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TGD BASED VIEW ABOUT LIVING MATTER AND REMOTE MENTAL INTERACTIONS

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Year 2018



Increase of the dimension of extension of rationals as the emergence of a reflective level of consciousness?

in TGD framework the hierarchy of extensions of rationals defines a hierarchy of adeles and evolutionary hierarchy. What could the interpretation for the events in which the dimension of the extension of rationals increases? Galois extension is extensions of an extension with relative Galois group Gal(rel)= Gal(new)/Gal(old). Here Gal(old) is a normal subgroup of Gal(new). A highly attractive possibility is that evolutionary sequences quite generally (not only in biology) correspond to this kind of sequences of Galois extensions. The relative Galois groups in the sequence would be analogous to conserved genes, and genes could indeed correspond to Galois groups (see this). To my best understanding this corresponds to a situation in which the new polynomial Pm+n defining the new extension is a polynomial Pm having as argument the old polynomial Pn(x): Pm+n(x)=Pm(Pn(x)).

What about the interpretation at the level of conscious experience? A possible interpretation is that the quantum jump leading to an extension of an extension corresponds to an emergence of a reflective level of consciousness giving rise to a conscious experience about experience. The abstraction level of the system becomes higher as is natural since number theoretic evolution as an increase of algebraic complexity is in question.

This picture could have a counterpart also in terms of the hierarchy of inclusions of hyperfinite factors of type II1 (HFFs). The included factor M and including factor N would correspond to extensions of rationals labelled by Galois groups Gal(M) and Gal(N) having Gal(M)⊂ Gal(M) as normal subgroup so that the factor group Gal(N)/Gal(M) would be the relative Galois group for the larger extension as extension of the smaller extension. I have indeed proposed (see this) that the inclusions for which included and including factor consist of operators which are invariant under discrete subgroup of SU(2) generalizes so that all Galois groups are possible. One would have Galois confinement analogous to color confinement: the operators generating physical states could have Galois quantum numbers but the physical states would be Galois singlets.

See the chapter Life and Death, and Consciousness or the article Does M8-H duality reduce classical TGD to octonionic algebraic geometry?.



Are toric Hamiltonian cycles consistent with genetic code?

The icosahedral model for bioharmony has ugly feature in that one must add tedrahedral harmony to obtain 64 rather than only 60 codons and a correspondence with the genetic code. This led to ask whether one could consider a modification of the icosahedral harmony by replacing one of the three isosahedral harmonies in bio-harmony plus tedrahedral harmony with toric harmony with 12 vertices and 24 (rather than 20) triangular faces having therefore 64 chords and 64 genetic codons

It seems that this is possible. The toric harmonies have by following argument 12 DNA doublets which each code single amino-acids. In icosahedral model one has 10 doublets. This corresponds to the almost exact U ↔ C and A ↔ G symmetries of the genetic code. In the following I give the argument in detail.

1. Some basic notions

First some basic notions are in order. The graph is said to be equivelar if it is a triangulation of a surface meaning that it has 6 edges emanating from each vertex and each face has 3 vertices and 3 edges (see this) Equivelarity is equivalent with the folllowing conditions;

  1. Every vertex is 6-valent.
  2. The edge graph is 6-connected.
  3. The graph has vertex transitive automorphism group.
  4. The graph can be obtained as a quotient of the universal covering tesselation (3,6) by a sublattice (subgroup of translation group). 6-connectedness means that one can decompose the tesselation into two disconnected pieces by removing 6 or more vertices
  5. Edge graph is n-connected if the elimation of k<n vertices leaves it connected. It is known that every 5-connected triangulation of torus is Hamiltonian (see this). Therefore also 6-connected (6,3)p=2,q=2 tesselation has Hamiltonian cycles.
  6. The Hamiltonian cycles for the dual tesselation are not in any sense duals of those for the tesselation. For instance, in the case of dodecahedron there is unique Hamiltonian cycle and for icosahedron has large number of cycles. Also in the case of 6,3) tesselations the duals have different Hamilton cycles. In fact, the problem of constructing the Hamiltonian cycles is NP complete.
2. What can one say about the number of Hamiltonian cycles?

Can one say anything about the number of Hamiltonian cycles?

  1. For dodecahedron only 3 edges emanates from a given vertex and there is only one Hamiltonian cycle. For icosahedron 5 edges emanate from given vertex and the number of cycles is rather large. Hence the valence and also closely related notion of n-connectedness are essential for the existence of Hamilton's cycles. For instance, for a graph consisting of two connected graphs connected by single edge, there exist no Hamilton's cycles. For toric triangulations one has as many as 6 edges from given vertex and this favors the formation of a large number of Hamiltonian cycles.
  2. Curves on torus are labelled by winding numbers (M,N) telling the homology equivalence class of the cycle. M and M can be any integers. Curve winds M (N) times around the circle defining the first (second) equivalence homology equivalence class. Also Hamiltonian cycles are characterized by their homology equivalence class, that is pair (M,N) of integers. Since there are only V=12 points, the numbers (M,N) are finite. By periodic boundary conditions means that the translations by multiples of 2e1+2e2 do not affect the tesselation (one can see what this means geometrically from the illustration at this). Does this mean that (M,N) belongs to Z2× Z2 so that one would have 4 homologically non-equivalent paths.

    Are all four homology classes realized as Hamiltonian cycles? Does given homology class contain several representatives or only single one in which case one would have 20 non-equivalent Hamiltonian cycles?

3. It is possible to find the Hamiltonian cycles

It turned out that there exist programs coding for an algorithm for finding whether given graph (much more general than tesselation) has Hamiltonian cycles. Having told to Jebin Larosh about the problem, he sent within five minutes a link to a Java algorithm allowing to show whether a given graph is Hamiltonian (see this): sincere thanks to Jebin! By a suitable modification this algorithm find all Hamiltonian cycles.

  1. The number NH of Hamiltonian cycles is expected to be rather large for a torus triangulation with 12 vertices and 24 triangles and it is indeed so: NH=27816! The cycles related by the isometries of torus tesselation are however equivalent. The guess is that the group of isometries is G= Z2,refl⋌ (Z4,tr⋌ Zn,rot). Zn,rot is a subgroup of local Z6,rot. A priori n∈{2,3,6} is allowed.

    On basis of the article about toric tesselations (see this) I have understood that one has n=3 but that one can express the local action of Z6,rot as the action of the semidirect product Z2,refl× Z3,rot at a point of tesselation. The identity of the global actions Z2,refl× Z3,rot and Z6,rot does not look feasible to me. Therefore G= Z2,refl⋌ (Z4,tr⋌ Z3,rot) with order ord(G)=24 will be assumed in the following (note that for icosahedral tesselation one has ord(G)=120 so that there is symmetry breaking).

    Z4 would have as generators the translations e1 and e2 defining the conformal equivalence class of torus. The multiples of 2(e1+e2) would leave the tesselation invariant. If these arguments are correct, the number of isometry equivalence classes of cycles would satisfy NH,I≥ NH/24=1159.

  2. The actual number is obtained as sum of cycles characterized by groups H⊂ Z12 leaving the cycle invariant and one can write NH,I= ∑H (ord(H)/ord(G)) N0(H) , where N0(H) is the number of cycles invariant under H.

4. What can one say about the symmetry group H for the cycle?

Simple arguments below suggest that the symmetry group of Hamiltonian cycles is either trivial or reflection group Z2,refl.

  1. Suppose that the isometry group G leaving the tesselation invariant decomposes into semi-direct product G= Z2,refl⋌ (Z4,tr⋌ Z3,rot), where Z3,rot leaves invariant the starting point of the cycle. The group H decomposes into a semi-direct product H=Z2,refl ⋌ (Zm,tr× Z3,rot) as subgroup of G=Z2,refl ⋌ (Z4,tr× Z3,rot).
  2. Zn,rot associated with the starting point of cycle must leave the cycle invariant at each point. Applied to the starting point, the action of H, if non-trivial - that is Z3,rot, must transform the outgoing edge to incoming edge. This is not possible since Z3 has no idempotent elements so that one can have only n=1. This gives H=Z2,refl ⋌ (Zm,tr. m=1,2 and m=4 are possible.
  3. Should one require that the action of H leaves invariant the starting point defining the scale associated with the harmony? If this is the case, then only the group H=Z2,refl would remain and invariance under Zrefl would mean invariance under reflection with respect to the axis defined by e1 or e2. The orbit of triangle under Z2,refl would consist of 2 triangles always and one would obtain 12 codon doublets instead of 10 as in the case of icosahedral code.

    If this argument is correct, the possible symmetry groups H would be Z0 and Z2,refl. For icosahedral code both Zrot and Z2refl occur but Z2,refl does not occur as a non-trivial factor of H in this case.

    The almost exact U ↔ C and A ↔ G symmetry of the genetic code would naturally correspond to Z2,refl symmetry. Therefore the predictions need not change from those of the icosahedral model except that the 4 additional codons emerge more naturally. The predictions would be also essentially unique.

  4. If H is trivial Z1, the cycle would have no symmetries and the orbits of triangles would contain only one triangle and the correspondence between DNA codons and amino-acids would be one-to-one. One would speak of disharmony. Icosahedral Hamiltonian cycles can also be of this kind. If they are realized in the genetic code, the almost exact U ↔ C and A ↔ G symmetry is lost and the degeneracies of codons assignable to 20+20 icosahedral codons increase by one unit so that one obtains for instance degeneracy 7 instead of 6 not realized in Nature.

5. What can one say about the characer of toric harmonies?

What can one say about the character of toric harmonies on basis of this picture.

  1. It has been already found that the proposal involving three disjoint quartets of subsequent notes can reproduce the basic chords of basic major and minor harmonies. The challenge is to prove that it can be assigned to some Hamiltonian cycle(s). The proposal is that the quartets are obtained by Z3rot symmetry from each other and that the notes of each quartet are obtained by Z4,tr symmetry.
  2. A key observation is that classical harmonies involve chords containing 1 quint but not 2 or no quints at all. The number of chords in torus harmonies is 24 =2× 12 and twice the number of notes. The number of intervals in turn is 36, 3 times the number of the notes. This allows a situation in which each triangle contains one edge of the Hamiltonian cycle so that all 3-chords indeed have exactly one quint.
  3. By the above argument harmony possesses Z2 symmetry or no symmetry at all and one has 12 codon doublets. For these harmonies each edge of cycle is shared by two neighboring triangles containing the same quint. A possible identification is as major and minor chords with same quint. The changing of the direction of the scale and the reflection with respect to the edges the Hamiltonian cycle would transforms major chords and minor chords along it to each other and change the mood from glad to sad and vice versa.

    The proposed harmony indeed contains classical chords with one quint per chord and for F,A,C # both minor and major chords are possible. There are 4 transposes of this harmony.

  4. Also Hamiltonian cycles for which n triangles contain two edges of Hamiltonian path (CGD type chords) and n triangles contain no edges. This situation is less symmetric and could correspond to a situtation without any symmetry at all.
  5. One can ask whether the classical harmonies corresponds to 24 codons assignable to the toric harmony and to the 24 amino-acids being thus realizable using only amino-acids. If so, the two icosahedral harmonies would represent kind of non-classical exotics.
See the chapter Geometric theory of harmony, the article Geometric theory of harmony or the article New results in the model of bio-harmony.



Can one imagine a modification of bio-harmony?

I have developed a rather detailed model of bio-harmony as a fusion of 3 icosahedral harmonies and tetrahedral harmony (see this and this). The icosahedral harmonies are defined by Hamiltonian cycles at icosahedron going through every vertex of the icosahedron and therefore assigning to each triangular face an allowed 3-chord of the harmony. The surprising outcome is that the model can reproduces genetic code.

The model for how one can understand how 12-note scale can represent 64 genetic codons has the basic property that each note belongs to 16 chords. The reason is that there are 3 disjoint sets of notes and given 3-chord is obtained by taking 1 note from each set. For bio-harmony obtained as union of 3 icosahedral harmonies and tetrahedral harmony note typically belongs to 15 chords. The representation in terms of frequencies requires 16 chords per note.

If one wants consistency one must somehow modify the model of icosahedral harmony The necessity to introduce tetrahedron for one of the 3 fused harmonies is indeed an ugly looking feature of the model. The question is whether one of the harmonies could be replaced with some other harmony with 12 notes and 24 chords. If this would work one would have 64 chords equal to the number of genetic codons and 5+5+6 =16 chords per note. The addition of tetrahedron would not be needed.

One can imagine toric variants of icosahedral harmonies realized in terms of Hamiltonian cycles and one indeed obtains a toric harmony with 12 notes and 24 3-chords. Bio-harmony could correspond to the fusion of 2 icosahedral harmonies with 20 chords and toric harmony with 24 chords having therefore 64 chords. Whether the predictions for the numbers of codons coding for given amino-acids come out correctly for some choices of Hamiltonian cycles is still unclear. This would require an explicit construction of toric Hamiltonian cycles.

1. Previous results

Before discussing the possible role of toric harmonies some previous results will be summarized.

1.1 Icosahedral bio-harmonies

The model of bio-harmony starts from a model for music harmony as a Hamiltonian cycle at icosahedron having 12 vertices identified as 12 notes and 20 triangular faces defining the allowed chords of the harmony. The identification is determined by a Hamiltonian cycle going once through each vertex of icosahedron and consisting of edges of the icosahedral tesselation of sphere (analog of lattice): each edge corresponds to quint that is scaling of the frequency of the note by factor 3/2 (or by factor 27/12 in well-tempered scale). This identification assigns to each triangle of the icosahedron a 3-chord. The 20 faces of icosahedron define therefore the allowed 3-chords of the harmony. There exists quite a large number of icosahedral Hamiltonian cycles and thus harmonies.

The fact that the number of chords is 20 - the number of amino-acids - leads to the question whether one might somehow understand genetic code and 64 DNA codons in this framework. By combining 3 icosahedral harmonies with different symmetry groups identified as subgroups of the icosahedral group, one obtains harmonies with 60 3-chords.

The DNA codons coding for given amino-acid are identified as triangles (3-chords) at the orbit of triangle representing the amino-acid under the symmetry group of the Hamiltonian cycle. The predictions for the numbers of DNAs coding given amino-acid are highly suggestive for the vertebrate genetic code.

By gluing to the icosahedron tetrahedron along common face one obtains 4 more codons and two slightly different codes are the outcome. Also the 2 amino-acids Pyl and Sec can be understood. One can also regard the tetrahedral 4 chord harmony as additional harmony so that one would have fusion of four harmonies. One can of course criticize the addition of tetrahedron as a dirty trick to get genetic code.

The explicit study of the chords of bio-harmony however shows that the chords do not contain the 3-chords of the standard harmonies familiar from classical music (say major and minor scale and corresponding chords). Garage band experimentation with random sequences of chords requiring conservability that two subsequent chords have at least one common note however shows that these harmonies are - at least to my opinion - aesthetically feasible although somewhat boring.

1.2 Explanation for the number 12 of notes of 12-note scale

One also ends up to an argument explaining the number 12 for the notes of the 12-note scale (see this). There is also second representation of genetic code provided by dark proton triplets. The dark proton triplets representing dark genetic codons are in one-one correspondence with ordinary DNA codons. Also amino-acids, RNA and tRNA have analogs as states of 3 dark protons. The number of tRNAs is predicted to be 40.

The dark codons represent entangled states of protons and one cannot decompose them into a product state. The only manner to assign to the 3-chord representing the triplet ordinary DNA codon such that each letter in {A,T,C,G} corresponds to a frequency is to assume that the frequency depends on the position of the letter in the codon. One has altogether 3× 4=12 frequencies corresponding to 3 positions for given letter selected from four letters.

Without additional conditions any decomposition of 12 notes of the scale to 3 disjoint groups of 4 notes is possible and possible chords are obtained by choosing one note from each group. The most symmetric choice assigns to the 4 letters the notes {C, C #, D, D#} in the first position, {E,F, F #, G} in the second position, and {G #, A, B b, B} in the third position. The codons of type XXX would correspond to CEG# or its transpose. One can transpose this proposal and there are 4 non-quivalent transposes, which could be seen as analogs of music keys.

Remark: CEG# between C-major and A-minor very often finishes finnish tango: something neither sad nor glad!

One can look what kind of chords one obtains.

  1. Chords containing notes associated with the same position in codon are not possible.
  2. Given note belongs to 6 chords. In the icosahedral harmony with 20 chords given note belongs to 5 chords (there are 5 triangles containing given vertex). Therefore the harmony in question cannot be equivalent with 20-chord icosahedral harmony. Neither can the bio-harmony with 64 chords satisfy the condition that given note is contained by 6 3-chords.
  3. First and second notes of the chords are separated by at least major third as also those second and third notes. The chords satisfy however octave equivalence so that the distance between the first and third notes can be smaller - even half step - and one finds that one can get the basic chords A-minor scale: Am, Dm, E7, and also G and F. Also the basic chords of F-major scale can be represented. Also the transposes of these scales by 2 whole steps can be represented so that one obtains Am, C #m, Fm and corresponding major scales. These harmonies could allow the harmonies of classical and popular music.
These observations encourage to ask whether a representation of the new harmonies as Hamiltonian cycles of some tesselation could exist. The tesselation should be such that 6 triangles meet at given vertex. Triangular tesselation of torus having interpretation in terms of a planar parallelogram (or perhaps more general planar region) with edges at the boundary suitable identified to obtain torus topology seems to be the natural option. Clearly this region would correspond to a planar lattice with periodic boundary conditions.

2. Is it possible to have toric harmonies?

The basic question is whether one can have a representation of the new candidate for harmonies in terms of a tesselation of torus having V= 12 vertices and F= 20 triangular faces. The reading of the article "Equivelar maps on the torus" (see this) discussing toric tesselations makes clear that this is impossible. One however have (V,F)= (12,24) (see this). A rather promising realization of the genetic code in terms of bio-harmony would be as a fusion of two icosahedral harmonies and toric harmony with (V,F)= (12,24). This in principle allows also to have 24 3-chords which can realize classical harmony (major/minor scale).

  1. The local properties of the tesselations for any topology are characterized by a pair (m,n) of positive integers. m is the number of edges meeting in given vertex (valence) and n is the number of edges and vertices for the face. Now one has (m,n)= (6,3). The dual of this tesselation is hexagonal tesselation (m,n)= (3,6) obtained by defining vertices as centers of the triangles so that faces become vertices and vice versa.
  2. The rule V-E+F=2(1-g)-h, where V, E and F are the numbers of vertices, edges, and faces, relates V-E-F to the topology of the graph, which in the recent case is triangular tesselation. g is the genus of the surface at which the triangulation is im eded and h is the number of holes in it. In case of torus one would have E=V+F giving in the recent case E=36 for (V,F)= (12,24) (see this) whereas in the icosahedral case one has E=32.
  3. This kind of tesselations are obtained by applying periodic boundary conditions to triangular lattices in plane defining parallelogram. The intuitive expectation is that this lattices can be labelled by two integers (m,n) characterizing the lengths of the sides of the parallelogram plus angle between two sides: this angle defines the conformal equivalence class of torus. One can also introduce two unit vectors e1 and e2 characterizing the conformal equivalence class of torus.

    Second naive expectation is that m× n × sin(θ) represents the area of the parallelogram. sin(θ) equals to the length of the exterior product |e1× e2|=sin(θ) representing twice the area of the triangle so that there would be 2m× n triangular faces. The division of the planar lattice by group generated by pe1+qe2 defines boundary conditions. Besides this the rotation group Z6 acts as analog for the symmetries of a unit cell in lattice. This naive expectation need not of course be strictly correct.

  4. As noticed, it is not possible to have triangular toric tesselations with (V,E,F)= (12,30,20). Torus however has a triangular tesselation with (V,E,F)=(12,36,24). An illustration of the tesselation can be found here). It allows to count visually the numbers V, E, F, and the identifications of the boundary edges and vertices. With good visual imagination one might even try to guess what Hamiltonian cycles look like.

    The triangular tesselations and their hexagonal duals are characterized partially by a pair of integers (a,b) and (b,a). a and b must both even or odd. The number of faces is F= (a2+3b2)/2. For (a,b)= (6,2) one indeed has V=12 and F=24. From the article one learns that the number of triangles satisfies F= 2V for a=b at least. If F= 2V holds true more generally one would have V= (a2+3b2)/8, giving tight constraints on a and b.

    Remark: The conventions for the labelling of torus tesselation vary. The above convention based on integers (a,b) is different from the convention based on integer pair (p,q) used in the article this). In this notation torus tesselation with (V,F)=(12,24) corresponds to (p,q)=(2,2) instead of (a,b)= (6,2). This requires (a,b)=(3p,q). In this notation one has V=p2+q2 +pq.

3. The number of triangles in the 12-vertex tesselation is 24: curse or blessing?

One could see as a problem that one has F=24>20? Or is this a problem?

  1. By fusing two icosahedral harmonies and one toric harmony one would obtain a harmony with 20+20+24 =64 chords, the number of DNA codons! One would replace the fusion of 3 icosahedral harmonies and tetrahedral harmony with a fusion of 2 icosahedral harmonies and toric harmony. Icosahedral symmetry with toric symmetry associated with the third harmony would be replaced with a smaller toric symmetry. Note however that the attachment of tetrahedron to a fixed icosahedral face also breaks icosahedral symmetry.

    This raises questions. Could the presence of the toric harmony somehow relate to the almost exact U ↔ C and A ↔ G symmetries of the third letter of codons. This does not of course mean that one could associated the toric harmony with the third letter. Note that in the icosa-tetrahedral model the three harmonies are assumed to have no common chords. Same non-trivial assumption is needed also now in order to obtain 64 codons.

  2. What about the number of amino-acids: could it be 24 corresponding ordinary aminoacids, stopping sign plus 3 additional exotic amino-acids. The 20 icosahedral triangles can corresponds to amino-acids but not to stopping sign. Could it be that one of the additional codons in 24 corresponds to stopping sign and two exotic amino-acids Pyl and Sec appearing in biosystems explained by the icosahedral model in terms of a variant of the genetic code. There indeed exists even third exotic amino-acid! N-formylmethionine (see this) but is usually regarded as as a form of methionine rather than as a separate proteinogenic amino-acid.
  3. Recall that the problem related to the icosa-tetrahedral harmony is that it does not contains the chords of what might be called classical harmonies (the chordds assignable to major and minor scales). If 24 chords of bio-harmony correspond to toric harmony, one could obtain these chords if the chords in question are chords obtainable by the proposed construction.

    But is this construction consistent with the representation of 64 chords by taking to each chord one note from 3 disjoint groups of 4 notes in which each note belongs to 16 chords. The maximum number of chords that note can belong to would be 5+5+6=16 as desired. If there are no common chords between the 3 harmonies the conditions is satisfied. Using for instance 3 toric representations the number would be 6+6+6=18 and would require dropping some chords.

  4. The earlier model for tRNA as fusion of two icosahedral codes predicting 20+20=40 tRNA codons. Now tRNAs as fusion of two harmonies allows two basic options depending on whether both harmonies are icosahedral or whether second harmony is toric. These options would give 20+20=40 or 20+24=44 tRNAs. Wikipedia tells that maximum number is 41. Some sources however tell that there are 20-40 different tRNAs in bacterial cells and as many as 50-100 in plant and animal cells.
See the chapter Geometric theory of harmony, the article Geometric theory of harmony or the article New results in the model of bio-harmony.



Dark valence electrons, dark photons, bio-photons, and carcinogens

The possible role of bio-photons in living matter is becoming gradually accepted by biologists and neuroscientists. It seems that the intensity of bio-photon emission increases in sick organisms and bio-photons are used as a diagnostic tool. Fritz Popp (see this) started his work with bio-photons with some observations about the interaction of UV light with carcinogens (see this). Veljckovic has also published results suggesting correlations between carcinogenity and the absorption spectrum of photons in UV (ultraviolet).

I have proposed that bio-photons emerge as ordinary photons from what I call dark photons, which differ from ordinary photons in that they have non-standard value heff= nh0 of Planck constant. Also other particles - electrons, protons, ions,..., can be dark in this sense.

One of the mysteries of biology, which mere biochemistry cannot explain, is that living systems behave coherently in macroscopic scales. The TGD explanation for this is that dark particles forming Bose-Einstein condensates (BECs) and super-conducting phases at magnetic flux tubes of what I call magnetic body possess macroscopic quantum coherence due to the large value of heff. This quantum coherence would force the coherent behavior of living matter. I have already earlier developed rather concrete models for bio-photons on basis of this assumption.

In the sequel I will discuss bio-photons from a new perspective by starting from bio-photon emission as a signature of a morbid condition of organism. The hypothesis is that in sick organism dark photons tend to transform to bio-photons in absence of metabolic feed increasing the value of heff. Hence BECs of dark photons and also of other dark particles decay and this leads to a loss of quantum coherence.

A further hypothesis is that at least a considerable part of bio-photons emerge in the transformations of dark photons emitted in the transitions of lonely dark valence electron of any atom able to have such. Since dark electron has a scaled up orbital radius, it sees the rest of atom as a unit charge and its spectrum is in good approximation hydrogen spectrum. Therefore the corresponding part of the spectrum of bio-photons would be universal in accordance with quantum criticality.

This picture allows to develop some ideas about quantum mechanisms behind cancer in TGD framework.

Some basic notions related to carcinogens

Before continuation it is good to clarify some basic notions. Toxins are poisonous substances created in metabolism. Carcinogens (this) are substances causing cancer, which often cause damage to DNA and induce mutations (mutagenicity).

Free radicals (see this) provide a basic example about carcinogens. They have one un-paired valence electron and are therefore very reactive. The un-paired electron has a strong tendency to pair with an electron and steals it from some molecule. The molecule providing the electron is said to oxidize and free radical to act as oxidant. The outcome is a reaction cascade in which carcinogen receives electron but electron donor becomes highly reactive. Anti-oxidants stop the reaction cascade by getting oxidized to rather stable molecules (this and this).

Benzo[a]pyrene (BAP) C20H12 (see this) is one example of carcinogen. It contains several carcinogenic rings and is formed as a product of incomplete burning and reacts with powerful oxidizers. As such BAP is not free radical but its derivatives BAP+/- obtained by one-electron reduction or oxidation are such (see this).

There are also carcinogens such as bentzene, which as such is not dangerous. What happens is that to the carbon at the ends of bentzene's double bond binds single oxygen atom and so called epoxy bond is formed. This molecule penetrates to the DNA chain and causes damage. Perhaps the fact that DNA nucleotide also contains aromatic 6-rings relates to this.

The emission of bio-photons (see this) increases if carcinogens such as oxidants are present. The idea is that bio-photons could be relevant concerning the understanding of the problem. It has been proposed that bio-photons could be created when anti-oxidants interact with molecules generating triplet states (spin 1) which decay by photon emission. The photons generated in this manner would have discrete spectrum whereas bio-photons seem to have continuous and rather featureless spectrum. Therefore this model must be taken with caution.

It could be that the origin of bio-photons is not chemical. If so, carcinogens would not produce bio-photons in ordinary atomic or molecular transitions. They could be however induce generation of bio-photons indirectly. The understanding of bio-photons might help to understand the mechanisms between carcinogenic activity. I have discussed bio-photons from TGD point of view earlier.

Some basic notions of TGD inspired quantum biology

In the sequel I try to develop a necessarily speculative picture about carcinogen action on basis of TGD based quantum about biology. The goal is to develop the general theory by developing a concrete model for a problem.

Magnetic flux tube and field body/magnetic body are basic notions of TGD implied by the modification of Maxwellian electrodynamics . Actually a profound generalization of space-time concept is in question. Magnetic flux tubes are in well-defined sense building bricks of space-time - topological field quanta - and lead to the notion of field body/magnetic body as a magnetic field identity assignable to any physical system: in Maxwell's theory and ordinary field theory the fields of different systems superpose and one cannot say about magnetic field in given region of space-time that it would belong to some particular system. In TGD only the effects on test particle for induced fields associated with different space-time sheets with overlapping M4 projections sum.

The hierarchy of Planck constants heff=n× h0, where h0 is the minimum value of Planck constant, is second key notion. h0 need not correspond to ordinary Planck constant h and both the observations of Randell Mills and the model for color vision suggest that one has h=6h0. The hierarchy of Planck constants labels a hierarchy of phases of ordinary matter behaving as dark matter.

Magnetic flux tubes would connect molecules, cells and even larger units, which would serve as nodes in (tensor-) networks Flux tubes would also serve as correlates for quantum entanglement and replace wormholes in ER-EPR correspondence proposed by Leonard Susskind and Juan Maldacena in 2014 (see this and this). In biology and neuroscience these networks would be in a central role. For instance, in brain neuron nets would be associated with them and would serve as correlates for mental images. The dynamics of mental images would correspond to that for the flux tube networks.

The proposed model briefly

In the sequel the basic hypothesis will be that dark photons emerging from the transitions of dark valence electrons of any atom possessing lonely unpaired valence electron could give rise to part of bio-photons in they decays to ordinary photons. The hypothesis is developed by considering a TGD based model for a finding, which served as a starting point of the work of Popp (see this): the irradiation of carcinogens with light at wavelength of 380 nm generates radiation with wavelength 218 nm so that the energy of the photon increases in the interaction. Also the findings of Veljkovic about the absorption spectrum of carcinogens have considerably helped in the development of the model.

The outcome is a proposal for dark transitions explaining the findings of Popp and Veljkovic. The spectrum of dark photons also suggests a possible identification of metabolic energy quantum of .5 eV and of the Coulomb energy assignable to the cell membrane potential. The possible contribution to the spectrum of bio-photons is considered, and it is found that spectrum differs from a smooth spectrum since the ionization energies for dark valence electrons depending on the value of heff as 1/heff2 serve as accumulation points for the spectral lines. Also the possible connections with TGD based models of color vision and of music harmony are briefly discussed.

See the chapter Dark valence electrons, dark photons, bio-photons, and carcinogens or the article with the same title.



Could also RNA and protein methylation be involved with expression molecular emotions?

Some time ago I wrote an piece of text ) (see this) about learning of slime molds. The proposal was based on the vision inspired by the model of bio-harmony and stating that harmony of music of light (and maybe of also sound) realized as 3-chords of dark photons with frequencies of 12-note scale expresses and creates emotions and that each harmony corresponds to a particular mood. The painful conditioning of the slime mold would generate a negative mood which would infect DNA and induce epigenetic change. This picture conforms also with the finding that RNA can induce learning of conditionings in snails (see this). Slime mold does not have central nervous system but a natural guess would be that also synaptic learning involves similar mechanism.

One can ask whether also RNA and protein methylation could be involved with learning. If molecular moods correspond to bio-harmonies and if the conditioning by say painful stimulus involves a change of the emotional state of RNA inducing that of DNA, it must change some of the chords of the bio-harmony. Since bio-harmony is essential for communications by dark photons between dark proton triplets representing dark variants of the basic biomolecules and also between communications between bio-molecules and their dark variants, one expects that the change of the harmony occurs for all dark analogs of biomolecules and also for their ordinary biomolecules.

Some chords represented by DNA-, RNA-, and tRNA codons, and amino-acids - briefly basic bio-molecules - would be affected.

  1. In the case of DNA epigenetic modifications (see this) affect mRNA and thus also protein expression. There are two basic mechanisms involved. Methylation of C nucleotide of DNA and protein modification for histone.

    Methylation (addition of CH3 to N) of C nucleotide leads to a silencing of gene expression. Methylation occurs typically for CpG pairs and for both strands. Before embryogenesis demethylation occurs for the entire DNA (stem cell state) but cell differentiation means methylation of genes not expressed. In vertebrates 60-80 percent of CpG is methylated in somatic cells. CpG islands form an exception involving no methylation. Demethylation (see this) as the reversal of methylation occurs either spontaneously or actively.

    The effects on gene expression can be also inherited to next generations. The mechanism of inheritance is poorly understood. The epigenetic change should be also somehow communicated to the DNA of germ cells but this seems impossible. The mystery is deepened because before embryogenesis demethylation occurs for the entire genome. It is difficult to understand how the chemical storage of the information about methylation patterns to be transferred to the next generation is possible at all.

    The TGD view about emotional expression inducing epigenesis by communications via dark photons between basic biomolecules and their dark variants suggests an elegant mechanism. What would be inherited would be the emotional states represented by bio-harmonies assignable to the dark variants of biomolecules.

  2. In the case of pre-RNA post-transcriptional chemical modifications (see this) - in particular methylation, are known to occur, and they affect RNA splicing rates and change the distribution of mRNAs and thus of proteins. The modifications affect also un-translated RNA (UTR) but not the protein translation from mRNA.
  3. Protein modifications (see this) in turn affect the dynamics of proteins - in particular their properties as enzymes by affecting therefore the rates for various basic processes.

    As already noticed, protein modifications are important in epigenesis by histone modification. Wikipedia article mentions lys acetylization by adding CH3=O group (see this), lys and arg methylation (see this), ser and thr phosphorylation, lys ubiquintination and sumoylation. For N-terminus (H2 group in the start of protein) the process is irreversible and new amino acid residues emerge. Methylation in C terminus (O=C-OH end of protein) can increase chemical repertoire. Note that the methylation occurs at the ends of the protein just like it tends to occur in the case of RNA as will be found.

RNA modifications deserve to be discussed in more detail. This field of study is known as epitranscriptomics (see this). These chemical modifications does not affect protein expression except in the case that they affect the rates of various alternative pre-RNA splicing so that the distribution of alternative protein outcomes changes. Clearly, the effect is somewhat like the effect of mood on overall activity. There are also many other modifications of RNA. One of the is A-I de-amination which changes in RNA but does not affect protein expression.

The methylation of RNA is the most common and best understood modification of RNA.

  1. The modelling of the methylation of both DNA and RNA is based on writer-reader-eraser model. Writing corresponds to methylation. Reading corresponds to attachment of enzymes involved in the splicing or protein synthesis with higher rate to methylated sites. Demethylation is example of erasing.
  2. Methylation is known to occur for various variants of RNA (ribosomal rRNA, tRNA, mRNA, and small nuclear RNA snRNA related to metabolic machinery) after transcription. The biochemical modifications of RNA are called epitranscriptomes (see this). N6-Methyladenosine (m6A) is the most common and best understood modification of RNA. m6A tells that nitrogen in position 6 of adenosine (A) is methylated by adding group CH3. m6A sites are often located in the last exon near the end of mRNA, in untranslated RNA (UTR) at 3' end, and inside long exons.

    It has been found that 3 members of so called YTH domain protein family acting as readers have larger affinity to bind to methylated sites. One of them shortens the lifetime of mRNA after translation.

  3. Methylation in general shortens the UTR (un-translated regions) of mRNA in its 5' and 3' ends (head and tail of mRNA) ). One speaks of alternative poly-adenylation (APA, see this) of the tail of the mRNA: poly-adenylation (PA) adds A-sequences to the end of mRNA affecting its dynamics: shortening of UTRs means shortening of PAs.
  4. Methylation affects the rates in the dynamics of translation but does not affect the product of translation itself. A-sequences shields mRNA and during its life cycle its length is reduced somewhat like telomere (see this) consisting of a repeated sequence TTAGGG and also shortening during the life cycle of DNA. APA affects rates for the dynamics of translation. Also stem loops of pre-RNA can be methylated and this can increase the rate of an alternative splicing and thus change relative rates of alternative gene expressions.
The basis question is which of the following options is correct.
  1. The chemical modification of the basic biomolecules required by the preservation of resonance condition. In this case the modification would be associated with all codons and mean a drastic change of both DNA and RNA and also amino-acids. The modifications, in particular methylation, are however associated with with highly restricted portions of DNA and RNA. On particular, only A nucleotide of RNA is methylated. Hence this option is definitely excluded.
  2. The basic bio-molecules have several resonance frequencies corresponding to various moods so that chemical modifications are not needed for preserving the resonance conditions. This was assumed about the emotional effect of RNA to DNA in the earlier considerations. Chemical modifications could be seen as emotional expression of dark variants of bio-molecules.

    This option conforms with the above facts about RNA methylation. Only UTRs at the ends of RNA and associated with the stem loops are sensitive to modifications and the interpretation is that these allow the emotional expression of RNA. Note that somewhat similar situation is encountered in the case of microtubules for which the other end is highly dynamical. One can ask whether the shortening of the A-sequences and telomeres could be seen as outcome of expression of negative emotions.

What inspired this piece of text was a highly interesting popular article "Methyl marks on RNA discovered to be key to brain cell connections" about methylation of RNA in brain (see this). The research article (see this) by Daria Merkuvjev et al has title "Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts".

The researchers isolated brain cells from adult mice and compared epitranscriptomes found at synapses to those elsewhere in the cells. At more than 4,000 spots on the genome, the mRNA at the synapse was methylated more often. In more than half of genes the epitranscriptomes were found in genes coding for proteins found mostly in synapses. If the methylation was disrupted, the brain cells did not function normally. It was concluded that the methylation probably makes signalling faster.

These findings conform with the idea about representation of molecular emotions as bio-harmony. Synaptic contacts are the places where emotions should be expressed to give rise to learning by conditioning realized in terms of changed synaptic strengths. Methylation would induced as emotional expression due to the changing of the 3-chords of the harmony.

See the chapter Emotions as sensory percepts about the state of magnetic body?, the article with the same title, or a shorter article Could also RNA and protein methylation of RNA be involved with the expression of molecular emotions?.



How life began?

The central question of biology is "How life began?" and dark variants of biomolecules suggest not only a solution to various paradoxes but also a concrete answer to this question.

The transcription machinery for rRNA including ribozymes and mRNA coding for the proteins associated with ribosomes is central for the translation. The DNA coding for rRNA is associated with nucleolus (see this) in the center of the nucleus.

  1. After the emergence of the first ribosome the ribosomes of the already existing nucleus can take care of the translation of the ribosomal proteins. But how could the first ribosome emerge? This question leads to a paradox bringing in mind self-reference - the basic theme of Gödel-Escher-Bach of Douglas Hofstadter, perhaps the most fascinating and inspiring book I have ever read. The ribosomal proteins associated with the first ribosomes should have been translated using ribosome, which did not yet exist!
  2. Could the translation of the first ribosomal proteins directly from the dark variants of these proteins solve the paradox? The idea of shadow dynamics induced by the pairing of basic biomolecules with their dark variants even allows to ask whether the replication, transcription, and translation could occur at dark level so that dark genes for ribosomes would be transcribed to dark ribosomal RNA and dark mRNA translated to dark AA associated with the ribosomes. These in turn would pair with ordinary ribosomal RNA and AA.
  3. But what about dark variants of ribosomes? One can encounter the same paradox with them if they are needed for the translation. Could it be that dark variants of the ribosomes are not needed at all for the translation but would only give rise to ordinary ribosomes by the pairings basic biomolecules and their dark variants. Dark DNA would pair with dark mRNA, which pairs spontaneously with dark tRNA. Once the ordinary ribosomes are generated from the dark ribosomes by pairing, they could make the translation much faster.
  4. There is however a problem. Both dark RNA and AA correspond to dark nuclear strings. Dark tRNA realized as nuclear string in the proposed manner does not have a decomposition to dark AA and dark RNA as ordinary tRNA has. The pairing of dark tRNA and dark mRNA should rise to dark AA and dark nuclear string - call it X - serving as the analog for the pairing of mRNA sequence with "RNAs" of tRNAs in the ordinary translation.
  5. How to identify X? Could the translation be analogous to a reaction vertex in which dark mRNA and dark tRNA meet and give rise to dark AA and X? X cannot be completely trivial. Could X correspond to the dark DNA?! If so, the process would transcribe from dark DNA dark RNA and translate from dark RNA and dark tRNA AA and dark DNA. This would lead to an exponential growth of dark DNA and other dark variants of bio-molecules. This exponential growth would induce exponential growth of the basic bio-molecules by pairing. Life would emerge! No RNA era or lipid era might be needed. All basic biomolecules or their precursors could emerge even simultaneously - presumably in presence of lipids - but this is not the only possibility.
One can take a more precise look at the situation and try to understand the emergence of bio-molecules and their basic reactions as shadows of the dark variants of bio-molecules appearing in dark particle reactions. The basic idea is that same dark reaction can give rise to several reactions of biomolecules if varying number of the external dark particles are paired with corresponding bio-molecules. Under what conditions this pairing could occur, is left an open question. Consider now the dark 2→ 2 reactions and possible reactions obtained by pairing of some particles.
  1. The reaction

    DmRNA+DtRNA→ DAA + DDNA

    gives rise to translation mRNA+tRNA → AA if DDNA-DNA pairing does not occur in the final state but other dark particles are paired with the their ordinary variants. If only DmRNA-mRNA and DDNA-DNA pairings occur, the reaction gives the reversal mRNA → DNA of transription.

    It should be easy to check whether this is allowed by the tensor product decomposition for the group representations associated with dark proton triplets. Same applies to other reactions considered below.

    If this reaction is possible then also the reversal

    DAA + DDNA → DmRNA+DtRNA.

    can occur. If only DDNA-DNA and DmRNA-mRNA pairings occur this gives rise to transcription of DNA→ mRNA. Also reverse translation AA → mRNA is possible.

  2. One can consider also the reaction

    DmRNA+DtRNA → DAA + DmRNA

    If all pairings except DAA-AA pairing are present, the outcome is instead of translation the replication of mRNA such that the amino-acid in tRNA serves the role of catalyzer. I have considered the possibility that this process preceded the ordinary translation: in a phase transition increasing heff the roles of AA and RNA in tRNA would have changed.

    If this reaction is possible then also its reversal

    DAA + DmRNA → DmRNA+DtRNA

    is allowed. If all pairing except DmRNA-mRNA occur, this gives rise to AA +RNA → tRNA allowing to generate tRNA from AA and RNA (not quite RNA).

  3. The replication of DNA strand would correspond at dark level to a formation of bound states by the reaction

    DDNA+DDNA→ DDNA +bound DDNA

    in which all particles are paired. The opening of DNA double strand would correspond to the reverse of this bound state formation.

These dark particle reactions behind the shadow dynamics of life should be describable by S-matrices, which one might call the S-matrix of life.
  1. For instance for

    DmRNA+DtRNA→ X,

    where X can be DmRNA+DtRNA (nothing happens - forward scattering) or DAA + DDNA and perhaps even DAA+DmRNA, one would have unitary S-matrix satisfying SSdagger=Id giving probability conservation as ∑n pm,n= |Smn|2 =1 as a special case. Writing S=1+iT unitarity gives i(T-T)+TT=0 giving additional constraints besides probability conservation.

    For

    DmRNA+DtRNA→ DAA + DDNA

    the non-vanishing elements of T are only between pairs [(DmRNA,DtRNA), (DAA,DDNA)] for which mRNA pairs with tRNA and DNA codes for AA. Unitary matrix would be coded by amplitudes t(AA,DNAi(A)) satisfying ∑ipi(DAA)=p(DDNA+DAA), pi(AA)=|t(DAA,DDNAi(A)|2. p(DDNA+DAA) equals to p(DDNA+DAA)= (1-p) Br(DDNA+DAA), where p is the probability that nothing happens (forward scattering) and Br(DDNA+DAA) is the branching ratio to DDNA+DAA channel smaller than 1 if Br(DDNA+DmRNA) is non-vanishing. The natural interpretation for pi(AA) would be as probability that DNAi codes for it.

  2. For the reverse reaction

    DAA + DDNA rightarrow DmRNA+DtRNA

    it is natural to assume that DtRNA corresponds to any tRNA, which pairs with RNA. The AA associated with this tRNA is always the same but the counterpart of RNA can vary (wobbling). One can speak of the decomposition of dark genetic code to DmRNA→ DtRNA → DAA to a pair of codes mapping DmRNA to DtNRA and DtRNA to DAA. There is a set tRNAi(mRNA) of tRNAs coding for given mRNA, and the probabilities pi(DmRNA) sum up to p= ∑i pi(DmRNA)= (1-p) Br(DmRNA+DtRNA) , where p is the probability for forward scattering and Br(DmRNA+DtRNA) is the branching fraction. The natural identification of pi(DmRNA) is as the probability that mRNA pairs with tRNAi.

A possible weak point of the proposal is pairing: what are the conditions under which it occurs and are different pairing patterns possible. Possible second weak point is purely group theoretic: one should check whether which reactions are allowed by the tensor product decompositions for the states of dark proton triplets

See the chapter Quantum Mind, Magnetic Body, and Biological Body or the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology.



TGD approach to the hen-or-egg problems of biology

Standard biology suffers from several hen-or-egg problems. Which came first: genes or metabolism? The problem is that genes require metabolism and metabolism requires genes! Genes-first leads to the vision about RNA world and metabolism-first to lipids world idea.

The emergence of basic biomolecules is the second problem. What selected these relatively few basic molecules from huge multitude of molecules? And again the hen-egg problems emerge. Which came first: proteins or the translation machinery producing them from RNA? Did RNA arrive before proteins or did proteins and RNAs necessary for their transcription and translation machinery emerge first. One can argue that ribozymes served as catalysts for RNA replication but how RNAs managed to emerge without replication machinery involving ribozymes? What about DNA: did it emerge before RNA or could it have emerged from RNA? It seems that something extremely important is missing from the picture.

p> TGD predicts the existence of dark variants of basic biomolecules DNA, RNA, tRNA, and amino-acids (AAs). One can of course ask whether something simpler could be imagined by utilizing the potential provided by dark variants of bio-molecules present already from beginning and providing both genes and metabolism simultaneously.

One can start from a couple of observations which forced myself to clarify myself some aspects of TGD view and also to develop an alternative vision about prebiotic period.

  1. Viruses are probable predecessors of cellular life. So called positive sense single stranded RNA (ssRNA) associated with viruses can form temporarily double strands and in this state replicate just like DNA (see this). The resulting single stranded RNA can in turn be translated to proteins by using ribosomal machinery. RNA replication takes place in so called viral replication complexes associated with internal cell membranes, and is catalyzed by proteins produced by both virus and host cell.

    Could ribozyme molecules have catalyzed RNA replication during RNA era? For this option AA translation would have emerged later and the storage of genetic information to DNA only after that. There is however the question about the emergence of AAs and of course, DNA and RNA. Which selected just them from enormous variety of options.

  2. Lipid membranes are formed by self-organization process from lipids and emerge spontaneously without the help of genetic machinery. It would be surprising if prebiotic life would not have utilized this possibility. This idea leads to the notion of lipid life as a predecessor of RNA life. In this scenario metabolism would have preceded genes (see this and this).
Consider now the situation in TGD.
  1. The dark variants of DNA, RNA, AA, and tRNA would provide the analogs of genes and all basic biomolecules present from the beginning together with lipid membranes whose existence is not a problem. They would also provide a mechanism of metabolism in which energy feed by (say) solar radiation creates so called exclusion zones (EZs) of Pollack in water bounded by a hydrophilic substance. EZs are negatively charged regions of water giving rise to a potential gradient (analog of battery) storing chemically the energy provided by sunlight and the formation of these regions gives rise to dark nuclei at magnetic flux tubes with scaled down binding energy.

    When the p-adic length scale of these dark nuclei is liberated binding energy is liberated as metabolic energy so that metabolic energy feed giving basically rise to states with non-standard value heff/h=n of Planck constant is possible. For instance, processes like protein folding and muscle contraction could correspond to this kind of reduction of heff liberating energy and also a transformation of dark protons to ordinary protons and disappearance of EZs.

    The cell interiors are negatively charged and this is presumably true for the interiors of lipid membranes in general and they would therefore correspond to EZs with part of protons at magnetic flux tubes as dark nuclei representing dark variants of basic biomolecules. Already this could have made possible metabolism, the chemical storage of metabolic energy to a potential gradient over the lipid membrane, and also the storing of the genetic information to dark variants of biomolecules at the magnetic flux tubes formed in Pollack effect.

  2. Biochemistry would have gradually learned to mimic dark variants of basic processes as a kind of shadow dynamics. Lipid membranes could have formed spontaneously in water already during prebiotic phase when only dark variants of DNA, RNA, AAs and tRNA, water, and lipids and some simple bio-molecules could have been present. The dark variants of replication, transcription and translation would have been present from the beginning and would still provide the templates for these processes at the level of biochemistry.

    Dark-dark pairing would rely on resonant frequency pairing by dark photons and dark-ordinary pairing to resonant energy pairing involving transformation of dark photon to ordinary photon. The direct pairing of basic biomolecules with their dark variants by resonance mechanism could have led to their selection explaining the puzzle of why so few biomolecules survived.

    This is in contrast with the usual view in which the emergence of proteins would have required the emergence of translation machinery in turn requiring enzymes as catalyzers so that one ends up with hen-or-egg question: which came first, the translation machinery or proteins. In RNA life option similar problem emerges since RNA replication must be catalyzed by ribozymes.

  3. Gradually DNA, RNA, tRNA, and AA would have emerged by pairing with their dark variants by resonance mechanism. The presence of lipid membranes could have been crucial in catalyzing this pairing. Later ribozymes could have catalyzed RNA replication by the above mentioned mechanism during RNA era: note however that the process could be only a shadow of much simpler replication for dark DNA. One can even imagine membrane RNAs as analogs of membrane proteins serving as receptors giving rise to ionic channels. Note however that in TGD framework membrane proteins could have emerged very early via their pairing with dark AA associated with the membrane. These membrane proteins and their RNA counterparts could have evolved into transcription and translation machineries.

    DNA molecules would have emerged through pairing with dark DNA molecules. The difference between deoxi-ribose and ribose would correspond to the difference between dark RNA and dark DNA manifesting as different cyclotron frequencies and energies making possible the resonant pairing for frequencies and energies. Proteins would have emerged as those proteins able to pair resonantly with dark variants of amino-acid sequences without any pre-existing translational machinery. It is difficult to say in which order the basic biomolecules would have emerged. They could have emerged even simultaneously by resonant pairing with their dark variants.

See the chapter Quantum Mind, Magnetic Body, and Biological Body or the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology.



Homeostasis and zero energy ontology

Homeostasis means that system is able to preserve its flow equilibrium under changing conditions. This involves many-layered hierarchies of pairs of control signals with opposite effects so that the system stays in equilibrium. For instance, we could not stand without this control system as one can easily check by using non-living test body! For instance, in bio-chemical homeostasis the ratios of concentrations remain constant. It is not at all clear whether ordinary chemistry can explain homeostasis.

In zero energy ontology (ZEO) one can imagine very fundamental mechanism of homeostasis.

  1. Zero energy states are pairs of ordinary 3-D states with members located at opposite boundaries of causal diamond (CD). Their total quantum numbers are opposite, which is only a manner to say that conservation laws hold true. The space-time surfaces connecting the 3-surfaces are preferred extremals of the action principle.

    In quantum field theory this picture can be seen only as a book keeping trick and one assumes that space-time continues beyond causal diamond. There is however no need for this in TGD framework although it is natural to assume that there is some largest CD beyond which space-time surfaces do not continue. CDs form a hierarchy and sub-CDs of this CD can be connected by minimal surfaces, which are analogs of external particles. One obtains networks analogs to twistor Grassmannian diagrams.

  2. Conscious entities (selves) correspond in ZEO to a sequences of state function reductions having interpretation as weak measurements, "small" state function reductions. In given weak measurement the members of the zero energy state at the passive boundary of CD are not affected: this is essentially Zeno effect associated with repeated measurements in ordinary quantum theory. The members of the state pairs at the active boundary of CD change and also the temporal distance between the tips of CD increases: this assigns a clock time to the experienced flow of time as sequence of state function reductions.

    Eventually it becomes impossible to find observables, whose measurement would leave the passive parts of the zero energy state invariant. First "big" state function reduction changing the roles of active and passive boundaries of CD takes place and time begins to run in opposite direction since the formerly passive boundary recedes away from the formerly active boundary which is now stationary. Self dies and re-incarnates with an opposite arrow of time. In TGD biology these two time-reversed selves are proposed to correspond to motor actions and sensory perceptions.

    Already Fantappie realized that two arrows of time seem to be present in living matter (consider only spontaneous assembly of bio-molecules as decay in opposite direction) and introduced the notion of syntropy as time-reversed entropy. For an observer with given arrow of time, a system with opposite arrow of time seems to break the second law. Temperature and concentration gradients develop, system self-organizes.

  3. These two quantal time evolutions with opposite arrows of time look very much like competing control signals in homeostasis. The 4-D conscious entities corresponding to control signals would have finite lifetime so that in their ensemble the effects of the signals with opposite arrows of time tend to compensate. This would give rise to homeostasis.
See the chapter Quantum Mind, Magnetic Body, and Biological Body or the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology.



Which came first: genes or metabolism?

The key hen-egg question in biology is which came first, genes or metabolism. Both seem to need the other one. Genes-first view has led to the notion of RNA era as prebiotic biology. Metabolism-first view assumes that lipid life preceded the life controlled by basic biomolecules. In TGD framework this hen-egg question disappears.

  1. Dark variants of DNA, RNA, tRNA, and AAs are dark proton sequences representing dark nuclei with scaled down nuclear binding energy. They come in different length scales and their decay to dark nuclei with shorter scale liberates dark nuclear binding energy, which could have been used as metabolic energy during the prebiotic period and could even in recent biology. Therefore genes and metabolic genes would have emerged simultaneously.
  2. In so called Pollack effect the irradiation of a water bounded by a hydrophilic material creates negatively charged exclusion zone (EZ). Positive charge must go somewhere and the TGD based proposal is that it goes to magnetic flux tubes and forms dark proton sequences provoding a representation of DNA,RNA,tRNA,AA and of vertebrate genetic code.

    This effect occurs for several light wavelengths but infrared light present in thermal radiation provides the most effective manner to generate the charge separation. One can say that charge separation generates a battery so that the energy of light is transformed to a usable chemical energy. EZs have presumably preceded cell membrane (cell interior has negative charge).

    According to Pollack protein unfolding and folding could involve Pollack effect and its reverse. Also muscle contraction liberating energy could involve the reverse of Pollack effect. This mechanism works also for humans and one can even say that photosynthesis which induces charge separation by splitting water to H+ and OH- works also for animals but in somewhat more complex manner. This could explain the positive effects of sunlight on well-being. Some spiritually oriented people are even claimed to survive by using only sunlight as metabolic energy: light and water would be enough.

  3. In this framework one can consider the possibility of lipid membranes living in symbiosis with dark variants DNA, RNA, tRNA, and AAs during prebiotic era. Membranes would have generated charge separation by Pollack effect in order to transform the energy of light to chemical energy usable as metabolic energy. The resulting dark nuclei at magnetic flux tubes would have given rise to a dark realization of genetic code realized later chemically perhaps in terms of some simpler molecules attached to the dark variants of DNA, RNA or AA. Replication at this period could have been simply splitting of the membrane to two pieces perhaps induced by the splitting of the magnetic body in the manner described.
See the chapter Quantum Mind, Magnetic Body, and Biological Body or the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology.



How does brain predict future?

Quanta Magazine is a real treasure trove. The gem was at this time titled " To Make Sense of the Present, Brains May Predict the Future" (see this). The article gives links to various research articles: here I mention only the article " Neural Prediction Errors Distinguish Perception and Misperception of Speech" by Blank et al > (see this) .

According to the article, brain acts as a prediction machine comparing predictions with what happened and modifying the predictions accordingly. Sensory perception would not be mere 3-D sensory time=constant snapshot as believed in last century but include also a prediction of future based on it that would be outcome of sensory perception and brain is able to modify the prediction by using the difference between prediction and reality.

In TGD framework one can go even further (see this). Sensory organs are the seats of sensory mental images constructed by repeated signalling between brain (maybe also magnetic body) and sensory organ using dark photons propagating forth and back with maximal signal velocity and contributing to the sensory input a virtual part. Nerve pulses would create by synaptic bridges connecting flux tubes to longer flux tubes acting as waveguides for dark photons to propagate. Sensory mental image would be essentially self organization pattern nearest to the actual sensory input. The percept itself would be artwork, a caricature selecting and emphasizing the features of sensory input important for the survival.

The term predictive coding used about the process reveals that the view about how brain achieves this relies on computational paradigm. This is one possible view. Personally I do cannot regard classical computation as a plausible option. A more neutral view relies on rather obvious assumption that that temporal sequences of associations giving rise to predictions. But how does this happen?

Neuroscientists speculate about deep connections between emotions and learning: the dopaminergic neurons are indeed very closely related to the neural reward system. If the difference between the predicted and actually perceived is large the reward is small - one might also call it punishment. "Surprise" would be rather neutral word to express it. Big discrepancy causes big surprise. The comparison of predicted and what really happened would be essential. This is was one of the first predictions of TGD and might apply to simple emotions but - as I have proposed - emotions such as experience of beauty, compassion or love need not correspond to emotions need not be mere reactions.

The finding suggests a connection with the ideas about the fundamental role of emotions in learning. I have already developed this theme in this article.

  1. The first finding made for snails (see this) was that RNA somehow codes the experience and induces epigenetic change at the level of DNA in turn inducing a change in behavior. The popular article " Scientists Sucked a Memory Out of a Snail and Stuck It in Another Snail" tells about the finding (see this).

    This led to a TGD based model based on the notion of bio-harmony for music of dark photon triplets representing 3-chords predicting genetic code correctly. Music expresses and creates emotions: same would happen already at RNA level. DNA would get in the same mood and by resonating with the 3-chords of RNA music and changing its harmony/mood coded by resonance frequencies of nuclei, which would slightly change. Epigenetic change would take place as a consequence and change the genetic expression in turn changing the behaviour.

    This brings in something genuinely new: TGD based view about dark matter, realizations of genetic code by dark proton sequences defining the dark analogs of DNA, RNA, tRNA, and amino-acids at the magnetic flux tubes of magnetic body of living system plus realization of the genetic code.

    It must be emphasized that magnetic body is 4-D and corresponds to a preferred extremals connecting to two 3-surfaces at the boundaries of causal diamond. Hence the basic objects are deterministic time evolutions, analogous to programs or behavioral patterns. The sequence of associations assignable to percept could be seen as space-time surface, a predicted space-time time evolution.

  2. Just a couple of days before writing this I learned about slime molds (this) , which are monocellulars, which contrary to expectations learn new behaviours. Nervous system is not therefore necessary for learning. Emotional RNA could be at work also here.
  3. RNA would be naturally also behind the learning in CNS as a change of synaptic strengths generating effectively different synchronously firing neuron groups representing mental images and new sequences of associations providing predictions. The mismatch between prediction and real percept would we represented in terms of dopamine concentration and this in turn would generate at RNA level emotion, which would be negative for mismatch and induce corresponding DNA emotion generating epigenetic change in turn changing synaptic strengths in turn changing the prediction as a sequence of associations regarded as temporal sequence in turn changing the behavior! Long sequence of causations!
Also the speculated unification of motor control and sensory perceptions is mentioned in the popular article. In sensory perception internal environment as a model for external environment is updated. In motor action it is external environment. Connection with arrow of time? Motor action as perception of changing environment where own biological body is part of environment. In TGD framework sensory perception and motor action would be time reversals of each other at the level of sensory mental images. This view is allowed by ZEO and encouraged by the discovery of Libet that volitional act is preceded by neural activity by a fraction of second.

Motor action would be generated by a negative energy signal to the geometric past which would correspond to mental images with reversed arrow of time in TGD inspired theory of consciousness. This duality would mean that in opposite time direction motor action would be a perceptions about say hand moving in desired direction! The counterpart of predictive coding would take care of comparisons and modifying the predicted "sensory percept" so that it corresponds to reality. This sounds strange but maybe the motor actions is just passive perception from the point of view of time reversed self!

See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



How do slime molds learn?

Quanta Magazine is a treasure trove of popular articles about hot topics in basic research and biology and neuroscience are the hottest topics now. The article "Slime Molds Remember — but Do They Learn?" about learning of slime molds (see this) serves as a good example of pleasant surprises popping up on weekly basis.

  1. The popular article tells that slime molds are monocellulars - for long time believed to belong to fungi - but actually somewhat like amoebas. They have neither neurons nor brains. The neuroscientific dogma says that neurons are necessary for learning so that slime molds should not learn. They should only adapt by selecting behaviors from a genetically inherited repertoir. Same would be true about plants, which are also known to learn.

    For physicist these beliefs look strange. Both animals and plants and also slime molds share the basic aspects about what it is to be alive, why should they be unable to learn? The research of biologist Audrey Dussutour and her team described in the article indeed shows that slime molds are indeed able to learn.

  2. Conditioning is the basic mechanism of learning, which by definition leads to a creation of a new kind of behavior rather than selecting some behavior from an existing repertoir as happens in adaptation. Typically the conditioning is created by associating unpleasant sensory stimulus such as electric shock to some other stimulus, which can be pleasant, say information about the presence of food. This leads to avoidance behavior and the mere presence of food can induce the avoidance behavior.
  3. It was found that slime mold learns a habit of avoiding the unpleasant stimulus - habituation is said to take place. Habituation generates of new behavior and is not mere adaption. For instance, habituation can mean stopping noticing stimulus like smell if it is not dangerous or important for survival. In the experiments the slime molds were conditioned to avoid noxious substances (having bitter "taste") and they remembered the behavior after a year of physiologically disruptive enforced sleep as the technical terms expresses it.
  4. Central nervous system has been believed to be responsible for habituation since neurons receive and process the sensory the stimuli, build kind of cognitive representations about them, and generate motor response. Neuroscientist believe that learning means strengthening of synaptic contacts eventually giving rise to a learned motor response to a sensory stimulus by a sequence of associations

    Against this background the ability of slime molds to learn looks mysterious. How do they perceive the stimulus, how do they process it, how do they respond to it? We know actually little about cognition and learning: we know a lof about the neural correlates of cognition but not what cognition is.

Forgetting for a moment the question about what cognition is, one can just ask what could lead to the change of behaviour of the slime mold. Some time ago I learned about another fascinating finding related to learning from the article "Scientists Sucked a Memory Out of a Snail and Stuck It in Another Snail" (see this). What was found that one can take RNA of a snail that has been conditioned by some painful stimulus and transfer it to another snail by scattering RNA on its brain neurons! Same can be achieved also by feeding snail with the conditioned snail. RNA must somehow represent memories. If this is true for snail it can be true also for the slime mold.

Usually learning is assigned with cognition regarded as kind of linguistic cognition. One speaks also of emotional intelligence: could learning be based on emotions? The TGD based model for emotions (see this) inspired by the model of music harmony (see this and this) leading to a model of genetic code predicting correctly vertebrate coderelies on this idea and leads to a model for what learning could be also in the case of slime molds.

  1. Music expresses and creates emotions coded in its harmony (think of major and minor scales as simple examples). This could be true in much more general sense. Not only music made of sound but also of light - dark photons in TGD framework - could realize these functions of music. DNA would have a representation in terms of a collection of 3-chords made of three dark photons with frequencies in proportions allowed by the harmony.
  2. The model of harmony based on icosahedral and tetrahedral geometries predicts a large number of harmonies representing emotional states, moods. The music of light makes possible communication between DNA, RNA, amino-acids (AAs), even tRNAs and their dark variants DDNA, DRNA, DAA, DtRNA. Communications are possible if the three chords can resonate note by not: ideal situation occurs if the harmony defining the mood is same in sender and receiver. Emphatics are those, who experience also the sufferings of the other people. Moods can be transferred from RNA to DNA and here they can induce epigenetic change leading to a change in behavior.
  3. The painful conditioning of snail would induce a new mood of RNA of snail (probably rather depressive!) and this would in turn infect the DNA of the snail (strong emotions are infective) and the mood of DNA would induce the epigenetic change leading to the avoidance behavior (see this and this). Emotions would be behind the learning and learning would take place at DNA level as epigenetic changes changing the gene expression. Habitutation would involve epigenetic changes and adaptation involve only activation of appropriate inherited genes.
It must be added that TGD also leads to a vision about the role of neurons in many aspects different from the neuroscientific view although agreeing with the basic facts and explaining quite a number of anomalies (see this).
  1. The notion of magnetic body (MB) containing dark matter as heff/h0=n phases of ordinary matter is central. The networks having as nodes objects consisting of ordinary matter (molecules, organelles, organs, even organisms) connected to a network made of flux tubes containing dark matter would give rise to both cellular and neuronal networks. Magnetic flux tube connecting two nodes would serve as a correlate of attention and communication pathway using supra currents or dark photons. Also classical signals can propagate along it.
  2. The primary function of nerve pulse activity at the level of CNS would not be communication between neurons but building of communication pathways from flux tubes along which dark photon signals can propagate with maximal signal velocity. The situation would be same in travel phone connections: the communication pathway would be created first and only then the communications with light velocity would begin. Synaptic transmission would build a bridge between otherwise non-connected flux tubes​. This would give rise to long waveguides. Dark photons transforming to ordinary photons would yield bio-photons, which have remained mysterious in standard bio-chemistry since their spectrum is not consistent with the discrete spectrum of lines produced if they were generated in molecular transitions.
  3. Sensory experiences would be basically at the level of sensory organs and sensory percepts would involve pattern recognition involving repeated feedback signal from brain an leading a standard perception nearest to the sensory input. The new view about time provided by zero energy ontology allows to circumvent the counter argument inspired by phantom leg phenomenon.
  4. Nerve pulse patterns would frequency modulate the generalized Josephson frequencies assignable to the membrane proteins acting as Josephson junctions and generating dark Josephson radiation as part of EEG propagating to the MB of the system. Thus nerve pulse patterns would code information but this information would be sent to MB.
  5. It is quite possible that the proposed RNA level mechanism is the microscopic mechanism behind strengthening of synaptic connections believed to be behind neuron level learning although also here new findings suggests that situation is not quite it has been believed to be (see this).
This did not say anything about cognition yet. TGD leads also to a view about mathematical correlates of cognition requiring profound generalization of the mathematical structure of theoretical physics. Real number field is tailor made for the description of the sensory world but how to describe the correlates of cognition. Here p-adic number fields come in rescue and in TGD framework one ends up to a unification of real physics and their p-adic analogs to what I call adelic physics (see this and this).

See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



Two different values for the metallicity of Sun and heating of solar corona: two puzzles with a common solution?

Solar corona could be also a seat of dark nucleosynthesis and there are indications that this is the case (see this) . The metallicity of stellar objects gives important information about its size, age, temperature, brightness, etc... The problem is that measurements give two widely different values for the metallicity of Sun depending on how one measures it. One obtains 1.3 per cent from the absorption lines of the radiation from Sun and 1.8 from solar seismic data. Solar neutrinos give also the latter value. What could cause the discrepancy?

Problems do not in general appear alone. There is also a second old problem: what is the origin of the heating of the solar corona. Where does the energy needed for the heating come from?

TGD proposal is based on a model, which emerged initially as a model for "cold fusion" (not really) in terms of dark nucleosynthesis, which produced dark scaled up variants of ordinary nuclei as dark proton sequences with much smaller binding energy. This can happen even in living matter: Pollack effect involving irradiation by IR light of water bounded by gel phase creates negatively charged regions from which part of protons go somewhere. They could go to magnetic flux tubes and form dark nuclei. This could explain the reported transmutations in living matter not taken seriously by academic nuclear physicists.

TGD proposal is that the protons transform to dark proton sequences at magnetic flux tubes with nonstandard value of Planck constant heff/h0=n. Dark nuclei with scaled up size. Dark nuclei can transform to ordinary nuclei by heff→ h (h= 6h0 is the most plausible option) and liberate almost all nuclear binding energy in the process. The outcome would be "cold fusion".

This leads to a vision about pre-stellar evolution. First came the dark nucleosynthesis, which heated the system and eventually led to a temperature at which the ordinary nuclear fusion started. This process could occur also outside stellar cores - say in planet interiors - and a considerable part of nuclei could be created outside star.

A good candidate for the site of dark nucleosynthesis would be solar corona . Dark nucleosynthesis could heat the corona and create metals also here. They would absorb the radiation coming from the solar core and reduce the measured effective metallicity to 1.3 per cent.

See the chapter Non-locality in quantum theory, in biology and neuroscience, and in remote mental interactions: TGD perspective or the article Morphogenesis in TGD Universe .



Morphogenesis in astrophysical scales?

The proposed general picture has interesting implications for the TGD view about stars and planets. Minimal surfaces have vanishing mean curvature vector Hk defined by the trace of the second fundamental form. The external curvatures sum up to zero and the surface looks like saddle surface locally. This strongly suggests that one cannot have (spherically symmetric) closed 3-surfaces obtained by taking two almost copies of 3-surface having a boundary and gluing them together along boundaries as the assumption that there are not boundaries requires. Could stars and planets be flow equilibria analogous to soap bubbles for which pressure difference is necessary and is provided by an external energy feed (blowing the bubble). When the energy feed ceases, the bubble collapses? The analogy with the stellar dynamics leading eventually to a collapse to a blackhole is obvious.

Morphogenesis and metabolic energy feed in astrophysical scales as explanations for puzzling findings?

The analogy with morphogenesis could allow to build a more coherent picture from several puzzling observations related to TGD made during years.

  1. One cannot obtain an imbedding of Schwartschild exterior metric without the presence of long range induced gauge field behaving like 1/r2. Any object with long range gravitational field must have also electroweak gauge charge. The charge can be made arbitrarily small but must be non-vanishing. The natural guess was that em charge - closely related to Kähler charge - is in question. If flow equilibrium analogous to soap bubble is in question, the charge must be Kähler charge with the energy momentum currents of Kähler field feeding energy to prevent gravitational collapse.
  2. During 1990s I did considerable amount of work t in attempts to construct spherically symmetric solutions of field equations using only Kähler action but failed. In this case, the field equations state the vanishing of the divergences of energy-momentum and color currents. All known extremals of both Kähler action and its twistor lift involving also volume term analogous to cosmological term are minimal surfaces and extremals of both Kähler action and volume term.

    The failure to discover extremals which are not minimal surface might be simply due to the fact that they are not simple. One can however ask whether there are actually no radially symmetric stationary extremals of Kähler action? Could volume term be needed to stabilize them?

  3. 4-surfaces with vanishing induced Kähler field are necessarily minimal surfaces. The vanishing of induced Kähler field is however not necessary. In fact all non-vacuum extremals of Kähler action are minimal surfaces. The known repertoire of minimal surfaces includes cosmic strings, massless extremals representing radiation, and CP2 type extremals with Euclidian signature of induced metric representing elementary particles. For these Kähler action is present but minimal surface field equations give extremal property separately in volume and Kähler degrees of freedom.

    Cosmic strings would dominate in the very early cosmology before space-time as a 4-surface with 4-D M4 projection had emerged. The vision is that the thickening of their M4 projection during cosmic expansion generated Kähler magnetic flux tubes carrying magnetic monopole fluxes. The thickening of cosmic strings need not leave them minimal surfaces but one expects that this is true approximately.

    The feed of energy and particles from flux tubes (suggesting that they are not minimal surfaces) would have generated visible matter and led to the formation of stars. The flux tubes would take the role of inflaton field in standard approach. Flux tubes would have also second role: they would carry the quanta of gravitational and gauge fields and thus would be mediators of various interactions.

    Dark matter identified as phases with non-standard value of Planck constant heff/h0=n having purely number theoretical origin in adelic physics > would reside at magnetic flux tubes and the general vision about TGD inspired biology is that it controls the ordinary biomatter, which would involve metabolic energy feed as a stabilizer of the flow equilibrium. This picture suggests a generalization.

  4. The vision about dark nucleosynthesis, which emerged from the model of "cold fusion" has led to the proposal that dark nucleosynthesis preceded ordinary nucleosynthesis. Dark proton sequences were generated first by the analog of Pollack effect at magnetic flux tubes suffering also weak decays to produce states involving dark neutrons. These states decayed to dark nuclei with smaller value of heff/h=n and eventually this process led to the formation of ordinary nuclei. This process liberated practically all nuclear energy and heated the system and led eventually to the ordinary nuclear fusion occurring in the cores of stars.

    In living systems dark nuclei realized as dark proton sequences realize dark analogs of DNA, RNA, amino-acids, and tRNA and would provide the fundamental realization of the genetic code. This picture predicts a hierarchy of dark nuclear physics and dark realizations of the genetic code and analogs of the basic biomolecules. Could biology be replaced by a hierarchy of "biologies" in a more general sense.

  5. In the generalized biology stellar cores would provide metabolic energy realized basically as energy flow associated with Kähler field in stellar core making possible to realize star as an analog of cell membrane as flow equilibrium. Also the flow of Kähler charge, presumably in radial direction, would be involved if the energy momentum current of the induced Kähler field is non-vanishing and could relate to the mass loss of stars.

    Even in the case of planets dark nucleosynthesis could provide a radial energy flow to guarantee stability. Nucleosynthesis could have occurred inside planets and have produced heavier nuclei. The standard picture about stars as providers of heavier elements and supernova explosions giving rise to fusion generating elements heavier than Fe could be wrong.

  6. This picture conforms with what we know about dark matter. Dark matter would consist of heff/h0=n phases of ordinary mater at magnetic flux tubes. If also magnetic flux tubes are minimal surfaces in good approximation, gravitational degrees of freedom assignable to the volume action as analog of Einstein-Hilbert action and stringy action would not interact with Kähler degrees of freedom appreciably except in the events in which dark energy and matter are transformed to ordinary matter. These events could be induced by collisions of magnetic flux tubes. The energy exchange would be present only in systems not representable as minimal surfaces. Dark matter in TGD sense has key role in TGD inspired quantum biology.
Blackhole collapse as an analog of biological death?

Before one can say something interesting about blackholes in this framework and must look more precisely what cosmic strings are. There are two kinds of cosmic strings identifiable as preferred extremals of form X2× Y2⊂ M4× CP2. X2 is minimal surface.

  1. Y2 can be homologically non-trivial complex sub-manifold of CP2 for which second fundamental form vanishes identically. Induced Kähler form is non-vanishing and defines monopole flux. Both Kähler and volume term (cosmological constant term formally at least) contribute to energy density but the energy momentum currents and also tensors have vanishing divergence so that there is no energy flux between gravitational and Kähler degrees of freedom.
  2. Y2 can be also homologically trivial geodesic sphere for which Kähler form and therefore Kähler energy density vanishes identically. In this case only cosmological constant Λ represents a non-vanishing contribution to the energy so that energy transfer between gravitational and Kähler degrees of freedom is trivially impossible.
What could happen in blackhole collapse?
  1. Blackhole is not able to produce "metabolic energy" anymore and preserve the spherically symmetric configuration anymore. The outcome of blackhole collapse could be a highly folded flux tube very near to minimal surface or perhaps, or even a cosmic string. The latter option is not however necessary.
  2. Is this string homologically non-trivial having large string tension or homologically trivial and almost vacuum for small values of Λ? The huge mass density of blackhole does not favour the latter option. This leaves under consideration only the homologically non-trivial cosmic strings or their deformations to flux tubes.

    The string tension for cosmic string is estimated to be a fraction of order 10-7 about the effective string tension of order 1/G determined by blackhole mass which is proportional to the Scwartschild radius. Therefore the cosmic string should be spaghetti like structure inside the horizon having length about 107 time the radius of blackhole. Note that TGD predicts also second horizon below Schwartschild horizon: the signature of the induced metric becomes Euclidian at this horizon and this could explain the echoes claimed to be associated with the observed blackhole formation.

  3. One could say that Big bang starting from homologically non-trivial cosmic strings would end with Big crunch ending with similar objects.
Living systems are conscious and there is indeed a strong analogy to TGD inspired theory of consciousness. One could say that the particular sub-cosmology corresponds to a conscious entity (many-sheeted space-time predicts a Russian doll hierarchy of them) which repeatedly lives and dies and re-incarnates with opposite arrow of time.
  1. In zero energy ontology (ZEO) key role is played by causal diamonds (CDs) carrying analogs of initial and final states at their boundaries are in key role. The M4 projection of CD is intersection of future and past directed light-cones. The shape of CD strongly suggests Big Bang followed by Big Crunch.
  2. TGD inspired theory of consciousness predicts that conscious entities - selves - correspond to a generalized Zeno effect. Self is identified as a sequence of "small" state function reductions (weak measurements) increasing gradually the size of CD by shifting the active boundary of CD farther away from that passive boundary which is not changed (Zeno effect).

    The states at the active boundary are affected unlike those at the passive boundary. Self dies when the first "big" state function reduction to the active boundary occurs and the roles of the active and passive boundary are changed. The arrow of geometric time identified as the distance between the tips of CD changes and the CD starts to grow in opposite time direction. The evolution of self is a sequence of births and deaths followed by a re-incarnation.

  3. In astrophysical context this evolution would be a sequence of lifes beginning with a Big Bang and ending with a Big Crunch with two subsequent evolutions taking in opposite time directions. Somewhat like breathing. This breathing would take place in all scales and gradually lead to a development of sub-Universes as the size of CD increases.
  4. In ZEO the first big state function reduction to active boundary of CD occurs when all weak measurements have been done and there are no observables commuting with the observables, whose eigenstates the states at the passive boundary are. Self dies and reincarnates.

    One can also try to build a classical view about what happens. Measurement involves always a measurement interaction generating entanglement. Could the transfer of quantum numbers and conserved quantities (also color charges besides Poincare charges) between Kähler and volume degrees of freedom define the measurement interactions in practice. When this transfer vanishes, there is no measurement interaction and no further measurements are possible. Also metabolism ceases and self dies in biological sense.

See the chapter Non-locality in quantum theory, in biology and neuroscience, and in remote mental interactions: TGD perspective or the article Morphogenesis in TGD Universe .



Morphogenesis in TGD Universe

All structures - including bio-molecules, membrane like structures, organelles, organs, ... - would be 4-D space-time surfaces in TGD Universe. This would reduce the notion of shape in biology to a precisely defined and testable geometrodynamics coupling to em fields and possibly also other induced gauge fields.

1. The dynamics of space-time surfaces

This dynamics predicts two kinds of space-time regions (see this).

  1. The regions of first kind are locally minimal surfaces. These minimal surfaces are as 4-D analogs of geodesic lines analogs of asymptotic states of particle physics for which interactions are not on. They also satisfy non-linear geometrization of massless field equations so that both particle and wave aspects are present. What is especially important is that static minimal surfaces have vanishing mean curvature and look like saddles locally. They cannot be closed surface if stationary.
  2. Second type of regions are not minimal surfaces: there is a non-trivial coupling of the minimal surface term to 4-force density analogous to the divergence of Maxwellian energy momentum tensor. This is a generalization of the dynamics of a point-like charged particle in Maxwell field. These regions are identified as interaction regions: in particle physics these two regions correspond to external free particles and the interaction region. Magnetic flux tubes play fundamental role in TGD based quantum biology are deformations of string like objects, which represent simplest 4-D minimal surfaces.

    Essential is the coupling between induced Kähler form (mathematically like Maxwell field) and the geometry of the surface: the divergence of energy momentum current assignable to the analog of cosmological term (4-volume) equals to the divergence of that assignable to Kähler action: this expresses local conservation of four-momentum. One could also speak about coupling between Kähler field and gravitational field: Penrose's intuition about the the role of gravitation in biology would be correct.

    When the coupling is absent, minimal surface property implies the separate vanishing of both divergences and separate conservation of corresponding energy-momenta. All the known extremals of Kähler action are minimal surfaces: this is due to their very simple algebraic properties making easy to discover them. Physically this correspond to quantum criticality: dynamics is universal and does not depend on coupling parameters.

2. General view about morphogenesis

These observations lead to a rather general view about morphogenesis.

  1. The presence of the Kähler field (em field is sum of Kähler field and second term) makes possible flow equilibria such as cell membrane, which are not minimal surfaces. These surfaces can be closed and stationary making possible isolation from environment crucial for living organisms.

    Spherical soap bubble is a good analogy: it is not minimal surface as the soap films spanned by frames are. They look locally like saddle surfaces with opposite external curvatures in two orthogonal directions, this implies that they cannot be closed surfaces. Bubble is not possible without a pressure difference Δ p between the interior and exterior of the bubble: the blowing of the soap bubble generates Δ p, and means external energy feed analogous to metabolic energy feed.

    Δ p is analogous to a non-vanishing voltage V over cell membrane. The electric field of cell membrane and the energy feed providing the energy of electric field as metabolic energy are essential for the stability. More generally, V would generalize to non-vanishing of energy momentum tensor of Kähler field with non-vanishing divergence serving as a correlate for the energy transfer between Kähler and volume (gravitational) degrees of freedom.

    This generalises to all morphologies, which correspond to closed surfaces. They necessarily involve both Kähler electric and magnetic fields coupling to the geometry to stabilize the morphology. This statement would give some content for the exaggerated claim that biology is nothing but electricity + Schrödinger equation that I heard during my first student year.

  2. For instance, the presence of Kähler electric field can correspond to electric fields of cell membrane or along a part of body. If it is too weak, things go wrong in development. As was found decades ago, consciousness is lost if the electric field between frontal lobes and hindbrain gets too weak or has wrong direction. Cell dies if the membrane potential becomes zero and EEG disappears in death. Also microtubules have electric field along their axes essential for their existence.

    Michael Levin and his collaborators have discovered further fascinating connections between electric fields and morphogenesis. One of the discoveries is that the electric fields of the embryo are controlled by neurons of the still developing brain (see this). This conforms with the view that neurons and their MBs correspond to a higher level in the hierarchy than ordinary cells and there take care of control in longer scales. The MB of the developing brain would be the controller.

  3. A non-trivial coupling (four-momentum transfer) between the volume and Kähler degrees of freedom requires that the energy momentum currents have opposite and non-vanishing divergences. For the energy momentum tensor of ordinary Maxwell field the divergence is proportional to the contraction of Maxwell current and Maxwell field so that the current must be non-non-vanishing.

    In TGD the energy momentum tensor is replaced with energy momentum current allowing to have well-defined notion of energy momentum and corresponding conservation laws. Now the divergence contains two terms. The first one is the contraction Tr(TKHk) of energy momentum tensor TK of Kähler action with the second fundamental form Hk: this term proportional to TK is new. Second term is proportional to the contraction jKJ∇ hk of the induced Kähler form J with Kähler current jK and gradients ∇ hk of imbedding space coordinates analogous the divergence of energy-momentum tensor jβFα in the case of ordinary Maxwell action. One expects both terms to be non-vanishing.

    For the mere Kähler action, which I believed for decades to determine the preferred extremals, jK is either vanishing or light-like. In presence of coupling it can be both non-vanishing and time-like. The realization that cosmological term is present was forced by the twistor lift of TGD whose existence is possible only for H=M4× CP2.

  4. The predicted stabilizing Kähler (and em) currents would naturally correspond to the DC currents flowing along the body in various scales discovered already by Becker and found to be essential for the survival of the organism. In particular, Becker's DC currents are essential for the healing of wounds and in the regeneration of organs. In the first first aid stage of the healing DC currents are generated locally and after than central nervous system (CNS) takes care of the generation of the current (for TGD based discussion of Becker currents see this). Also this is easy to understand from the proposed stability criterion.
3. More quantitative view

The emergence of life would require the coupling between Kähler and volume degrees of freedom. The following gives a quantitative discussion based on p-adic length scale hypothesis and twistor lift of TGD.

  1. The coefficient Λ/8π G == 1/L4 of the volume term in the action is analogous to cosmological constant in general relativity. The predicted wrong sign of Λ is the stumbling block of superstring theories. In TGD framework the sign is correct.
  2. p-Adic coupling constant evolution predicts that the cosmological constant depends on p-adic length scale L(k) characterizing the size scale of the Universe, most naturally as that of horizon size. In zero energy ontology (ZEO) L(k) is identifiable as the size scale of causal diamond (CD).

    One important implication is a solution to the problem of cosmological constant. Although cosmological constant is huge at very early times (or more precisely, in very short p-adic length scales), it is small in the length scales of recent cosmology. The values of cosmological constant at smaller p-adic lengths scales are however visible also in the recent day physics in many-sheeted space-time and biology could make them visible as the following arguments show.

  3. There are two paired p-adic length scales: short p-adic length scale L(k1) and long p-adic length scale L(k). The vacuum energy density ρvac=Λ/8π G is naturally proportional to 1/L4(k1). One has energy E=1/L(k1) per 3-volume L(k1)3.

    ρvac=Λ/8π G is also naturally proportional to 1/GL2(k) since Λ =x/L(k)2 is natural by dimensional considerations. If L(k) corresponds to the size scale of the horizon, Λ degreases during cosmic evolution and the problem of cosmological constant disappears. One has

    1/L4(k1) = Λ/8π G ,

    Λ/8π = x2/L2(k) .

    Here the p-adic length scale L(k) could characterize the p-adic size scale of CD. G=lPl2 is gravitational constant, lPl Planck length scale, and L=L(k1) is a smaller length scale. L(k1) expressible using the geometric mean

    L(k1)=(8π GΛ)1/4 = x-1/2(L(k)lPl)1/2 .

    of L(k) and Planck length lPl and allows an identification as a p-adic length scale for a suitable choices of the parameter x. One has (8π)1/4≈ 2.4.

    What could this pairing of short and long p-adic length scales mean? The notion of magnetic body (MB) could provide and explanation. MB has onion-like layered structure with layers labelled by p-adic length scales up to some maximum size scale. This suggests that a biological structure with size scale L(k1) has MB for which the largest layer has the size scale L(k). L(k1) would correspond to smallest length scale in the hierarchy. Both scales could correspond to size scales of CDs.

    Remark: When L(k1) is scaled by 2r (k1→ k1+r), L(k) is scaled by 22r (k→ k+2r).

  4. From the parameterization

    ρvac= yH2/8π G

    of the dark energy density in terms of Hubble constant at given space-time sheets one obtains an estimate for the inverse of the Hubble constant H, which depends on space-time sheet in terms of L(k), as

    1/H(k) = (y/8π x)1/2 L(k) .

    H(k) refers now to Hubble constant in given p-adic length scale characterizing a level in the hierarchy of space-time sheets and is not the ordinary Hubble constant defined in very long scales at GRT limit of TGD. Naturality suggests the condition y/8π x=1.

One expects that the coupling between Kähler action and volume term can be non-vanishing only if the two contributions to the energy momentum tensor are of the same order of magnitude. Otherwise minimal surface property takes care that field equations are satisfied, and one does not obtain closed membrane like structures crucial for life.
  1. To achieve this, Kähler action ∝ E2-B2 must be of the same order of magnitude as (Λ/8π G)== x/GL2(k) giving in the case of cell membrane for the Kähler electric field strength the rough estimate

    E ∼ (x/lPlL(k))1/2 .

    Remark: The electric field of the cell membrane corresponds to E ∼ 5× 10-4 eV2 in the units of particle physicist (hbar=1 and c=1) in which unit of distance is 1/eV and one has 1 m ↔ 1.24× 106 eV-1.

  2. If an estimate for the typical strength E of bio-electric field is given, one can get some idea about the length scale L(k) as

    L(k)= x/lPlE .

    By feeding in Planck length lPl∼ 1.6× 10-35 m and the electric field E∼ 5× 106 V/m of the cell membrane, one obtains for the cell membrane the estimate

    L(k)∼ x1/2 L0 ,

    L0= 1.1× 106 ly .

    L(k1)= x-1/4 L1 ,

    L1=(lPlL0)1/2=4.2× 10-7 m .

    Note that L(k) scales as x1/2 and L(k1) as x-1/4.

  3. The value of electric field for cell membrane is essential for the argument. If one wants to generalize the argument from cell membrane to other systems, one must have an idea about how it scales. Membrane potential is near the value for which the potential energy ZeV0 for a Cooper pair is slightly above the thermal energy at physiological temperature. Hence the possible magnetic flux tube assignable to membrane proteins acting as Josephson junctions through cell membrane carry weakest possible electric field: this conforms with metabolic economy. A natural generalization would be that for a flux tube of length L one has E= V0/L. This gives the scalings

    L(k)∝ L/Lc ,

    L(k1)∝ (L/Lc)1/2 .

The value of the parameter x is open and one can make only guesses. Naturality would suggest that x is not too far from unity.

Option I: The size of the Milky Way is estimated to be about LMW=105 ly. L(k)=LMW would be obtained for x=.01. One should be however cautious with this estimate: also x∼ 1 might be acceptable.

  1. For L(k1) the formula L(k1)= x-1/2(L(k)lPl)1/2 gives for x=.01

    L(k1)= 4 nm .

    This is near the p-adic length scale L(149)=5 nm assignable to the ordinary cell membrane. There are indeed indications that galactic year defines a biorhythm. For x=1 giving L(k)= 106 ly one would have L(k1)= 1.26 nm, which does not correspond to cell membrane length scale.

  2. For the inverse of the Hubble constant H(149) one obtains for x=.01 the estimate

    1/H(k) ≈ 2(y/8π x)1/2 L(k) .

    H(149) does not correspond to standard cosmological constant. One has H(149)=L(k) for y=2π x=.0628.

  3. The scaling L(k) → 105L(k) the size scale of the observed Universe about 15 Gly scales L(k1=149) to L(k1)= 1.3 μm, which corresponds to L(165)=1.25 μm in a reasonable approximation (L(167)=2.5 μm is the p-adic length scale of nuclear membrane). This scale would correspond to a distance through which one has membrane potential V0. Could the size scales of galaxy and observed Universe indeed correspond to those of lipid layer of cell membrane and cell membrane?
Option II: One could argue that the long length scales correspond to the size scale of Earth. In TGD based view about EEG MB as onion-like structure has also layer with size scale of Earth radius RE.
  1. The condition that L(k)=RE=6.3× 106 m gives x=6.4× 10-16 and L(k1)= 6.7 mm. L(k1) could characterize a brain structure involved in the generation of EEG. Note that the estimate assumes the electric field of cell membrane. One can argue that the value of x=6.4× 10-16 is highly un-natural.
  2. There are indications for the existence of life in Mars, whose radius is 1/2 of that for Earth. L(k) would scale down by 1/2 as also the cell membrane thickness. Could this be assumed also for the Option I? By the proposed criterion the strength of electric field E for cell membrane should be 2 times stronger than for Earthly cell (for same physiological temperature). For instance, membrane potential could be same but membrane thickness could be 1/2 of that for Earthly membrane.

    Interestingly, the TGD based version of Expanding Earth model predicts that Earth experienced a rapid expansion doubling its radius. Even more, neuronal cell membranes are 2 times thicker than ordinary cell membranes. Animals utilizing aerobic respiration emerged in Cambrian explosion and eventually also neurons and TGD suggests an explanation in terms of oxygenation as the life in underground oceans entered to the surface through the cracks generated by the expansion.

See the chapter Non-locality in quantum theory, in biology and neuroscience, and in remote mental interactions: TGD perspective or the article Morphogenesis in TGD Universe .



Getting philosophical: some comments about the problems of physics, neuroscience, and biology

A reaction to not so thoughtful comments of a young otherwise friendly fellow in FB inspired me to ask why the young people who have got through the the basic courses are not only ignorant but sometimes also - well - arrogant. Why they are ignorant is easy to understand but arrogance remains a mystery for me. Personally I was also extremely ignorant as also the my fellow students but quite too shy to be arrogant: could I have been as arrogant as other if I had not been so hopelessly shy? This fellow had not understood much of what I had written - something completely acceptable, understandable, and predictable since something completely new is in question and text book wisdom or what professor said is simply not enough.

So he concluded that I am writing only weird fairy tales and that it seems that I have never heard about mathematics, electrodynamics, or thermodynamics. According to him these fields of science allow to understand biology more or less completely: I do not know whether this wisdom originated form from a text book or whether a professor told it. My FB friend also wanted to know whether I have read any book about biology during my lifetime.

I responded that I have not only heard the word "biology" but have even written a book about quantum consciousness and quantum biology (1000+ something pages). I forgot to mention that I have also written two published books about TGD and there are 17 online books at my homepage (9 of them about quantum biology) plus numerous articles both published articles and at homepage. I told that I have also recently published a long article in a book published by Springer about adelic physics: the goal of adelic physics is to describe the correlates of cognition and consciousness in terms of number theory and whose most important applications are to biology.

I also informed that I have also heard the word "thermodynamics" and even developed what I call p-adic thermodynamics providing a first principle approach to particle massivation replacing Higgs mechanism. I forgot to mention that quantum TGD can be seen formally as a complex square root of thermodynamics replacing Boltzman weights with the complex square roots defining vacuum functionals and that the generalization of so called microcanonical leads to extremely predictive view about scattering amplitudes serving as the building bricks of zero energy states.

1. Importance of philosophical thinking

This discussion once again made manifest both the extreme importance and regrettable lack of philosophical thinking - not only biology but in natural sciences in general. I do not mean with philosophical thinking academic philosophy, which I have found mostly deadly boring. Rather, for me good philosophical thinking means posing critical questions - rather than personal insults.

What we really know and what we do not know? What do we believe and what part of this is just beliefs? Are there facts challenging these beliefs? What is consciousness: is it really a property of something as "-ness" suggests? What is free will? How it manifests itself? Is it an essential aspect of consciousness so that AI hype could be forgotten? Are free will and non-determinism really in conflict with physics as physicalist has decided to believe? Concerning consciousness, what guidelines come from modern, physics, biology, and neuroscience?

In physics critical thinking would have allowed to avoid the numerous fads and fashions that have plagued us during last 4 decades: GUTs that led to the wrong track, inflation theory, various ad hoc models of dark matter postulating some exotic strong AI, supersymmetry in its GUT form, superstring models, loop gravity,...

Critical thinking would have challenged various "interpretations" of quantum theory and we could have continued immediately the work of the fathers of quantum theory rather than waiting for almost a century. Critical thinking would have also inspired the question whether the non-determinism of state function reduction has something to do with free will and how one should generalize the ontology of physics (Copenhagen ontology gives is it up altogether) to build a logically consistent framework.

Unfortunately critical thinking tends to lengthen the time spent in academic assembly line so that it is strongly discouraged. Thinkers tend also to become isolated from their social groups since everyone of us wants desperately to belong to some group and this requires sharing of its beliefs. It is easier to believe what professor and text book tell and get the research position and funding.

People are also very lazy. AI scientist decides that consciousness is running computer program or a property of the network structure or something equally ad hoc: no need to learn huge amount of physics, biology, neuroscience. Biologist decides that biology is nothing but Schrödinger equation and electromagnetism (or mere chemistry as in the older variant of the belief still prevailing). Neuroscientist desides that physicalism is correct and brain is the seat of the consciousness module. Brain as a computer paradigm makes the situation even easier. Physicist decides to believe in physicalism stating in its modern version that all physics reduces to Planck length scale: one can safely forget all other branches of sciences as a kind of taxonomy and specialize to apply one particular algorith to build CV.

2. Basic dogmatics

The key dogmas common to all branches of natural science are physicalism and reductionism. Physicalism states that matter is all that matters and consciousness is mere epiphenomenon and that world is deterministic - in the quantum version of the dogma it obeys statistical determinism. Reductionist sees natural sciences are a victorious march towards shorter and shorter space and time scales. Science is an imperium that grows conquest by conquest.

We are told that super string theorists have taken the last step to Planck scale by building the only possible theory of everything. This step is really gigantic: from electroweak length scale there are 16 orders of magnitude to Planck length scale. Before this every order of magnitude has contained a lot of su4prises but now the situation would be different as already GUT theorists revealed to us.

The surprise was however that the theory in Planck length scale does not allow to predict anything in long length scales: situation is like trying to predict the behavior of initial value sensitive system. The question of philosopher would be obvious: could something have gone wrong? This question has been made by some theoreticians. The decision of elite however seems to be that physics has reached its end. Nothing can be predicted and we should be happy about this marvellous feature of the only possible theory.

This series of conquests is marked by transitions. From biology to biochemistry, from biochemistry in vivo to organic chemistry in vitro, from chemistry to molecular physics, from molecular physics to atomic physics. Then follows a transition from atomic physics to nuclear physics: the assumption is that these two physics have practically nothing to do with each other. There are numerous experimental anomalies found during the last century challenging this belief. "Cold fusion" people were labelled next to criminals for their scandalous claims. Luckily the situation has now changed. But people talking about water memory belong still to the pariah of science.

After this jump we jump from nuclear physics to hadron physics to physics at quark-gluon level and then comes the really really big Planck jump. So simple.

There is however a little problem. Every successful conqueror must build a lot of bridges, without them the maintenance fails. Reductionistic conquerors were so hasty that they did not have time to to build the bridges between these different physics. We do not understand how nuclear physics emerges from hadron physics emerges from quark physics. We do not understand how biochemistry emerges from organic chemistry emerges from molecular physics emerges from atomic physics. But we can decide that this is only a technical difficulty: if we had enough computational power we could fill these gaps.

Actually, I know a couple of finnish fellows who tried to fill a gap. The first one has read from text book that the notion of chemical bond emerges from atomic physics. He wrote a lot of computer programs and did not find a slightest indication for this. Second fellow had learned that cell membrane emerges and started to study a model in which one has just molecules and molecular dynamics simplifying the situation. Not a slightest indication.

3. Restricting the attention to biology and neuroscience

In the following the attention is restricted mostly to the philosophical problems of biology and neuroscience. It however turns that these problems are actually also problems of physics.

3.1 Biology as nothing but biochemistry and electromagnetism

The basic dogmatics says that life is nothing but chemistry plus a little bit of electromagnetism needed to model cell membrane and neuronal membrane. There is also EEG but this is taken as noise due to neural circuits so that there is no need to waste time with it. Luckily, not all experimentalists know or care about dogmatics and have found correlations of EEG with behavior and physiology and they are used as a diagnostic tool. Most of them however refuse to consider seriously the possibility that EEG might possibly communicate something from brain somewhere. Where would this somewhere could reside: outside brain?

No! Philosopher must be producing totally weird fairy tale now! Says the mainstreamer inside me with such a friendly ut delicate tone that it becomes clear that he regards the poor philosopher as a screwball.

But philosopher continues asking. Didn't Libet discover that our sensory data is fraction of second old? Could it take fraction of second of this data to propagate as EEG signals from brain to this something. As a matter fact, Libet discovered also that the conscious decision to raise finger is preceded by neural activity starting for a fraction of second earlier. One cannot understand this unless one decides that it supports the absence of free will.

Philosopher asks also whether our decision that experienced time and the time of physicist are one and the same thing is be wrong. They are indeed different in many respects as any first year physics student understands. Should we trust facts instead of textbook wisdom? And what about Libet's second finding: could we give up our firm decision that signals propagate in only single direction of geometric time?

There is also a second strange electromagnetic phenomenon in biology: bio-photons. Already discovered almost century ago, they are still taken as pseudoscience by many biologists. They appear in visible and UV range but it seems that they are not produced in molecular reactions (this would mean peaks in the distribution). What is their origin?

3.1 Why vivo-vitro difference?

Even the basic dogmatist must admit that one must speak about organic chemistry in vivo and in vitro. In vitro one can build models for reactions, deduce estimates for the excitation energies of molecules, construct thermodynamical models for reactions in terms of thermodynamics involving parameters like activation energies and chemical potentials, one can develop complex networks of reaction pathways.

The typical assumption of these models is that everything is homogenous and isotropic: one has spatially constant concentrations of various reactions obeying differential equations determined by the kinetics. One can however construct more complex structure by allowing diffusion making possible spatial gradients.

The problem is that this dynamics has very little to do with what happens in living cell. The in vitro estimates for the rates of reactions are many many orders of magnitudes too low as compared to those in living matter. We do not understand anything about bio-catalysis. We know that enzymes and ribozymes somehow make the miracle but that's all. We do not have slightest clue about how reactants manage to find each other in the molecular soup full of different molecules. We have no idea wherefrom the reactants get the energy to jump over potential wall making the reaction quite too slow.

Philosopher would say that here is an excellent opportunity for new physics to enter in biology. How can reactants find each other? Could they possibly be connected by something, which shortens as the reactants meet? Could the notion of tensor network involving quantum entanglement be essential element of biology and entire physics. Particles would not be lonely riders but could be connected by something at least temporarily. Could this something liberate energy quanta allowing to get over the potential wall making reaction so slow? Could these networks have dynamical topology and make living systems what they are.

Unfortunately, standard space-time picture does not allow this something. Also Planck constant is quite too small. Should we conclude that the philosopher is weirdly fairytaling again?

3.2 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?

Easy to guess the reaction of me the mainstreamer: fairy-taling again.

3.3 Where does the coherence come from?

A further mystery is how the biochemical reactions can occur coherently in length scales longer than atomic scale. Without this coherence I could not write this, play piano, or even raise my hand. If we were just sacks of water containing some chemicals we would be doing science and arts. We would be indeed just sacks of water containing some chemicals in chemical and thermodynamical equilibrium and microscopic sample from this water would characterize us completely.

Mysteriously the coherence of biodynamics in scales up to the size of the organism emerges somehow. The required coherence need not be quantum coherence - and probably it is not - but it could be induced by quantum coherence. Quantum coherence of what? There is also the problem due to quite too small value of Planck constant. We have learned about the effects supporting the vision about quantum biology. It is now however becoming clear that these effects would however require large value of Planck constant.

Here the philosopher remembers the findings of Blackman and other pioneers of bio-electromagnetism. They found that the irradiation of vertebrate brain by ELF radiation at EEG frequencies scale had effects on both behavior and physiology and these effects look quantal occurring at harmonics of endogenous magnetic field of .2 Gauss. E=h× f makes these effects extremely small and totally masked by thermal noise. What if the value of Planck constant were so large that the energies were above thermal energy?

Now the mainstream physicist inside us is getting really angry: is this recklessly speculating philosopher really suggesting that our cherished quantum theory might not be the final word of science?

3.4 Morphogenesis

The problem of structure formation in biology - morphogenesis - was put under the rug by most biologists after the emergence of genetics. Sheldrake is one of those who have taken it seriously and has been labelled as a crackpot by mainstreamers. One just assumes that the structures are there and performs chemistry around these structures. This approach is very practical and has given an enormous amount of data but practically no understanding.

In standard physics the description of spatial structure would be in terms of enhanced densities of biomolecules or of their gradients in some space-time region. This is the only possibility because the space-time of standard physics is topologically and geometrically utterly trivial. Empty Minkowski space is an excellent approximation for it.

What philosopher has to say about this? If space-time topology were topologically non-trivial, situation would change dramatically. Already Wheeler saw this possibility and in the biology inspired by TGD (for which Wheeler suggested its name) all structures correspond to structures of topologically non-trivial space-time identified as surface in certain 8-D space-time: space-time sheets, magnetic flux tubes, etc... The entire TGD inspired quantum biology relies on this vision. The structures that we see around us would represent the non-trivial topology of space-time surface.

All structures - including bio-molecules, membrane like structures, organelles, organs, ... - would be 4-D space-time surfaces. Again philosopher gets excited since this would reduce the notion of shape in biology to a precisely defined and testable geometrodynamics coupling to em fields.

3.4.1. The dynamics of space-time surfaces

This dynamics predicts two kinds of space-time regions (see this.

  1. The regions of first kind are locally minimal surfaces. These minimal surfaces are as 4-D analogs of geodesic lines analogs of asymptotic states of particle physics for which interactions are not on. They also satisfy non-linear geometrization of massless field equations so that both particle and wave aspects are present. What is especially important is that static minimal surfaces have vanishing mean curvature and look like saddles locally. They cannot be closed surface if stationary.
  2. Second type of regions are not minimal surfaces: there is a non-trivial coupling of the minimal surface term to 4-force density analogous to the divergence of Maxwellian energy momentum tensor. This is a generalization of the dynamics of a point-like charged particle in Maxwell field. These regions are identified as interaction regions: in particle physics these two regions correspond to external free particles and the interaction region. Magnetic flux tubes play fundamental role in TGD based quantum biology are deformations of string like objects, which represent simplest 4-D minimal surfaces.

    Essential is the coupling between induced Kähler form (mathematically like Maxwell field) and the geometry of the surface: the divergence of energy momentum current assignable to the analog of cosmological term (4-volume) equals to the divergence of that assignable to Kähler action: this expresses local conservation of four-momentum. One could also speak about coupling between Kähler field and gravitational field: Penrose's intuition about the the role of gravitation in biology would be correct.

    When the coupling is absent, minimal surface property implies the separate vanishing of both divergences and separate conservation of corresponding energy-momenta. All the known extremals of Kähler action are minimal surfaces: this is due to their very simple algebraic properties making easy to discover them. Physically this correspond to quantum criticality: dynamics is universal and does not depend on coupling parameters.

3.4.2 General view about morphogenesis

These observations lead to a rather general view about morphogenesis.

  1. The presence of the Kähler field (em field is sum of Kähler field and second term) makes possible flow equilibria such as cell membrane, which are not minimal surfaces. These surfaces can be closed and stationary making possible isolation from environment crucial for living organisms.

    Spherical soap bubble is a good analogy: it is not minimal surface as the soap films spanned by frames are. They look locally like saddle surfaces with opposite external curvatures in two orthogonal directions, this implies that they cannot be closed surfaces. Bubble is not possible without a pressure difference Δ p between the interior and exterior of the bubble: the blowing of the soap bubble generates Δ p, and means external energy feed analogous to metabolic energy feed.

    Δ p is analogous to a non-vanishing voltage V over cell membrane. The electric field of cell membrane and the energy feed providing the energy of electric field as metabolic energy are essential for the stability. More generally, V would generalize to non-vanishing of energy momentum tensor of Kähler field with non-vanishing divergence serving as a correlate for the energy transfer between Kähler and volume (gravitational) degrees of freedom.

    This generalises to all morphologies, which correspond to closed surfaces. They necessarily involve both Kähler electric and magnetic fields coupling to the geometry to stabilize the morphology. This statement would give some content for the exaggerated claim that biology is nothing but electricity + Schrödinger equation that I heard during my first student year.

  2. For instance, the presence of Kähler electric field can correspond to electric fields of cell membrane or along a part of body. If it is too weak, things go wrong in development. As was found decades ago, consciousness is lost if the electric field between frontal lobes and hindbrain gets too weak or has wrong direction. Cell dies if the membrane potential becomes zero and EEG disappears in death. Also microtubules have electric field along their axes essential for their existence.

    Michael Levin and his collaborators have discovered further fascinating connections between electric fields and morphogenesis. One of the discoveries is that the electric fields of the embryo are controlled by neurons of the still developing brain (see this). This conforms with the view that neurons and their MBs correspond to a higher level in the hierarchy than ordinary cells and there take care of control in longer scales. The MB of the developing brain would be the controller.

  3. A non-trivial coupling (four-momentum transfer) between the volume and Kähler degrees of freedom requires that the energy momentum currents have opposite and non-vanishing divergences. For the energy momentum tensor of ordinary Maxwell field the divergence is proportional to the contraction of Maxwell current and Maxwell field so that the current must be non-non-vanishing.

    In TGD the energy momentum tensor is replaced with energy momentum current allowing to have well-defined notion of energy momentum and corresponding conservation laws. Now the divergence contains two terms. The first one is the contraction Tr(TKHk) of energy momentum tensor TK of Kähler action with the second fundamental form Hk: this term proportional to TK is new. Second term is proportional to the contraction jKJ∇ hk of the induced Kähler form J with Kähler current jK and gradients ∇ hk of imbedding space coordinates analogous the divergence of energy-momentum tensor jβFα in the case of ordinary Maxwell action. One expects both terms to be non-vanishing.

    For the mere Kähler action, which I believed for decades to determine the preferred extremals, jK is either vanishing or light-like. In presence of coupling it can be both non-vanishing and time-like. The realization that cosmological term is present was forced by the twistor lift of TGD whose existence is possible only for H=M4× CP2.

  4. The predicted stabilizing Kähler (and em) currents would naturally correspond to the DC currents flowing along the body in various scales discovered already by Becker and found to be essential for the survival of the organism. In particular, Becker's DC currents are essential for the healing of wounds and in the regeneration of organs. In the first first aid stage of the healing DC currents are generated locally and after than central nervous system (CNS) takes care of the generation of the current (for TGD based discussion of Becker currents see this). Also this is easy to understand from the proposed stability criterion.
3.5 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.

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 parametrization of the situation involving a lot of parameters. TGD leads to a quantum model for the situtation. Also the interpretation about the role of nerve pulse patterns at neuronal level changes dramatically.

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. 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.

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 and claims that it leads to a theory of consciousness as a generalization of quantum measurement theory. Irritating.

3.6 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. Adelic physics in turn predicts - surprise- surprise - a hierarchy of phases of matter labelled by the value of Planck constant. These phases residing at these somethings defining the networks - magnetic flux tubes - make possible macroscopic quantum coherence inducing the coherence of living matter.

3.7 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 in information theoretic sense? And could also radiation provide realization of genetic code necessary for communications?

3.8 The mystery of replication

Replication is one of the deepest mysteries of biology. It is really something totally counterintuitive if cell is seen as a sack of water plus some chemicals. We have a lot facts about what happens in the replication at DNA level but how this miracle happens is a mystery. At cell level the situation gets even more complex.

Philospher thinks that behind the chemistry there might lurk a much simpler quantum dynamics and that chemistry only makes its best to mimic this deeper dynamics. Is biochemistry controlled by something? Does this something provide a template for the dynamics at chemical level? The idea about the presence of this something popped up already in the mystery of EEG. What could this something perhaps receiving sensory information from vertebrate brain and maybe providing feedback as control signals affecting also chemistry?

Now our brave philosopher attacks the length scale reductionism again. Isn't it quite too much to require that all these replications in different length scales would result as accidental "emergences" due to thermodynamical fluctuations? Could the dynamics be fractal with same patterns - for instance replication - occurring in different scales. Could this dynamics be induced what happens on this something.

Philosopher also suggests a concrete model for the controlling level: dark matter with large value of Planck constant heff/h0=n at magnetic flux tubes and asks whether the conjectured dark realization of DNA in various scales performs the fundamental replication inducing in turn the biological replication in various scales as a mimicry? Morphogenesis controlled by the hierarchy of dark realizations of genetic code would be the basic vision. This would simplify the situation enormously but in totally different manner than length scale reductionism.

3. 9 Evolution

I forgot perhaps the most important piece from the original text. Philosopher cannot avoid the question "What is evolution?"

In standard biology evolution is mystery. If one believes on standard thermodynamics, evolution is impossible by second law and the eventual heat death is unavoidable. Evolution means generation of structures and second law indeed states that all gradients die so that the finals state is totally uninteresting homogenous stuff.

I already mentioned the weird proposal that biology is just an enormous thermodynamical fluctuation. Boltzmann brain was indeed a kind of fad of pop physicists for some years ago. The idea - if you want to call it such - was that Boltzmann brains - and also ours - popped up from the multiverse by a complete accident. One could even argue that this occurred only at planet Earth to make the claim more plausible. This is however not science anymore, this is just pure plain idiocy.

Philosopher asks questions and now the most obvious questions are following. Is evolution something much more general than biological evolution? Is evolution a basic aspect of physics as already cosmological evolution suggests? Is evolution "must", something completely unavoidable? What could force it?

The Universe governed by second law certainly does not allow evolution: just the contrary. Could the increase of entropy and increase of conscious information and development of cognition relate somehow? It has been argued by that biological evolution involves increase of the rate of entropy production as any-one can see by just looking around. These two things are not the same but are they somehow related.

Philosopher gets now childishly excited. We must just tolerate. Our philosopher already mentioned that p-adic physics as physics of cognition not only leads to a measure for conscious information - something very non-trivial - but to adelic physics fusing physics in various number fields. Adeles form a hierarchy labelled by the dimension of the extension of rationals inducing the extension of p-adic number fields labelled by primes. This dimension corresponds to the effective value of Planck constant and the larger it is, the larger the scale of quantum coherence is.

This has been already said but now comes the basic point and philosopher gets really excited. Since the number of extensions of rationals with dimension larger than given integer n is finite and the number of those with dimension larger than n is infinite, this dimension is bound to increase in statistical sense in the sequence of state function reductions recreating the quantum Universe again and again. Evolution is unavoidable! This is like random work from origin upwards. The height from the origin unavoidably increases.

Even more, the total negentropy coming from various p-adic sectors turns out to be larger than the entropy coming from the real sector. The bad news - not actually a news - is that increase of this negentropy is accompanied by the increase of entropy: civilizations indeed have the bad habit of polluting their environments. The good news is that negentropy increases faster than entropy: for a trivial extension of rationals from which everything would have started, negentropy equals to entropy. But for more complex extensions it is larger.

See the chapter Quantum Mind, Magnetic Body, and Biological Body or the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology.



Geometric theory of bio-harmony

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

  1. The model relies on the geometries of icosahedron and tetrahedron and representation of 12-note scale as so called Hamiltonian cycle at icosahedron going through all 12 vertices of icosahedron. The 20 faces correspond to allowed 3-chords for harmony defined by given Hamiltonian cycle. This brings in mind 20 amino-acids (AAs).
  2. One has three basic types of harmonies depending on whether the symmetries of icosahedron leaving the shape of the Hamiltonian cycle is Z6, Z4 or Z2. For Z2 there are two options: Z2,rot is generated by rotation of π and Z2,refl by reflection with respect to a median of equilateral triangle.
  3. Combining together one harmony from each type one obtains union of 3 harmonies and if there are no common chords between the harmonies, one has 20+20+20 3-chords and a strong resemblance with the code table. To given AA one assigns the orbit of given face under icosahedral isometries so that codons correspond to the points of the orbit and orbit to the corresponding AA. 4 chords are however missing from 64. These one obtains by adding tetrahedron. One can glue it to icosahedron along chosen face or keep is disjoint.
  4. The model in its original form predicts 256 different harmonies with 64 3-chords defining the harmony. DNA codon sequences would be analogous to sequences of chords, pieces of music. Same applies to mRNA. Music expresses and creates emotions and the natural proposal is that these bio-harmonies correlate with moods that would appear already at molecular level. They could be realized in terms of dark photon triplets realized in terms of light and perhaps even music (living matter is full of piezo-electrets). In fact, also the emotions generated by other art forms could be realized using music of dark light.
The model of music harmony is separate from the model of genetic code based on dark proton triplets and one of the challenges has been to demonstrate that they are equivalent. This inspires several questions.
  1. Could the number of harmonies be actually larger than 256 as the original model predicts? One could rotate the 3 fused Hamilton's cycles with respect to each by icosahedral rotations other leaving the face shared by icosahedron and tetrahedron invariant. There are however conditions to be satisfied.
    1. There is a purely mathematical restriction. If the fused 3 harmonies have no common 3-chords the number of coded AAs is 20. Can one give up the condition of having no common 3-chords and only require that the number of coded AAs is 20?
    2. There is also the question about the chemical realizability of the harmony. Is it possible to have DNA and RNA molecules to which the 3-chords of several harmonies couple resonantly? This could leave only very few realizable harmonies.
  2. The model predicts the representation of DNA and RNA codons as 3-chords. Melody is also an important aspect of music. Could AAs couple resonantly to the sums of the frequencies (modulo octave equivalence) of the 3-chords for codons coding for given AA? Could coding by the sum of frequencies appear in the coupling of tRNA with mRNA by codewords and coding by separate frequencies to the letterwise coupling of DNA and RNA nucleotides to DNA during replication and transcription?
  3. What about tRNA. Could tRNA correspond to pairs of harmonies with 20+20+444 codons? What about single 20+4=24 codon representation as kind of pre-tRNA?
  4. What is the origin of 12-note scale? Does genetic code force it? The affirmative answer to this question relies on the observation that 1-1 correspondence between codons and triplets of photons requires that the frequency assignable to the letter must depend on its position. This gives just 12 notes altogether. Simple symmetry arguments fix the correspondence between codons and 3-chords highly uniquely: only 4 alternatives are possible so that it would be possible to listen what DNA sequences sounds in given mood characterized by the harmony.
  5. What disharmony could mean? A possible answer comes from 6 Hamiltonian cycles having no symmetries. These disharmonies could express "negative" emotions.
See the new chapter Geometric theory of bio-harmony or the article New results in the model of bio-harmony .



Did RNA replicate in codon-wise manner during RNA era?

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

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

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

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

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

  1. During RNA era amino-acids associated with pre-tRNA molecules would served as catalysts for replication of RNA codons. The linguistic mode would have been "holistic" during RNA er in accordance with the findings of the above experiments. RNA codon would have been the basic unit.
  2. This would have led to a smaller number of RNAs since RNA and RNA like molecules in tRNA are not in 1-1 correspondence. A more realistic option could have been replication of subset of RNA molecules appearing in tRNA in this manner.
  3. Then a great evolutionary leap leading from RNA era to DNA era would have occurred. AA catalyzed replication of RNA would have transformed to a translation of RNA to proteins and the roles of RNA and AA in tRNA would have changed. [Perhaps the increase of heff in some relevant structure as quantum criticality was reached led to the revolution?]
  4. At this step also (subset of) DNA and its transcription to (a subset of) mRNA corresponding to tRNA had to emerge to produce mRNA in transcription. In the recent biology DNA replicates and is transcribed nucleotide by nucleotide rather than using codon as a unit so that DNA and RNA polymerases catalyzing replication and transcription should have emerged at this step. An alternative option would involve the "tDNA" as the analog of "tRNA" and the emergence of polymerases later: this does not however look attractive if one accepts the idea about the transition from holistic to analytic mood.

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

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

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

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

The communication between dark and ordinary variants of biomolecules involves resonance mechanism and would also involve genetic code represented as 3-chords, music of light, and it is interesting to see whether this model provides additional insights.
  1. The proposal is that 3-chords assignable to nucleotides as music of light with allowed 64 chords defining what I have called bio-harmony is essential for the resonance (see this, this, and this). The 3 frequencies must be identical in the resonance: this is like turning 3 knobs in radio. This 3-fold resonance would correspond to the analytic mode. The second mode could be holistic in the sense that it would involve only the sum only the sum of the 3 frequencies modulo octave equivalence assigning a melody to a sequence of 3-chords.
  2. The proposal is that amino-acids having not triplet decomposition are holistic and couple to the sum of 3 frequencies assignable to tRNA and mRNA in this manner. Also the RNAs in tRNA could couple to mRNA in this manner. One could perhaps say that tRNA, mRNA and amino-acids codons sing whereas DNA provides the accompaniment proceeding as 3-chords. The couplings of DNA nucleotides to RNA nucleotides would realy on the frequencies assignable to nucleotides.
  3. If the sum of any 3 frequencies associated with mRNA codons is not the same except when the codons code for the same amino-acids, the representation of 3-chords with the sum of the notes is faithful. The frequencies to DNA and RNA nucleotides cannot be however independent of codons since the codons differing only by a permutation of letters would correspond to the same frequency and therefore code for the same amino-acid. Hence the information about the entire codon would be needed also in transcription and translation and could be provided either by dark DNA strand associated with DNA strand or by the interactions between the nucleotides of the DNA codon.
  4. The DNA codon itself would know that if is associated with dark codon and the frequencies assignable to nucleotides are determined by the dark DNA codon. It would be enough that the frequency of the letter depends on its position in the codon so that there would be 3 frequencies for every letter: 12 frequencies altogether.

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

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

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

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

      CEG# ↔ DF#Bb , C#FA↔ D#GB .

    2. One could have

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

      or

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

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

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

    That the position the frequency associated with the nucleotide depends on its position in the codon would also reflect the biochemistry of the codon and this kind of dependence would be natural. In particular, different frequencies associated with the first and third codon would reflect the parity breaking defining orientation for DNA.
See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



Dark valence electrons and color vision

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

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

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

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

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

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

See the chapter Dark valence electrons and color vision or the article with the same title .



Does RNA code for pain?

Again an extremely interesting finding from neuroscience. The popular article "Scientists Sucked a Memory Out of a Snail and Stuck It in Another Snail" tells that the conditionings of snails produced by painful sensations can be transferred to other snails or even snail neurons in Petri dish by adding just the RNA of the conditioned snails to the dish! The article can be found at here .

Let us summarize the findings.

  1. RNA from snails is transferred to snails or to even populations of snail neurons in Petri dish!
  2. The effect involves epigenetic changes in DNA by methylation induced by RNA somehow. The reaction is to the serotonin informing for the stimulus. Avoidance behavior emerges as a response.
  3. How does RNA induce the epigenetic change? RNA should couple to a a specific part of DNA and induce the effect. A pairing of DNA with RNA in question occurring also in transcription suggests itself strongly.
  4. What in the RNA of the conditioned snail is different? RNA should somehow code for the conditioning induced by a painful sensory experience. RNA of sensory receptors should change somehow and communicate this change to DNA in brain by some mechanism. DNA-RNA pairing does not seem plausible. Could the pairing occur by some other means?
Before continuing it is good to summarize the TGD based models for music harmony providing also a model of genetic code (see this), for sensory perception (see this), for emotions (see this), and for impriting of emotions in water (see this).
  1. TGD based model for emotions and communication of emotions suggests that the communication takes place in terms of what I call music of light (also sound might be involved). Music expresses and creates emotions. Emotional state, mood, is coded by harmony or disharmony for music of light.

    12-note is fundamental for music and is represented as a closed self-non-intersecting path (Hamilton cycle) at icosahedron having 12 vertices. Icosahedron has 20 faces (triangles) and for given Hamilton cycle one can assign a 3-chord to each triangle. This gives 20-chord harmony (or disharmony). There is quite large number of 20-chord harmonies and those allowing Z6,Z4 and Z2 as symmetries is quite large. Besides this there 6 cycles with no symmetries and these could be identified as dis-harmonies.

  2. 20 is also the number of amino-acids so that it is not totally surprising that the model for bioharmony as a union of 3 different 20-chord harmonies plus 4-chord harmony assignable to tetrarhedron turns out to give a model of genetic code as 64 chord bioharmony. There are 64 basic 3-chords in one-one correspondence with DNA and RNA codons. tRNA corresponds to a union of 2 20-chord harmonies. Given amino-acid corresponds to the orbit of 3-chord under symmetries of the harmony so that number of 3-chords at the orbit is the number of DNAs coding for the amino-acid. These numbers come out correctly.
  3. There are two other representations of genetic code. The ordinary chemical representation and the representation in terms of dark proton sequences at magnetic flux tubes. The model for dark proton triplet predicts that its states divided to 64 analogs of DNA codons, 64 analogs of RNA codons, 40 analogs of tRNA codons, and 20 analogs of amino-acids. Genetic code comes out correctly also now by a natural pairing of dark proton triplets. One must couple these 3 representations of genetic code with themselves and with each other.
  4. There is indeed resonant coupling by 3-chords realized in terms of free frequencies of dark photons. The frequencies are rather low (E =heff× f, heff/h=n) but energies are same as for biophotons with energies in visible and UV range.

    Also dark variants of DNA, etc couple with each other via dark photon resonance. Dark DNA,etc couple with ordinary DNA, etc.. by energy resonance to form double strands. This means that dark photon transforms to ordinary photon in the coupling. Amino-acid couples to single frequency, which is the sum of codon frequencies coding for it.

    There is quite large number of 3-chord 3-harmonies defining DNA and RNA moods, and 3-chord 2-harmonies tRNA moods, and amino-acid 1-chord harmonies. There also 6 disharmonies with 20 chords each possible assignable to negative moods such as those generated by pain.

So: Is the communication chemical by DNA-RNA pairing or by some other means? TGD based model suggests "some other means".
  1. Pain in sensory receptor is certainly involved. In TGD based model differs from neuroscience view in that for sensory experiences sensory receptors are seats of the sensory qualia and brain only forms cognitive representations about them and also entangles with sensory receptors to share the pain. Somehow pain must affect RNA in sensory receptors? How?
  2. In this framework the stimulus in nocireceptors would induce a disharmony expressed in terms of the disharmony associated with the expression of RNA in terms of 3-chords. The dark variant of RNA in pain receptors would entangle with the dark DNA in certain neurons in brain of the snail. Nerve pulse patterns from the nociceptors would generate also magnetic flux tube connections parallel to the sensory pathway in question and make possible the communication by dark biophoton triplets to brain possible. The dark variant of DNA in brain would have resonant coupling with ordinary DNA and induce the epigenetic change by methylation as a response to the negative mood with the mediary of biophotons. After this the organism would have avoidance behaviour towards the stimulus inducing the pain.
  3. The presence of mere RNA and associated dark RNA dis-harmonious mood would do the same for any neuron by the resonance mechanism. This would allow to transfer emotions even to snail neurons in Petri dish, not only those in living snails.
The proposed mechanism provides insights to many other poorly understood problems.
  1. This mechanism also allows to understand how the transfer of emotions conditioning induces epigenetic chance also in the germ cell DNA: this is not easy to understand in the standard framework requiring chemical communication through the germ cell membrane.
  2. The models for learning (memories restricted to conditionings) based on formation of synaptic contacts on one hand and involving RNA are seen as exclusive in standard neuroscience. In TGD framework the formation of synaptic contacts might rely at the fundamental level on the same epigenetic mechanism. Neuromodulators might induce the emotional states in RNA in turn doing the epigenetic editing.

    In human brain the genomes differ in various neurons and epigenetic editing by the proposed mechanism might cause this. An interesting question is whether humans could edit their genomes intentionally. All conditionings are not useful and maybe it becomes someday possible to affect these conditionings at the level of dark DNA.

  3. Squid and octopus are known to be able to edit their mRNA (see this). Instead of DNA the mRNA produced in the transcription so that the translation produce different protein. The effect of emotional states of the dark variant of RNA associated with mRNA could be the mechanism involved.
  4. The strong emotional state of single individual induces very effectively the same emotional state in people around: consider only concert as an example. Could the "music of dark light" mediate the emotions from the dark RNA of individual - say artist - to people around. If so all art would be basically music of light!
To sum up: this finding provides rather concrete support for the vision that emotions are coded by the music of light at molecular level.

See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



The experiments of Masaru Emoto with emotional imprinting of water

Sini Kunnas sent a link to a video telling about experiments of Masaru Emoto (see this) with water, which is at criticality with respect to freezing and then frozen. Emoto reports is that words expressing emotions are transmitted to water: positive emotions tend to generate beautiful crystal structures and negative emotions ugly ones. Also music and even pictures are claimed to have similar effects. Emoto has also carried out similar experiments with rice in water. Rice subjected to words began to ferment and water subject to words expressing negative emotions began to rotten.

Remark: Fermentation is a metabolic process consuming sugar in absence of oxygen. Metabolism is a basic signature of life so that at least in this aspect the water+rice system would become alive. The words expressing positive emotions or even music would serve as a signal "waking up" the system.

One could define genuine skeptic as a person who challenges existing beliefs and pseudo-skeptic (PS in the sequel) as a person challenging - usually denying - everything challenging the mainstream beliefs. The reception of the claims of Emoto is a representative example about the extremely hostile reactions of PSs as aggressive watchdogs of materialistic science towards anything that challenges their belief system. The psychology behind this attitude is same as behind religious and political fanatism.

I must emphasize that I see myself as a thinker and regard myself as a skeptic in the old-fashioned sense of the word challenging the prevailing world view rather than phenomena challenging the prevailing world view. I do not want to be classified as believer or non-believer. The fact is that if TGD inspired theory of consciousness and quantum biology describes reality, a revolution in the world view is unavoidable. Therefore it is natural to consider the working hypothesis that the effects are real and see what the TGD based explanation for them could be.

The Wikipedia article about Masaru Emoto (see this) provides a good summary of the experiments of Emoto and provides a lot of links so that I will give here only a brief sketch. According to the article Emoto believed that water was a "blueprint for our reality" and that emotional "energies" and "vibrations" could change the physical structure of water. The water crystallization experiments of Emoto consisted of exposing water in glasses to different words, pictures or music, and then freezing and examining the aesthetic properties of the resulting crystals with microscopic photography. Emoto made the claim that water exposed to positive speech and thoughts would result in visually "pleasing" crystals being formed when that water was frozen, and that negative intention would yield "ugly" crystal formations.

In 2008, Emoto and collaborators published and article titled "Double-Blind Test of the Effects of Distant Intention on Water Crystal Formation" about his about experiments with water in the Journal of Scientific Exploration, a peer reviewed scientific journal of the Society for Scientific Explorations (see this). The work was performed by Masaru Emoto and Takashige Kizu of Emoto’s own IHM General Institute, along with Dean Radin and Nancy Lund of the Institute of Noetic Sciences, which is on Stephen Barrett's Quackwatch (see this) blacklist of questionable organizations. PSs are the modern jesuits and for jesuits the end justifies the means.

Emoto has also carried experiments with rice samples in water. There are 3 samples. First sample "hears" words with positive emotional meaning, second sample words with negative emotional meaning, and the third sample serving as a control sample. Emoto reports (see this) that the rice subjected to words with positive emotional content began to ferment whereas water subject to words expressing negative emotions began to rotten. The control sample also began to rotten but not so fast.

In the article The experiments of Masaru Emoto with emotional imprinting of water I will consider the working hypothesis that the effects are real, and develop an explanation based on TGD inspired quantum biology. The basic ingredients of the model are following: magnetic body (MB) carrying dark matter as heff/h=n phases of ordinary matter; communications between MB and biological body (BB) using dark photons able to transform to ordinary photons identifiable as bio-photons; the special properties of water explained in TGD framework by assuming dark component of water implying that criticality for freezing involves also quantum criticality, and the realization of genetic code and counterparts of the basic bio-molecules as dark proton sequences and as 3-chords consisting of light or sound providing a universal language allowing universal manner to express emotions in terms of bio-harmony realized as music of light or sound. The entanglement of water sample and the subject person (with MBs included) realized as flux tube connections would give rise to a larger conscious entity expressing emotions via language realized in terms of basic biomolecules in a universal manner by utilizing genetic code realized in terms of both dark proton sequences and music of light of light and sound.

See the chapter Emotions as sensory percepts about the state of magnetic body? or the article The experiments of Masaru Emoto with emotional imprinting of water.



How molecules in cells "find" one another and organize into structures?

The title of the popular article How molecules in cells 'find' one another and organize into structures expresses an old problem of biology. Now the group led by Amy S. Gladfelter has made experimental progress in this problem. The work has been published in Science (see this).

It is reported that RNA molecules recognize each other to condense into the same droplet due to the specific 3D shapes that the molecules assume. Molecules with complementary base pairing can find each other and only similar RNAs condense on same droplet. This brings in mind DNA replication, transcription and translation. Furthermore, the same proteins that form liquid droplets in healthy cells, solidify in diseases like neurodegenerative disorders.

Some kind of phase transition is involved with the process but what brings the molecules together remains still a mystery. The TGD based solution of this mystery is one of the first applications of the notion of many-sheeted space-time in biology, and relies on the notion of magnetic flux tubes connecting molecules to form networks.

Consider first TGD based model about condensed and living matter. As a matter fact, the core of this model applies in all scales. What is new is there are not only particles but also bonds connecting them. In TGD they are flux tubes which can carry dark particles with nonstandard value heff/h=n of Planck constant. In ER-EPR approach in fashion they would be wormholes connecting distance space-time regions. In this case the problem is instability: wormholes pinch and split. In TGD monopole magnetic flux takes care of the stability topologically. The flux tube networks occur in all scales but especially important are biological length scales.

  1. In chemistry the flux tubes are associated with valence bonds and hydrogen bonds (see this). In biology genetic code would be realized as dark nuclei formed by sequences of dark protons at magnetic flux tubes. Also RNA, amino-acids, and even tRNA could have dark counterparts of this kind (see this). Dark variants of biomolecules would serve as templates for their ordinary variants also at the level of dynamics. Biochemistry would be shadow dynamics dictated to high degree by the dark matter at flux tubes.
  2. Dark valence bonds can have quite long length and the outcome is entangled tensor net (see this). These neuronal nets serve as correlates for cognitive mental images in brain (see this) emotional mental images in body (see this). Dark photons propagating along flux tubes (more precisely topological light rays parallel to them) would be the fundamental communication mechanism (see this). Transmitters and nerve pulses would only change the connectedness properties of these nets.
The topological dynamics of flux tubes has two basic mechanisms (I have discussed this dynamics from the point of view of AI here).
  1. Reconnection of flux tubes serves is the first basic mechanism in the dynamics of flux tube networks and would give among other things rise to neural nets. The connection between neurons would correspond basically to flux tube pair which can split by reconnection. Also two flux tube pairs can reconnect forming Y shaped structures. Flux tube pairs could be quite generally associated with long dark hydrogen bonds scaled up by heff/h=n from their ordinary lengths. Flux tube pairs would carry besides dark protons also supra phases formed by the lone electron pairs associated quite generally with hydrogen bonding atoms. Also dark ions could appear at flux tubes.

    Biomolecules would have flux loops continually scanning the environment and reconnecting if they meet another flux loop. This however requires that magnetic field strengths are same at the two loops so that a resonance is achieved at level of dark photon communications. This makes possible recognition by cyclotron frequency spectrum serving as signature of the magnetic body of the molecule.

    Water memory (see this) would rely on this recognition mechanism based on cyclotron frequencies and also immune system would use it at basic level (here one cannot avoid saying something about homeopathy although I know that this spoils the day of the skeptic: the same mechanism would be involved also with it). For instance, dark DNA strand accompanying ordinary DNA and dark RNA molecules find each other by this mechanism (see this). Same applies to other reactions such as replication and translation .

  2. Shortening of the flux tubes heff/h reducing phase transition is second basic mechanism explaining how biomolecules can find each other in dense molecular soup. It is essential that the magnetic fields at flux tubes are nearly the same for the reconnection to form. A more refined model for the shortening involves two steps: reconnection of flux tubes leading to a formation of flux tube pair between molecules and shortening by heff/h reducing phase transition.
Also ordinary condensed matter phase transitions involve change of the topology of flux tube networks and the model for it allows to put the findings described in the article in TGD perspective.
  1. I just wrote an article (see this) about a solution of two old problems of hydrothermodynamics: the behavior of liquid-gas system in the critical region not consistent with the predictions of statistical mechanics (known already at times of Maxwell!) and the behavior of water above freezing point and in freezing. Dark flux tubes carrying dark protons and possibly electronic Cooper pairs made from so called lone electron pairs characterizing atoms forming hydrogen bonds.
  2. The phase transition from gas to liquid occurs when the number of flux tubes per molecule is high enough. At criticality both phases are in mechanical equilibrium - same pressure. Most interestingly, in solidification the large heff flux tubes transform to ordinary ones and liberate energy: this explains anomalously high latent heats of water and ammonia. The loss of large heff flux tubes however reduces "IQ" of the system.
The phase transitions changing the connectedness of the flux tube networks are fundamental in TGD inspired quantum biology.
  1. Sol-gel transition would correspond to this kind of biological phase transitions. Protein folding (see this) - kind of freezing of protein making it biologically inactive - and unfolding would be second basic example of this transition. The freezing would involve formation of flux tube bonds between points of linear protein and assignable to hydrogen bonds. External perturbations induce melting of the proteins and they become biologically active as the value of heff/h=n characterizing their maximal possible entanglement negentropy content (molecular IQ) increases. External perturbation feeds in energy acting as metabolic energy. I have called this period molecular summer.
  2. Solidification of proteins reducing is reported to be associated with diseases such neurodegenerative disorders. In TGD picture this would reduce the molecular IQ since the ability of system to generate negentropy would be reduced when heff for the flux tubes decreases to its ordinary value. What brings molecules together is not understood and TGD provides the explanation as heff reducing phase transition for flux tube pairs.
See the chapter Artificial Intelligence, Natural Intelligence, and TGD or the article with the same title.



Is time reversal involved with Pollack effect?

In Pollack effect negatively charges Exclusion Zeones (EZs) are formed. EZs have the very strange property that the impurities are spontaneously removed from them. This seems to be in conflict with the second law of thermodynamics according to which both temperature and concentration gradients should tend to disappear. Could one understand this as being due to a reversal of the arrow of time?

Indeed, TGD inspired theory of consciousness relying on zero energy ontology (ZEO) predicts the possibility of time reversed selves (see this). When conscious entity - self - dies, it reincarnates as a self with opposite arrow of geometric time.

  1. In ZEO zero energy states replace ordinary quantum states assigned with time=constant snapshots of time evolution in space-time. Zero energy states are pairs of ordinary quantum states at opposite light-like boundaries of causal diamond (CD) identifiable as counterparts of initial and finals states of a physical event. Conservation quantum numbers translates to a mathematical statement that the quantum numbers associated with the members of pairs are opposite. One can also say that zero energy state is analogous to a deterministic computer program or a behavioral mode. The act of free will replaces this program/behavior with a new one so that one avoids the paradox between the non-determinism of free will and determinism of physics.
  2. Causal diamond (CD) defines the imbedding space correlate of self. One can assign to the opposite light-like boundaries the attributes active and passive. During the sequence of analogs of "small" state function reductions analogous to weak quantum measurements (resembling classical measurements) the passive boundary remains unaffected as also the members of state pairs defining zero energy states associated with it. Active boundary recedes farther away from the passive boundary and the members of state pairs at it change. The size of CD thus increases and gives rise flow of geometric time as an increase of the temporal distance between the tips of CD.
  3. Eventually the first state function reduction to the opposite boundary of CD must occur, and active and passive boundary change their roles. Self dies and re-incarnates as a self with opposite arrow of geometric time: the formerly passive boundary of CD becomes now active and moves in opposite time direction reduction by reduction. In the next re-incarnation self continues almost from the moment of geometric time at which it died. It might be that we die repeatedly without noticing it at all!
  4. The many-sheeted space-time approximated with slightly curved regions of Minkowski space would certainly tend to mask the time reversals in given length scale. In elementary particle length scales the state function reductions would indeed change the arrow of time but this would occur so often that there would be no arrow of time in statistical sense: one would speak of microscopic reversibility. In time scales considerably longer than those of human consciousness the observed arrow of time would correspond to that associated with selves with very large CDs and with lifetime much longer than ours. The change of the arrow of time could be detectable in time scales relevant to living matter and human consciousness and just these scales are the scales where the anomalies occur!
Could the ghostly space-time regions - time reversed selves - have some physical signatures making possible to prove their existence empirically?
  1. Second law would still hold true but in opposite direction of geometric time for the space-time sheets with non-standard arrow of time. The effects implied by second law would be present as their reversals. The observer with standard direction of geometric time would see temperature and density gradients to develop spontaneously. Also parameters describing dissipation rates such as Ohmic resistance and viscosity could have in some situations negative values.

    This indeed seems to take place in living matter. For instance, the building bricks of molecules spontaneously arrange to molecules: DNA replication, transcription and translation of RNA to proteins are basic examples about this. The development of concentration gradients is also clear in the strange ability of EZs to get rid of impurities. Also the charge separation creating EZs could be seen as disappearence of charged separatio in reversed direction of time. Healing of living organism could be a basic example of the process in which the arrow of time changes temporarily at some level of hierarchy of space-time sheets.

  2. The generation of temperature gradients would be a clear signature for the reversal of the arrow of time. Water is the basic stuff of life, and the thermodynamics of water involves numerous anomalies summarized at Martin Chaplin's homepage "Water structure and science". TGD based explanation could be naturally in terms of dark variants of protons at magnetic flux tubes and possible change of the arrow of geometric time.
  3. There is a lot of anecdotal evidence for the effects challenging our beliefs about standard arrow of time. A spontaneous generation of temperature differences is basic example. There is a nice popular document about this boundary region of science by Phie Ambo, which even skeptic might enjoy as art experience.

    It was a great surprise for me that one of the key personalities in the document is Holger B Nielsen, one of the pioneers of string models. I have had the honor to have intense discussions with him in past: he is one of the very few colleagues who has shown keen interest on the basic ideas of TGD. The document discusses strange phenomena associated with the physics of water possibly having interpretation in terms of time reversal and formation of EZs. From the document one also learns that in Denmark physics professionals are beginning to take these anomalies seriously.

    Unfortunately, the people who claim having discovered this kind of effects - often not science professionals - are labelled as crackpots. The laws of science also tell what we are allowed to observe (and think), at least if we want to be called scientists!

  4. The ghost stories might also reflect something real - this real need of course not be ghost but something deep about consciousness. Could it be that it is sometimes possible to consciously experience the presence of a space-time region - self - with an opposite arrow of geometric time? Ghost stories typically involve a claim about the reduction of temperature of environment in presence of ghost: could this be something real and a signature for the reversal of time at some level of dark matter hierarchy affecting also dark matter? As a matter of fact, in TGD Universe our conscious experience could involve routinely sub-selves (mental images) with non-standard arrow of time (see this): motor actions could be identified as sensory mental images with opposite arrow of time.
For background see the chapter How to test TGD Based Vision about Living Matter and Remote Mental Interactions or the article Pollack's Findings about Fourth phase of Water: TGD View.



Dance of the honeybee and New Physics

For more than two decades ago mathematician Barbara Shipman made rather surprising finding while working with her thesis. The 2-D projections of certain curves in flag manifold F=SU(3)/U(1)× U(1) defined by the so called momentum map look like the waggle part of the dance of the honey bee. Shipman found that one could reproduce in this framework both waggle dance and circle dance (special case of waggle dance) and the transition between these occurring as the distance of the food source from the nest reduces below some critical distance. Shipman introduced a parameter, which she called α, and found that the variation of α allows to integrate various forms of the honeybee dance to a bigger picture. Since SU(3) is the gauge group of color interactions, this unexpected finding led Shipman to as whether there might be a profound connection between quantum physics at quark level and macroscopic physics at the level of honeybee dance.

The average colleague of course regards this kind of proposal as crackpottery: the argument is that there simply cannot be any interaction between degrees of freedom in so vastly different length scales. Personally I however found this finding fascinating and wrote about the interpretation of this finding in the framework of TGD and TGD inspired consciousness. During more than two decades a lot of progress has taken place in TGD, in particular I have learned that the flag manifold F has interpretation as twistor space of CP2 and plays a fundamental role in twistor lift of TGD. Hence it is interesting to look what this could allow to say about honeybee dance.

It turned out that one could understand the waggle parts of the honeybee dance at space-time level in terms of the intersection of the space-time surface with the image of the Cartan sub-algebra of SU(3) represented in CP2 using exponential map. This allows to code the positional data about the food source. The frequencies assignable to the wing vibrations and waggling turn could have interpretation as cyclotron frequencies as expected if the magnetic body of the bee controls the waggle dance utilizing resonance mechanism. They could also correspond to the momenta (frequencies) defining constants of motion for geodesic in U(1)× U(1) defining one particular point of flag manifold F. Also a connection with the Chladni effect emerges: the waggle motion is along time-like curve at which Kähler force vanishes. Also the transition from waggle dance do circle dance.

See the new chapter Dance of the honeybee and New Physics or the article with the same title.



How brain selectively remembers new places?

There was a very interesting link in Minding Brain related to the storage of new memories. The title of the popular article is "How brain selectively remembers new places?". The following represents TGD based view about what might happen.

  1. In TGD framework brain/body corresponds to 4-D geometric object classically - a space-time surface with complex topology (zero energy ontology, ZEO). Brain and biological body are accompanied by magnetic body (MB) defining a topological time evolution of flux tube network having neurons (and also body cells) as its nodes and it is MB, which seems to be of fundamental significance (see this and this). Memories are located in 4-D brain (body) for the first time to the time-place, where they were formed, later successful memory recalls form new copies of them.
  2. To remember is to see in time direction to geometric past. The signal sent from hippocampus backwards in geometric time scatters back in standard time direction: this is nothing but seeing in 4 dimensions. 4-D memory storage means that there is practically no limitations on memory storage since new storage capacity is created all the geometric time! Making careful distinction between experienced and geometric times allows to both avoid paradoxes and solve the paradoxes of existing theory. Remark: Also the possibility of quantum entanglement also increases exponentially the memory storage capacity (and destroys the dreams of AI afficionados about copying human consciousness as bits telling whether neuron fires or not to a computer file!).
  3. Brain is able to detect whether the sensory percept - say completely new place - is indeed new. Brain acts as novelty detector. This requires scanning of 4-D brain to see whether there are sensory percepts in geometric past, which share common features with the recent sensory percept. This requires high level conceptualization so that perceptive field is decomposed to objects with some attributes. If common objects are not found, the percept is regarded as something new. In this case a new symbolic memory representation about perceptive field is formed.
  4. This strongly suggests that the signal sent from hippocampus scatters back from brain of past and is then compared with the recent sensory percept. If they the signals are very similar - this might give rise to some kind of resonance - the experience is "I have seen this before". The information provided by the already existing memory is utilized. If not then sensory percept is regarded as new and memory representation is formed.
Where is this new memory representation constructed?
  1. The article suggests that locus coeruleus (LC) and area CA3 of hippocampus are involved. It was found that the modulation of CA3 by LC is was involved in the formation of new memory: if the modulation was prevented, no new memory was formed and the the mice behaved next day as if the place were still new.
  2. In ZEO the new memory would correspond to a collection of activated neurons in LC and CA3 accompanied by connected flux tube structure represented the new mental image as a quantum entangled structure - tensor network. This kind of mental images would have formed for some period of time in the brain of the mice and given rise to a 4-D representation of new place to be read later by sending signals backwards in geometric time.
See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



Getting memories by eating those who already have them

While writing article about emotions as sensory percepts about the state of magnetic body I learned about extremely interesting findings. I have already earlier written about some of the finding that both pieces of split planaria have the memories (identified as learned skills or conditionings) of the original planaria (see this). The news at this time was that planaria get the memories of planaria that they have eaten!

To begin with, one must carefully distinguish between genuine memories and memories as behavioral patterns) (conditionings, skills).

  1. Cognitive memories as behavioral patterns are assumed to be due to the strengthening of synaptic contacts (long term potentiation (LPT) giving rise to nerve circuits, which are active or easily activated. In TGD framework activation means formation of flux tube network giving rise to quantum entangled state with neurons at the nodes: neural activity generates transmitters serving as bridges between flux tubes associated with axons and create flux tube network carrying a conscious mental image. A quantum coherent entangled tensor network is formed and also classical communications using dark photons are possible in this state. These neurons are firing synchronously. Nerve pulses would not be signals between neurons but would induce communications to magnetic body in scales even larger than body.
  2. Genuine memories - say episodal memories - would in TGD (zero energy ontology, ZEO) correspond to neural activities in geometric past: kind of seeing in time direction. These are typically verbal memories but also sensory memories are possible and can be induced by electric stimulation of brain.
Consider now the experiments discussed in the popular article Somewhere in the brain is a storage device for memories). They all relate to the identification of memory as a behavioral pattern induced by conditioning and are therefore emotional memories.
  1. In one experiment sea slugs learned to avoid painful stimulus. This led to a generation of synaptic contacts between neutrons involving increased synaptic strength - long term potentiation (LPT). Then some drug was used to destroy the LPT. The problem was that the lost contacts were not those formed when the memory was formed!
  2. In second experiment mice were used. A conditioned fear (LPT) was induced in mice and again the generation of synaptic contacts was observed. Then the contacts - long term potentiation - was destroyed completely. Memories as conditioned fear however remained!
It was an amusing accident to learn about this just when I was building a model for emotions as sensory percepts about the state of magnetic body (MB) fundamental in TGD inspired quantum biology.
  1. MB consists of a part formed from highly dynamical flux tube tensor networks having cells and also other structures with other size scales (fractality) as nodes. MB has also a part outside body involving rather large values of heff= n× h and having to higher cognitive IQ. Corresponding emotions would be higher level emotions (like experience of beauty) whereas bodily emotions are primitive and involve positive/negative coloring inducing a desire to preserve/change the situation in turn inducing an emotional counterpart of motor activity as excretion of hormones from emotional brain with hypothalamus in the role of highest motor areas and lower glands (both in brain and in body) in the role of lower motor areas.
  2. In the recent case the memories are definitely emotional memories and in TGD framework they would be naturally at the level of body and generated as mental images associated with large numbers of ordinary cells appearing as nodes of quantum entangled flux tube networks giving rise to tensor networks (see this). Hormones would be the tool to modify and generate these networks.
  3. Emotional memories would be represented by the conditioning and analog of LPT at the level of body rather than at the level of brain! Hormones like also other information molecules would act as relays connecting existing pieces of network to larger ones! The neural activity would be involved only with the generation of memories and induce hypothalamus to generate the fear network using the hormones controlling hormonal activities of lower level glands.
  4. The model could also explain the finding that in the splitting of flatworm the both new flatworms inherit the memories and that even non-trained flatworms eating trained flatworms get their memories (defined as behavioral patterns involving emotional conditioning).
See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



Emotions as sensory percepts about the state of magnetic body?

What emotions are? How emotions are created? How are they represented: in brains, at body, or perhaps somewhere else? One can consider these questions from the point of view of neuroscience, endocrinology, and quantum physics. Emotions can be divided to lower level emotions accompanied by intention/need/desire (hunger is accompanied by the need to eat) and thus distinguishing them from sensory qualia whereas higher level emotions like catharsis and the experience of beauty not accompanied by any desire. What does does this division correspond to?

  1. TGD inspired answer to the questions is that emotions are sensory percepts about the state of magnetic body (MB). Sensory-motor loop generalizes: various glands excreting hormones to blood stream and binding to receptors give rise to the analog of motor output.
  2. Consider first neuronal level. Neural transmitters binding to receptors serve as bridges allowing to build connected networks of neurons from existing building bricks. They are accompanied by flux tube networks giving rise to tensor networks as quantum coherent entangled structures (tensor nets) serving as correlates of mental images and allowing classical signalling with light velocity using dark photons. These tensor networks represent our mental images only if they correspond to our sub-selves (see this).

    In a similar manner hormones give rise to networks of ordinary cells implying in particular that emotional memories are realized in (biological) body (BB). Nervous system gives information about the state of these networks to brain and hypothalamus serves as the analog of motor cortex sending hormones controlling the excretion of hormones at lower level glands.

  3. The hierarchy of Planck constants defines a hierarchy of dark matters and heff=n× defines a kind of IQ. The levels of MB corresponding to large/small values of n would correspond to higher/lower emotions.
MB decomposes to two basic parts: the part in the scale of BB and formed by networks having cells and larger structures as nodes (forming a fractal hierarchy) and the part in the scales larger than BB.
  1. In the scales larger than that of BB (long scales) the change the topology is not easy and the dynamics involves oscillations of MB - analogs of Alfwen waves - and analogs of ordinary motor actions changing the shape of flux tubes but leaving its topology unaffected (these actions might represent or serve as templates for ordinary motor actions in body scale (see this).
  2. In the scales larger than that of BB (long scales) the change the topology is not easy and the dynamics involves oscillations of MB - analogs of Alfwen waves - and analogs of ordinary motor actions changing the shape of flux tubes but leaving its topology unaffected (these action might represent or serve as templates for ordinary motor actions in body scale).

    Alfwen waves with cyclotron frequencies and generalized Josephson frequencies assignable to cell membrane as Josephson junction would be involved see this). The size scale of particular onion-like layer of MB corresponds to the wavelength scale for cyclotron frequencies and is proportional to heff/h=n for dark photons. For instance, alpha band in EEG corresponds to the scale of Earth but the energy scale of dark photons is that of bio-photons.

    The TGD inspired model of music harmony (see this) gives as a side product a model of genetic code predicting correctly the numbers of codons coding for aminoacids for vertebrate code. The model allows to see sensory percepts about the dynamics in large scales as analog of music experience. The notes of 3-chords of the harmony correspond to light as dark photons and frequencies defining the notes of the chord: cyclotron radiation and generalized Josephson radiation from cell membrane would represent examples of dark light. Music expresses and creates emotions and music harmonies would correspond to various emotional states/moods realized at the level of DNA and its dark counterpart (dark nuclei represented as dark proton sequences). MB would be like a music instrument with flux tubes serving as strings. It is difficult to assign any specific desire to large scale sensory percepts about MB and the interpretation as higher emotions - or rather feelings - makes sense.

See the chapter Emotions as sensory percepts about the state of magnetic body? or the article with the same title.



What could idiot savants teach to us about Natural Intelligence?

Recently a humanoid robot known as Sophia has gained a lot of attention in net (see the article by Ben Goertzel, Eddie Monroe, Julia Moss, David Hanson and Gino Yu titled with title " Loving AI: Humanoid Robots as Agents of Human Consciousness Expansion (summary of early research progress)" .

This led to ask the question about the distinctions of Natural and Artificial Intelligence and about how to model Natural Intelligence. One might think that idiot savants could help answering this kind of question but so it turned out to be!

Mathematical genii and idiot savants seem to have something in common

It is hard to understand the miraculous arithmetical abilities of both some mathematical genii and idiot savants lacking completely conceptual thinking and conscious information processing based on algorithms. I have discussed the number theoretical feats here.

Not all individual capable of memory and arithmetic feats are idiot savants. These mathematical feats are not those of idiot savant and involve high level mathematical conceptualization. How Indian self-taught number-theoretical genius Ramajunan discovered his formulas remains still a mystery suggesting totally different kind of information processing. Ramanujan himself told that he got his formulas from his personal God.

Ramajunan's feats lose some of their mystery if higher level selves are involved. I have considered a possible explanation based on ZEO, which allows to consider the possibility that quantum computation type processing could be carried out in both time directions alternately. The mental image representing the computation would experience several deaths following by re-incarnations with opposite direction of clock time (the time direction in which the size of CD increases). The process requiring very long time in the usual positive energy ontology would take only short time when measured as the total shift for the tip of either boundary of CD - the duration of computations at opposite boundary would much longer!

Sacks tells about idiot savant twins with intelligence quotient of 60 having amazing numerical abilities despite that they could not understand even the simplest mathematical concepts. For instance, twins "saw" that the number of matches scattered along floor was 111 and also "saw" the decomposition of integer to factors and primality. A mechanism explaining this based on the formation of wholes by quantum entanglement is proposed here. The model does not however involve any details.

Flux tube networks as basic structures

One can build a more detailed model for what the twins did by assuming that information processing is based on 2-dimensional discrete structures formed by neurons (one can also consider 3-D structures consisting of 2-D layers and the cortex indeed has this kind of cylindrical structures consisting of 6 layers). For simplicity one can assume large enough plane region forming a square lattice and defined by neuron layer in brain. The information processing should involve minimal amount of linguistic features.

  1. A natural geometric representation of number N is as a set of active points (neurons) of a 2-D lattice. Neuron is active it is connected by a flux tube to at least one other neuron. The connection is formed/strengthened by nerve pulse activity creating small neuro-transmitter induced bridges between neurons. Quite generally, information molecules would serve the same purpose (see this and this).

    Active neurons would form a collection of connected sets of the plane region in question. Any set of this kind with given number N of active neurons would give an equivalent representation of number N. At quantum level the N neurons could form union of K connected sub-networks consisting Nk neurons with ∑ Nk=N.

  2. There is a large number of representations distinguished by the detailed topology of the network and a particular union of sub-networks would carry much more information than the mere numbers Nk and N code. Even telling, which neurons are active (Boolean information) is only part of the story.

    The subsets of Nk points would have large number of representations since the shape of these objects could vary. A natural interpretation would be in terms of objects of a picture. This kind of representation would naturally result in terms of virtual sensory input from brain to retina and possibly also other sensory organs and lead to a decomposition of the perceptive field to objects.

    The representation would thus contain both geometric information - interpretation as image - and number theoretic information provided by the decomposition. The K subsets would correspond to one particular element of a partition algebra generalizing Boolean algebra for which one has partition to set and its complement (see this).

  3. The number N provides the minimum amount of information about the situation and can be regarded as a representation of number. One can imagine two extremes for the representations of N.
    1. The first extreme corresponds to K linear structures. This would correspond to linear linguistic representation mode characteristic for information processing used in classical computers. One could consider interpretation as K words of language providing names for say objects of an image. The extreme is just one linear structure representing single word. Cognition could use this kind of representations.
    2. Second extreme corresponds to single square lattice like structure with each neuron connected to the say 4 nearest neighbors. This lattice has one incomplete layer: string with some neurons missing. This kind of representation would be optimal for representation of images representing single object.

      For N active neurons one can consider a representation as a pile of linear strings containing pk neurons, where p is prime. If N is divisible by pk: N= Mpk one obtains a M× pk lattice. If not one can have M× pk lattice connected to a subset of neurons along string with pk neurons. One would have representation of the notion of divisibility by given power of prime as a rectangle! If N is prime this representation does not exist!

Flux tube dynamics

The classical topological dynamics for the flux tube system induced by nerve pulse activity building temporary bridges between neurons would allow phase transitions changing the number of sub-networks, the numbers of neurons in them, and the topology of individual networks. This topological dynamics would generalize Boolean dynamics of computer programs.

  1. Flux tube networks as sets of all active neurons can be also identified as elements of Boolean algebra defined by the subsets of discretize planar or even 3-D regions (layer of neurons). This would allow to project flux tube networks and their dynamics to Boolean algebra and their dynamics. In this projection the topology of the flux tube network does not matter much: it is enough that each neurons is connected to some neuron (bit 1). One might therefore think of (a highly non-unique) lifting of computer programs to nerve pulse patterns activating corresponding subsets of neurons. If the dynamics of flux tube network determined by space-time dynamics is consistent with the Boolean projection, topological flux tube dynamics induced by space-time dynamics would define computer program.
  2. At the next step one could take into account the number of connected sub-networks: this suggests a generalization of Boolean algebra to partition algebras so that one does not consider only subset and its complement but decomposition into n subsets which one can think as having different colors (see this). This leads to a generalization of Boolean (2-adic) logic to p-adic logic, and a possible generalization of computer programs as Boolean dynamical evolutions.
  3. At the third step also the detailed topology of each connected sub-network is taken into account and brings in further structure. Even higher-dimensional structures could be represented as discretized versions by allowing representation of higher-dimensional simplexes as connected sub-networks. Here many-sheeted space-time suggests a possible manner to add artificial dimensions.
This dynamics would also allow to realize basic arithmetics. In the case of summation the initial state of the network would be a collection of K disjoint networks with Nk elements and in final state single connected set with N=∑ Nk elements. The simplest representation is as a pile of K strings with Nk elements. Product M× N could be reduced to a sum of M sets with N element: this could be represented as a pile of M linear strings.

Number theoretical feats of twins and flux tube dynamics

Flux tube dynamics suggests a mechanism for how the twins managed to see the number of the matches scattered on the floor and also how they managed to see the decomposition of number into primes or prime powers. Sacks indeed tells that the eyes of the twins were rolling wildly during their feats. What is required is that the visual perception of the matches on the floor was subject to dynamics allowing to deform the topology of the associated network. Suppose that some preferred network topology or network topologies allowed to recognize the number of matches and tell it using language (therefore also linear language is involved). The natural assumption is that the favored network topology is connected.

The two extremes in which the network is connected are favored modes for this representation.

  1. Option I corresponds to any linear string giving a linguistic representation as the number neurons (which would be activated by seeing the matches scattered on the floor). A large number of equivalent representations is possible. This representation might be optimal for associating to N its name. The verbal expression of the name could be completely automatic association without any conceptual content. The different representations carry also geometric information about the shape of the string: melody in music could be this kind of curve whereas words of speech would be represented by straight lines.
  2. Option II corresponds to a maximally connected lattice like structure formed as pile of strings with pk neurons for a given prime: N= M1× pk+M2, 0≤ Mi < pk. The highest string in the pile misses some neurons. This representation would be maximally connected. It contains more information than that about the value of N.
Option II provides also number theoretical information allowing a model for the feats of the twins.
  1. As far the checking the primeness of N is considered, one can assume k=1. For the primes pi dividing N one would find a representation of N as a rectangle. If N is prime, one finds no rectangles of this kind (or finds only the degenerate 1× p rectangle). This serves a geometric signature of primeness. Twins would have tried to find all piles of strings with p neurons, p=2,3,5,... A slower procedure checkes for divisibility by n=2,3,4,....
  2. The decomposition into prime factors would proceed in the similar manner by starting from p=2 and proceeding to larger primes p=3,5,7,.... When a prime factor pi is found only single vertical string from the pile is been taken and the process is repeated for this string but considering only primes p>pi. The process would have been completely visual and would not involve any verbal thinking.
For the storage of memories the 2-D (or possibly 3-D representation) is non-economical and the use of 1-D representation replacing images with their names is much more economic. For information processing such as decomposition into primes, the 2-D or even 3-D representation are much more powerful.

See the chapter Artificial Intelligence, Natural Intelligence, and TGD or the article with the same title.



Artificial Intelligence, Natural Intelligence, and TGD

Recently a humanoid robot known as Sophia has gained a lot of attention in net (see the article by Ben Goertzel, Eddie Monroe, Julia Moss, David Hanson and Gino Yu titled with title " Loving AI: Humanoid Robots as Agents of Human Consciousness Expansion (summary of early research progress)" .

Sophia uses AI, visual data processing, and facial recognition. Sophia imitates human gestures and facial expressions and is able to answer questions and make simple conversations on predefined topics. The AI program used analyzes conversations, extracts data, and uses it to improve responses in the future. To a skeptic Sophia looks like a highly advanced version of ELIZA.

Personally I am rather skeptic view about strong AI relying on a mechanistic view about intelligence. This leads to transhumanism and notions such as mind uploading. It is however good to air out one's thinking sometimes.

Computers should have a description also in the quantal Universe of TGD and this forces to look more precisely about the idealizations of AI. This process led to a change of my attitudes. The fusion of human consciousness and presumably rather primitive computer consciousness but correlating with the program running in it might be possible in TGD Universe, and TGD inspired quantum biology and the recent ideas about prebiotic systems provide rather concrete ideas in attempts to realize this fusion.

TGD also strongly suggests that there is also what might be called Natural Intelligence relying on 2-D cognitive representations defined by networks consisting of nodes (neurons) and flux tubes (axons with nerve pulse patters) connecting them rather than linear 1-D representation used by AI. The topological dynamics of these networks has Boolean dynamics of computer programs as a projection but is much more general and could allow to represent objects of perceptive field and number theoretic cognition.

See the chapter Artificial Intelligence, Natural Intelligence, and TGD or the article with the same title.



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