Has dark matter at the magnetic flux tubes been photographed?

I spent a very pleasant week in Hungary in second Unified Theories conference (thanks for organizers for creating extremely warm atmosphere) and had the opportunity to listen Peter Gariaev's lecture about the fascinating experimental discoveries made by his group about the interaction of laser light and also ordinary light with DNA. The lecture and the discussions with Peter led to an updating of eight-year old model for these effects and summarized the updated model in the article that I titled The Notion of Wave-Genome and DNA as Topological Quantum Computer. I glue below the introduction of the article.

The Notion of Wave-Genome and DNA as Topological Quantum Computer

For about eight years ago - inspired by a representation in CASYS^¢2000 conference [1] - I developed a model (see this) for the fascinating effects of laser light on genome discovered by Peter Gariaev and his collaborators [1,2,3,4,5]. This model is somewhat obsolete since it does not involve the recent TGD inspired vision about quantum biology and DNA, and the discussions with Peter in the second Unified Theories conference 2008 in Budapest made clear the need to update this model containing also some misinterpretations.

In this article the effects of laser light on living matter are discussed only briefly with a stronger emphasis on the photographs produced by the scattering of ordinary light on DNA reported in [5]. In TGD framework these photographs could be interpreted as photographs of wormhole magnetic flux tubes containing dark matter. This would realize the dream of making directly visible the basic new structure predicted by TGD inspired quantum biology.

1 The findings of Peter Gariaev and collaborators

These findings include the rotation of polarization plane of laser light by DNA [1], phantom DNA effect [4], the transformation of laser light to radiowave photons having biological effects [4], the coding of DNA sequences to the modulated polarization plane of laser light and the ability of this kind of light to induce gene expression in another organisms provided the modulated polarization pattern corresponds to an "address" characterizing the organism [1,4], and the formation of images of what is believed to be DNA sample itself and of the objects of environment by DNA sample in a cell irradiated by ordinary light in UV-IR range [5].

Gariaev and collaborators have introduced the notion of wave genome [1] requiring the coding of DNA sequences to temporal patterns of coherent em fields forming a bio-hologram representing geometric information about the organism. Code could mean that nucleotide is represented by a characteristic rotation angle for the polarization plane of linearly polarized laser radiation scattering from it. This kind rotation is known to be induced by chromosomes by a mechanism which to my best knowledge is poorly understood. Other open questions concern the precise identification of the substrate of the bio-hologram, of the reference wave and of information carrying wave, and of the mechanism making possible (quantum) coherence in macroscopic length scales.

The reading of the DNA sequence to a radiation pattern is assumed to rely on the propagation of an acoustic soliton along DNA [1]. Whatever this process is, one should also identify the reverse process inducing the activation of the genome as the target organism receives the radiation coding for the DNA provided the "address" is correct. One should also identify the mechanism transforming laser radiation to radio-waves at various frequencies as well as the mechanism creating what is believed to be the image of DNA sample and replicated images of some instruments used in experiment.

2 The relevant aspects of TGD based view about living matter

The called massless extremals (MEs or topological light rays) distinguish between TGD and Maxwell's electrodynamics: they represent classically signals propagating with light velocity in a precisely targeted and dispersion free manner, and are therefore excellent candidates for the communication and control tools in the TGD based model for a living system as a conscious hologram (see this) and this). The notion of magnetic/field body, which can have layers of even astrophysical size, is an essential element of the model. Magnetic body uses biological body as a sensory receptor and motor instrument and MEs mediate sensory input and control signals between the two kinds of bodies (see this). I have already earlier applied MEs and the notion of magnetic body in an attempt to understand Gariaev's findings (this).

The new element is the model for DNA as topological quantum computer (tqc) (see this) based on time-like braidings of so called wormhole magnetic flux tubes connecting nucleotides to the lipids at lipid layers nuclear and cell membranes. The model leads to a wide variety of predictions about DNA itself (see this), to a universal model for a tissue memory in terms of space-like braidings of wormhole magnetic flux tubes (see this), to a more detailed model of nerve pulse explaining also the origin of EEG and its synchrony (this), to a model for the evolution of the genetic code (see this), to a model of catalyst action involving a phase transition reducing the value of Planck constant inducing the shortening of the flux tubes connecting the reacting molecules and thus forcing them to the vicinity of each other, and to a model of for protein folding (this) in which the presence of wormhole magnetic flux tubes connecting bio-molecules becomes almost a definition for what it is to be living. It is interesting to combine these new ideas with the earlier [1,2,2,4] and more recent [5] findings of Gariaev. Basically the challenge is to fuse the DNA as tqc model with the model of living systems as a conscious hologram (see this).

3 The basic assumptions of model explaining findings of Gariaev

The basic assumptions of the model to be discussed are following.

1. The hierarchy of Planck constants requires a generalization of the notion of 8-D imbedding space H=M⁴×CP₂ obtained by gluing together almost copies of H like pages of book along common back. The pages of the book carry matter with various values of Planck constant and the particles at different pages of the book are dark relative to each other in the sense that they cannot appear in the same vertex of Feynman diagram. The particles at different pages of the book can however interact via classical fields and via the exchange of (for instance) photons which suffer a phase transition changing Planck constant as they leak between different pages of the book. In principle it is therefore possible to photograph the magnetic flux tubes carrying dark matter, and the proposal is that this is what Gariaev and collaborators have actually achieved [5].
2. Braid strands realized as wormhole magnetic tubes are correlates for a directed attention. DNA connected by strands to (say) experimental instrument directs its attention to the instrument. One could perhaps say that DNA "sees" the surrounding world. Also ordinary attention for vision and other senses could involve flux tubes connecting DNA to the object of perception. This explains the ability of DNA to generate images of objects of external world [5]. The hierarchy of Planck constants explains the transformation of laser light to radio waves [3] as a phase transition increasing Planck constant and thus also wavelength but keeping the energy of photons as such.
3. Wormhole flux tubes carrying super-conducting matter in large hbar phase are characterized by anomalous em charges characterizing the nucleotides (see this), and thus define an excellent candidate for the substrate of bio-hologram. A coding of DNA nucleotides to the rotation of polarization plane results for photons traversing through these flux tubes if a large parity breaking making possible rotation of the polarization plane (Faraday effect) is assumed. This is made possible by large parity breaking of fractally scaled up variant of weak physics (see this) explaining also chiral selection.
4. The model for the nerve pulse (see this) leads to the model of EEG waves in which EEG rhythms induce a complete analog of reference waves whereas nerve pulse induces the analog of information carrying wave. The model predicts a fractal hierarchy of EEGs (EXGs) and their counterparts associated with long ranged color and electro-weak gauge fields having MEs as classical correlates. EEG rhythms are associated with propagating soliton sequences and nerve pulse corresponds to a propagating perturbation associated with this soliton sequence rather than soliton. The model predicts automatically the synchrony and spatiotemporal coherence of neural firing. EEG photons correspond to a large value of Planck constant implying that their energies are above thermal energy at physiological temperatures so that their effects on living matter are not masked by thermal noise.
   This model generalizes essentially as such to the recent context: the counterparts of nerve pulses propagate along the complex formed by DNA connected to the nuclear or cell membrane or even to another cell nucleus by flux tubes. The prediction is that gene expression can be coherent in the scale of organ and even that of population. This conforms with the notion of super-genome stating that the sequences of DNA strands in different nuclei organize along magnetic flux sheet like text lines at the page of a book. The notion of hyper-genome means that these books from different organisms in turn organize to a pages of a book at higher level of fractal hierarchy and give rise to a gene expression at the level of population or even biosphere.

References

[1] P. Gariaev et al (2000), The DNA-wave-biocomputer, CASYS'2000, Fourth International Conference on Computing Anticipatory Systems, Liege, 2000. Abstract Book, Ed. M. Dubois.

[2] P. Gariaev, Brief introduction into WaveGenetics. Its scope and opporturnities., http://www.wavegenetics.jino-net.ru.

[3] P. P. Gariaev et al(2002), The spectroscopy of bio-photons in non-local genetic regulation, Journal of Non-Locality and Remote Mental Interactions, Vol 1, Nr 3. http://www.emergentmind.org/gariaevI3.htm .

[4] P. P. Gariaev, V. I. Chudin, G. G. Komissarov, A. A. Berezin , A. A. Vasiliev (1991), Holographic Associative Memory of Biological Systems, Proceedings SPIE - The International Society for Optical Engineering. Optical Memory and Neural Networks. v.1621, p. 280- 291. USA.

[5]P. P. Gariaev, G. G. Tertishni, A. V. Tovmash (2007), Experimental investigation in vitro of holographic mapping and holographic transposition of DNA in conjuction with the information pool encircling DNA, New Medical Tehcnologies, #9, pp. 42-53. The article is in Russian but Peter Gariaev kindly provided a translation of the article to English.

[6] F. A. Popp, B. Ruth, W. Bahr, J. Böhm, P. Grass (1981), G. Grolig, M. Rattemeyer, H. G. Schmidt and P. Wulle: Emission of Visible and Ultraviolet Radiation by Active Biological Systems. Collective Phenomena(Gordon and Breach), 3, 187-214.

[7]Faraday effect, http://en.wikipedia.org/wiki/Faraday_-effect.

For more details see the chapter DNA as a Topological Quantum Computer of "Genes and Memes". See also the article The Notion of Wave-Genome and DNA as Topological Quantum Computer.

From Equivalence Principle to Zero Energy Ontology

The tension between analytic and constructive approaches is present even in Einstein's own theory and was the basic stimulus leading to TGD. Equivalence Principle states that gravitational and inertial masses are identical. This statement is however rather problematic as Einstein himself was first to admit. Einstein's equations express the identity for gravitational and inertial energy momentum densities as a consequence of a variational principle. There is however no global version of this statement because one cannot define the notions of inertial and gravitational four-momenta without adherence to perturbative approach.

The hypothesis that space-times are 4-D surfaces of a higher-dimensional space-time of form H=M⁴×S resolves the problem: since Poincare symmetries become symmetries of H rather than space-time itself. Inertial four-momentum can be defined as a conserved Noether charge and also gravitational four-momentum can be regarded as a Noether charge albeit non-conserved. Equivalence Principle can hold true only under some additional conditions. For instance, for the imbeddings of Robertson-Walker cosmologies inertial four-momentum density vanishes unlike gravitational four-momentum density, which for a long time remained quite a mystery. The real understanding of the situation became possible only after the introduction of what I call zero energy ontology.

In zero energy ontology one replaces positive energy states with zero energy states with positive and negative energy parts of the state at the boundaries of future and past direct light-cones forming a causal diamond. All conserved quantum numbers of the positive and negative energy states are of opposite sign so that these states can be created from vacuum. Äny physical state is creatable from vacuum" becomes thus a basic principle of quantum TGD and together with the notion of quantum jump resolves several philosophical problems (What was the initial state of universe?, What are the values of conserved quantities for Universe, Is theory building completely useless if only single solution of field equations is realized?).

At the level of elementary particle physics positive and negative energy parts of zero energy state are interpreted as initial and final states of a particle reaction so that quantum states become physical events. Equivalence Principle would hold true in the sense that the classical gravitational four-momentum of the vacuum extremal whose small deformations appear as the argument of configuration space spinor field is equal to the positive energy of the positive energy part of the zero energy quantum state. Equivalence Principle is expected to hold true for elementary particles and their composites but not for the quantum states defined around non-vacuum extremals.

More precisely, the inertial four-momentum assignable to the 3-D Chern-Simons action is non-vanishing only if one adds to the CP₂ Kähler form a pure gauge part A_a=constant, where a denotes light cone proper time . A breaking of Poincare invariance is implied which is however compensated by the fact that configuration space corresponds to the union of configuration spaces associated with future and past directed light-cones. If the vacuum extremal is also an extremal of the curvature scalar, gravitational four-momentum is conserved.

In the case of CP₂ type vacuum extremal gravitational stationarity transforms the M⁴ projection of the extremal from a random light-like curve to a light-like geodesic allowing an interpretation as incoming or outgoing on mass shell particle. General vacuum extremal corresponds to a virtual particle. At the classical level Equivalence Principle requires that the light-like gravitational four-momentum of CP₂ vacuum extremal co-incides with the light-like inertial four-momentum associated with Chern-Simons action in this situation. This condition relates the value of A_a to gravitational constant G and CP₂ radius R. G would thus appear as a fundamental constant and quantum criticality should dictate the ratio G/R². The topologically condensed CP₂ type vacuum extremal necessarily creates a non-vacuum region around it and the resulting inertial four-momentum would correspond to the gravitational four-momentum.

The strong form of Equivalence Principle would require that the classical 4-momentum associated with Kähler action of allowed small deformations co-incides with the conserved gravitational four-momentum of the vacuum extremal extremizing curvature scalar: this might have a natural interpretation in terms of Bohr orbitology but is not be consistent with zero energy ontology inspired picture unless one has double sheeted structure with sheets possessing opposite energies such that double sheeted structure is approximated by single sheet with Robertson-Walker cosmology in GRT framework. The identification of gauge bosons as wormhole contacts and gravitons as pairs of wormhole contacts supports double sheeted structure with sheets possessing opposite arrows of geometric time. Near the vicinity of wormhole contacts (pieces of CP₂ type vacuum extremals) the sheets which are originally vacuum extremals are deformed to non-vacuum extremals and carry inertial four-momentum which should be equal to the gravitational four momentum of the vacuum extremal.

For background see the chapter TGD and GRT of "Classical Physics in Many-Sheeted Space-time". See also the article "Topological Geometrodynamics: an Overall View".

Infinite primes and algebraic Brahman=Atman identity

The hierarchy of infinite primes (and of integers and rationals) was the first mathematical notion stimulated by TGD inspired theory of consciousness. The construction recipe is equivalent with a repeated second quantization of super-symmetric arithmetic quantum field theory with bosons and fermions labeled by primes such that the many particle states of previous level become the elementary particles of new level. The hierarchy of space-time sheets with many particle states of space-time sheet becoming elementary particles at the next level of hierarchy and also the hierarchy of n:th order logics are also possible correlates for this hierarchy. For instance, the description of proton as an elementary fermion would be in a well defined sense exact in TGD Universe.

This construction leads also to a number theoretic generalization of space-time point since given real number has infinitely rich number theoretical structure not visible at the level of the real norm of the number a due to the existence of real units expressible in terms of ratios of infinite integers. This number theoretical anatomy suggest kind of number theoretical Brahman=Atman principle stating that the set consisting of number theoretic variants of single point of the imbedding space (equivalent in real sense) is able to represent the points of the world of classical worlds or even quantum states of the Universe . Also a formulation in terms of number theoretic holography is possible.

Just for fun and to test these ideas one can consider a model for the representation of the configuration space spinor fields in terms of algebraic holography. I have considered guesses for this kind of map earlier and it is interesting to find whether additional constraints coming from zero energy ontology and finite measurement resolution might give. The identification of quantum corrections as insertion of zero energy states in time scale below measurement resolution to positive or negative energy part of zero energy state and the identification of number theoretic braid as a space-time correlate for the finite measurement resolution give considerable additional constraints.

1. The fundamental representation space consists of wave functions in the Cartesian po wer U⁸ of space U of real units associated with any point of H. That there are 8 real units rather than one is somewhat disturbing: this point will be discussed below. Real units are ratios of infinite integers having interpretation as positive and negative energy states of a super-symmetric arithmetic QFT at some level of hierarchy of second quantizations. Real units have vanishing net quantum numbers so that only zero energy states defining the basis for configuration space spinor fields should be mapped to them. In the general case quantum superpositions of these basis states should be mapped to the quantum superpositions of real units. The first guess is that real units represent a basis for configuration space spinor fields constructed by applying bosonic and fermionic generators of appropriate super Kac-Moody type algebra to the vacuum state.
2. What can one say about this map bringing in mind Gödel numbering? Each pair of bosonic and corresponding fermionic generator at the lowest level must be mapped to its own finite prime. If this map is specified, the map is fixed at the higher levels of the hierarchy. There exists an infinite number of this kind of correspondences. To achieve some uniqueness, one should have some natural ordering which one might hope to reflect real physics. The irreps of the (non-simple) Lie group involved can be ordered almost uniquely. For simple group this ordering would be with respect to the sum N=N_F+N_F,c of the numbers N_F resp. N_F,c of the fundamental representation resp. its conjugate appearing in the minimal tensor product giving the irrep. The generalization to non-simple case should use the sum of the integers N_i for different factors for factor groups. Groups themselves could be ordered by some criterion, say dimension. The states of a given representation could be mapped to subsequent finite primes in an order respecting some natural ordering of the states by the values of quantum numbers from negative to positive (say spin for SU(2) and color isospin and hypercharge for SU(3)). This would require the ordering of the Cartesian factors of non-simple group, ordering of quantum numbers for each simple group, and ordering of values of each quantum number from positive to negative.
3. The presence of conformal weights brings in an additional complication. One cannot use conformal as a primary orderer since the number of SO(3)×SU(3) irreps in the super-canonical sector is infinite. The requirement that the probabilities predicted by p-adic thermodynamics are rational numbers or equivalently that there is a length scale cutoff, implies a cutoff in conformal weight. The vision about M-matrix forces to conclude that different values of the total conformal weight n for the quantum state correspond to summands in a direct sum of HFFs. If so, the introduction of the conformal weight would mean for a given summand only the assignment n conformal weights to a given Lie-algebra generator. For each representation of the Lie group one would have n copies ordered with respect to the value of n and mapped to primes in this order.
4. Cognitive representations associated with the points in a subset, call it P, of the discrete intersection of p-adic and real space-time sheets, defining number theoretic braids, would be in question. Large number of partonic surfaces can be involved and only few of them need to contribute to P in the measurement resolution used. The fixing of P means measurement of N positions of H and each point carries fermion or anti-fermion numbers. A more general situation corresponds to plane wave type state obtained as superposition of these states. The condition of rationality or at least algebraicity means that discrete variants of plane waves are in question.
5. By the finiteness of the measurement resolution configuration space spinor field decomposes into a product of two parts or in more general case, to their superposition. The part Y₊, which is above measurement resolution, is representable using the information contained by P, coded by the product of second quantized induced spinor field at points of P, and provided by physical experiments. Configuration space örbital" degrees of freedom should not contribute since these points are fixed in H.
6. The second part of the configuration space spinor field, call it Y_-, corresponds to the information below the measurement resolution and assignable with the complement of P and mappable to the structure of real units associated with the points of P. This part has vanishing net quantum numbers and is a superposition over the elements of the basis of CH spinor fields and mapped to a quantum superposition of real units. The representation of Y_- as a Schrödinger amplitude in the space of real units could be highly unique. Algebraic holography principle would state that the information below measurement resolution is mapped to a Schrödinger amplitude in space of real units associated with the points of P.
7. This would be also a representation for perceiver-external world duality. The correlation function in which P appears would code for the information appearing in M-matrix representing the laws of physics as seen by conscious entity about external world as an outsider. The quantum superposition of real units would represent the purely subjective information about the part of universe below measurement resolution.
8. The condition that Y represents a state with vanishing quantum numbers gives additional constraints. The interpretation inspired by finite measurement resolution is that the coordinate h associated with Y corresponds to a zero energy insertion to a positive or negative energy state localizable to a causal diamond inside the upper or lower half of the causal diamond of observer. Below measurement resolution for imbedding space coordinates Y(h) would correspond to a nonlocal operator creating a zero energy state. This would mean that Brahman=Atman would apply to the mini-worlds below the measurement resolution rather than to entire Universe but by algebraic fractality of HFFs this would would not be a dramatic loss.

There is an objection against this picture. One obtains an 8-plet of arithmetic zero energy states rather than one state only. What this strange 8-fold way could mean?

1. The crucial observation is that hyper-finite factor of type II₁ (HFF) creates states for which center of mass degrees of freedom of 3-surface in H are fixed. One should somehow generalize the operators creating local HFF states to fields in H, and an octonionic generalization of conformal field suggests itself. I have indeed proposed a quantum octonionic generalization of HFF extending to an HFF valued field Y in 8-D quantum octonionic space with the property that maximal quantum commutative sub-space corresponds to hyper-octonions . This construction raises X⁴ Ì M⁸ and by number theoretic compactification also X⁴ Ì H in a unique position since non-associativity of hyper-octonions does not allow to identify the algebra of HFF valued fields in M⁸ with HFF itself.
2. The value of Y in the space of quantum octonions restricted to a maximal commutative subspace can be expressed in terms of 8 HFF valued coefficients of hyper-octonion units. By the hyper-octonionic generalization of conformal invariance all these 8 coefficients must represent zero energy HFF states. The restriction of Y to a given point of P would give a state, which has 8 HFF valued components and Brahman=Atman identity would map these components to U⁸ associated with P. One might perhaps say that 8 zero energy states are needed in order to code the information about the H positions of points P.

For background see the chapter Was von Neumann right after all? of "Towards S-matrix".

Configuration space gamma matrices as hyper-octonionic conformal fields with values in HFF

The fantastic properties of HFFs of type II₁ inspire the idea that a localized version of Clifford algebra of configuration space might allow to see space-time, embedding space, and configuration space as emergent structures.

Configuration space gamma matrices act only in vibrational degrees of freedom of 3-surface. One must also include center of mass degrees of freedom which appear as zero modes. The natural idea is that the resulting local gamma matrices define a local version of HFF of type II₁ as a generalization of conformal field of gamma matrices appearing super string models obtained by replacing complex numbers with hyper-octonions identified as a subspace of complexified octonions. As a matter fact, one can generalize octonions to quantum octonions for which quantum commutativity means restriction to a hyper-octonionic subspace of quantum octonions . Non-associativity is essential for obtaining something non-trivial: otherwise this algebra reduces to HFF of type II₁ since matrix algebra as a tensor factor would give an algebra isomorphic with the original one. The octonionic variant of conformal invariance fixes the dependence of local gamma matrix field on the coordinate of HO. The coefficients of Laurent expansion of this field must commute with octonions.

The world of classical worlds has been identified as a union of configuration spaces associated with M⁴_± labeled by points of H or equivalently HO. The choice of quantization axes certainly fixes a point of H (HO) as a point remaining fixed under SO(1,3)×U(2) (SO(1,3)×SO(4)). The condition that hyper-quaternionic inverses of M⁴ Ì HO points exist suggest a restriction of arguments of the n-point function to the interior of M⁴_±.

Associativity condition for the n-point functions forces to restrict the arguments to a hyper-quaternionic plane HQ=M⁴ of HO. One can also consider the commutativity condition by requiring that arguments belong to a preferred commutative sub-space HC of HO. Fixing preferred real and imaginary units means a choice of M²=HC interpreted as a partial choice of quantization axes. This has quite strong implications.

1. The hyper-quaternionic planes with a fixed choice of M² are labeled by points of CP₂. If the condition M² Ì T⁴ characterizes the tangent planes of all points of X⁴ Ì HO it is possible to map X⁴ Ì HO to X⁴ Ì H so that HO-H duality ("number theoretic compactification") emerges. X⁴ Ì H should correspond to a preferred extremal of Kähler action. The physical interpretation would be as a global fixing of the plane of non-physical polarizations in M⁸: it is not quite clear whether this choice of polarization need not have direct counterpart for X⁴ Ì H. Standard model symmetries emerge naturally. The resulting surface in X⁴ Ì H would be analogous to a warped plane in E³. This new result suggests rather direct connection with super string models. In super string models one can choose the polarization plane freely and one expects also now that the generalized choice M² Ì M⁴ Ì M⁸ of polarization plane can be made freely without losing Poincare invariance with reasonable assumption about zero energy states.
2. One would like to fix local tangent planes T⁴ of X⁴ at 3-D light-like surfaces X³_l fixing the preferred extremal of Kähler action defining the Bohr orbit. An additional direction t should be added to the tangent plane T³ of X³_l to give T⁴. This might be achieved if t belongs to M² and perhaps corresponds to a light-like vector in M².
3. Assume that partonic 2-surfaces X belong to dM⁴_± Ì HO defining ends of the causal diamond. This is obviously an additional boundary condition. Hence the points of partonic 2-surfaces are associative and can appear as arguments of n-point functions. One thus finds an explanation for the special role of partonic 2-surfaces and a reason why for the role of light-cone boundary. Note that only the ends of lightlike 3-surfaces need intersect M⁴_± Ì HO. A stronger condition is that the pre-images of light-like 3-surfaces in H belong to M⁴_± Ì subset HO.
4. Commutativity condition is satisfied if the arguments of the n-point function belong to an intersection X²ÇM² Ì HQ and this gives a discrete set of points as intersection of light-like radial geodesic and X² perhaps identifiable in terms of points in the intersection of number theoretic braids with dH_±. One should show that this set of points consists of rational or at most algebraic points. Here the possibility to choose X² to some degree could be essential. For the pre-images of light-like 3-surfaces commutativity would allow one-dimensional curves having interpretation as braid strands. These curves would be contained in plane M² and it is not clear whether a unique interpretation as braid strands is possible (how to tell whether the strand crossing another one is infinitesimally above or below it?). The alternative assumption consistent with virtual parton interpretation is that light-like geodesics of X³ are in question.

To sum up, this picture implies HO-H duality with a choice of a preferred imaginary unit fixing the plane of non-physical polarizations globally, standard model symmetries, and number theoretic braids. The introduction of hyper-octonions could be however criticized: could octonions and quaternions be enough after all? Could HO-H duality be replaced with O-H duality and be interpreted as the analog of Wick rotation? This would mean that quaternionic 4-surfaces in E⁸ containing global polarization plane E² in their tangent spaces would be mapped by essentially by the same map to their counterparts in M⁴×CP₂,and the time coordinate in E⁸ would be identified as the real coordinate. Also light-cones in E⁸ would make sense as the inverse images of M⁴_±.

For background see the chapter Was von Neumann right after all? of "Towards S-matrix". See also the article "Topological Geometrodynamics: an Overall View".

Topological Geometrodynamics: an Overall View

The participation in a conference inspired me to write a brief overall view about the recent situation in TGD. This was badly needed since even the last year has brought many important steps of progress. I glue here only the abstract of the article.

A brief summary of various competing visions about the basic principles of quantum Topological Geometrodynamics (TGD) and about tensions between them is given with emphasis on the recent developments.

1. Physics as the classical spinor field geometry of the world of classical worlds is the oldest and best developed approach to TGD and means generalization of Einstein's program of geometrizing classical physics so that it applies to entire quantum physics.

2. Parton level formulation of quantum TGD as an almost topological quantum field theory using light-like 3-surfaces as fundamental objects allows a detailed understanding of super-conformal symmetries generalizing those of super string models. A category theoretical interpretation of M-matrix as a functor is possible. This picture has tight connections to the physics as configuration space geometry approach and implies it.

3. Physics as generalized number theory represents third vision about TGD. Number theoretic universality meaning a fusion of real and p-adic physics to single coherent whole forces a formulation in terms of so called number theoretic braids. The symmetries of classical number fields strongly suggest the interpretation in terms of standard model symmetries and a number theoretic interpretation of the imbedding space M⁴× CP₂. Associativity condition would define laws of classical and quantum TGD. The notion of infinite prime defines a third thread in the braid of number theoretical ideas and it is now possible to give a surprisingly realization for the number theoretic Brahman=Atman identity (algebraic holography) based on the generalization of the number concept by allowing infinite number of real units representable as ratios of infinite integers having interpretation as representations for physical states of super-symmetric arithmetic QFT. The infinitely rich number theoretic anatomy for the points of number theoretic braids allows to represent the information about quantum state of the Universe which remains below measurement resolution.

4. The idea about hierarchy of Planck constants was inspired by certain empirical facts. The hierarchy leads to a generalization of the notion of imbedding space emerges naturally from the requirement that the choice of quantization axes has a geometric correlate also at the level of imbedding space. The physical implication is the identification of dark matter in terms of a hierarchy of macroscopically quantum coherent phases with quantized values of Planck constant having arbitrarily large values and playing a key role, not only in biology but also in astrophysics and cosmology of TGD Universe. The hierarchy of Planck constants can be seen as necessary for the realization of quantum criticality. The generalization of imbedding space is also essential for the construction of the Kähler function of configuration space.

5. The fifth vision about quantum TGD is that the mere finiteness of measurement resolution fixes the scattering matrix of quantum TGD. In zero energy ontology S-matrix must be generalized to M-matrix identified as time-like entanglement coefficients between positive and negative energy parts of zero energy states. M-matrix can be regarded as a "complex square root" of density matrix expressible as product of a real square root of density matrix and unitary S-matrix: thermodynamics becomes part of quantum theory. Hyper-finite factors of type II₁ (HFFs) emerge naturally through Clifford algebra of the "world of classical worlds" and allow a formulation of quantum measurement theory with a finite measurement resolution. The notion of finite measurement resolution expressed in terms of inclusion of HFFs with included algebra defining the measurement resolution leads to an identification of M-matrix in terms of Connes tensor product and a simple argument shows that M-matrix is unique apart from the presence of the square root of density matrix needed by thermodynamics. Coupling constant evolution corresponds to a hierarchy of measurement resolutions and p-adic coupling constant hypothesis follows as a consequence with an additional prediction assigning to particles an additional time scale characterizing temporal distance between positive and negative energy parts of corresponding zero energy state: for electron this time scale is .1 second, fundamental biorhythm. Thus zero energy ontology implies a direct connection between elementary particle physics and biology.

6. Consciousness theory interpreted as generalization of quantum measurement theory the most plausible vision about quantum TGD and has already shown its power and brought into theory notions which cannot be imagined in the standard conceptual framework of quantum physics.

The mystery of mini galaxies and the hierarchy of Planck constants

New Scientist informs that a team led by Pieter van Dokkum at Yale University measured the light of distant galaxies from around 3 billion years after the big bang. They had the same mass as the Milky Way, but were 10 times smaller (The Astrophysical Journal, vol 677, p L5). Peering at younger regions of the sky shows that galaxies this size are no longer around, but it's not clear what happened to them. "This is a very puzzling result," says Simon White of the Max Planck Institute for Astrophysics in Garching, Germany. "Galaxies cannot disappear." Team member Marijn Franx of Leiden Observatory, the Netherlands, suspects they have since merged with extremely massive galaxies.

The evidence of Bohr quantization of planetary orbits with a gigantic value of Planck constant led originally to the idea that Planck constant in TGD Universe has a spectrum of discrete values. The hierarchy of Planck constants leads to generalization of the imbedding space H=M⁴×CP₂ so that it becomes a book like structure with pages characterized partially by the value of Planck constant (see this). This generalization is not anymore ad hoc but is essential for the realization of quantum criticality and the construction of quantum TGD proper: for instance, Higgs mechanism and the manner how space-time sheet is assigned with light-like 3-surfaces defining the fundamental dynamical objects of quantum TGD can be understood in this framework (see this ).

The matters at different pages would be dark relative to each other since the particles from different pages cannot appear in the same interaction vertex (see for instance this). The particles at different pages can however interact via classical gauge- and gravitational fields leaking between the pages via the back of the book, and by the exchange of particles tunneling in the same manner and thus experiencing a phase transition changing Planck constant. The model for living matter and gravitational interactions suggests that the space-time sheets containing dark matter are magnetic and gravimagnetic flux tubes (perhaps the attribute "wormhole magnetic" is more accurate characterization) (see this).

These assumptions guarantee consistency with what is known about dark matter (long range classical gauge fields do not - or at least are not believed to- exist) so that only the classical gravitational interaction and graviton exchanges necessarily involving hbar changing phase transition remain in astrophysical length scales. The interactions with particles of visible matter via graviton exchanges are predicted to differ from what GTR predicts (see this): ordinary gravitons could appear as bursts corresponding to the decays of gigantic gravitons with large hbar to ordinary gravitons. These kind of bursts would be interpreted as external perturbations and would not be counted as gravitons.

This framework also explains various really weird anomalies in neuroscience and biology, in particular those associated with living cell, if considerable part of biologically important ions are in phase with large Planck constant phase at what I call wormhole magnetic flux tubes (see this, this, this, and this).

Consider now the mysterious disappearance of mini galaxies. The smooth cosmic expansion of standard cosmology is in TGD replaced by quantum leaps analogous to quantum transitions of atoms in which the Planck constant associated with the space-time sheet increases by a factor which is most naturally power of 2. The expansion of dark matter forces the visible matter condensed around it to follow. There are several applications: in particular, the piecewise expansion of Earth explains those forgotten facts about the evolution of continents which Wegener's theory failed to explain.

The disappearance of the mini galaxies would be due to this mechanism. From the assumption that this mechanism gives rise to the same outcome as smooth expansion within factor of two at given moment, one could estimate their recent size. If the galaxies are assumed to have roughly the size of Milky Way now, an upwards scaling would be roughly by a factor 8. This would mean that recent age of Universe would be about 24 billion years.

Heart memory, braids, and some comments about skepticism

I have discussed in the previous postings a model for DNA as topological quantum computer based on braidings defined by "wormhole magnetic" flux tubes (wormholes have elementary particle size now). Among other things the model leads also to a detailed model of the evolution of genetic code and to a model of protein folding discussed in previous postings. Also testable "almost"-predictions about DNA itself follow and many of them have been already verified.

The model predicts also a hierarchy of memories based on the braiding of the flux tubes. For instance, one can say that the space-like braidings write in memory time like braidings (dancing pattern is a good metaphor for them) defining running topological quantum computer programs. This is like connecting the legs of dances to wall by thin threads so that dancing patterns are recorded to the braiding of these threads.

In TGD Universe entire body and also magnetic body are conscious so that brain is not in any preferred position as far as memories are considered and one can speak about tissue memory. Brain would be responsible for highly symbolic representations of memories whereas sensory organs would serve as seats of sensory qualia and sensory memories. It is quite possible that different organs are specialized to store special types of memories. For instance, anyone who has been fallen in love would guess that heart might be specialized to emotional memories.

It should be added that in TGD Universe memories are represented in the body of the geometric past and memory recall corresponds to a communication with geometric past or to sharing of mental images in geometric past and geometric now by time like quantum entanglement. For instance, a pain in phantom leg would correspond to a sharing of the mental image about the pain located in the geometric past where the leg still exists (note that experienced and geometric time are not one and same thing in TGD based ontology).

The prediction is that organ transplants can transfer various kinds of memories and habits to the patient and induce changes of personality. One can even say that the entire 4-D body of the donor -with brain included - becomes part of the acceptor of the transplant. This raises difficult ethical issues. For instance, what happens if the donor has performed a suicide: is there a danger that the acceptor suffers the same fate?

There is evidence that heart transplants induce this kind of changes: see the list of references below, which I found from an article "Organ transplants and tissue memories" by Paul Pearsall, Gary E. Scwartz and Lind G. Russek. Unfortunately, the article was a finnish translation so that it is not much point to give a link. The article Cellular memory in organ transplants by Leslie A. Takeuchi however gives a summary about various findings. One report tells about a 7-year old boy who received the heart of six-year old boy. The mother of the donor tells that when boy saw her for the first time he run to her and rubbed his nose against her nose in the same manner has his own son had done.

The stimulus for writing this comment came from a discussion stimulated by a newspaper article relating to heart memory. The article told about a patient, Sonny Graham, who received heart from a man, Terry Cottie, who had performed suicide. Graham wanted to express his gratitude for the wife of the donor, Cheryl, and met her. After this Graham felt a compelling need to write to Cheryl. They fell in love and were married. Graham had told that he felt that he had known Cheryl for years. They were happy but 12 years after the operation Graham suddenly performed a suicide in exactly the same manner as the donor. This suggests that ethical issues must be taken very seriously; heart - consisting of neurons as also brain - might be much more than a mechanical pump.

The story created a heated discussion in Skepsis, the discussion group of finnish skeptics - exceptionally hard nosed and exceptionally immune to facts. The stupidity, arrogance, and intellectual inhonesty of these besserwissers creates always a strange feeling in me: kind of diametric opposite of the feeling of awe created by the music of a great master like Chopin or Beethoven. This particular discussion was however exceptional in that it created a completely new standard of skeptic silliness very hard to surpass.

The general strategy of skeptics was of course the same as always: try to avoid any discussion about the content as long as possible. The debate was opened with the demand that journalists writing something like this should be immediately fired. As it became clear that the article had been also published in Daily Mail, skeptics represented their second standard argument: references are lacking and therefore the newspaper article cannot be taken seriously. Needless to mention that skeptics followed their standard habit by giving not a single reference to support their own claims. When someone gave a link to the above mentioned article written by three PhDs and containing also the references below, it became impossible to avoid a discussion about the topic itself.

Skeptics began to explain. The explanations followed the standard "nothing-but" format: the reports published in the refereed journals are nothing but fabulations of "scientists" since it is known that heart is nothing but a mechanical pump; if the reported events are true they are nothing but accidents (accident is the skeptic's best friend); if the personality changes were real they were nothing but after effects of a heavy medication; and so on. Not a single proposal trying to explain why the personality of receiver began to resemble that of the donor in the reported cases.

The reader might argue that I should not waste my precious time by killing flies. After all, the "skepticism" of Skepsis has nothing to do with science nor with real skepticism, which means critical attitude towards any theoretical framework. Just the opposite is true. The "skepticism" of Skepsis means materialistic and reductionistic world view taken to extreme. The universe of the vulgar skeptic is a strange mixture of mutually contradictory beliefs.

• Good skeptic believes in clockwork dogma: Universe is nothing but a deterministic machine without anything which might be called free will. Consciousness is an epiphenomenon: there is nothing to explain.
• Good skeptic believes in reductionism: universe is nothing but a dance of elementary particles. That the non-deterministic character of quantum laws is in conflict with the clockwork dogma does not perturb good skeptic.
• Good skeptic believes in randomness dogma: life is nothing but a result of completely random events which just happened. This dogma is in obvious conflict with the clockwork dogma but extremely powerful weapon against hard facts in discussions such as above.
• Good skeptic believes also in vulgar Darwinism stating that biological evolution is nothing but a fight for survival. Of course, only intentional agents possessing some free will can be said to fight for their survival so that there is conflict with with both clockwork dogma and randomness dogma.

The source of problems and my motivation for commenting the above discussion is that academic world and Skepsis form a kind of unholy alliance resembling the marriage of state and church. For this reason the young academic career builder quite often finds it safer to become a member of Skepsis which means that he becomes a victim of an intense brain washing. This means also unavoidably corruption and misuse of academic power. Skepsis has indeed taken the role of former KGB in Soviet Union doing the dirty work of labeling academic dissidents as mad scientists: also I have experienced this fate. On the positive side one must admit that the discussion culture in Skepsis has improved during last years thanks to the moderation removing comments in which non-skeptics are given the label of nazi, psychopath, homosexual, pedophile, mentally ill, or something comparable.

References

1. Lunde DT. Psychiatric complications of heart transplants. Am J Psychiatry 1967; 124:1190-1195.
2. Kuhn WF et al. Psychopathology in heart transplant candidates. J Heart Transplants 1988; 7:223-226.
3. Mai FM. Graft and donor denial in heart transplant recipients. Am J Psychiatry 1986; 143:1159-1161.
4. Miller JG. Living Systems. New York, NY: McGraw-Hill, 1978.
5. Schwartz GE, Russek LG. Dynamical energy systems and modern physics: Fostering the science and spirit of complimentary and alternative medicine. Alter Therapies Health Med 1997; 3(3):46-56.
6. Schwartz GE, Russek LG. Do all dynamical systems have memory? Implications of the systemic memory hypothesis for science and society. In KH Pribram (ed.). Brain and Values: Is a Biological Science of Values Possible? Hillsdale, NJ: Lawrence Erlbaum Associates, 1998.
7. Schwartz GER, Russek LGS. The origin of holism and memory in nature: The systemic memory hypothesis. Frontier Perspectives 1998; 7(2):23-30.
8. Schwartz GER, Russek LGS. The plausibility of homeopathy: The systemic memory mechanism. Integrative Med 1998; 1(2):53-60.
9. Sylvia C, with Novak W. A Change of Heart. New York, NY: Little, Brown, 1997.
10. Pearsall P. The Heart's Code. New York, NY: Broadway Books, 1998.
11. Song LZYX, Schwartz GER, Russek LGS. Heart-focused attention and heart-brain synchronization: Energetic and physiological mechanisms. Alter Therapies Health Med 1998; 4(5):44-63.
12. Russek LG, Schwartz GE. Energy cardiology: A dynamical energy systems approach for integrating conventional and alternative medicine. Advances. J Mind-Body Health 1996; 12(4):4-24.
13. Tiller WA. Science and Human Transformation: Subtle Energies, Intentionality and Consciousness. Walnut Creek, CA: Pavior, 1997.
14. Russek LR, Schwartz GE. Interpersonal heart-brain registration and the perception of parental love: A 42-year follow-up of the Harvard Mastery of Stress study. Subtle Energies 1994; 5(3):195-208.
15. Hameroff SR, Penrose R. Orchestrated reduction of quantum coherence in brain microtubules: A model for consciousness. In SR Hameroff, AW Kaszniak, AC Scott (eds). Toward a Science of Consciousness. Cambridge, MA: The MIT Press, 1996.
16. Schwartz GER, Russek, LGS. The Living Energy Universe. Charlottesville, VA: Hampton Roads Publishing, 1999.

TGD based model for the evolution of genetic code: VI

First some context. I have discussed the model for the evolution of genetic code and the ideas inspired by this model in previous postings (I, II, III, IV,V).

The model for the evolution of genetic code leads to the idea that the folding of proteins obeys a code inherited from genetic code in the sense that aminoacid behaves like the conjugate Y_c of the middle nucleotide of the codon XYZ coding for it and that flux tubes connecting aminoacids to each other connect conjugate aminoacids behaving like Y and Y_c. Also catalyst action would reduce to effective base pairing in this picture. After some trials one ends up with a general conceptualization of the situation with the identification of wormhole magnetic flux tubes as correlates for attention at molecular level so that a direct connection with TGD inspired theory of consciousness emerges at quantitative level. This allows a far reaching generalization of the DNA as topological quantum computer paradigm and makes it much more detailed. Also earlier vision about function of neurotransmitters and other information molecules as carriers of links in the web formed by living body becomes very concrete. The final outcome is very simple quantitative model for folding and catalyst action based on minimization of energy and consistent with basic experimental facts as well as general ideas.

Because the model represents a quantitative breakthrough in the evolution of the TGD based view about quantum biology and to save the time required by the painstaking manual tex-html translation, I decided to represent the material also as article entitled From Genetic Code to Code for Folding and Catalysis. The background making it easier to understand can be found in the chapter Evolution in Many-Sheeted Space-time of "Genes and Memes" containing also the article as a section.

TGD based model for the evolution of genetic code: V

First some context. I have discussed the model for the evolution of genetic code and the ideas inspired by this model in previous postings (I, II, III, IV).

Biochemistry represents extremely complex and refined choreography. It is hard to believe that this reduces to a mere an unconscious and actually apparent fight for chemical survival. In TGD Universe consciousness would be involved even at the molecular level and magnetic body would be the choreographer whose dance would induce the molecular activities. This picture combined with the idea of standard plugs through and terminals at which flux tubes end, leads to a third trial to understand catalytic code.

The third trial differs from the second trial in that the letters X,Y,Z of the codon XYZ coding for the aminoacid do not correspond to COOH, residy R, and NH₂ group. Rather, free aminoacid behaves like XY as in the first trial and X and Y correspond to flux tubes ending at OH and =O in COOH group. For the new option all - not only alpha helical and beta sheeted - aminoacids in the interior of the aminoacid sequence behave like the conjugate of letter Y for the codon XYZ coding for the aminoacid. The new model predicts that DNA, mRNA, tRNA, and aminoacids are in general connected by braid strands and provides a detailed picture about the role of braidings in transcription and translation. The topological dynamics of the magnetic body, its motor activities, would induce catalytic dynamics. Also a far reaching generalization of DNA as tqc paradigm emerges (see the postings I, II, III, IV, V, VI, VII, VIII, IX, X, XI, XII,XIII).

1. Flux tubes as a correlate for directed attention

Molecular survival is the standard candidate for the fundamental variational principle motivating the molecular intentional actions. There is entire hierarchy of selves and the survival at the higher level of hierarchy would force co-operation and altruistic behavior at the lower levels. One might hope that this hypothesis reduces to Negentropy Maximization Principle, which states the information contents of conscious experience is maximized. If this picture is accepted, the evolution of molecular system is analogous to the evolution of a society.

Directed attention is the basic aspect of consciousness and the natural guess would be that directed attention corresponds to the formation of magnetic flux tubes between subject and target. The directedness property requires some manner to order the subject and target.

1. The ordering by the values of Planck constant is what first comes in mind. The larger space-time sheet characterized by a larger value of Planck constant and thus at a higher level of evolutionary hierarchy would direct its attention to the smaller one.
2. Also the ordering by the value of p-adic prime characterizing the size scale of the space-time sheet could be considered but in this case directedness could be questioned.
3. Attention can be directed also to thoughts. Could this mean that attention is directed from real space-time sheets to p-adic space-time sheets for various values of primes but not vice versa? Or could the the direction be just the opposite at least in the intentional action transforming p-adic space-time sheet to real space-time sheet. Perhaps directions are opposite for cognition and intention.

The generation of wormhole magnetic flux tubes could be the correlate for the directed attention, not only at molecular level, but quite generally. Metaphorically, the strands of braid would be the light rays from the eyes of the perceiver to the target and their braiding would code the motions of the target to a topological quantum computation like activity and form a memory representation at least. The additional aspect of directed attention would be the coloring of the braid strands, kind of coloring for the virtual light rays emerging from the eyes of the molecular observer. In the case of DNA this can induce a coloring of braid strands emerging from aminoacids and other molecules so that it would indeed become possible to assign to aminoacid the conjugate of the middle nucleotide of the codon XYZ coding for it.

Attention can be also redirected. For this process there is a very nice topological description as a reconnection of flux tubes. What happens is that flux tubes A→ B and C → D fuse for a moment and become flux tubes A→ D and C→ B. This process is possible only if the strands have same color so that the values of the quark charges associated with A and B are same.

This kind of process can modify tqc programs. For instance, in the case of the flux tubes coming from nucleotides X and X_c and ending to the lipid layer this process means that X and X_c and corresponding lipids become connected and genome builds memory representation about this process via similar link. If proteins are connected with mRNA connected to DNA in this manner, this process would allow the formation of flux tubes between aminoacids of two proteins in such a manner that protein would inherit from DNA codon the color of the middle nucleotide and its interactions effectively reduce to base pairing.

DNA would have memory representation about molecular processes via these changing braiding topologies, and one could say that these molecular processes reflect the bodily motions of the magnetic body. Entire molecular dynamics of the organism could represent an enormous tqc induced by the motor activities of the magnetic body. At the level of sensory experience similar idea has been discussed earlier: Out of Body Experiences and illusions such as train illusion could be understood in terms of motor action of magnetic body inducing virtual sensory percepts.

Attention can be also switched on and off. Here the structure of the lipid ends containing two nearby situated =O:s suggest the mechanism: the short flux tube connecting =O:s disappears. The minimization of Coulomb interaction energy at each end implies that re-appearance of the flux tubes creates a short flux tube with the original strand color.

2. Where do flux tubes begin from?

The view about magnetic body as a controller of biological body using genome as a control tool suggests that DNA is to a high degree responsible for directed attention and other molecules as targets so that flux tubes emanate from DNA nucleotides. The reason would be that the aromatic cycles of DNA correspond to larger value of Planck constant.

Some chemical or geometric property of DNA nucleotides or of DNA nucleotides of DNA strand could raise them to the role of subject. Aromatic cycle property correlates with the symmetries associated with large value of Planck constant and is the best candidate for this property. If this is accepted then also some aminoacid residues might act as subjects. Phe, His, Trp, Tyr contain aromatic cycle. The derivatives of Trp and Tyr act as neurotransmitters and His is extremely effective nucleophilic catalyst. This would make possible more specific catalytic mechanisms through the pairing of Phe, His, Trp, and Tyr with residues having flux tube terminals.

This raises the question about the physical interaction determining the color of the strand emerging from the aromatic cycle. The interaction energy of quark at the end of flux tube with the classical electromagnetic fields of nuclei and electrons of the ring should determine this. The wormhole contact containing quark/antiquark at the throat at space-time sheet containing nuclei and electrons could also delocalize inside the ring. One of the earliest hypothesis of TGD inspired model for living matter was that wormhole Bose-Einstein condensates could be crucial for understanding of the behavior of biomolecules. Wormhole throats with quark and antiquark at their throats appear also in the model of high T_c superconductivity. The only manner for the electronic space-time sheet to feed its electromagnetic gauge flux to larger space-time sheets using exactly two wormhole contacts is to use wormhole contacts with u_c and d at their "upper" throat (T,G). For proton one would have d_c and u at their "upper" throat (A,C). The presence of electron or proton at nucleotide space-time sheet near the end of flux tube might allow to understand the correlation. The transfer of electrons and protons between space-time sheets with different p-adic length scale is basic element of TGD based model of metabolism so that there might be some relation.

3. What aminoacids can act as plugs and terminals of flux tubes?

Standardization constraint suggests that flux tubes are attached to standard plugs and terminals. The explicit study of various biological molecules and the role of water in biology suggests that =O serves as a plug to which flux arrives and from which it continues. The intuitive reason for the proposal is that =O allows two hydrogen bonds. OH would in turn correspond to a terminal at which flux tube ends. One might be very naive and say that conscious biomolecules have learned the fundamental role of oxygen and water in the metabolism and become very attentive to the presence of =O and OH. =O appears in the residues of Asp, Glu, Asn, Gln. OH groups appear inside the residues of Asp,Glu and Ser, Thr.

It might not be very wise to restrict the molecular attention to only =O and OH and it is probably better to speak about probabilities for the flux tubes to attach to various kinds of terminals. Both SH and NH₂ are chemically like OH both these them could act as terminals of flux tubes: NH₂ (Asp,Gly,Glu,Arg) contain NH₂ and Cys contains SH.

4. Directed attention generates memory representations and tqc like processes

Directed attention induces braiding if the target is moving and changing its shape. This gives rise to a memory representation of the behavior of the object of attention and also to a tqc like process. A considerable generalization of tqc paradigm suggests itself. Tqc could be induced by the braiding between DNA and lipids, DNA and proteins via folding processes, DNA RNA braiding and braiding between DNA and its conjugate, DNA and protein braiding. The outcome of tqc would be represented as the temporal patterns of biochemical concentrations and rates and there would be hierarchy of p-adic time scales and those associated with the dark matter hierarchy.

For instance, the protein content of lipid membranes is about 50 per cent and varies between 25 and 75 per cent so that protein folding and lipid flow could define tqc programs as self-organization patterns. The folding of protein is dynamical process: alpha helices are created and disappear in time scale of 10^-7 seconds and the side chains of protein can rotate.

The details of the tqc like process depend on what one assumes. The minimal scenario is deduced from the transcription and translation processes and from the condition that magnetic body keeps control or at least keeps book about what happens using genome as a tool. The picture would be essentially what one might obtain by applying a rough model for web in terms of nodes and links.

1. mRNA and mRNA and DNA must remain connected by flux tubes after transcription. The Y_c of mRNA codon could be connected to =O plug in the aminoacid of tRNA molecule and this to Y in tRNA anticodon so that one would have DNA-aminoacid-tRNA link. Z_c in mRNA would be connected to Z in tRNA anticodon giving mRNA-tRNA link. OH in aminoacid would be connected to X in tRNA dicodon XY giving aminoacid-tRNA link.

2. When tRNA donates its aminoacid to the growing chain, the formation of the peptide bond separates one H₂O and the X connection to OH becomes a connection to water molecule so that one obtains tRNA-H₂O link. DNA-mRNA-aminoacid-tRNA link with color Y is preserved. Dn depolymerization of mRNA H₂O molecule is used and the reverse change for linkings takes place.

3. The recombination process for two conjugate DNA-mRNA-aminoacid-tRNA links can transform the flux tubes in such manner that one obtains aminoadic-aminoacid Y link between the =O:s of aminoacids A₁ and A₂ characterized by Y and Y_c. As proposed, this mechanism could be central in the enzyme substrate interaction. The process would pair tRNAs corresponding to Y and Y_c together to give DNA-mRNA-tRNA-tRNA-mRNA-DNA link providing a memory representation about aminoacid pairing A₁-A₂. One can say that magnetic body creates with the mediation of the genome dynamical tqc programs to which much of the biomolecular activity reduces. Not all however, since two aminoacid pairs A₁-A₂ and A₃-A₄ can recombine to A₁-A₄ and A₃-A₂ without DNA knowing anything about it. Magnetic body however knows.

4. The constant part of the aminoacid inside aminoacid would behave like Y_c if aminoacid is coded by XYZ whereas the ends and the protein would behave like dicodons XY (in second trial it would have behaved like YZ). If one assigns to the hydroxyl and amino groups of the residue the roles of object and subject also flux tubes connecting the residue groups become possible and protein does not behave like single nucleotide anymore although one can still say that everything reduces in a well-define sense to the genetic code.

4. Introns and DNA-protein attachment

An example is the situation in which protein acts as an enzyme attaching on DNA. Suppose that this process effectively reduces to a base pairing between aminoacid and DNA nucleotide. Protein can attach to any portion of DNA. Since nucleotide triplets and aminoacids in the first approximation correspond to same length in the respective chains, amino-acid is expected to correspond to nucleotide triplet. The simplest interaction is the attachment to the gene coding for the aminoacid itself but much more general enzymatic interactions are possible. This works if the gene does not contain introns or if the attachment is along single exon.

It is known that DNA can change its conformation from strand during enzyme-DNA action and the contraction of DNA strand might make possible to have enzyme-DNA interaction also in the case that attachment region corresponds to several exons. One can of course ask whether genes containing introns tend to code for proteins which are used for topological quantum computations. Introns, perhaps the repeating sequences with no obvious function, would have at least this useful function but very probably much more useful ones too (they are now known to be transcribed to RNA and TGD suggest that language corresponds to intronic gene expression). The emergence of introns might be somewhat like the emergence of information society.

The foldings of proteins tend to be conserved in the evolution whereas primary structure can change quite a lot apart from some aminoacids critical for enzymatic action. This confirms with the effective base pairing interaction between aminoacids and DNA and would mean that DNA-aminoacid tqc programs are rather robust against mutations.

5. Evolution and braidings

The evolution at the molecular level corresponds to the emergence of increasingly complex molecules using as basic building blocks aminoacid chains and non-translated residues attached to them in the post-translational processing of the aminoacid chains. Also increasingly complex reaction paths emerge. Molecular survival and the competition for the metabolic resources at molecular level could be seen as the basic driving force of this evolution.

Typically, in the original situation the enzymes would have received the substrate molecules from the environment but sooner or later this would have become difficult. The solution would have been a synthesis of the substrate from simpler ingredients by starting from some precursor.

If molecules (with magnetic bodies included) are conscious entities able to direct attention, one can imagine that magnetic body controlling them with the mediation of genome and able to actively modify it, could help through modifications of the genome to create to the catalyst a binding site able to bind the precursor. Immune system is doing this very intensively. If the enzyme binding the precursor already exists, a combination of genes coding for the enzyme and the enzyme having the metabolites as ligands could allow to achieve this. All this would reduce to the motor activities of magnetic body, in particular reconnection of flux tubes, kind of Shivas dance. Genome would not be anymore a sequence of DNA developing through random mutations under selection pressures.

Can one make any clear cut predictions about preferred mutations?

1. Mutations are not expected to be always random point mutations but could be a result of a purposeful action of the magnetic body. Chemical similarity is expected to be conserved in good mutations. This is known to be the case. Allowed point mutations should conserve Y. Also bi-local mutations might occur and could be crucial for the coherence of the organisms. As found, the formation of flux tube between aminoacids A₁ and A₂ induces a flux tube between nucleotides Y and Y_c at the corresponding genes. This flux tube could force the possibly intentional mutations to occur as simultaneous point mutations of the two genes conserving the conjugacy property and leaving thus braiding invariant.

2. Folding is known to be more conserved than aminoacid sequence. Since folding is a collective property of gene, local chemistry might not be enough and the proposed non-local conservation laws might be needed. Bilocal mutations would also correlate the mutations of the binding sites of protein and ligand so that the crucial geometric conjugacy proposed to reduce to conjugation for Y would not be lost. The prediction would be conserved Y-Y_c pairs in genes coding for protein and ligand and these pairs might allow to deduce the paired points. The paired nucleotides need not belong to the same strand since genes are evenly distributed between strand and its conjugate and characterized by A,G surplus. Strong form of conjugacy stating that paired genes belong to the strand and its conjugate sounds beautiful in the ears of mathematician at least and would be mirror image for the mutual avoidance of quark matter and antimatter at protein level. Some examples are in order. Ala/Ser, Ser/Thr, Ile/Val/Leu, Asp/Glu do not change Y. Lys/Arg (A/G)), Tyr/Phe (A/U), Gly/Ala (G/C),... are also prevalent and one might hope that they correspond to binary mutations in some important cases.

3. If the flux tubes can connect also side chains the situation becomes more complex. There is a temptation to think that these flux tubes would connect only the nearby aminoacids and do not affect the large scale dynamics of folding. This would be the case if the value of Planck constant associated with these flux tubes is smaller than for the flux tubes connecting aminoacids as basic units. This kind of pairing would be consistent with Y-Y_c rule since hydrophobic and hydrophilic residues would tend to be connected by a long flux tube. If flux tubes can begin from the aromatic side chains, the replacement of an aromatic side chain with an aromatic side chain is favored (also chemical similarity explains this). The most basic facts about folding do not provide obvious support the idea about flux tubes between residues.
   1. Hydrophobic residues tend to cluster in dense packing in protein interior (antimatter at quark level) and Val (T), Leu (T), Ile (T), Phe (T), Ala (C), and Gly (G) make 63 percent of the interior of protein: the special role of Gly (matter rather than antimatter) is due to the reduction of the side chain to hydrogen atom.
   2. Asp (A), Glu (A), Lys (A) and Arg (G) with ionized residues are mostly at the surface of protein and make 23 per cent of protein surface and 4 per cent of interior. As noticed earlier, matter and antimatter at quark level tend to be far from each other.
   3. Polar groups tend to be paired by hydrogen bonds and oppositely charged groups tend to be near each other. Acidic Cys residues tend to be in positions where they can form S-S bonds. This cannot be explained by Y-Y_c pairing nor by the presence of bonds connecting residues in the proposed scenario. Aromatic residues tend to have favorable electrostatic interactions with each other and with S, O and amino groups.

In this framework aminoacids would have appeared before their precursors and possessed some function in RNA world, say the catalysis of join of RNA₂ dinucleotides to the increasing chain as I have proposed. Competition might have led to the situation in which RNA₂ learned to catalyze selectively generation of aminoacids from much simpler precursors (three of the proposed precursors contain only C,=O, and O^-). The reduced genetic code would have been present at two levels: reader can decide whether this is a shortcoming of the model or a fundamental biochemical duality implying an exponential amplification of RNA and aminoacid populations.

For details see the chapter Prebiotic Evolution in Many-Sheeted Space-time of "Genes and Memes".