radius the continents fit nicely together to cover entire surface of Earth. This lead to the proposal that during Cambrian explosion in which highly developed life formed mysteriously emerged, the Earth radius grew by factor 2 in a relatively short time. The life would have evolved in Mother Gaia's womb, underground oceans perhaps between crust and astenosphere at depth not larger than 80 km, shielded from cosmic rays and meteoric bombardment.
   
   
2. The sudden expansion can be modelled in TGD inspired new physics as a phase transition increasing the p-adic length scale of Earth and reducing the scale dependent cosmological constant assignable to Earth by factor 1/4: these kind of phase transitions replace smooth cosmological expansion in TGD inspired cosmology.
   

   This led to the splitting of the continuous crust to continents and oceans emerged as the the water from underground oceans containing the highly developed life forms bursted to the surface.
   
   

3. The intriguing coincidence is that Mars has radius which is 1/2 of Earth's recent radius. Could also Mars have underground ocean with rather developed life forms waiting for the moment of birth? Magnetic field is necessary in TGD based model of life and the article tells that Mars has unexpectedly strong magnetic field. It also tells about underground ocean at death about 100 km! The boundary between Earth's core and astenosphere, where the ancient oceans might have been is at dept of about 80 km.
   
   

Some comments about the magnetic field Mars

Some comments about the magnetic field of Mars are in order.

1. Wikipedia article about Earth's magnetosphere (see this) gives a criterion for the height below which magnetic field can survive under the pressure caused by solar wind. The criterion reads
   

   R_CFR_P= (B²/ρ_sw v_sw²)^{1/6 .}
   

   Here R_P is planet radius, B is the strength of the magnetic field at its surface, and ρ_sw and v_sw are the mass density and velocity of solar wind. The ratio R_CF/R_P is essentially the ratio of the density of magnetic energy and density of kinetic energy. This implies that the strength of B is about 10 times higher than the strength of the Earth's magnetic field at surface about .5 Gauss. The recent findings should increase the earlier estimate R_CF/R_P∼ 1 given in Wikipedia. For Earth the thickness of magnetosphere is about 10 times Earth radius giving R_CF/R_P∼ 11 .
   
   

2. The strength of magnetic field behaves like 1/r³ in dipole approximation and scaling R_P by factor 2 would reduce magnetic field strength at surface down by factor 1/8, which is near to value of the Earth's magnetic field strength B_E. Could one think that also Earth had similar magnetic field before the expansion that the expansion of Earth radius by factor 2 gave rise to the recent magnetic field? B_Mars∼ 10B_E however suggests that the magnetic field of Mars in dipole
   approximation should actually extend equally far as the Earth's magnetic field! This does not seem to make sense.
   

   Could one think that the matter at the flux tubes of Martian magnetic field is dark matter as h_eff= nh₀ phases and is not visible in the ordinary sense. For instance, cyclotron energies proportional to h_effeB/m would be much higher than expected. Another option is that the magnetic field corresponds carries monopole fluxes at its flux tubes carrying dark particles.
   
   

Paradox and its solution

What looks mysterious is that if Martian magnetic field is dipole field in reasonable approximation it should be more or less like Earth's magnetic field! One would expect cyclotron radiation and Al. Why it is not seen? The answer could be simple.

1. Also Earth's magnetic field would decompose to stable part for which flux tubes carry quantized monopole flux and ordinary part. Monopole part does not need current to sustain it and this has been used to explain why Earth's magnetic field has not disappeared long time ago. The varying part of the Earth's magnetic field would be created by convection currents in the solar. Since Mars does not have outer core, it would not have this part of magnetic field. I have proposed this model for the maintenance of Earth's magnetic field at (see this.
   
   
2. I have assumed that dark matter as h_eff=n×h₀ phases of ordinary matter essential for life resides at the flux tubes of this field having strength which is 2/5 of the Earth's ordinary magnetic field. I have called this field endogenous magnetic field and its existence and existence of h_eff hierarchy was deduced from the explanation of quantal effects of ELF em fields on vertebrate brain. If Mars has only dark magnetic field, the magnetic field of Mars is invisible! The ordinary part of this magnetic field should appear in the analog of Cambrian explosion as the radius of Mars increases to that of Earth and core radius increase by factor 2 and the core becomes unstable against division to to two layers.
   
   
3. It has been thought that Martian magnetic field is so weak because the outer core of Mars has been seized up in distant past leading to a collapse of the magnetic field. Could one think that the reverse of this process took place for Earth in the expansion and created the outer core, perhaps by splitting of the core to inner and outer core. This picture would fit nicely with the p-adic length scale hypothesis suggesting layered structures with thickness of layer coming as some power of 2: the thickness of core would have double and core would have divided to two layers. If the strength of the Earth's magnetic field has been stronger by factor 8 before Cambrian explosion, this should be seen in magnetic records.
   

   Same would have happened also in Earth and would explain how oxygen atmosphere emerged. Before that various ions from solar wind would have entered to the dark flux tubes and entered to the interior of Earth. Same would happen in Mars now.
   

   The rotation of the outer core would create ordinary magnetic field after the expansion. Before that various ions from solar wind would have entered to the dark flux tubes and entered to the interior of Mars. Same would have happened also in Earth and would explain how oxygen atmosphere emerged in Cambrian explosion and life could burst safely to the surface of Mars.
   
   

4. Intriguingly, Mars has its own version of Norther lights (see this). Without magnetic field auroras should not exist! Could it be that they are dark auroras associated with dark magnetic field of Mars. In reconnections of the magnetic field o Martian magnetic field and those associated with solar wind dark ions would transform to ordinary ones and create Norther and Souther lights. Van Allen belts are in the height range .6-58 Mm (Earth radius is 6,4 Mm). Mars should have dark van Allen belts along which ions of solar wind would end down to the interior of Mars.
   
   
5. What about the pulsed oscillations of Martian magnetic field at frequency around 10 ms, which corresponds to a period of 3.33... minutes detected at the night-side of Mars?
   

   The pulsations could correspond to a biorhythm. Also Earth's magnetic field has pulsations with frequencies varying between 1 mHz and 1 Hz. 1 mHz corresponds to 3/3.6 minutes and 1 Hz to average DNA cyclotron frequency in endogenous magnetic field B_end = .2 Gauss identifiable as dark magnetic field.
   

   Could these pulsations correspond to a heartbeat or breathing of Martian magnetic Mother Gaia - rather concrete pulsation of its magnetic body made from flux tubes and/or sheets? Why the pulsations appear only at the dark side? Could the pressure of the solar wind prevent the pulsations at the day-side?
   
   

One can wonder what the measured magnetic field is. Is it the sum of dark and ordinary part or only ordinary part. If test particles touch all space-time sheets involved, they experience the sum of the magnetic fields so that the usual measurements should give the sum. If it is only the ordinary part, one still would have problem why this field having strength near to Earth's magnetic field is not visible as van Allen belts for instance. The QFT limit of TGD indeed corresponds to the replacement of space-times sheets with single region of Minkowski space and the identification of fields as the sums of the induced fields from various space-time sheets.

About intraplanetary life

The new observations allow to make the existing model for intra-planetary life much more details. The following applies to both Earth and Mars.

1. At Earth the multicellular life forms would have emerged in Cambrian explosion suddenly from the Earth interior as its size increased by factor 2. The expansion would be one stepwise cosmic expansion and associated with the decrease of length scale dependent cosmological constant associated with Earth. Same should happen in Mars sooner or later. So that there is no reason to worry. If we destroy our species and many other at the same time, intelligent life forms will develop in Mars.
   
   
2. If the multicellular life forms represented intraterrestrial life, photosynhesis and even oxygen based life should have evolved in underground ocean. The breathing animals would be like fishes using the oxygen in water.
   
   
3. The dark magnetic flux tubes of planet would have served as channels for solar photons propagating as dark photons to the the ocean in the interior of the planet. Dark photons would have transformed to ordinary photons and used in photosynthesis making possible chemical energy storage. Photosythesis would have produced oxygen O₂ which would not have been lost to outer space now: a good reason for intraplanetary life when oxygen atmosphere is missing.
   

   Thus breathing animals would have become possible besides plants like organisms performing the photosynthesis. Also animal-plants doing photosynthesis themselves can be considered. Even we could use the metabolic energy stored chemically in manner analogous to photosynthesis. The machinery is very similar and there is evidence that even humans can use sunlight as metabolic energy. Pollack effect would be key element here. Pollack effect generates charge separation and thus voltage and this gives rise to a battery.
   
   

See the article New support for the view about Cambrian explosion being caused by rapid increase of Earth radius, shorter article Could Mars have intra-planetary life?, or the chapter 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.

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 h_eff=nh₀ larger than its standard value and responsible for long range quantum correlations. This because the larger the value of h_eff characterizing the phase of ordinary matter is, the larger the energy of the system is, and because h_eff tends to decrease spontaneouly. Phase of ordinary mattter with nonstandard value of h_eff has interpretation as dark matter.
   

   Quantum scales are typically proportional to h_eff 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.

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 h_eff 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 h_eff. 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.

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 h_eff=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 h_eff=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 h_eff(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.

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 h_eff 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 h_eff 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 h_eff 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 h_eff? Could the reduction of h_eff bringing nucleotides together induce the reduction of flux tube lengths giving rise to ordinary codon? If the reduction of h_eff 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 h_eff 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 h_eff. 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.

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 2^1/12 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.

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 h_eff 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 R_gal of galaxy is estimated to be in the range [.75,1.0]× 10⁵ ly. The length of string within galactic radius would satisfy L_gal=[.8,3.3]R_gal. The estimate excludes the lower bound. For the upper bound the one has L_gal ∼ 3.3 × R_gal.
   

   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 L_BH∼ .1 ly. The size of the galactic blackhole (see this) is R_S,BH∼ 4.4× 10^-5 ly giving R_S,BH/L_gal∼ 4.4× 10^-4. One has T_max∼ 10^-6/G and blackhole corresponds effectively to a string with tension T_G∼ 1/2G and length R_S,BH so that the ratio would be R_S,BH/L_gal ∼ 2G/T_max∼ 2× 10^-6. The straight string with length L_BH would have been compressed to a volume of Schwartchild radius R_B,S∼ 2^-11L_BH.
   
   
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 L_gal=3.3× R_gal. 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 L_gal∈ [.3× 10^-6,1.0]× R_gal. 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.

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 R_CZ= .724R. The predicted He abundance at surface is Y_surf=.231. These values are in conflict with R_CZ= .713R and Y_surf=.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 h_eff=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.

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.

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 h_eff=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 h_eff=nh₀ protons at magnetic flux tubes parallel to nanoparticle chains. The "IQ" of the system or its magnetic body characterized by h_eff 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.

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.