What's new in

Genes and Memes

Note: Newest contributions are at the top!



Year 2014



TGD inspired model for the formation of exclusion zones from coherence regions

At Thinking Allowed Original there is a link to the talk of Mae-Wan Ho in Conference on the Physics, Chemistry and Biology of Water 2014. It is a very nice representation and I learned new facts highly relevant for my own work.

The main points of Mae were that protons make water aconductor, maybe even superconductor. In TGD framework the statement would be that dark protons flowing along magnetic flux tubes make this possible. I however believe that electronic and even ionic Cooper pairs are are involved. Mae believes also that water associated with collagen networks appears as superfluid in nano-scales. Also this is very attractive idea and if the heff= hgr condition holds as some arguments suggest, then superfluidity allowing macroscopic quantum coherence with gravitational Compton length having no dependence on the mass of particle becoems possible. One of the effects is fountain effect explained elegantly by macroscopic quantum gravitational coherence: water would effectively defy gravitation: this effect might allow testing of the hypothesis.

CDs and EZs

Mae Wan-Ho talked about and compared two notions: CDs (coherent domains of water with size of about micrometer postulated by quantum field theoreticians, in particular Emilio del Giudice) and EZs (exclusion domains with size about 200 micrometers discovered by Gerald Pollack and collaborators experimentally). By the way, in Zero Energy Ontology (ZEO) I talk about causal diamonds (CDs), which are typically much larger than CDs of Giudice et al.

  1. Inside EZ the water forms layered structure consisting of hexagonal layers and the stoichiometry is H1.5O so that every fourth proton must be outside EZ (proton is not accompanied by electron if charge separation takes place: EZ is indeed negatively charged so that one obtains different pHs inside EZ and in its exterior). This state is experimentally heavier than ordinary water.
  2. So called tetrahedral or 4-coordinated water is assigned with CDs. CDs and EZs could correspond to two different p-adic length scales in TGD framework. This state would be less dense than ordinary water. Both CD and EZ contain plasma of almost free electrons. CDs are excited to 12.06 eV just .5 eV below the ionizing potential 12.56 eV. .5 eV which is the nominal value of metabolic energy quantum - probably not an accident.

TGD inspired model for CDs and EZs

I try my best to summarise some very interesting points of the talk and develop in more detail TGD inspired model for EZs and their formation, and the TGD view of metabolism leading to a prediction of new form of metabolism involving dark UV photons from Sun.

  1. The splitting of ordinary water H2O to 2H++2e- + O is a key step in photosynthesis. In particular, it produces oxygen without which which we cannot survive. The splitting process involves two ionizations. The ionisation energy of the first electron 12.56 eV and in ultraviolet much above the metabolic energy quantum around .5 eV. How the splitting of water can be achieved at all? This looks like a very real problem!
  2. CDs/EZs could be the solution to the problem. Inside CD the energy for the splitting of water is much smaller due to the fact that electrons are almost free as already mentioned: if the splitting energy equals to the so called formation energy, it is about .41 eV for CD: nothing but the metabolic energy quantum! Also at the interace of EZ just above the boundary of EZ the electronic states are excited and only an energy of .51 eV - known as formation energy - is needed for the splitting. This suggests that metabolic energy quanta are used to generate EZs and/or CDs in the fundamental step metabolism. Also irradiation at these energies generates CDs/EZs.
  3. My layman logic says that formation energy for EZ must correspond to the energy needed to increase the size of /EZ by a minimum amount. In TGD model this would mean creating one proton-electron pair such that electron remains inside the EZ, whose size thus increases and proton becomes dark proton at dark magnetic flux tube. This step would be also a key step in the splitting of water. Splitting of water and growth of EZ would be essentially the same process. In the case of CD it would seem that charge separation takes place inside CD in the splitting and proton can go outside.

    What comes in mind that the formation of CDs requiring large excitation UV energy of 12.06 eV precedes that of EZs. After the formation of CD and almost free electrons only metabolic energy quantum per proton is required to kick single proton to dark magnetic flux tube. This would conform with the fact that CD radius is about 200 times larger than that of CD meaning that volumes are related by a factor 8×106≈ 223. The formation of EZ would transform tetrahedral water to the hexagonal H1.5O and suck protons to dark protons at magnetic flux tubes. If this picture is correct, the proper identification of formation energy for CD would be as absorption energy for CD equal to 12.06 eV and in UV. Recall that biophoton spectrum extends to UV and dark photons with this energy could be responsible for the formation of CDs. This would adde dark photons transforming to biophotons to the picture.

    The formation of EZ can be seen as pulling out one ordinary proton from ordinary water just above the surface of the EZ and making it dark proton at a magnetic flux tube assignable to the EZ and perhaps connecting it to neighboring EZ for form a quantum coherent network. Dark proton would serve as a current carrier and make water a conductor and perhaps even super-conductor. Even superfluidity can be considered.

  4. The metabolic energy quantum .5 eV can be also assigned with hydrogen bond. Could the process of generating dark proton and increasing the size of EZ by one electron involve cutting of the hydrogen bond binding the proton to the water outside. If so then the only thing keeping the excited water inside CD as a coherent phase would be the bond energy of hydrogen bonds! Maybe this is too simplistic.

    I have proposed earlier that hydrogen bonds are short magnetic flux flux tubes, which can suffer heff increasing phase transition. These flux tubes could in turn experience reconnections with U shaped large heff flux tubes and get connected to the dark web. Mae-Wan Ho also tells that the transfer of proton from covalent OH bond to the middle of hydrogen bond happens with a considerable probability. Could this step precede the increase of heff and reconnection? This would give a connection with hydrogen bonding about which Mae also talked about. These naive models of course cannot be correct in detail but give hopes about fusion of existing chemical thinking and new quantal notions.

  5. A process bringing in mind the formation of EZs occurs as one perturbs molecular bio-systems - that is feeds energy into it. The system "wakes up" from "winter sleep", the globular proteins, which are in resting state with hydrogen bonds at their surface forming kind of ice layer unfold and protein aggregates are formed. Molecular summer begins and ceases when the energy feed is over. Cellular winter begins again. Maybe cellular summer is just temporary formation of EZ layers around the protein involving melting of hydrogen bonds and generation of dark protons making system conscious!

Is a new source of metabolic energy needed?

What remains to be understood is the process generating CDs: where could the UV photons with energy 12.06 eV come? Clearly a new form of metabolism is involved and the only source of energy seems to be the Sun!

  1. Solar radiation cannot however provide UV photons as ordinary photons since UV radiation at these wavelengths is absorbed by the atmosphere. In TGD framework a reasonable candidate for dark radiation with energies in UV range is dark cyclotron radiation with energy E=heff×f: biophotons would be produced in the transformation of dark cyclotron photons to ordinary photons.
  2. Could part of solar UV radiation transform to dark UV photons at magnetic flux tubes of even size scales larger than that of Earth predicted by the model of EEG and arrive along them through the atmosphere? The presence of a new source of metabolic energy is in principle a testable prediction: is the energy feed from the visible part of solar radiation really enough to cover the metabolic energy needs? Here one must however take into account the fact that the UV energy would be received by water. The water from which CDs are eliminated would not allow photosynthesis.
To sum up, if the proposed picture is correct photosynthesis involves formation of EZs and cellular respiration the inverse of this process. As discussed earlier, the purpose of metabolic processes would be basically generation and transfer of negentropic entanglement assignable to large heff states.

See the chapter Quantum gravity, dark matter, and prebiotic evolution or the article TGD inspired model for the formation of exclusion zones from coherence regions. .



How bio-polymers were associated with their dark counterparts?

Ulla gave in the comment section of previous posting a link to article Hydrogen cyanide polymers, comets and the origin of life helping me to discover a new big gap in my knowledge about biology. HCN is everywhere and Miller demonstrated in his classic experiments that 11 out of 20 amino-acids emerge in presence of HCN. It has been later found that well over 20 amino-acids were produced. In my own belief system amino-acids could have appeared first as concrete something "real" and DNA as symbolic representations of this something "real". First at dark matter level and then biochemically.

In TGD Universe one can imagine - with inspiration coming partially from Pollack's experiments - that dark variants DNA, RNA and amino-acids were realized first as dark proton sequences at flux tubes- dark nuclei - I call them just dark DNA, RNA and amino-acids although dark proton sequences are in question. The genetic machinery involving translation and transcription was realized as dark variant and dark DNA was a symbolic representation for dark amino-acids.

How did this dark life give rise to bio-chemical life as its image? This is the question! I can only imagine some further questions.

  1. Was this process like master teaching to a student a skill? Master does it first, and then student mimics. If so, the emergence of amino-acids, mRNA and DNA polymers would not have been purely chemical process. Dark variants of these polymers would have served as templates for the formation of ordinary basic biopolymers, for transcription, and for translation. These templates might have been necessary in order to generate long RNA and DNA sequences: mere chemistry might have not been able to achieve this. Without dark polymers one obtains only bio-monomers, with dark polymers as template one obtains also bio-polymers. Dark polymers would have been the plan, biopolymers the stuff used to build.
  2. Are dark DNA, RNA, amino-acids, etc indeed still there and form binary structures with their biochemical variants as I have indeed proposed?
  3. Are dark translation and transcription processes still an essential part of ordinary translation and transcription? Master-student metaphor suggest that these dark processes actually induce them just like replication of magnetic body could induce the replication of DNA or cell. Visible chemistry would only make visible the deeper "dark chemistry". Apologies for all biochemists who have done heroic work in revealing chemical reaction paths!;-)

How the process assigning biochemical life to dark life could have proceeded? The minimalistic guess is that the only thing that happened was that dark life made itself gradually visible! As a consciousness theoretician I have a temptation to see religious statements as hidden metaphors, at least they provide an excellent manner to irritate skeptics: Dark matter - "the God" made us- the biological life - to its own image;-).

  1. First dark amino-acid sequences were accompanied by ordinary amino-acid sequences so that the dark translation process had now a visible outcome. At this step the presence of HCN was crucial and made the step unavoidable. Also the presence of template was necessary.
  2. Dark mRNA got a visible counterpart in the same manner: the presence of template made possible long RNA polymers. The translation remained basically dark process but made visible by mRNA.
  3. Dark DNA got a visible companion: again the presence of the template was and still is crucial.
What about generation of DNA and RNA? It is known that in reducing atmosphere DNA and RNA nucleobasis are obtained in an environment believed to mimick prebiotic situation: the presence of HCN and ammonia are necessary (see this). Reducing atmosphere does not oxidize, in other worlds does not contain oxygen and other oxidizing agents and can contain also actively reducing agents such as hydrogen and carbon monoxide. There are however some problems.
  1. There is evidence that early Earth atmosphere contained less reducing molecules than thought during times of Miller. If life emerged in the underground water reservoirs as TGD strongly suggests, the usual atmosphere was absent and there are good hopes about reducing atmosphere.
  2. The experiments using reducing gases besides those used in Miller's experiments produce both left and right handed polymers so that chiral selection is missing. This is not a surprise since weak interactions generate extremely small parity breaking for visible matter. If dark proton strings or even dark nuclei are involved, the Compton length of weak gauge bosons can be of the order of atomic length scale or even longer and weak interactions would be as strong as electromagnetic interactions. Therefore chiral selection becomes possible. The simplest option is that chirality selection occurred already for the helical magnetic flux tubes and induced that of biopolymers.
For background see the chapter Evolution in Many-Sheeted Space-time.



Where did the oceans come from?

TGD based vision about life has been developing rapidly thanks to the realization that hierarchy of Planck constants and dark matter could relate directly to criticality: consider only long range correlations, phase separation, and classical non-determinism near critical point as common aspects. Ulla's facebook group (maybe I dare to give the link here) has served as a valuable source of links to the findings which challenge the recent mainstream views and provide inspiration for developing my own views. One of the interesting links today was from Elizabeth Maas to the popular article "Half of the Earth's water formed before the sun was born". The article describes research results providing additional support for the TGD inspired idea about the occurrence of prebiotic evolution in underground water reservoirs shielded from meteorites and cosmic rays. The idea relies on TGD inspired variant of Expanding Earth hypothesis.

  1. Article represents first a standard argument in favor of late formation of seas. The collisions by astreroids and meteorites could have evaporated the water or blown off it in to space. Hence surface water at Earth should have emerged much later. Note that one can replace "water" with "life" in the argument. A related problem is Cambrian explosion: it seems impossible that the evolution could have occurred so fast that highly evolved life forms emerged suddenly.
  2. The researchers however end up to propose that the water emerged already before Sun, and also oceans did so rather early. Carbonaceous chondrites, which formed at the same time as Sun and well before the planets, could have served as a source of water. These meteorites were formed very early, already earlier than Sun. Their composition resembles that of bulk solar system composition. By studying basaltic meteorites from asteroid Vesta, which is known to be formed in the same region as Earth, the reaserachers found that they contain same hydrogen isotopic composition as carbonaeous chondrites.

    This motivates the proposal that chondrites contained the water. A further proposal is that the water reservoirs formed at the surface of Earth as it formed. Here I beg to disagree: the objection represented in the beginning is difficult to circumvent!

The article stimulates several interestig questions in TGD based conceptual framework.
  1. Why not to assume formation of underground water reservoir so that meteorites and UV radiation would not have been a problem? And there is indeed recent evidence for the previous existence of large underground reservoirs. The formation process for Earth could have naturally led to the evaporation of of chondrite water from the interior of Earth and its transfer nearer to surface and getting caught inside reservoirs.

    Also prebiotic life could have evolved in the underground reservoirs and already in chondrites (DNA, RNA, aminoacids, tRNA represented as dark proton sequences at flux tubes) and transformed to the life as we know. Mother Gaia's womb was nice place: no meteorite bombardment, no cosmic rays, and metabolic energy provided by Mother Gaia as dark photons. Cambrian explosion as Earth's radius increased by a factor of two was the birthday of the life as we identify it, the (child;-) water burst to the surface and seas were formed and life began to evolve at the surface of Earth. The greatest stories have fractal structure;-).

    Recall that in TGD continous cosmological expansion at level of space-time sheets is at quantum level replaced with a sequence of phase transitions increasing heff and/or p-adic length scale of the space-time sheet - by p-adic length scale hypothesis most naturally by a factor of two. This kind of transition explains why the continents of Earth fit nicely together to cover entire Earth if the radius is half of its recent value, the emergence of gigantic life forms, etc... (see this).

  2. The basic objection relates to the basic mechanisms of metabolism. What replaced plants receiving metabolic energy from solar light as source of metabolic energy? What replaced Sun? Did the dark photon radiation generated by Earth - or maybe also Sun - and penetrating ordinary matter as dark radiation, replace sun light? Any critical system could generate this radiation and it should not be difficult to identify this kind of system: the boundary between core and mantle is the most obvious candidate for a critical system as also for a rapid self-organization process). I proposed for more than decade ago this option half-jokingly as metabolic sources of IT (intraterrestrial) life as I called it.

  3. Dark photon adiation would have had a universal energy spectrum - the spectrum of biophotons in visible and UV range. Part of it would have transformed to biophotons taking the role of solar radiation as a metabolic energy source. An interesting question is whether the life at the bottom of oceans could give some hints about the counterpart of photosynthesis based on bio-photons? I remember also that also quartz has been mentioned as a source of biophotons but cannot find the reference. The discovery that the metabolic reactions thought to require complex catalytic maschinery can take place in the environment similating ocean bottom (see this) supports the idea about the evolution of life from prebiotic life forms in the womb of Mother Gaia. In TGD framework these prebiotic life forms could correspond to dark proton sequences (dark nuclei) at magnetic flux tubes associated with the negatively charged exclusion zones discovered by Pollack).
About Expanding Earth Hypothesis see the chapter Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life. About criticality see the article Criticality and dark matter.



Harmony, music, and religious myths

I have talked about the notion of harmony based on icosahedral representation of 12-note scale and its connection with biology and consciousness coming from the observation that the number of faces of icosahedron is 20 - the number of amino-acids. The link connecting music with biology would be via the geometry of Platonic solids: icosahedron and also tetrahedron.

The 12 vertices of icosahedron correspond to the notes of the 12-note scale and to some Hamilton's cycle defining a closed curved connecting nearest neighbour vertices: it is closed by octave equivalence and does not intersect itself. Quint cycle assigns to each vertex a note of the scale and thus also to every face (triangle) of the icosahedron a chord. These chords define the harmony and there are 11 cycles/harmonies allowing symmetries (6 cycles without symmetries). They fall in three types corresponding to symmetry group Z6= Z3rot× Z2refl, Z4=Z2rot× Z2refl , and Z2= Z2rot or Z2=Z2refl, which is subgroup of icosahedral isometries A5× Z2refl having 2× 60 elements. Just these groups appeared in the model of genetic code inspired by observations about the structure of the code table telling the numbers N(d) of amino-acids coded by d codons.

These symmetries define a hierarchy of symmetry breakings. This hierarchy has amazing connections with the myths, which I believe to reflect deep facts about consciousness and biology at fundamental level. The story of genesis is a good representative in this respect.

  1. The hierarchy of symmetry breakings proceeding from Z6 down to Z2refl brings strongly in mind evolution as loss of innocence. For Z6 one as 4 orbits. One orbit contains 2 triangles (chords, DNA codons assignable to ile). The other orbits correspond to six codons assignable to amino-acids ser, arg, and leu. The chords at the orbits are major chords and 7-chords, and minor chords and 6-chords for the inverse of the harmony.

    There are no dissonant chords in 0-quint sector: dissonances appear only for the remaining groups as 0-quint chords. This is musical representation of paradize. This harmony is based on 6-note scale for the basic notes of the chords and used by impressionistic composers. Amino-acids correspond to selections of preferred chord from each orbit and there are only four different chords: this sub-harmony is very simple. Life in paradize is simple!

  2. Next comes an intriguing observation. The number of amino-acids obtained as projections of the icosahedral DNA orbits is 19, not 20! One chord does not correspond to amino-acid: it is non-playable chord! Could it be impossible to have 20 amino-acids as projections of the orbits and that 19 is the maximum number? The reason for 19 is that the number of amino-acid of type Z6 is 3+1=4 rather than 5. Therefore there is one "non-playable" chord - located at the "paradize orbit" -, which does not correspond to any amino-acid. The natural identification of the non-playable chord is as one of the aug type chords (say CEG#, which is the last breath in many finnish tangos telling about unhappy love end - something between happy CM and sad Am, "raueta" is finnish word for this manner to come to an end: "expire" might be the nearest english counterpart). This chord is located at the 2-chord orbit related to the other chord of the orbit by half-octave shift (chords could be CEG# and F#BbD), the tritonus denied by church.

    One cannot avoid the associations between non-playable chord and the denied fruit hanging in the tree of good and bad knowledge in the story of Adam and Eve, and its analog in many fairy tales. The non-playable chord also brings in mind the hilarious story of Gödel-Escher-Bach about non-playable record (a truth unprovable in given axiom system).

  3. The hierarchy of symmetry breakings leading from Z6 to Z2refl encourages one to continue with the biblical analogies. Z6, Z4 and Z2rot cycles have half-octave shift as a symmetry: good and evil do not exist in paradise, but dissonances are already there for Z4 and Z2 harmonies - the evil snake! These states correspond to the consciousness of animals, children, and saints. Note that bio-harmony corresponds to the presence of one sub-harmony of type Zn, n=6,4,2.
  4. The banishing from the paradize takes place as Z2refl symmetric harmony replaces Z2rot harmony: half-octave shift is not a symmetry anymore, and one can tell between good and evil, and eventually church decides to deny tritonus as a symbol of evil! Paradise is left as icosahedral and tetrahedral code are fused to form the tetra-icosahedral code - the ordinary genetic code leading to the breaking of Z2refl symmetry.
  5. In banishment punct ("empty" amino-acid) as a counterpart of chord shared by tetrahedron and icosahedron emerges and means stopping of the music piece altogether. Death of the sinner! For unfused codes this chord is playable as Sec/Pyl and the music piece is never-ending: life is eternal in paradise! No notion of time, no sin, no death! Amusingly, impressionist music with 6-note scale is music of "now", attempt to catch this moment.

For details see the chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems or the article Geometric theory of harmony.



Updated version of geometric theory of harmony

For some time ago I introduced the notion of Hamiltonian cycle as a mathematical model for musical harmony and also proposed connection with biology: motivations came from two observations. The number of icosahedral vertices is 12 and corresponds to the number of notes in 12-note system and the number of triangular faces of icosahedron is 20, the number of amino-acids and the number of basic chords for the proposed notion of harmony. This led to a group theoretical model of genetic code and replacement of icosahedron with tetra-icosahedron to explain also the 21st and 22nd amino-acid and solve the problem of simplest model due to the fact that the required Hamilton's cycle does not exist.

This article was meant to be a continuation to the eralier article providing a proposal for a theory of harmony and detailed calculations. It however turned out that the proposed notion of bio-harmony was too restricted: all isosahedral Hamilton cycles with symmetries turned out to be possible rather than only the 3 cycles forced by the assumption that the polarity characteristics of the amino-acids correlate with the properties of the Hamiltonian cycle. This working hypothesis had to be given up. The fuel of the minirevolution was the observation the symmetries of the Hamiltonian cycles (Z6, Z4, Z2) are nothing but the icosahedral symmetries needed to predict the basic numbers of the genetic code and its extension to include also 12st and 22nd amino-acids! Thus icosahedral Hamiltonian cycles predict genetic code without further assumptions. Mathematician cannot simply neglect this kind of connection!

One also ends up with a proposal for what harmony is leading to non-trivial predictions both at DNA and amino-acid level.

  1. 3-adicity and also 2-adicity are essential concepts allowing to understand the basic facts about harmony. The notion of harmony at the level of chords is suggested to reduce to the notion of closeness in the 3-adic metric using as distance the distance between notes measures as the minimal number of quints allowing to connect them along the Hamilton's cycle. In ideal case, harmonic progressions correspond to paths connecting vertex or edge neighbors of the triangular faces of icosahedron.
  2. An extension of icosahedral harmony to tetra-icosahedral harmony was proposed as an extension of harmony allowing to solve some issues of icosahedral harmony relying on quint identified as rational frequency scaling by factor 3/2.

    This extension is kept also now. One must however give up the idea about correlation between polarity characteristics of proteins and properties of Hamilton cycles. One must allow all 11 icosahedral harmonies with symmetries as bio-harmonies: their symmetry groups Z6, Z4, Z2 can be identified as the symmetry groups defined the decomposition of 60 DNA codons to 20+20+20 codons in the model of the genetic code. The 4 remaining DNAs and amino-acids can be assigned to both tetra-icosahedron and tetrahedron and icosahedron regarded as defining separate genetic codes. This explains why stopping codons can code for the 21st and 22nd amino-acid under some circumstances.

    Tetrahedral code is second member in the hierarchy of genetic codes inspired by the notion of Combinatorial Hierarchy M(n+1)= MM(n)= 2M(n)-1 giving the numbers 2, 4,7, 64, 2126,... as numbers of DNA codons. The fourth member would correspond to what I called "memetic code" allowing representation of codons as sequences of 21 DNAs. It is not known whether the Combinatorial Hierarchy of Mersenne primes continues as Hilbert conjectured.

  3. The notion of bio-harmony is partially characterized by the triplet n= (n0,n1, n2), characterizing the numbers of 0-, 1-, and 2-quint chords which in turn correspond to DNA codons in consistency with the observation that codons indeed correspond to triplets of nucleotides. n-quint chord corresponds to a triangle (face of icosahedron) containing n edges of the Hamiltonian. Particular bio-harmony requires a selection of a specific Hamiltonian cycle from each class of cycles (1 Z6 symmetric cycle having n= (2,12,6), 2 Z4 symmetric cycles n ∈{(0,16,4), (4,8,8)}, 3 Z2=Z2rot with n∈{(0,16,4),(2,12,6),(4,8,8)} and 5 Z2=Z2refl symmetric cycles with (n∈ {(2,12,6), (4,8,8)}. Note that the are only three different triplets n.
  4. The model gives for the fusion of icosahedral and tetrahedral cycles just the ordinary genetic code so that it is consistent with the proposal that genetic code is realized also by dark proton sequences. For de-fused icosahedral and tetrahedral codes the common face would code for Pyl and Sec, the well-known 21st and 22nd amino-acid. An amusing "co-incidence" is that met to which genes realized as mRNA code is the first codon of gene. At the level of music met would correspond to the basic chord, "home" from which the simple music pieces often begin!
  5. The original idea was that the rules of bio-harmony could be applied to amino-acid sequences interpreted as sequences of basic 3-chords. DNA would have represented the notes of the music. For given choice of harmony as Hamiltonian cycle meaning selection of of 4, 5 or 10 amino-acids coded by the 20 DNAs in question, the hypothesis had to be modified by replacing amino-acid sequences with DNA sequences.

    These DNA sequences however define also amino-acid sequences identifiable as specific triangle at the orbit of Zn defining the DNA codons assigned to that amino-acid (there is a singular fiber space structure). Together the three 20-plets of DNAs define an amino-acid harmony with (4+5+10 =19 chords with tetrahedral extension defining a harmony with 22 chords/amino-acids). Hence both DNA sequences and amino-acid sequences define "bio-music".

  6. The assumption that harmonic transitions between chords (DNA codons) minimize the distance between chords defined by quint-metric leads to highly non-trivial and testable predictions about both DNA sequences and amino-acid sequences. Negentropy Maximization Principle (NMP) suggests that evolution favors the generation of harmony which should thus increase in the proposed sense for DNA sequences defining particular genes or other functional units of DNA during evolution. Large quint-distances between subsequent codons/chords would tend to polished out under evolutionary pressures.
  7. Could icosahedron, tetrahedron, and tetra-icosahedron have direct physical counterparts in living matter? For instance, water molecules form icosahedral clusters and the chlathrates associated with synaptic contacts have icosahedral symmetries. Tetra-icosahedron has 13 vertices with the added vertex representing one note- say E- in C-key as note with slightly different frequency to resolve the basic problem of rational number based 12-note scale (12 quints give slightly more that 7 octaves). Intriguingly, microtubules consist of basic structures consisting of 13 tubulins with 2 states defining bit: could these bit sequences define representation for the 3-chords and thus representation of sequence of DNA codons and realization of genetic code.
  8. Music is language of emotions and peptides are molecules of emotion as Candace Pert expressed it. Could bio-harmonies serve as direct correlates for emotions? What is bio-music? A natural TGD inspired guess is that sounds can be replaced with heff=n× h dark photons with low frequencies and having energies in the range of bio-photons (visible and UV range maximally effective biologically) as proposed on basis of some physical facts and theoretical ideas kenociteallb/hearing. The frequency spectrum of dark cyclotron photons along magnetic flux tubes would define bio-music as "music of dark light" and bio-harmonies would correlate with emotions and moods.
If one can find various icosahedral Hamilton's cycles one can immediately deduce corresponding harmonies. This would require computer program and a considerable amount of analysis. My luck was that the all this has been done. One can find material about icosahedral Hamilton's cycles in web, in particular the list of all 1024 Hamilton's cycles with one edge fixed (this has no relevance since only shape matters). If one identifies cycles with opposite internal orientations, there are only 512 cycles. If the cycle is identified as a representation of quint cycle giving representation of 12 note scale, one cannot make this identification since quint is mapped to fourth when orientation is reversed. The earlier article about icosahedral Hamiltonian cycles as representations of different notions of harmony is helpful.

The tables listing the 20 3-chords of associated with a given Hamilton's cycle make it possible for anyone with needed computer facilities and music generator to test whether the proposed rules produce aesthetically appealing harmonies for the icosahedral Hamiltonian cycles. Biologist with access to DNA sequences could experiment with DNA codons to see whether their are harmonious in the sense that the distance between subsequent chords assignable to DNA codons tend to be small in quint metric. Note that DNA decomposes to pieces corresponding to different Hamiltonian cycles (harmonies) so that the comparison is not quite straightforward.

For details see the chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems or the article Geometric theory of harmony.



Geometric theory of harmony

For some time ago I introduced the notion of Hamiltonian cycle as a mathematical model for musical harmony and also proposed a connection with biology: motivations came from two observations (see this). The number of icosahedral vertices is 12 and corresponds to the number of notes in 12-note system and the number of triangular faces of icosahedron is 20, the number of aminoacids and the number of basic chords for the proposed notion of harmony. This led to a group theoretical model of genetic code and replacement of icosahedron with tetraicosahedron to explain also the 21st and 22nd amino-acid and solve the problem of simplest model due to the fact that the required Hamilton's cycle does not exist.

This led also to the notion of bioharmony. This article is a continuation to the mentioned article providing a proposal for a theory of harmony and detailed calculations.

  1. 3-adicity and also 2-adicity are essential concepts allowing to understand the basic facts about harmony. The notion of harmony at the level of chords is suggested to reduce to the notion of closeness in the 3-adic metric using as distance the distance between notes measures as the minimal number of quints allowing to connect them along the Hamilton's cycle. In ideal case, harmonic progressions correspond to paths connecting vertex or edge neighbors of the triangular faces of icosahedron.
  2. An extension of icosahedral harmony to tetraicosahedral harmony was proposed as an extension of harmony allowing to solve some issues of icosahedral harmony relying on quint identified as rational frequency scaling by factor 3/2.
  3. The idea that the rules of bioharmony realized on amino-acid sequences interpreted as sequences of basic 3-chords leads to highly non-trivial and testable predictions about amino-acid sequences.
If one can find various icosahedral Hamilton's cycles one can immediately deduce corresponding harmonies. This would require computer program and a considerable amount of anlysis. My luck was that the all this has been done. One can find material about icosahedral Hamilton's cycles in web, in particular the list of all 1024 Hamilton's cycles with one edge fixed (see ) (this has no relevance since only shape matters). If one identifies cycles with opposite internal orientations, there are only 512 cycles. If the cycle is identified as a representation of quint cycle giving representation of 12 note scale, one cannot make this identication since quint is mapped to fourth when orientation is reversed. The earlier article about icosahedral Hamiltonian cycles as representations of different notions of harmony is helpful.

The tables listing the 20 3-chords of associated with a given Hamilton's cycle make it possible for anyone with needed computer facilities and music generator to test whether the proposed rules produce aesthetically appealing harmonies for the icosahedral Hamiltonian cycles.

For details see the chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems or the article Geometric theory of harmony.



More precise view about remote DNA replication

Both Luc Montagnier and Peter Gariaev have found strong evidence for what might be called remote replication of DNA. I have developed a TGD inspired model for remote replication using the data from Peter Gariaev, who has developed the notion of wave DNA waveDNA supported by Montagnier's findings.

Polymer chain reaction (PCR) provides a manner to buildcopies of piece of DNA serving as template. Once single copy is produced, it serves as a template for a further copy so that exponential amplification is achieved. Montagnier's and Gariaev's works suggest however that the synthesis of DNA could also occur without a real matrix DNA as remote replication. According to the proposal of Gariaev DNA template would be remotely represented as what he calls wave DNA. Montagnier uses 7 Hz ELF radiation to obtain the effect whereas Gariaev uses scattering of laser light into large interval of frequencies to achieve the effect.

In TGD approach magnetic body containing dark matter with large Planck constant, the associated cyclotron radiation for which energy scale is proportional to effective Planck constant heff=n× h having large values implying conjectured macroscopic quantum coherence of living matter, dark analog of DNA represented as dark proton sequences at magnetic flux tubes and accompanying ordinary DNA, plus reconnection of U-shaped magnetic flux tubes assignable to the magnetic bodies of bio-molecules and allowing them to recognize each other, are the basic elements. The model has evolved from the attempts to understand water memory and homeopathy in TGD framework (see this).

Both 7 Hz ELF radiation and scattering of laser light would both generate dark photon (large Planck constant) spectrum with a wide spectrum of frequencies but with the same energy which in Gariaev's experiments would naturally be the energy of scatter laser light. The dark photons would provide representation for DNA codons. If 7 Hz frequency radiation involves dark photons with energies of visible photons transforming to ordinary photons before scattering from DNA the outcome would be same as in Gariaev's experiments.

The updated model involves same elements as the model discussed in (see this) but there are also new elements due to the developments in the model of dark DNA allowing to imagine a detailed mechanism for how water can represent DNA and how DNA could be transcribed to dark DNA. The transcription/association represents a rule and rules are represented in terms of negentropic entanglement in TGD framework with pairs of states in superposition representing the instances of the rule. Transition energy serves as a characterizer of a molecule - say DNA codon - and the entangled state is a superposition of pairs in which either molecule is excited or dark DNA codon is excited to higher cyclotron state with same energy: this requires tuning of the magnetic field and sufficiently large value of heff at the flux tube. Negentropic entanglement is due to the exchange of dark photons: this corresponds to wave DNA aspect. Dark cyclotron photons also generate negatively charged exclusion zones (EZs) discovered by Pollack and in this process transform part of protons to dark ones residing at the magnetic flux tubes associated with EZs and forming dark proton sequencies.

For details see the chapter Quantum gravity, dark matter, and prebiotic evolution or the article More Precise View about Remote DNA Replication .



Quantum gravity, dark matter, and prebiotic evolution

The ideas related to prebiotic evolution have developed rather rapidly after the discovery of the hierarchy of Planck constants around 2003 providing a general manner to understand living orgnisms as macroscopic quantum systems.

  1. Magnetic body as carrier of dark matter realized as phases with non-standard value heff=n× h of Planck constant is the key concept in the developments and brings to the description of the living matter a third level besides organism and environment.
  2. EEG and its predicted fractal variants have interpretation in terms of communication from biological body to to magnetic body and as control of biological body by magnetic body. EEG photons are identified as dark photons and the energy spectrum of dark EEG photons is conjectured to correspond to that for bio-photons. Bio-photons would result in the transformation of dark photons to ordinary ones and their energy spectrum would directly reflect the spectrum of endogenous magnetic fields. If heff for given ion is proportional to its mass number, the spectrum of energies for bio-photons resulting from dark cyclotron photons is universal and does not depend on charged particle.
  3. One can now understand the mechanism making Cooper pairs of bio-superconductors stable, possibly even above room temperatures. Also the understanding of cell membrane as Josephson junction has increased considerably. The recent view is that generalized Josephson junction is in question. The Josephson energy identified as the Coulombic energy difference at two sides of the membrane is generalized by including also the difference of cyclotron energies. This contribution dominates, and this explains why the value of metabolic energy currency is roughly 5-10 times higher than the value of Josephson energy.

    One ends up with a model of transmembrane proteins as generalized Josephson junctions by taking a "square root" of the thermodynamical model meaning that Boltzman weights are replaced with their complex square roots. The chemical potential difference of thermodynamical model is replaced with the difference of cyclotron energies. Generalized Josephson energies correspond to the differences of cyclotron energies in the first approximation since Coulombic contribution is small. The communications to the magnetic body by dark photons rely on frequency modulation due to variations of membrane voltage, in particular those induce by nerve pulses.

  4. The totally unexpected observation was that the states of dark protons forming dark nuclei as string like objects correspond in natural manner to DNA,RNA, aminoacids and even tRNA molecules and that vertebrate genetic code is realized naturally, led to the proposal that prebiotic life relies on dark nuclear physics .
  5. Taking seriously the findings related to water memory and homeopathy as well as the findings of Gariaev et al has led to a further progress. In this framework water memory and homeopathy provide direct evidence for the role of dark proton sequences at magnetic flux tubes as prebiotic life forms. The preparation of the homeopathic remedy would induce evolutionary process leading to a generation of a population of regions of water mimicking the magnetic body of the invader molecule. The challenge is to identify these regions.
  6. The understanding of negentropic entanglement as entanglement described by n× n unit matrix and by unitary matrix for entanglement coefficient allowed a more precise understanding of Negentropy Maximization Principle and led to the conjecture that n is nothing but the integer characterizing heff. NMP implies that Universe generates negentropic entanglement, "Akashic records", being analogous to huge library extending quantum jump by quantum jump. It is perhaps not an accident that in quantum computation entanglement matrix is unitary.
  7. There was also another thread related to the ideas about hierarchy of Planck constants. The findings of Nottale suggest that planets correspond to Bohr orbits with gigantic gravitational Planck constant. It took quite a time to realize that the same predictions follow if hgr is associated with pairs formed by microscopic systems and Sun and that in this case the values of hgr could be identified with those of heff.

    Already during first years emerged the idea that the Planck constant characterizes magnetic flux tubes connecting two systems and depends on the quantum numbers of the systems assignable to the interactions in question. Therefore one can speak also about hem assignable to electromagnetic interactions. A vision developed stating that when interaction gets too strong, heff increases so that the perturbation series in powers of 1/heff converges and perturbation theory works. At space-time level this means non-determinism, which is key feature of the basic varioational principle: the space-time sheets connecting initial and final 3-surface at boundaries of CD are n-sheeted for heff=n× h and the sheets co-incide at ends.

  8. The findings of Pollack about exclusion zones and fourth phase of water meant a further breakthrough and led to the proposal that negatively charged exclusion zones (EZs) of water with H1.5O stoichiometry are accompanied by magnetic body carrying dark proton nuclei at the flux tubes. EZs are excellent candidates for primitive life forms and can be identified as the primitive life forms making possible water memory and homeopathy.
  9. The last step of progress relates to the proposal of Tajmar et al that gravimagnetic effect could explain the well-established anomaly relating to the measurement of the mass of Cooper pair in rotating super-conductor. The GRT prediction for the effect is however 28 orders of magnitude too small so that new physics would be needed. The Thomson gravimagnetic field is proportional to h2 so that large value of Planck constant could explain the effect. The value can be estimated and it is of the order of 1014 as required! If it is equal to heff then the energy spectrum of dark EEG photons is that of bio-photons as conjectured earlier!

The following sections describe in detail the outcome of this progress.

  1. In the first section gravimagnetic effect and its biological implications are discussed from TGD point of view.
  2. In the second section the model for water memory and homeopathy is discussed and shown to lead to a general model for how immune system and bio-catalysis could have developed from their primordial versions,how dark proteins might have emerged as concrete representations for invader molecules making it possible to make the invader non-dangerous by attaching to its magnetic body, how DNA and genetic code could have emerged as symbolic representations for the magnetic bodies of invader molecules and later as symbolic representation of the magnetic body of the system itself. ZEO implies that actually time evolution of the magnetic body can be coded by DNA and protein folding could provide a concrete representation for this time evolution.

For details and background see the new chapter Quantum gravity, dark matter, and prebiotic evolution.



To the index page