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Bio-Systems as Conscious Holograms

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Year 2011



Latest view about water memory

The notion of water memory has several aspects. Water memory was introduced by Benveniste to explain the claimed ability of homeopathically treated water to behave as if it contained the original molecules. Already Benveniste discovered the connection with very low frequency electromagnetic radiation and claimed that the patterns of this radiation carry the information about the molecule and represent its biologically relevant aspects. Water memory has been also assigned to the observation suggesting that the human intent has effect on the crystal structures formed as water near criticality freezes.

Basic aspects of water memory

The first aspect of water memory relates to homeopathy and is discussed from strongly skeptic point of view in Wikipedia article. Mae Wan-Ho takes a more balanced view on homeopathy in her article discussing the recent findings of the research group of HIV Nobelist Luc Montagnier providing strong support for water memory and suggesting also a connection with gene level (see this and this).

The basic principle of homeopathy is "let like be cured by like". Homeopathic remedies are highly diluted preparations believed to cause in the healthy individuals effects similar to the undesired symptoms of the person treated. Homeopathy is not in accordance with the naive materialistic beliefs about what water is (just the letters H2O!) and what happens in succussion process producing the remedy. Not surprisingly, hard-nosed skeptics are not able to discuss the subject without bursts of rage. Obviously, the claimed effect of homeopathic remedy resembles that of vaccine and one might say that the harmful substance serves as its own antibody eliminating the effect of the harmful substance. If one takes homeopathy seriously, the challenge is to explain this auto-antibody behavior. One can of course ask whether this behavior could in some sense be the basic mechanism of immune system.

In Benveniste's experiments antibodies of human basophils were dissolved in water and the claim of experiments was that basophils added to the homeopathically treated water produced allergic reaction serving usually as a signature for the presence of antibody. As if water were able to mimic the antibodies in biologically relevant aspects. Later Benveniste was labeled as a fraud but the research has continued and it has been for long time thought that low frequency electromagnetic fields are essential for water memory. The frequencies in question extend to kHz range and cannot relate to molecular transitions. Cyclotron frequencies assignable to charged particles at the magnetic body of the molecule are the natural candidate in TGD framework.

Second aspect of water memory relates to the claim that human intent has an effect on the molecular structure of water. Clearly a special variant of remote mental interaction would be in question. Masaru Emoto has photographed water crystals resulting from water contained by a glass and subject to human intent. Depending on the origin of water the resulting water crystals can vary from random to very organized and aesthetic. Words, pictures, and music are used to generate the crystals. It is important to not forget that human intent is a decisive factor so that water need not be able to read as one especially simplistic and aggressive fanatic ridiculizing Emoto claimed! Emoto has published several books containing pictures of the crystals and makes explicit that he is not a scientist but photographer who has discovered a fascinating new phenomenon and loves to document it.

Mae Wan-Ho has written an article titled Crystal Clear - Messages from Water in which she discusses Emoto's work with intellectual honesty and giving primacy for facts instead of dogmas. The basic argument of skeptic is that water is just H2O as we learned in school and therefore Emoto must be a swindler. The Wikipedia article about Masaru Emoto's work represents a rather civilized skeptic reaction as compared to Harriet Hall's piece of bad rhetorics filled with nasty ad hominem attacks. More ambitious skeptic believer bothers to develop an argument claiming that aesthetic appeal is highly subjective measure to characterize the water crystals. Here common sense and intellectual honesty clash with materialistic dogmas categorically denying this kind of effects, and the reader of these books must make a personal decision about what might be the truth - unless they decide to become photographers of water crystals.

The reader can also form his or her opinion about this aspect of water memory by looking the You tube video Water has Memory prepared in Aerospace Institute in Stuttgart illustrating that the effect of human intent on the structure of water droplets is same for droplets from same source, is repeatable, and characterizes the operator. Also the effect of flowers dropped into the water is illustrated. All drops from a given source give rise to same structure characterizing the flower. It is suggested that water is a huge information source and serves as a kind of data medium. This proposal is highly trivial and would mean a profound modification of world view.

A simple model for water memory

Suppose that we just for a moment decide to overcome our intellectual laziness and are not satisfied with the standard rhetoric tricks of skeptics to convince ourselves that water memory researches must be swindlers or fools. In other words, we take the experimental evidence supporting water memory as something worth of considering seriously and try to build a model for the claimed phenomena. We can indeed imagine when we do not know. The challenge of the model for water memory is to explain the claimed basic aspects of water memory with minimal assumptions. Let us the restrict the model building further by assuming that we live in TGD Universe and that our vision about this Universe is roughly correct.

The ability of water molecule clusters to mimic the possibly harmful substances - call them just H - dissolved in water in some biologically relevant aspects could explain the effectiveness of homeopathic remedies. Water should make possible a symbolic representation of the molecules or their magnetic bodies.

  1. Suppose H is a polar molecule so that it is biologically effective and that magnetic body characterizes the relevant biological effects of a polar molecule. Suppose that mechanical agitation causes some polar molecules to lose their magnetic bodies so that they attach to water molecule clusters, which therefore become "actors" representing H. In the dilution the density of the fake molecules is also reduced but if the energy provided by shaking can be used as metabolic energy makes possible for the "actors" to replicate and their population can survive and even evolve in the sequence of "environmental catastrophes" induced by repeated succussions possibly also inducing evolution as an increase of Planck constant for the magnetic body of the "actor". Also the replication of the magnetic body of the "actor" is required. Cyclotron frequency spectrum would serve as a characterizer of molecule's magnetic body and cyclotron radiation would make possible communications between fake molecules and their magnetic body.

  2. What the dropping of magnetic bodies really means? To answer the question consider a general vision about what happens as energy is fed into a system consisting of proteins dissolved in water. The proteins originally in closed globular configuration open as the ordered water covering their surfaces with "ice" melts. This leads to a protein aggregation during the short "molecular summer" provided by the energy feed. The outcome is braiding and reconnection of flux tubes.

    Suppose that this mechanism is at work also when proteins are replaced with harmful polar molecules. During "molecular summer" a reconnection process for closed loops emerging from water clusters and polar molecules would connect them with water clusters. Also the magnetic bodies of polar molecules would generate connections to water clusters via molecules. Self-reconnection for the flux tubes going through H molecules makes possible the transfer of the magnetic body of H to water molecule cluster. Water molecule cluster would "steal" the magnetic coat of H and H molecules would be left with short-cut closed flux tubes after the reconnection.

  3. What is required that these water clusters or something associated with them can replicate and develop to a population representing the original molecules. The needed metabolic energy would come from mechanical agitation. Note that this replication should involve also the replication of magnetic bodies which suggests that linear structures generating planar flux tubes emanating from the basic building bricks of the structure are involved. This will be discussed below.

What could then be the healing mechanism in homeopathy? Why the presence of the fake molecules in organism would prevent the harmful actions of real molecules in the organism? What could be the translation of "Let like be cured by like" to the language of quantum TGD?

  1. Suppose that the effects of H on bio-molecules are due to cyclotron radiation along the flux tubes of its magnetic body connecting it to bio-molecules of the organism. Suppose that the fake representatives of H contained by the homeopathic remedy and real molecules H reconnect so that the flux loops associated with H and fake H reconnect to a pair of flux tubes connecting H and fake H. Suppose that this happens with such high a rate that the fraction of the connections to other biomolecules remains low.

  2. If so, fake H would effectively act antibody of H and the effects of H via its magnetic body on organism would be minimized. Like would indeed cure like. Could this reconnection mechanism be at work also when antibody attaches to the harmful molecule? If so, the basic mechanism of immunization would be universal and involved the notion of magnetic manner in an essential manner.

Dark nucleon genetic code as realization of water memory, and homeopathic mechanism as basic mechanism of immune system

The proposal says nothing about the detailed structure of water clusters, and does not mention dark nucleons nor the proposal for the realization of genetic code based on them. A more refined model would include also these and give a connection for how immune system would utilize the reconnection of flux tubes defining the basic mechanism of homeopathy.

  1. TGD predicts a realization of vertebrate genetic code at the level of dark nucleons. Dark nucleons correspond to the states of DNA, RNA, tRNA, and amino-acids and represent vertebrate genetic code under rather general assumptions (see this). One could even consider the extension of the genetic code to a naming of polar molecules by sequences of representatives of DNA letters. Suppose that dark proton sequences are attached to a polar molecule dissolved in water, and define a representation of the molecule in terms of code letters realized as exotic protons with Compton length in nano-scale. The assignment of the magnetic body of the molecule to water cluster would give it the same "name" as for the original molecule. It is of course possible to have other representation and one of them would be in terms of dark u quarks providing representation of A,T,C,G in terms of spin states.

  2. If the population of dark DNA molecules assigned with the harmful substance H is able to use the energy provided by the succussion process as a metabolic energy for replication, the disappearance of H is compensated by the replication of dark DNA representing it. Dark DNA becomes the representative of H. The growing population would consist of dark DNA and the flux tubes of the magnetic body connect to dark DNA strands. Replication would be the analog of that for ordinary DNA and involve also the replication of magnetic bodies. The water would contain pairs of dark DNA and its conjugate connected by a flux tube and these flux tubes would reconnect with flux tubes connecting the dark DNA sequence representing H and connected by flux tubes to its conjugate.

  3. It is known that the DNA of the immune system evolves with an especially high rate. Could the universal naming mechanism allow the immune system to generate new immune responses via the transcription of the dark DNA sequence representing the harmful molecule to a real DNA, which in turn codes for amino-acid attaching to the harmful molecules along the dark nucleon sequence? A model for homeopathy would extend to a model for the functioning of immune system. This would be of course also a mechanism of evolution as a reaction to changing chemical environment. This would explain also the effect of the homeopathic remedy as an effect at gene level.

    It is difficult to exaggerate the potential significance of this mechanism for biology, genetic engineering, and medicine. Understanding of the contemptible homeopathy could induce decisive step in the understanding of biology. This possibility shows how dangerous it is to take the claims forced by a particular belief system like materialism as final truths.

Reader has certainly noticed that reconnection mechanism pops up again and again in the model and would be also the fundamental mechanism of ordinary DNA replication, transcription, translation of mRNA to proteins, and of process catching tRNA molecules carrying amino-acids to form protein at mRNA. This mechanism would be realized even in the mutual interactions between living organisms and between living organisms and inanimate matter.

Braiding represents as a higher level aspect of water memory

Braiding represents another aspect of water memory relating to the representation as dark nucleon sequences as the quantum computer programs represented by braidings to DNA in the model of DNA as topological quantum computer (see this). The memories represented by braiding would be about the flow of water and molecules rather than about substances present in the water. The model of qualia (see this) is based on flux tube connections between system representing self and environment. For polar molecules the qualia would relate to charge and electric polarization. Could the qualia assignable to polar molecule plus environment have scaled down fractal variants at the level of water clusters of environment? If this were the case then water would effectively produce representations about molecule at the level of qualia. Could also these relate to water memory?

Effects of intent on water crystallization

One should understand the effect of intent on water in terms of water memory. The proposed representation of polar molecules in terms of dark DNA sequences is one possible realization of water memory reducing naming of molecules to genetic code letters. Essentially addressing of molecules would be in question. This aspect of water memory is not relevant now. Rather, what matters is the interaction of water with human operator and reconnection of flux tubes of magnetic bodies is a good guess for how this interaction is realized. The same mechanism is involved also with the interaction of homeopathic remedy and harmful substance.

How could one understand the effect of intent on water crystallization, which characterizes the operator involved. The situation would be very much like that in the experiments of Tiller. The magnetic bodies assignable to the operator and water must interact and produce the effects. This would not be surprising if similar interaction takes place in the case of dissolved substances.

A concrete model for the interaction would be in terms of the reconnections of closed flux tubes emerging from the biological body of subject person with the flux tubes of the magnetic body of water creating direct flux tube contacts between the two bodies. The presence of magnetic flux tube connections between water sample and operator's magnetic and biological body would induce the effects on crystallization of water. Water memory should be stable in human time scales. This requires that these flux tube patterns are rather stable modification of the magnetic body of water. Large values of Planck constant assignable to the magnetic body of human agent would be needed. What is required is that the crystallization patterns and therefore structures of water clusters correlate with the structure of the magnetic body of the water sample.

Magnetic body and migrating birds

What happens when the water glass in the experiments of Emoto is taken to a large distance from operator? Does the effect prevail? If the magnetic flux tubes stretch, this interaction need not cease as the distance between operator and water glass increases unless the double flux tube splits by self-reconnection. If so, water could indeed act as a data medium as proposed in the video about water memory.

Magnetic body could play key role in understanding how birds and fish manage to find their birth places during migration is one of the many unresolved mysteries of biology. It has been suggested that orienteering in magnetic field of Earth using neuron level compass is in question but this proposal has its difficulties. Could it be that the birds and fish are connected by the magnetic flux tubes of their personal magnetic body or of that of the species to the birth place so that they would only follow Ariadne's thread?

For background see the chapter Homeopathy in Many-sheeted Space-time.



Constraints on the fermionic realization of genetic code from the model for color qualia

The original model for DNA as topological quantum computer assigns to DNA nucleotides quarks at ends of flux tubes or quark pairs at the ends of wormhole flux tubes. This is only the realization that came first to my mind in TGD Universe where dark variants of quarks can define QCD like physics even in cellular length scales. One can actually imagine several realizations of the genetic code and the first realization is far from being the simplest one. It is enough to have four different particles or many-particle quantum states to build at least formally a map from A,T,C, G to four states. It is obvious that the number of possible formal realizations is limited only by the imagination of the theoretician. Additional conditions are required to fix the model.

Fermionic representation

Consider first the fermionic representations in the general case without specifying what fermions are.

  1. The original proposal was that DNA nucleotides correspond to flux tubes with quark q and antiquark qbar at the ends of the parallel flux sheets extremely near to each other. Second options relies on wormhole magnetic flux tubes in which case quark pair qqbar is at both ends. Quarks u, d and their antiquarks would code for A,T,C,G. The spin of quarks is not taken into account at all in this coding: why not restrict the consideration to single quark. The total quark charge at given end of flux tube pair vanishes and flux tube ends carry opposite quark charges.

    The nice feature of this option is that one could understand the generation of color qualia in the model of sensory receptor in simple manner to be discussed below. Even if one accepts the arguments supporting the view that dark quarks in cell scale are natural outcome of the hierarchy of Planck constants, one could argue that the presence of both quarks and antiquarks does not conform with matter antimatter asymmetry (not that one can however identify the analog of matter antimatter asymmetry at DNA level).

  2. Spin states for fermion pairs assigned with two parallel magnetic flux tubes with the magnetic field generated by spin provide much simpler representation for nucleotides. Similar fermion pair would reside at the second end of flux tube pair.
    1. It is is essential that rotational symmetry is broken and reduces to rotational symmetry around the direction of flux tubes so that spin singlet and spin 0 state of triplet mix to form states for which each fermion is in spin eigenstate. The states must be antisymmetric under exchange of the protons and spin 1/0 states are antisymmetric/symmetric in spatial degrees of freedom (wave functions located to the ends of flux tubes). The states with definite spin for given flux tube are mixtures of s=1 states with vanishing spin projection and s=0 state.
    2. It is not quite clear whether one should treat fermion pairs as identical bosons with 3+1 spin states since in TGD framework one considers disjoint partonic 2-surfaces and the situation is not that of QFT in M4. This interpretation would require totally symmetry of the states under permutations of bosonic states defined by the 3+1 spin states. Coding by spin requires that each nucleotide corresponds to a state with a well defined spin. In field theory language the state would be obtained by applying bosonic oscillator operators generating states of given spin localized to a given nucleotide position.
    3. The classical correlate for the permutations of coordinates of fermions has interpretation as braiding for the flux tubes of the flux tube pair. In the similar manner the permutation of the flux tube pairs associated with nucleotides has interpretation as braiding of the 3-braids formed form from flux tube pairs. Braiding therefore gives a representation of spin analogous to the well-known orientation entanglement relation invented by Dirac and providing geometric representation of spin 1/2 property.
Various options for the fermionic representation of A,T,C,G

Fermionic representations allows several options since fermion can be electron, u or d quark, or proton. Wormhole magnetic fields would not be needed in this case.

  1. The problem of electron and proton options is that it does not allow realization of color qualia. There is also the well-known problem related to the stability of DNA caused by the phosphate charge of -2 units per nucleotide. Somehow this charge should be screened. In any case, the charge -2 should correspond to the electron pair at the DNA end of the flux tube for electron option. For proton option the charge would be screened completely. One could of course consider also the large hbar color excitations of ordinary protons instead of quark at its nucleotide ends. This option would however require the modification of quark wave functions inside proton and this option will not be discussed here.
  2. Quark option would give rise to both color and allow also to reduce the electronic charge of -2 units by 4/3 units to -2/3 units in the case of u quark pair. This would help to stabilize DNA. In the case of d quarks the charge would increase to -10/3 units and is not favored by stability argument. Flux tube pairs assigned to single nucleotide define diquarks with spin 1 or spin 0.
    1. Diquarks behave ass identical bosons with 3+1 spin states and 3× 3 color states. The states with well defined symmetry properties in spin degrees of freedom have such properties in spatial degrees of freedon. This means that one obtains a superposition of flux tube pairs with are either braided or unbraided. Triplet/singlet state is symmetric/antisymmetric and total asymmetry could be guaranteed by assuming symmetry/antisymmetry in spatial degrees of freedom and antisymmetry/symmetry in color degrees of freedom. This would give anti-triplet/6-plet in color degrees of freedom. Spatial symmetry would favor antitriplet and diquark would behave like antiquark with respect to color. Let us assume antitriplet state for definiteness.
    2. DNA codon corresponds to three-di-quark state. This state must be totally symmetric under the exchange of bosons. One can have total symmetry in both spatial and color degrees of freedom or total antisymmetry/symmetry in spatial and total antisymmetry/symmetry in color degrees of freedom.The first option gives 10-dimensional color multiplet and the second one color singlet. Braiding is maximal and symmetric/antisymmetric in these case. One can consider also mixed symmetries. In this case one has color octet which is antisymmetric with respect to the first nucleotide pair and symmetric with respect to first nucleotide pair and third nucleotide. The braiding of the first two nucleotides must be antisymmetric and the braiding of this pair with third nucleotide. The conclusion would be that color multiplets correspond to well defined braidings and one would therefore have directed connection with topological quantum computation. Color octet is especially interesting concerning the representation of color qualia.
The challenge of all these options (note that the representability of color selects quark option) is to find a good justification for why the assignment of A,T,C,G to quark states or spin states is unique dynamically. Stability argument is expected to help here.

Realization of color qualia for quark option

Consider now how one could understand the generation of qualia for quark option.

  1. The generation of qualia involves interaction with external world giving rise to a sensory percept. In the case of visual colors it should correspond to a measurement of quark color and should give rise to eigenstages of color at the ends of flux tubes at DNA nucleotides for a nucleus or cell of photoreceptor. A modification of capacitor model is needed. Color polarization is still essential but now polarization in nucleus or cell scale is transformed in the generation of color quale to a polarization in longer length scale by the reconnection of flux tubes so that their ends attach to "external world". The nucleus/cell becomes color and state function reduction selects well defined quantum numbers. It is natural to assume that the entanglement in other degrees of freedom after color measurement is negentropic.
  2. Does the "external world" corresponds to another cell or to the inner lipid layers of the cell membrane containing the nucleus. In the first case flux tubes would end to another cell. If the nuclei of receptor cells are integrate to a larger structure by magnetic flux sheets traversing through them one can also consider the possibility that the polarization in the scale of cell nucleus (recall that the nucleus has also double lipid layer) is transformed to a polarization in cell scale so that similar process in cell scale gives rise to qualia.
  3. The entire receptor unit must have net color after the state function reduction. This requires that there are flux tubes connecting the receptor unit to a unit representing "external world". If second cell is the "external world" these flux tubes must go through the pair of lipid layers of both cell membrane and end up to the nucleus of cell in the environment. If external world corespond to the complement of nucleus inside cell the inner layers of cell membrane represents external world. Cell membrane indeed serves as sensory receptor in cell length scale. One can of course have sensory qualia in various length scales so that both options are probably correct and a kind of fractal hierarchy is very natural giving rise also to our qualia at some higher level.
  4. Consider now how the color qualia are generated.
    1. There must be two flux tube states. In the first state there are two flux tube beginning from cell nucleus A and ending to the inner lipid layer a1 and flux tube beginning from the outer lipid layer a2 and ending cell nucleus B. Both flux tubes have vanishing net color so that cells have vanishing net colors. This could be regarded as the resting state of the receptor. The lipids in layers a1 and a2 are connected by another short flux tube. Same for b1 and b2.
    2. The second flux tube state corresponds to long flux tubes connecting the nuclei of cells A and B. The ends carry opposite color charges. In this case the net color of both A and B is non-vanishing. This state would be an outcome of a reconnection process in which the flux tubes from A to a1 and B to a2 re-connect with the short flux tube connecting lipid layers a1 and a2.
    3. When these flux tubes carry opposite colors numbers at their ends, the cell possess net color charge and can represent color quale. Or rather, creation of this kind of flux tube connections would give rise to the color charging of the receptor cell with external world carrying opposite color charge.
One can argue that this mechanism is not quite in spirit with color capacitor model. Polarization is still essential but now polarization in receptor scale is transformed to polarization in longer length scale by the reconnection of flux tubes. This model is neither consistent with the naive expectation that the quale is generated after state function reduction. Rather, the beginning of sensation of quale means beginning of negentropic entanglement and fusion with external world and state function usually associated with the quantum measurement would mean the end of the sensation and separation from the external world! Maybe one can say that state function reduction means that experience is replaced with a memory "I had the sensation of quale"! Krishnamurti would certainly agree!;-)

The unexpected prediction of the model is that braiding would correlate directly with qualia. This would mean also a connection between quantum computation and qualia. This condition emerges from Fermi/Bose-Einstein statistics correlating braiding with symmetry properties of color states and spin states. Quite generally, the correlation of braiding with the symmetries of wave functions as functions of points of braid end points would allow to have direct geometric correlate between induced entanglement and braiding as naive intuitive expectations have suggested.

For background see the chapter General Theory of Qualia.



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