What's new in
Bio-Systems as Conscious Holograms
Note: Newest contributions are at the top!
In earlier posting Comparison of Maxwellian and TGD views about classical gauge fields I compared Maxwellian and TGD based notions of classical fields. The comparison was restricted to the linear superposition of fields which in TGD framework is restricted to linear superposition of effects of classical fields: the space-time sheets representing classical fields are indeed separate and it is enough that their M4 projections intersect. Summation of effects means at classical level summation of forces caused by them due to the fact that p"../articles/ have topological sum contacts to both space-time sheets. The notion of hologram relies crucially on the superposition of fields and this this forces to reformulate the notion of hologram in TGD framework.
In TGD inspired theory of consciousness the idea about living system as a conscious hologram is central. It is of course far from clear what this notion means. Since the notions of interference and superposition of fields are crucial for the description of the ordinary hologram, the proposed general description for the TGD counterpart for the superposition of fields is a natural starting point for the more precise formulation of the notion of conscious hologram. In the following only the notion of conscious hologram is discussed. Also the formulation of the notion of ordinary hologram in TGD framework is an interesting challenge.
One can imagine several applications in TGD inspired quantum biology.
In TGD Universe gauge fields are replaced with topological field quanta. Examples are topological light rays, magnetic flux tubes and sheets, and electric flux quanta carrying both magnetic and electric fields. Flux quanta form a fractal hierarchy in the sense that there are flux quanta inside flux quanta. It is natural to assume quantization of Kähler magnetic flux. Braiding and reconnection are basic topological operations for flux quanta.
One important example is the description of non-perturbative aspects of strong interactions in terms of reconnection of color magnetic flux quanta carrying magnetic monopole fluxes. These objects are string like structures and one can indeed assign to them string world sheets. The transitions in which the thickness of flux tube increases so that flux conservation implies that part of magnetic energy is liberated unless the length of the flux quantum increases, are central in TGD inspired cosmology and astrophysics. The magnetic energy of flux quantum is interpreted as dark energy and magnetic tension as negative "pressure" causing accelerated expansion.
This picture is beautiful and extremely general but raises challenges. How to describe interference and linear superposition for classical gauge fields in terms of topologically quantized classical fields? How the interference and superposition of Maxwellian magnetic fields is realized in the situation when magnetic fields decompose to flux quanta? How to describe simple systems such as solenoidal current generating constant magnetic field using the language of flux quanta?
Superposition of fields in terms of flux quanta
The basic question concerns the elegant description of superposition of classical fields in terms of topological field quanta. What it means that magnetic fields superpose.
Time varying magnetic fields described in terms of flux quanta
An interesting challenge to describe time dependent fields in terms of topological field quanta which are in many respects static structures (for instance, flux is constant). The magnetic fields created by time dependent currents serves as a good example from which one can generalize. In the simplest situation the magnetic field strength experiences time dependent scaling. How to describe this scaling?
Consider first the scaling of the magnetic field strength in flux tube quantization.
Consider as the first example slowly varying magnetic field created by an alternating running in current in cylindrical solenoid. There are flux tubes inside the cylindrical solenoid and return flux tubes outside it flowing in opposite direction. Flux tubes get thicker as magnetic field weakens and shift from the interior of solenoid outside. For some value x of the time dependent scaling B→ B/x the elementary flux quantum Φ0 reaches the radius of the solenoid. Quantum effects must become important and make possible the change of the sign of the elementary flux quantum. Perhaps quantum jump turning the flux quantum around takes place. After this the size of the flux quantum begins to decrease as the magnitude of the magnetic field increases. At the maximum value the size of the flux quantum is minimum.
This example generalizes to the magnetic field created by a linear alternating current. In this case flux quanta are cylinderical flux sheets for which magnetic field strength and thickness oscillators with time. Also in this case the maximum transversal area to the system defines a critical situation in which there is just single flux sheet in the system carrying elementary flux. This flux quantum changes its sign as the sign of the current changes.
For background see the chapter Bio-Systems as Conscious Holograms.
The idea about remote replication, transcription and translation of genes in terms of electromagnetic field patterns is very attractive and would be in accordance with the wave DNA vision. This requires a coding of DNA nucleotides. I have proposed several codings of this kind.
In the sequel a model for the coding of DNA in terms of radiation patterns is discussed. There are three experimental guidelines: the phantom DNA identified as dark nucleon sequences in TGD framework and the evidence for remote activation of DNA transcription - both discovered by Gariaev's group - are assumed as the first two key elements of the model. The remote replication of DNA suggested by the experimental findings of Montagnier's group serves as a further guideline in the development of the model.
Polymerase chain reaction (PCR) is the technique used in the experiments of Montagnier's group. DNA polymerase catalyzes the formation of DNA from existing DNA sequences serving as a template. Since the catalytic interaction of DNA polymerase takes place with already existing DNA sequence, the only possibility is that first some conjugate DNA sequences are generated by remote replication after which DNA polymerase uses these sequences as templates to amplify them to original DNA sequences. Whether the product consists of original DNA or its conjugate can be tested.
The model inspires the proposal that the magnetic body of a polar molecule codes for it using dark nucleon sequences assignable to the hydrogen bonds between the molecule and surrounding ordered water layer. Quantum antenna mechanism would allow the immune system to modify itself by developing ordinary DNA coding for amino-acids attaching to and thus "catching" the polar molecule. The mechanism could be behind water memory and homeopathic healing. Every polar molecule in living matter would have dark nucleon sequence or several of them (as in the case of amino-acids) serving as its name. This would also associate unique dark nucleon sequence also with the magnetic body of DNA so that DNA-dark DNA association would be automatic. Same applies to mRNA and tRNA and amino-acids.
Before continuing I want to express my gratitude to Peter Gariaev for posing a question which led to the realization of the connection between quantum antenna hypothesis, remote replication, and genetic code and its generalization.
1. The findings that one should understand
It is good to start by summarizing the experimental findings that the model should explain.
2. The model of remote replication consistent with DNA as topological quantum computer model
The basic assumptions are that the scattered radiation, the flux tubes of the magnetic body of DNA along which the radiation propagates, and quarks and antiquarks at the ends of the flux tubes from system able to serve as a template for the formation of conjugate of ordinary DNA. To understand how remote remote replication could take place, some further assumptions are necessary.
Quantum antenna mechanism is extremely general and flexible and might be a fundamental mechanism of bio-catalysis allowing also communication between visible and dark matter sectors. Antenna mechanism is of course central also in ordinary communications. If the biologically most relevant interactions of biomolecules via quantum antenna mechanism then also water memory and the claimed effects of homeopathically treated water might be understood (see this). The testing of the dark photon aspect of the hypothesis would require the detection of the dark photons somehow: the decay to a bunch of n ordinary photons with same wavelength is the obvious manner to achieve this.
1. Identification of phantom DNA
The observed residual coherent scattering from a chamber from which ordinary DNA is removed inspired the notion of phantom DNA. The questions are what phantom DNA is and is it relevant to remote replication of the ordinary DNA.
Phantom DNA identified observed in the scattering experiments could correspond to dark nucleon sequences realizing vertebrate genetic code with dark nucleons consisting of three quarks representing both DNA,RNA, tRNA, and aminoacids as particular nucleon states (see this). The resonant interaction between ordinary and dark DNA would explain why light at same frequencies scatters also from dark DNA in phantom DNA experiments. In Montagnier's experiments it could give rise to a positive feedback amplifying the radiation from second sample containing DNA. Water would be living in the sense that it contains "dark DNA" and dark DNA might allow remote transcription to ordinary DNA sequences in presence of ordinary DNA codons (triplets) and vice versa.
Skeptic can of course ask whether one could explain the experimental findings without assuming phantom DNA.
2. Dark DNA and frequency coding by quantum antenna mechanism
The remote transcription of dark DNA (phantom DNA) to ordinary DNA and vice versa would have quite far reaching implications for evolution since dark DNA/RNA/tRNA/amino-acids could define a virtual world serving as Rkeno&D lab where new DNAs could be developed and if needed translated to ordinary DNA. The dark DNA could be also transferred through cell membranes without difficulty, in particular to germ cells. Also the genetic transfer between different organisms would become possible. Second possibility is that the magnetic flux tubes mediating the dark photons traverse the cell membranes so that even the transfer of dark nucleons through the cell membrane is un-necessary. The implications for genetic engineering would be obvious.
Could one generalize the quantum antenna mechanism to the interaction between dark nucleons representing DNA triplets as entangled states of three quarks and ordinary DNA codons consisting of three unentangled nucleotides? Could similar mechanism realize genetic code assigning to dark DNA dark variants of RNA, tRNA and amino-acids via the analogs of transcription and translation processes? It seems that frequency coding, which - somewhat disappointingly - did not look natural for remote replication of ordinary DNA, is ideal for these processes so that the original idea of wave DNA would be realized at the level of dark-visible and dark-dark interactions.
The flux tubes would be associated with entire codons -DNA triplets - rather than individual nucleotides. Different DNA triplets do not form interacting groups in the sense that they should be connected by flux tubes. Therefore the simplest possibility would be frequency coding with specific resonance frequency for each DNA triplet. No quarks at the ends of the flux tubes connecting codons (not nucleotides) are needed. If one assumes that octaves correspond to the same frequency this would require odd multiples
λ(n)= (2n+1)λ0 , n=0,...,63
of λ0 so that the longest wavelength would be 127λ0. In the number theoretic model of the genetic code based on the notion of Combinatorial Hierarchy (see this codons are indeed labeled by 64 integers in the range 0,...,127=27-1. These integers are however not assumed to be odd. One can also consider the possibility that the frequencies are coded by the value of Planck constant and this option leads to an interpretation of the earlier proposed TGD inspired realization of the so called divisor code suggested by Khrennikov and Nilsson in terms of quantum antenna hypothesis. This will be discussed later on.
Support for this option comes from the phenomenon of phantom DNA demonstrating that resonant scattering of light from DNA and dark DNA occurs for the same frequencies.
Can one imagine remote transcription of dark DNA to ordinary DNA using only nucleotides as building bricks? This process would require coupling of DNA nucleotides to dark nucleons representing DNA triplets and it is not easy to imagine any simple mechanism making this possible. Already existing DNA triplets seem to be necessary.
3. Common explanation for the recent findings of Montagnier and earlier findings of Gariaev
In the experiments of Montagnier's group the outcome is remote replication whereas the earlier experiments Gariaev's group give evidence for remote activation of DNA transcription. Hence one expects a common underlying mechanism.
What is nice from TGD point of view that the consistency between the two experiments give support also for the notion of dark DNA and its identification as phantom DNA.
The basic assumptions of the model of remote replication deserve a short summary.
3. Possible implications
The proposed realization of remote replication seems to have rather far reaching implications for the understanding of the mechanism of homeopathy and basic mechanisms of immune system as well as to the understanding of how DNA -dark nucleon sequence association. One can also interpret the proposed TGD based realization of the divisor code suggested by Khrennikov (see this) as frequency coding of DNA triplets by the value of Planck constant assignable to flux tubes emerging from DNA triplets.
1. Possible relevance for homeopathy and immune system
TGD inspired vision about water memory assumes that the magnetic bodies of molecules dis-solved into water represent the molecules in terms of cyclotron frequencies characterizing its magnetic body. Molecules can lose their magnetic bodies as the hydrogen bonds connecting the molecule to the magnetic body are split. The population of these lost magnetic bodies would define a representation for the dissolved substance able to mimic it.
The hitherto unanswered questions concern the detailed structure of the magnetic body of the molecule and how it codes for the molecule. The hydrogen bonds connecting the molecule to the ordered water forming a kind of ice covering the molecule in the inactive state should be crucial aspect of the coding. If dark nucleon sequences are associated with the hydrogen bonds of this "ice layer" or generated in their splitting as I have proposed, one can ask whether dark nucleon sequences could characterize the molecular magnetic body. If so, cyclotron resonance frequencies or more general frequencies associated with the dark DNA sequences could code for the molecule. DNA sequences would define a universal language allowing for the system to name for polar molecules.
Quantum antenna mechanism would in turn associate ordinary DNA sequences with the dark nucleon sequences coding for the molecule. Hence one can imagine a development of a mechanism allowing the organism to modify its DNA by adding to it genes coding for proteins characterized by the same resonance frequencies as the magnetic bodies of the invader molecules. These proteins would couple strongly to the invader molecules via quantum antenna mechanism and the phase transition reducing Planck constant would allow them to catch the invader molecules by attaching to them. The fact that the DNA of immune system evolves very rapidly conforms with this vision.
2. Frequency coding for DNA sequences by the value of Planck constant as a realization of divisor code
The realization of dark magnetic bodies of polar molecules in terms of dark nucleon sequences allows to understand the association of dark DNA with ordinary DNA, RNA, and tRNA making among other things possible the transcription of dark DNA to DNA and vice versa. Dark nucleon sequences would be associated with the magnetic bodies of DNA, mRNA, and tRNA. This would apply also to amino-acid sequences. Dark DNA would separate from ordinary DNA as it loses its magnetic body in the splitting of hydrogen bonds and suffers denaturation. Similar mechanism would cause denaturation of other biomolecules and would mean that they "lose their names" and thus information content and become mere organic molecules instead of living bio-molecules. This kind of association would make the emergence of the genetic code and its generalization to the naming of molecules by DNA sequences trivial.
Genetic code can be understood from the proposed natural correspondence between dark nucleon sequences and DNA, RNA, tRNA, and acmino-acids). I have however developed also another realizaton based on TGD based realization of so called divisor code first suggested by Khrennikov and Nilsson and the following argument allows to interpret in terms of frequency for fixed value of photon energy with frequencies coded by the value of Planck constant.
For background see the chapter Homeopathy in Many-Sheeted Space-time.
I have discussed in the chapter About the Nature of Time of "Matter, Mind, Quantum" how the arrow of geometric time as a correlate for the experienced arrow of geometric time might be selected in TGD Universe. The discussion does not touch the question what arrow of time means at the level of quantum states. Therefore the notion of negative energy signal propagating backwards in geometric time crucial for TGD inspired quantum biology remains somewhat fuzzy.
The recent progress in the understanding of the basic properties of zero energy states makes it possible to understand what arrow of geometric time and the notion of negative energy state and signals propagating to the direction of geomeric past mean at the level of zero energy states. This understanding has surprisingly non-trivial philosophical implications. In the following I shall briefly the quantum view about arrow of time.
Arrow of time as an inherent property of zero energy states?
The basic idea can be expressed in very conscise form. In positive energy ontology arrow of time characterizes dynamics. In zero energy ontology arrow of time characterizes quantum states.
Does state function-state preparation sequence correspond to alternating arrow of geometric time?
The state function reduction at light-like boundary of CD implies delocalization at the opposite boundary. This inspires so fascinating questions.
The arrow of geometric time and the arrow of logical implication
If physics is mathematics in the sense that there is nothing behind quantum states regarded as purely mathematical objects, Boolean logic must have a direct manifestation in the structure of physical states. Physical states should represent quantal Boolean statements which get their meaning via quantum jumps. In TGD framework WCW ("world of classical worlds") spinor fields represent quantum states of the Universe and WCW spinors correspond to fermionic Fock states for second quantized induced spinor fields at space-time surface. Fock state basis has interpretation in terms of Boolean algebra. In positive energy ontology the problem is that fermion number as a super-selection rule would allow very limited number of Boolean statements to be represented. In ZEO the situation changes.
The fermionic parts of positive and negative energy parts can be seen as quantum superpositions of Boolean statements with fermion number in given mode (equal to 0 or 1) representing yes/no or true/false. Also various spin like quantum numbers associated with oscillator operators have same interpretation. Zero energy state could be seen as quantum superposition of pairs of elements of Boolean algebras associated with positive and negative energy parts of the zero energy state.
The first - and incorrect - interpretation is that zero energy state represents a quantum superposition of equivalent statements a↔ b and thus abstraction A<---> B involving several instances of A and B. The breaking of time reversal invariance allowing localization to definite fermionic quantum numbers at single end of CD only however implies that quantum states can only represent abstraction of logical implication to A→ B rather than equivalence. p-Adic physics for various primes p (see this) would represent correlates for cognition and intentionality.
For background see the chapter Time, Space-time, and Consciousness.
Isotope effect of odor perception as an additional guideline to TGD inspired model of odor perception
Flies can smell the difference between normal hydrogen and deuterium. This is not in accordance with the standard theory of olfaction which says that olfaction relies on the shape of the molecule but conforms with the theory of Luca Turin, who is one of the co-authors of the article
Franco, M. I., Turin, L., Mershin, A. & Skoulakis, E. M. C. Proc. Natl Acad. Sci. USA doi:10.1073/pnas.1012293108 (2011)
reporting the discovery. The theory assumes that olfaction relies on molecular vibrational frequencies depending on the mass of the isotope. You can make your day perfect by enjoying the summary of the vibrational theory of scents by Luca Turin himself (I am grateful for Fischer Gabor for the link). There is also a Wikipedia article about Vibration Theory of Olfaction.
1. Turin's theory
From Turin's lecture and WIkipedia article one learns why reductionism is so nice when it can be applied.
In Turin's theory vibrational frequencies are interpreted in terms of a model of receptor based on the idea that electron tunneling occurs between odor molecule and receptor and generates odor sensation if the energies of the electron states at the both sides are same. In general the ground state energies of the electron at the two sides are different but it can happen that the condition is satisfied for some excited state of electron of the acceptor so that odor perception is due to a tunneling to an excited state. The model requires the fusion of the odorant molecule to the receptor so that there is a close relationship with the standard theory assuming lock-and-key mechanism.
2. Callahan's theory
The finding conforms also with the old discovery of Callahan that the olfaction of insects is analogous to seeing at IR frequencies. This hypothesis explains among other things the finding that insects seem to love candles. See this:
Callahan, P. S. (1977). Moth and Candle: the Candle Flame as a Sexual Mimic of the Coded Infrared Wavelengths from a Moth Sex Scent. Applied Optics. 16(12) 3089-3097.
If I have understood Callahan's theory correctly, the IR photons emitted by the odorant would induce transitions of electrons or Cooper pairs of the odor receptor. This would allow "radiative smelling" without a direct contact between odor molecules and olfactory receptors and at the first glance this seems like an unrealistic prediction. However, since the average power of radiation is proportional to 1/r2, where r is the distance between the receptor and molecule, radiative smelling would in practice be limited to rather short distances unless the radiation is guided. Maybe this could be tested experimentally by using coherent beam of IR light as a candidate for an artificial odorant.
3. TGD based theory
In TGD inspired theory of qualia one must distinguish between the sensory input inducing the quale and its secondary representation in terms of Josephson and cyclotron frequencies.
For the general theory of qualia including also a model of odor perception see the chapter General Theory of Qualia.
HIV Nobelist L. Montagnier's group has published two "../articles/ challenging the standard views about genetic code and providing strong support for the notion of water memory. Already the results of the first article suggested implicitly the existence of a new kind nano-scale representation of genetic code and the the recent article makes this claim explicitly. The model for the findings was based on the notion of magnetic bodies assignable with molecules and with water structures representing biologically relevant aspects of molecules in terms of cyclotron frequencies. The model involves also the realization of genetic code using electromagnetic field patterns and as dark nucleon strings and led to a proposal that the analogs of trancription and translation are realized for the dark variants of DNA,RNA, tRNa, and aminoacids represented in terms of dark nucleon strings. Also analogs of these processes between ordinary and dark variants of the biomolecules in question were proposed. This would make possible R&D like controlled evolution based on experimentation using dark representations of biomolecules.
The recent findings of Montagnier's group allow a more detailed formulation of the model and suggest a general mechanism for generalized transcription and translation processes based on reconnection of magnetic flux tubes connecting the molecules involved. A new element in the model is the role of ordered water and hydrogen bonds in the formation of water memories. These representation would result from the dropping of the magnetic bodies of molecules as the hydrogen bonds connecting the molecule to water molecules of the ordered water layer around it are split during the mechanical agitation. A similar process occurs quite generally when external energy feed excites the resting state of cell and induces protein folding and its reversal and the formation of protein aggregates. The necessity of repeated dilution and mechanical agitation could be understood if it provides metabolic energy for the replication of the magnetic bodies and gives rise to a series of "environmental catastrophes" inducing evolutionary leaps increasing the typical value of Planck constant associated with the magnetic bodies until the energy E= hf of 7 Hz dark photons becomes larger than thermal energy at room temperature.
For a detailed description of the model see the chapter Homeopathy in Many-Sheeted Space-Time.