There are several grand visions about TGD Universe. One of them is as a topological quantum computer in a very general sense. This kind of visions are always oversimplifications but the extreme generality of the braiding mechanism suggest that also simpler systems than DNA might be applying tqc. The detailed model for tqc performed by DNA indeed leads to the idea that so called water memory could be realized in terms of braidings.
A. Braid strands as flux tubes of color magnetic body
The flux tubes defining braid strands carry magnetic field when the supra current is on. In TGD Universe all classical fields are expressible in terms of the four CP2 coordinates and their gradients so that em, weak, color and gravitational fields are not independent as in standard model framework. In particular, the ordinary classical em field is necessarily accompanied by a classical color field in the case of non-vacuum extremals. This predicts color and ew fields in arbitrary long scales and quantum classical correspondence forces to conclude that there exists fractal hierarchy of electro-weak and color interactions.
Since the classical color gauge field is proportional to Kähler form, its holonomy group is Abelian so that effectively U(1)× U(1)subset SU(3) gauge field is in question. The generation of color flux requires colored particles at the ends of color flux tube so that the presence of pairs of quark and antiquark assignable to the pairs of wormhole throats at the ends of the tube is unavoidable if one accepts quantum classical correspondence.
In the case of cell, a highly idealized model for color magnetic flux tubes is as flux tubes of a dipole field. The preferred axis could be determined by the position of the centrosomes forming a T shaped structure. DNA strands would define the idealized dipole creating this field: DNA is indeed negatively charged and electronic currents along DNA could create the magnetic field. The flux tubes of this field would go through nuclear and cell membrane and return back unless they end up to another cell. This is indeed required by the proposed model of tqc.
It has been assumed that the initiation of tqc means that the supra current ceases and induces the splitting of braid strands. The magnetic flux need not however disappear completely. As a matter fact, its presence forced by the conservation of magnetic flux seems to be crucial for the conservation of braiding. Indeed, during tqc magnetic and color magnetic flux could return from lipid to DNA along another space-time sheet at a distance of order CP2 radius from it. For long time ago I proposed that this kind of structures -which I christened "wormhole magnetic fields" - might play key role in living matter. The wormhole contacts having quark and antiquark at their opposite throats and coding for A, T, C, G would define the places where the current flows to the "lower" space-time sheet to return back to DNA. Quarks would also generate the remaining magnetic field and supra current could indeed cease.
The fact that classical em fields and thus classical color fields are always present for non-vacuum extremals means that also the motion of any kind of particles (space-time sheets), say water flow, induces a braiding of magnetic flux tubes associated with molecules in water if the temporary splitting of flux tubes is possible. Hence the prerequisites for tqc are met in extremely general situation and tqc involving DNA could have developed from a much simpler form of tqc performed by water giving perhaps rise to what is known as water memory (see this, this and this). This would also suggest that the braiding operation is induced by the a controlled flow of cellular water.
B. Water memory: general considerations
With few exceptions so called "serious" scientists remain silent about the experiments of Benveniste and others relating to water memory (see this, this and this) in order to avoid association with the very ugly word "homeopathy".
The Benveniste's discovery of water memory initiated quite dramatic sequence of events. The original experiment involved the homeopathic treatment of water by human antigene. This meant dilution of the water solution of antigene so that the concentration of antigene became extremely low. In accordance with homeopathic teachings human basophils reacted on this solution.
The discovery was published in Nature and due to the strong polemic raised by the publication of the article, it was decided to test the experimental arrangement. The experimental results were reproduced under the original conditions. Then it was discovered that experimenters knew which bottles contained the treated water. The modified experiment in which experimenters did not possess this information failed to reproduce the results and the conclusion was regarded as obvious and Benveniste lost his laboratory among other things. Obviously any model of the effect taking it as a real effect rather than an astonishingly simplistic attempt of top scientists to cheat should explain also this finding.
The model based on the notion of field body and general mechanism of long term memory allows to explain both the memory of water and why it failed under the conditions described.
- Also molecules have magnetic field bodies acting as intentional agents controlling the molecules. Nano-motors do not only look co-operating living creatures but are such. The field body of molecule contains besides the static magnetic and electric parts also dynamical parts characterized by frequencies and temporal patterns of fields. To be precise, one must speak both field and relative field bodies characterizing interactions of molecules. Right brain sings-left brain talks metaphor might generalize to all scales meaning that representations based on both frequencies and temporal pulse with single frequency could be utilized.
The effects of complex bio-molecule to other bio-molecules (say antigene on basofil) in water could be characterized to some degree by the temporal patterns associated with the dynamical part of its field body and bio-molecules could recognize each other via these patterns. This would mean that symbolic level in interactions would be present already in the interactions of bio-molecules.
If water is to mimic the field bodies of molecules using water molecule clusters, at least vibrational and rotational spectra, then water can produce fake copies of say antigenes recognized by basofils and reacting accordingly.
Also the magnetic body of the molecule could mimic the vibrational and rotational spectra using harmonics of cyclotron frequencies. Cyclotron transitions could produce dark photons, whose ordinary counterparts resulting in de-coherence would have large energies due to the large value of hbar and could thus induce vibrational and rotational transitions. This would provide a mechanism by which molecular magnetic body could control the molecule. Note that also the antigenes possibly dropped to the larger space-time sheets could produce the effect on basofils.
- There is a considerable experimental support for the Benveniste's discovery that bio-molecules in water environment are represented by frequency patterns, and several laboratories are replicating the experiments of Benveniste as I learned from the lecture of Yolene Thomas in the 7:th European SSE Meeting held in Röros . The scale of the frequencies involved is around 10 kHz and as such does not correspond to any natural molecular frequencies. Cyclotron frequencies associated with electrons or dark ions accompanying these macromolecules would be a natural identification if one accepts the notion of molecular magnetic body. For ions the magnetic fields involved would have a magnitude of order .03 Tesla if 10 kHz corresponds to scaled up alpha band. Also Josephson frequencies would be involved if one believes that EEG has fractally scaled up variants in molecular length scales.
- Suppose that the representations of bio-molecules in water memory rely on pulse patterns representing bit sequences. The simplest realization of bit would be as a laser like system with bit 1 represented by population inverted state and bit 0 by the ground state. Bits could be arranged in sequences spatially or by variation of zero point energy defining the frequency: for instance increase of frequency with time would define temporal bit sequence. Many-sheeted lasers are the natural candidates for laser like systems are in question since they rely on universal metabolic energy quanta. Memory recall would involve sending of negative energy phase conjugate photons inducing a partial transition to the ground state. The presence of metabolic energy feed would be necessary in order to preserve the memory representations.
C. Water memory in terms of molecular braidings
It is interesting to look water memory from the point of view of tqc. Suppose that the molecules and water particles (space-time sheet of size of say cell length scale) are indeed connected by color flux tubes defining the braid strands and that splitting of the braid strands can take place so that water flow can gives rise to a braiding pattern and tqc like process.
The shaking of the bottle containing the diluted homeopathic remedy is an essential element in the buildup of water memories also in the experiments of Benveniste. Just like the vigorous flow of sol near the inner monolayer, this process would create a water flow and this flow creates a braiding pattern which could provide a representation for the presence of the molecules in question. Note that the hardware of braiding could carry information about molecules (cyclotron frequencies for ions for instance).
The model for the formation of scaled down variants of memories in hippocampus discussed above suggests that each half period of theta rhythm corresponds to tqc followed by a non-computational period during which the outcome of tqc is expressed as 4-D nerve pulse patterns involving cyclotron frequencies and Josephson frequency. Josephson currents at the second half period would generate dark Josephson radiation communicating the outcome of the calculation to the magnetic body. Entire hierarchy of EEGs with varying frequency scale would be present corresponding to the onion like structure of magnetic body. This pattern would provide an electromagnetic representation for the presence of the antigene and could be mimicked artificially [1,2,3].
This picture might apply be the case also in the case of water memory.
- The shaking might drop some fraction of antigene molecules to dark space-time sheets where they generate a dark color magnetic field. Because of the large value of Planck constant super-conductivity along color flux tubes running from molecular space-time sheets could still be present.
- TGD based model of super conductivity involves double layered structures with same p-adic length scale scale as cell membrane (see this). The universality of p-adic length scale hierarchy this kind of structures but with a much lower voltage over the bilayer could be present also in water. Interestingly, Josephson frequency ZeV/hbar would be much lower than for cell membrane so that the time scale of memory could be much longer than for cell membrane for given value of hbar meaning longer time scale of memory recall.
- Also in the case of homeopathic remedy the communication of the result of tqc to the magnetic body would take place via Josephson radiation. From the point of view of magnetic body Josephson radiation resulting in shaking induced tqc induced would replace the homeopathic remedy with a field pattern. The magnetic bodies of basophils could be cheated to produce allergic reaction by mimicking the signal representing the outcome of this tqc. This kind of cheating was indeed done in the later experiments of Benveniste involving very low frequency electromagnetic fields in kHz region allowing no identification in terms of molecular transitions (magnetic body and cyclotron frequencies) .
D. Why experimenter had to know which bottle contained the treated water?
Why experimenter had to know which bottle contained the treated water? The role of experimenter eliminates the possibility that the (magnetic bodies of) clusters of water molecules able to mimic the (magnetic bodies of) antigene molecules electromagnetically are present in the solution at geometric now and produce the effect. The earlier explanation for experimenter's role was based on the idea that memory storage requires metabolic energy and that experimenter provides it. Tqc picture suggests a variant of this model in which experimenter makes possible the recall of memories of water represented as braiding patterns and realized via tqc.
D.1 Does experimenter provide the metabolic energy needed to store the memories of water?
What could be then the explanation for the failure of the modified experiment? Each memory recall reduces the occupation of the states representing bit 1 and a continual metabolic energy feed is needed to preserve the bit sequence representations of antibodies using laser light systems as bit. This metabolic energy feed must come from some source.
By the universality of metabolic energy currencies population inverted many-sheeted lasers in living organisms define the most natural source of the metabolic energy. Living matter is however fighting for metabolic energy so that there must be some system willing to provide it. The biological bodies of experimenters are the best candidates in this respect. In this case experimenters had even excellent motivations to provide the metabolic energy. If this interpretation is correct then Benveniste's experiment would demonstrate besides water memory also psychokinesis and direct action of desires of experimenters on physics at microscopic level. Furthermore, the mere fact that we know something about some object or direct attention to it would mean a concrete interaction of our magnetic with the object.
D.2 Does experimenter make possible long term memory recall?
The alternative explanation is that experimenter makes possible long term memory recall which also requires metabolic energy.
- If braiding pattern represents, the water memory the situation changes since the robustness of the braiding pattern suggests that this representation is still in the geometric past (which is replaced with a new one many times). If the dark variants of molecules created in the process are still in the water, the braid representation of water memories could be available even in the geometric now but it is better to not make this assumption. The challenge is to understand how this information can be made conscious.
- What is certainly needed is that the system makes the tqc again. This would mean a fractal quantum jump involving unitary U process and state function reduction leading to the generation of generalized EEG pattern. Only the sums and differences of cyclotron frequency and Josephson frequency would matter so that the details of the flow inducing braiding do not matter. The shaking process might be continuing all the subjective time in the geometric past so that the problem is how to receive information about its occurrence. Experimenter might actually help in this respect since the mechanism of intentional action initiates the action in the geometric past by a negative energy signal.
- If the magnetic body of the water in the geometric now can entangle with the geometric past, tqc would regenerate the experience about the presence of antigene by sharing and fusion of mental images. One can however argue that water cannot have memory recall in this time scale since water is quite simple creature and levels with large enough hbar might not be present. It would seem that here the experimenter must come in rescue.
- The function of experimenter's knowledge about which bottle contains the homeopathic solution could be simply to generate time-like entanglement in the required long time scale by serving as a relay station. The entanglement sequence would be water now -experimenter now - water in the past with "now" and "past" understood in the geometric sense. The crucial entanglement bridge between the magnetic body of water and experimenter would be created in the manufacturing of the homeopathic remedy.
This picture is of course just one possible model and cannot be taken literally. The model however suggest that magnetic bodies of molecules indeed define the braiding; that the generalized EEG provides a very general representation for the outcome of tqc; that liquid flow provides the manner to build tqc programs - and also that shaking and sudden pulses is the concrete manner to induce visible-dark phase transitions. All this might be very valuable information if one some day in the distant future tries to build topological quantum computers in laboratory.
E. Little personal reminiscence about flow
I cannot resist a temptation to bore the reader with something which I have already told quite too many times. The reason why I started to seriously ponder consciousness was the wonderful experience around 1985 or so, which lasted from week two two - I do not remember precisely. To tell quite honestly and knowing the reactions induced in some hard nosed "serious" scientists: my experience was that I was enlightened. The depth and beauty of this state of consciousness was absolutely stunning and it was very hard to gradually realize that I would not get this state back.
To characterize the period of my life which I would without a hesitation choose if I had to select the most important weeks of my life, the psychologist needed only two magic words - acute psychosis. The psychologist had even firmly predicted that I would soon fall in a totally autistic state! This after some routine examinations (walking along straight line and similar tests). What incredible idiots can an uncritical belief on science make of us!
This experience made with single stroke clear that in many respects the existing psychology does not differ much from the medicine at middle ages. The benevolent people believing in this trash - modern psychologists - can cause horrible damage and suffering to their patients. As I started serious building of consciousness theory and learned neuroscience and biology, I began to grasp at more general level how insane the vision of the official neuroscience and biology about consciousness was. We laugh for the world view of people of middle ages but equally well they could laugh for our modern views about what we are.
Going back to the experience. During it I saw my thoughts as extremely vivid and colorful patterns bringing in mind paintings of Dali and Bosch. What was strange was the continual and very complex flow at the background consisting of separate little dots. I can see this flow also now by closing my eyes lightly when in a calm state of mind. I have proposed many explanations for it and tried to figure out what this flow tries to tell to me. Sounds pompous and a little bit childish in this cynic world, but this is the first time that I dare hope of having understood the deeper message I know is there.
 J. Benveniste et al (1988). Human basophil degranulation triggered by very dilute antiserum against IgE. Nature 333:816-818.
 J. Benveniste et al (198?). Transatlantic transfer of digitized antigen signal by telephone link. Journal of Allergy and Clinical Immunology. 99:S175 (abs.). For recent work about digital biology and further references about the work of Benveniste and collaborators see this .
 L. Milgrom (2001), Thanks for the memory. An article in Guardian about the work of professor M. Ennis of Queen's University Belfast supporting the observations of Dr. J. Benveniste about water memory.
 E. Strand (editor) (2007), Proceedings of the 7th European SSE Meeting August 17-19, 2007, Röros, Norway. Society of Scientific Exploration.
For details see the chapter DNA as Topological Quantum Computer of "Genes and Memes".