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Bio-Systems as Conscious Holograms

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Year 2016

Taos hum as remote metabolism?

I have been considering an explanation of taos hum. Hints come from the observations that it begins after sunset as microwave presumably "static" generated by living organisms, and also from the phenomenon of microwave hearing: microwaves modulated with sound frequencies can be heard. Taos hum is claimed to correlate also with the acoustics of the building which suggests that it is a real phenomenon. Taos hum can be an (extremely) unpleasant experience. It sounds like an idling diesel engine. I know this from personal experience since I suffered from taos hum when I was younger (as I realized while developing a model for it!).

Could the microwaves transformed inbody to sounds or directly to nerve pulse patterns generating sensation of hearing be the reason for taos hum.

Why taos hum? Could animals use microwaves for "seeing" in absence of sunlight? But for what purpose plants would use microwaves? Could organisms send negative energy heff=n×h microwaves to environment and suck metabolic energy quanta with energy around .5 eV in this manner? Remote metabolism! Or maybe time reversed photosynthesis in dark! Biophotons indeed have energy spectrum in visible and UV as also sunlight does. This would require non-standard value of Planck constant.

This hypothesis would explain why the microwaves causing taos hum not hum are not observed directly. And if something is sucking metabolic energy from you, it is would be rather natural to experience very unpleasant feelings and try to find a place to hide as many sufferers of taos hum try to do!

For background see the chapter Bio-Systems as Conscious Holograms .

Brain metabolic DNA as an indication for genomic R&D based on dark DNA

I learned a lot in SSE-2016 conference. For instance, the notion of brain metabolic DNA (BMD) (see this) about which Antonio Giuditta had a nice poster was a new notion to me. TGD suggests active R&D like process driving genetic evolution and I have been a little bit disappointed since epigenetics is too passive in this respect. BMD would fit with my crazy speculations.

I try to summarize my first impressions about brain metabolic DNA.

  1. The profiles for both the repetitive and non-repetitive fractions differ from native DNA and for learning rats differs from those for control rats. Stress and learning situations induce this process and it occurs at least in brain.
  2. Wikipedia lists DNA replication and repair as the basic mechanisms of DNA synthesis. They would yield essentially a copy of native DNA. Does this mean that there could be some new mechanism responsible for the synthesis?
I have worked with two new new mechanisms of DNA synthesis emerging from TGD based new biophysics for which MB consisting of magnetic flux tubes carrying dark matter identified as large heff=n× h, n integer, phases is crucial.

These new phases of ordinary particles identifiable as dark matter would make possible macroscopic quantum coherence in much longer length scales than usually for large values of n since Compton length is proportional to heff. Large heff would make living matter a macroscopic quantum system. Large heff phases would be created at quantum criticality: the large values of Compton lengths would be correlates for long range correlations and quantum fuctuations. Quantum criticality is indeed emerging as a basic aspect of living matter.

  1. The experiments of Montagnier et al suggest that remote replication of DNA involving sending information about the template strand using light is possible. Peter Gariaev's group has made similar claims much earlier. Together with Peter Gariaev we published an article in Huping Hu's journal DNADJ about remote replication of DNA before the work of Montagnier (the article is also at homepage).

    The idea is that what I call dark photons (see below) carry genetic information. Dark photons would have energies in visible and UV range and could transform to biophotons with same energy. This would make them bio-active since biomolecules have transition energy spectrum in this range. The challenge is to understand the details of the information transfer mechanism. What would be needed would be regeneration DNA or dark DNA at the receiver end using the information. How this precisely occurs is of course only a subject of speculation.

    This mechanism as such would not however apply to this situation since the ordinary DNA could not serve as template.

  2. The notion of dark DNA is one of the key new physics notions of TGD and the transcription of dark DNA to ordinary DNA could be involved with generation BMD.
    1. The proposal is that genetic code has realization at the level of "dark" nuclear physics (see this). Dark DNA would correspond to dark proton sequences having interpretation as dark nuclei. Darkness would mean that the protons are in phase with non-standard value of Planck constant given by heff=n× h, n integer which can vary. The value of heff learns as a kind of intelligence quotient since it tells the scales of long term memory and intentional action and also the size scale of the system). It could serve as intelligence quotient of cells and pyramidal neurons generating EEG as Josephson radiation (frequency of Josephson radiation is f= 2eV/heff in terms of membrane potential V) could be the neuronal intellectuals).
    2. Dark DNA could accompany ordinary DNA as parallel dark proton strands. The negative phosphate charge would neutralize the positive charge of dark protons so that the system would be classically stable. The ability to pair in this manner would quite generally select preferred biomolecules as winners in evolution.
    3. For instance, the transcription of dark DNA to ordinary DNA is possible: dark DNA would serve as template for the ordinary DNA codons. Dark variants of biomolecules could make possible R&D in living matter. Evolution would not be by random mutations plus selection but intentional and more analogous to occurring in R&D laboratories.
    4. If dark DNA strands were used as tempates in the generation of BMD one could understand why learning BMD differs from the native DNA. Primarily the dark DNA would be modified as a response to learning and the modification would be transcribed to that of ordinary DNA.

      The interesting question is whether these changes could also be transferred to the germ cells say by sending the information in form of light and generating copies of newly generated DNA portions replacing the original ones.

See the chapter Homeopathy in many-sheeted space-time. See also the article Comments about the representations in SSE-2016 conference about consciousness, biology, and paranormal phenomena .

Comparing TGD view about quantum biology with McFadden's views

McFadden has very original view about quantum biology: I have written about his work for the first time for years ago, much before the emergence of ZEO, of the recent view about self as generalized Zeno effect, and of the understanding the role of magnetic body containing dark matter (see this). The pleasant surprise was that I now understand McFadden's views much better from TGD viewpoint.

  1. McFadden sees decoherence as crucial in biological evolution: here TGD view is diametric opposite although decoherence is a basic phenomenon also in TGD.
  2. McFadden assumes quantum superpositions of different DNAs. To me this looks an unrealistic assumption in the framework of PEO. In ZEO it is quite possible option.
  3. McFadden emphasizes the importance of Zeno effect (in PEO). In TGD the ZEO variant of Zeno effect is central for TGD inspired theory of consciousness and quantum biology. Mc Fadden suggests that quantum effects and Zeno effect are central in bio-catalysis: the repeated measurement keeping reactants in the same position can lead to an increase of reaction rate by factors of order billion. McFadden describe enzymes as quantum mousetraps catching the reactants and forcing them to stay in same position. The above description for how catalysis catches the reactants using U-shaped flux tube conforms with mousetrap picture.

    McFadden discusses the action of enzymes in a nice manner and his view conforms with TGD view. In ZEO the system formed by catalyst plus reactants could be described as a negentropically entangled sub-self, and self indeed corresponds to a generalized Zeno effect. The reactions can proceed in shorter scales although the situation is fixed in longer scales (hierarchy of CDs): this would increase the length of the period of time during which reactions can proceed and lead to catalytic effect. Zeno effect in ZEO plus hierarchies of selves and CDs would be essentially for the local aspects of enzyme action.

  4. Protons associated with hydrogen bonds and electronic Cooper pairs play a universal role in McFadden's view and the localization of proton in quantum measurement of its position to hydrogen bond is the key step of enzyme catalysis. Also TGD dark protons at magnetic flux tubes giving rise to dark nuclear strings play a key role. For instance, McFadden models enzyme catalysis as injection of proton to a very special hydrogen bond of substrate. In TGD one has dark protons at magnetic flux tubes and their injection to a properly chosen hydrogen bond and transformation to ordinary proton is crucial for the catalysis. Typical places for reactions to occur are C=O type bonds, where the transition to C-OH can occur and would involve transformation of dark proton to ordinary proton. The transformation of dark proton to ordinary one or vice versa in hydrogen bonds would serve as a biological quantum switch allowing magnetic body to control biochemistry very effectively.

    What about electronic Cooper pairs assumed also by McFadden? They would flow along the flux tube pairs. Can Cooper pairs of electrons and dark protons reside at same flux tubes? In principle this is possible although I have considered the possibility that particles with different masses (cyclotron frequencies) reside at different flux tubes. For hgr =heff this would make possible both frequency and energy resonance for cyclotron transitions.

McFadden has proposed quantum superposition for ordinary codons: This does not seem to make sense in PEO since the chemistries of codons are different) but could make sense in ZEO. In TGD one could indeed imagine quantum entanglement (necessary negentropic in p-adic degrees of freedom) between dark codons. This NE could be either between additional degrees of freedom or between spin degrees of freedom determining the dark codons. In the latter case complete correlation between dark and ordinary DNA codons would imply also the superposition of their tensor products with ordinary codons.

The NE between dark codons could also have a useful function: it could determine physically gene as a union of disjoint mutually entangled portions of DNA. Genes are known to be highly dynamical units, and after pre-transcription splicing selects the portions of the transcript translated to protein. The codons in the complement of the real transcript are called introns and are spliced out from mRNA after the pre-transcription (see this).

What could be the physical criterion telling whether a given codon belongs to exonic or intronic portion of DNA? A possible criterion distinguish between exons and introns is that exons have NE between themselves and introns have no entanglement with exons (also exons could have NE between themselves). Introns would not be useless trash since the division into exonic and exonic region would be dynamical. The interpretation in terms of TGD inspired theory of consciousness is that exons correspond to single self.

An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Homeopathy in Many-Sheeted Space-time and in the article About physical representations of genetic code in terms of dark nuclear strings.

Is bio-catalysis a shadow of dark bio-catalysis based on generalization of genetic code?

Protein catalysis and reaction pathways look extremely complex (see this) as compared to replication, transcription, translation, and DNA repair. Could simplicity emerge if biomolecules are identified as chemical shadows of objects formed from dark nuclear strings consisting of dark nucleon triplets and their dynamics is shadow of dark stringy dynamics very much analogous to text processing?

What if bio-catalysis is induced by dark catalysis based on reconnection as recognition mechanism? What if contractions and expansions of U-shaped flux tubes by heff increasing phase transitions take that reactants find each other and change conformations as in the case of opening of DNA double strand? What if codes allowing only the dark nucleons with same dark nuclear spin and flux tubes spin to be connected by a pair of flux tubes?

This speculation might make sense! The recognition of reactants is one part of catalytic action. It has been found in vitro RNA selection experiments that RNA sequences are produced having high frequency for the codons which code for the amino-acid that these RNA molecules recognize (this). This is just what the proposal predicts!

Genetic codes DNA to RNA as 64→ 64 map, RNA to tRNA as 64→ 40, tRNA to amino-acids with 40→ 20 map are certainly not enough. One can however consider also additional codes allowed by projections of (4⊕ 21⊕ 22) ⊗ (5⊕ 3 (⊕ 1)) to lower-dimensional sub-spaces defined by projections preserving spins. One could also visualize bio-molecules as collections of pieces of text attaching to each other along conjugate texts. The properties of catalysts and reactants would also depend by what texts are "visible" to the catalysts. Could the most important biomolecules participating biochemical reactions (proteins, nucleic acids, carbohydrates, lipids, primary and secondary metabolites, and natural products, see this) have dark counterparts in these sub-spaces.

The selection of bio-active molecules is one of the big mysteries of biology. The model for the chemical pathway leading to the selection of purines as nucleotides (see this) assumes that the predecessor of purine molecule can bind to dark proton without transforming it to ordinary proton. A possible explanation is that the binding energy of the resulting bound state is higher for dark proton than the ordinary one. Minimization of the bound state energy could be a completely general criterion dictating which bio-active molecules can pair with dark protons. The selection of bio-active molecules would not be random after all although it looks so. The proposal for DNA-nuclear/cell membrane as topological quantum computer with quantum computations coded by the braiding of magnetic flux tubes connecting nucleotides to the lipids wlead to the idea that flux tubes being at O=-bonds (see this).

An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Homeopathy in Many-Sheeted Space-time and in the article About physical representations of genetic code in terms of dark nuclear strings.

Are sound-like bubbles whizzing around in DNA are essential to life?

I got a link to a very interesting article about sound waves in DNA (see this). The article tells about THz de-localized modes claimed to propagate forth and back along DNA double strand somewhat like bullets. These modes involve collective motion of many atoms. These modes are interpreted as a change in the stiffness of the DNA double strand leading to the splitting of hydrogen bonds in turn leading to a splitting into single strands. The resulting gap is known as transcriptional bubble propagating along double strand is the outcome. I do not how sound the interpretation as sound wave is.

It has been proposed that sound waves along DNA give rise to the bubble. The local physical properties of DNA double strand such as helical structure and elasticity affect the propagation of the waves. Specific local sequences are proposed to favor a resonance with low frequency vibrational modes, promoting the temperary splitting of the DNA double strand. Inside the bubble the bases are exposed to the surrounding solvent, which has two effects.

Bubbles expose the nucleic acid to reactions of the bases with mutagens in the environment whereas so called molecular intercalators may insert themselves between the strands of DNA. On the other hand, bubbles allow proteins known as helicases to attach to DNA to stabilize the bubble, followed by the splitting the strands to start the transcription and replication process. The splitting would occur at certain portions of DNA double strand. For this reason, it is believed that DNA directs its own transcription.

The problem is that the strong interactions with the surrounding water are expected to damp the sound wave very rapidly. Authors study experimentally the situation and report that propagating bubbles indeed exist for frequencies in few THz region. Therefore the damping deo not seem to be effective. How this is possible? As an innocent layman I also wonder how this kind of mechanism can be selective: it would seem that the bullet like sound wave initiates transcription at many positions along DNA. The transcription should be localized to a region assignable to single gene. What could guarantee this?

Can TGD say anything interesting about the mechanism behind transcription and replication?

  1. In TGD magnetic body controls and coordinates the dynamics. The strongest hypothesis is that basic biochemical process are induced by those for dark variants of basic bio-molecules (dark variants of DNA, enzymes,...). The belief that DNA directs its own transcription translates to the statement that the dark DNA consisting most plausibly from sequences of dark proton triplets ppp at dark magnetic flux tubes controls the transcription: the transcription/replication at the level of dark DNA induces that at the level of ordinary DNA.
  2. If the dark DNA codons represented as dark proton triplets (ppp) are connected by 3 flux tube pairs, the reverse of the reconnection should occur and transform flux tube pairs to two U-shaped flux tubes assignable to the two dark DNA strands. Dark proton sequences have positive charge +3e per dark codon giving rise to a repulsive Coulomb force between them. There would be also an attractive force due to magnetic tension of the flux tubes. These two forces would compensate each other in equilibrium (there also the classical forces due to the negatively charged phosphates associated with nucleotides but these would not be so important).

    If the flux tube pairs are split, the stabilizing magnetic force however vanishes and the dark flux tubes repel each other and force the negatively charged DNA strands to follow so that also ordinary DNA strand splits and bubble is formed. The primary wave could therefore be the splitting of the flux tube pairs: whether one can call it as a sound wave is not clear to me. Perhaps the induced propagating splitting of ordinary DNA double strand could be regarded as an analog of sound wave.

    The splitting of flux tube pairs for a segment of DNA would induces a further splitting of flux tubes since repulsive Coulomb force tends to drive the flux tubes further away. The process could be restricted to DNA if the "upper" end of the split DNA region has some dark DNA codons which are not connected by flux tubes pairs. This model reason why for dark proton sequences.

  3. This model does not yet explain how the propagating splitting wave is initiated. Could a quantum phase transition increasing the value of heff associated with the flux tube pairs occur for some minimal portion of dark DNA "below the region associated with gene and lead to the propagating wave induced by the above classical mechanism? That the wave propagates in one direction only could be due to chirality of DNA double helix.
An interesting question is how the RNA world vision relates to this general picture.
  1. There are strong conditions on the predecessor of DNA and RNA satisfies many of them: reverse transcription to DNA making possible transition to DNA dominated era is possible. Double stranded RNA exists in cells and makes possible RNA genome: this would however suggest that cell membrane came first. RNA is a catalyst. RNA has ability to conjugate an amino-acid to the 3' end of RNA and RNA catalyzes peptide bond formation essential for translation. RNA can self-replicate but only relatively short sequences are produced.
  2. TGD picture allows to understand why only short sequences of RNA are obtained in replication. If the replication occurs at the level of dark ppn sequences as it would occur for DNA in TGD framework, long RNA sequences might be difficult to produce because of the stopping of the propagation of the primary wave splitting the flux tube pairs. This could be due to the neuron pairs to which there is associated no Coulomb repulsion essential for splitting.
  3. In TGD framework RNA need not be the predecessor of DNA since the evolution would occur at the level of dark nucleon strings and DNA as the dark proton string is the simpest dark nucleon string and might have emerged first. Dark nuclear strings would have served as templates and biomolecules would have emerged naturally via the transcription of their dark counterparts to corresponding bio-polymers.

An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Homeopathy in Many-Sheeted Space-time and in the article About physical representations of genetic code in terms of dark nuclear strings.

Could dark DNA, RNA, tRNA and amino-acids correspond to different charge states of codons?

If dark codons correspond to dark nucleon triplets as assumed in the following considerations there are 4 basic types of dark nucleon triplets: ppp,ppn, pnn, nnn. Also dark nucleons could represent codons as uuu,uud,udd,ddd: the following discussion generalizes as such also to this case. If strong isospin/em charge decouples from spin the spin content is same independently of the nucleon content. One can consider the possibility of charge neuralization by the charges assignable to color flux tubes but this is not necessarily. In any case, one would have 4 types of nucleon triplets depending on the values of total charges.

Could different dark nucleon total charges correspond to DNA,RNA, tRNA and amino-acids? Already the group representation content - perhaps correlating with quark charges - could allow to distinguish between DNA, RNA, tRNA, and amino-acids. For amino-acids one would have only 4× 5 and ordinary statistics and color singlets. For DNA and RNA one would have full multiplet also color non-singlets and for tRNA one could consider (4⊕ 21⊕ 22)× 5 containing 40 states. 31 is the minimum number of tRNAs for the realization of the genetic code. The number of tRNA molecules is known to be between 30-40 in bacterial cells. The number is larger in animal cells but this could be due to different chemical representations of dark tRNA codons.

If the net charge of dark codon distinguishes between DNA,RNA, tRNA, and amino-acid sequences, the natural hypothesis to be tested is that dark ppp, ppn, pnn, and nnn sequences are accompanied by DNA,RNA, tRNA, and amino-acid sequences. The dark beta decays of dark protons proposed to play essential role in the model of cold fusion could transform dark protons to dark neurons. Peptide backbones are neutral so that dark nnn sequence could be also absent but the dark nnn option is more natural if the general vision is accepted.

Is this picture consistent with what is known about charges of amino-acids DNA,RNA, tRNA, and amino-acids?

  1. DNA strand has one negative charge per nucleotide. Also RNA molecule has high negative charge. This conforms with the idea that dark nucleons accompany both DNA and RNA. DNA codons could be accompanied by dark ppp implying charge neutralization in some scale and RNA codons by dark ppn. The density of negative charge for RNA would be 2/3 for that for DNA.
  2. Arg, His, and Lys have positively charged side chains and Asp,Glu negative side chains (see (see this). The charge state of amino-acid is sensitive to the pH value of solution and its conformation is sensitive to the counter ions present. Total charge for amino-acid in peptide however vanishes unless it is associated with the side chain: as in the case of DNA and RNA it is the backbone whose charge is expected to matter.
  3. Amino-acid has central C atom to which side chain, NH2, H and COOH are attached. For free amino-acids in solution water solution NH2→ NH3+ tends to occur pH=2.2 by receiving possibly dark proton whereas COOH tends to become negatively charged above pH= 9.4 by donating proton, which could become dark. In peptide OH attach to C and one H attached to N are replaced with peptide bond. In the pH range 2.2-9.4 amino-acid is zwitterion for which both COOH is negatively charged and NH2 is replaced with NH3+ so that the net charge vanishes. The simplest interpretation is that the ordinary proton from negatively ionized COOH attaches to NH2 - maybe via intermediate dark proton state.
  4. The backbones of peptide chains are neutral. This conforms with the idea that dark amino-acid sequence consists of dark neutron triplets. Also free amino-acids would be accompanied by dark neutron triplets. If the statistics is ordinary only 4 dark nnn states are possible as also 5 dark color flux tube spin states.
  5. tRNA could involve dark pnn triplet associated with the codon. An attractive idea is secondary genetic code assigning RNA codons to tRNA-amino-acid complex and projecting 8⊗ (5⊕ 3) containing 64 dark RNA spin states to 8⊗ 5 containing 40 dark tRNA spin states with same total nucleon and flux tube spins. Dark tRNA codons would in turn be attached to dark amino-acids by a tertiary genetic code projecting spin states 8⊗ 5 to 4⊗ 5 by spin projection. In the transcription dark tRNA would attach to dark mRNA inducing attachment of dark amino-acid to the growing amino-acid sequence and tRNA having only dark tRNA codon would be left. The free amino-acids in the water solution would be mostly charged zwitterions in the pH range 2.2-9.4 and the negative charge of COO- would be help in the attachement of the free amino-acid to the dark proton of tRNA codon. Therefore also the chemistry of free amino-acids would be important.

    An interesting question is why pnn triplets for tRNA would only 5 in flux tube degrees of freedom entire 8 in nucleon degrees of freedom. For RNA consisting of ppn triplets also 3 would be possible. What distinguishes between ppn and pnn?

    An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Homeopathy in Many-Sheeted Space-time and in the article About physical representations of genetic code in terms of dark nuclear strings.

About physical representations of genetic code in terms of dark nuclear strings

The standard view about evolution as a random process suggests that genetic code is pure accident. My own view is that something so fundamental as life cannot be based on pure randomness. TGD has led to several proposals for genetic code, its emergence, and various realizations based on purely mathematical considerations or inspired by physical ideas. One can argue that genetic code is realized in several manners just like bits can be represented in very many manners. Two especially interesting proposals have emerged. The first one is based on geometric model of music harmony involving icosahedral and tetrahedral geometries. Second one having two variants is based on dark nuclear strings. Both models predict correctly the numbers of DNA codons coding for a given amino-acid.

An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Homeopathy in Many-Sheeted Space-time and in the article About physical representations of genetic code in terms of dark nuclear strings.

Gut cells without mitochondria can survive: proof for the notion of remote metabolism?

Gut cells can survive without mitochondria (see this)! There are many other strange findings. Visible and IR light energize human skin cells transferring energy for the cells- the analog of photosynthesis. Some spiritual groups and also traditionally the people called saints are reported to survive by using only sunlight as their source of metabolic energy. NASA has studied sleigh dogs able to run for days without eating and showing no signs of getting tired.

Could photosynthesis work also in animal mitochondrial cells? The basic mechanism could be essentially the same: electron transfer chain providing energy to pump protons through cell membrane against potential gradient. This is the key step of both photosynthesis and cellular respiration. After that protons flow spontaneously back through ATP synthase and liberate energy to build ATP from ADP. This is like power plant. In plants solar photons provide the energy for electrons. In the animal cells dark photons with large heff=n×h (transforming now and then to biophotons) could do it. In the case of IR lmetabolism electrons could send to the energy source dark negative energy IR photons, which decay to ordinary IR photons. This would be an active variant of metabolism and time reversal of the usual mechanism: I have called it quantum credit card mechanism or remote metabolism. I wrote about this a blog posting some time ago.

Now even mitochondria are missing! Could remote metabolism work also without mitochondria? ADP→ ATP transformation should occur since ATP is the universal energy currency. Could it take place as remote metabolism by sending negative energy photons to the cells having the mitochondria. The electron transfer chain is preceded by Krebs cycle extracting the energy from nutriens: could the absorption of negative energy photons induce the decay of nutrient without transfer of energy to electron chain of the mitochondria. The hungry gut cell without mitochondria would be allowed to eat in the table of the luckier ones. Again one quantum objection against vulgar darwinism. This would be like kicking laser from population reversed state to ground state by phase conjugate negative energy irradiation.

For background see the chapter Macroscopic quantum coherence and metabolism as different sides of the same coin or the article Pollack's mechanism and photosynthesis.

Pollack's mechanism and photosynthesis

An obvious idea is that Pollack's mechanism is the predecessor of photosynthesis. The question is therefore whether photosynthesis could involve the formation of exclusion zones (EZs) by the analog of Pollack's mechanism leading to charge separation taking place also in photosynthesis. Pollack's mechanism creates in presence of radiation and water bounded by a gel at the boundary of water and gel an EZ, which is a layer negatively charged water with effective stoichiometry H1.5O consisting of layers with hexagonal structure. The TGD inspired proposal is that hydrogen bonded pairs of H2O molecules are formed and that each of them loses one proton as dark proton at magnetic flux tubes outside EZ. The notion of many-sheeted space-time and topological ield quantization are essential elements of the proposal. Same phenomenon could be caused also by irradiation by sun light.

The light dependent step 2H2O → 4H+ +4e- + O2 of photosynthesis pumps protons through thylakoid mebranes (see the illustration). The electrons excited by photons of sunlight are transferred along electron transfer chain and lose energy used to pump protons through the thylakoid membrane and being thus transferred from stroma (outside of the membrane) to grana (inside of the membrane) against electric gradient. ADP transforms to ATP as these protons return to back through ATP synthase. This step is repeated again and again.

Could dark protons created by the analog of Pollack's mechanism be involved with photosynthesis as its fundamental step already present in its primordial variant? In what step the protons are transformed to dark protons by this mechanism?

  1. The model of cell membrane leads to a proposal that pumps and channels quite generally are dark magnetic flux tubes and protons (and also other ions) are transferred through them as dark protons (dark ions). This would imply almost dissipationless transfer.
  2. The protons are pumped as dark protons through the thylakoid membrane along dark magnetic flux tubes serving as pumps using the energy provided by electrons flowing down in the electron chain. The dark protons return from grana through ATPase as dark protons as ATP is generated and transform with some rate back to ordinary protons in stroma. Otherwise the fraction of dark protons would steadily increase.
  3. This leaves two options under consideration. Already the step 2H2O → 4H+ +4e- + O2 step 2H2O → 4H+ +4e- + O2 creates dark protons by a generalization of Pollack's mechanism or this step creates ordinary protons transformed by Pollack's mechanism to dark protons as they are transferred to dark magnetic flux tubes serving as pumps. The first option looks more plausible.
What is interesting is the electron transfer chain is involved also with the cellular breathing. There are various light therapies using red or IR light, and they seem to provide basically metabolic energy. Cells would act like plant cells and the analog of photosynthesis could be in question. This would explain the claims that the members of some religious cults can practically live utilizing only sunlight. I have actually proposed that analog of photosynthesis storing the energy by ADP+Pi→ ATP type process using standard machinery could be actually involved and transfer the energy of IR light to metabolic energy further distributed by ATP.

The metabolic machinery for cellular breathing contains so called oxidative phosphorylation (OP) as a basic step: OP adds to ADP a phosphate giving metabolic currency ATP. ATP in turn distributes the metabolic energy further. OP uses electron transport chain to transfer metabolic energy from NADH by NADH → NAD+ H+ +2e-. The electrons go through the electron transport chain as in photosynthesis and transfer protons outside the mitochondrial membrane very much like in photosynthesis. The protons return through ATP-synthase and induce ADP+Pi → ATP.

The metabolic energy must come from somewhere and OP indeed follows Krebs cycle in which the energy is extracted from nutrients and given to the NADP molecule. The photon energy could be feeded directly to OP electron transfer chain just as photon energy is transferred to this chain in photosynthesis. The presence of electron transfer chain is necessary and one must feed the electrons and protons to this chain somehow.

  1. Could the analog of photosynthetic reaction 2H2O → 4H+ +4e- + O2 with visible photons replaced with IR photons produce dark protons? Whether this is energetically possible and whether the electrons have high enough energies to drive the dark protons through the membrane is far from clear. One can of course imagine, that the number of pumped protons per electron is lower than usually.
  2. A mechanism that I have called quantum credit card and remote metabolism looks more plausible. The splitting 2H2O → 4H+ +4e- + O2 could occur - not by absorption of positive energy photon but by emission of negative dark IR photon with the energy of visible photon. Cell would actively suck metabolic energy from IR light source. The emitted dark negative energy IR photon would decay to ordinary IR photons in reverse time direction, which would look like fusion in standard time direction and is thermodynamically non-favoured. ZEO predicting kind of syntropic processes to occur in living matter would be an essential prerequisite.

At deeper level metabolic energy might correspond to negentropic entanglement and thus information. Information could be the basic metabolic currency.

For background see the chapter Macroscopic quantum coherence and quantum metabolism as different sides of the same coin: Part I.

Confirmation of Santilli's detection of antimatter galaxies via a telescope with concave lenses: really?

I encountered in Facebook a really bizarre sounding title reading The incredible pictures scientists say prove invisible alien entities ARE here on Earth (see this) and just for curiosity decided to add one click to the web page in question (means higher income from ads) knowing that this is just what they want me to do! The story involves aliens spying us so that that the street credibility index of the story reduced zero. The tool to detect the spies would be Santilli's telescope using concave lenses. Santilli, who is familiar to me, also talks about two types of invisible terrestrials detected by his telescope. It would be easy to ridicule but let us be patient.

An earlier article with title Apparent detection of antimatter galaxies via a telescope with convex lenses (see this) reports a detection of antimatter galaxies. There is also an article with title "Confirmation of Santilli’s detection of antimatter galaxies via a telescope with concave lenses" published in American Journal of Modern Physics claiming an independent observation of antimatter galaxies, antimater asteroids, and antimatter cosmic rays by Santilli's telescope (see this). These articles say nothing about aliens spying us.

Since I suffer from a pathological trait of taking half-seriously even the weirdest stories, I decided to learn what Santilli's telescope using concave lenses might mean. Ordinary telescope uses convex lenses (see this). The light rays coming from the other side converge to form a picture of the source. For concave lense the light rays coming from the other side diverge so that concave lense does not sound like a good idea for detecting light coming from distant objects.

It is however claimed that Santilli's telescope detects light sources in darkness. This is only possible if the index of refraction n=c/v characterizing the medium via the ratio of light velocity in vacuum to the velocity of light in medium changes sign. From Snell's law n1sin(θ1)= n2sin(θ2) follow the basic facts about lenses (see this). It is possible to construct lenses which have negative index of refraction so that concave lense behaves like convex one. Presumably this is not be the case now since according to the existing theory, ordinary light would have the negative index of reflection (unless it is somehow transformed when arriving to the lense).

Concerning the theoretical arguments Santilli makes several claims, which do not make sense to me.

  1. The photons are identified as antimatter photons assumed to have negative energies. These antimatter photons are assumed to have repulsive gravitational interaction with ordinary matter. The claim is that this implies negative index of refraction. This does not make sense since gravitational interaction is quite too weak to cause refraction. Electromagnetic interaction must be in question. Antimatter photons are claimed to propagate with superluminal speeds and arrive instantaneously from remote galaxies. The assumption is in dramatic conflict with what we know about antimatter.
  2. Refractive index is claimed to be a property of light. This does not make sense: refractive index characterizes medium. Its sign however changes when the energy of photon changes sign. From Snell's law the sign of refractive index must change sign as the light enters to the concave lense. This would require that Santilli's antimatter photons transform to ordinary photons.
These arguments are more than enough for dooming the claims of Santilli as pseudoscience but what if there is something in it? The experimental finding is so simple that if it is not an artefact of poor experimentation, some interesting - possibly new - physics could be involved. So let us looks the situation from different point of view forgetting the theory behind it and taking seriously the claimed observations. Could one explain the findings in TGD framework?

Zero energy ontology (ZEO) is one of the cornerstones of TGD and could indeed explain the claims of Santilli and colleagues. In ZEO zero energy states are pairs of positive and negative energy states at opposite light-like boundaries of causal diamonds (CD) forming a scale hierarchy. Zero energy states are counterparts of physical events in standard ontology.

  1. ZEO predicts that the arrow of time can have both directions. In ZEO based quantum measurement theory state function reductions occur at either boundary of CD. Conscious entities correspond to sequences of reductions leaving everything unaffected at the boundary (Zeno effect) but changing the situation at the opposite boundary, in particular increasing its distance from the fixed boundary, which gives rise to the experienced flow of time. The first reduction to opposite boundary replaces the zero energy state with time reversed one. This can happen also for photons.
  2. The particles with non-standard arrow of time are not antimatter (I have considered also this possibility since it might explain the experimental absence of antimatter) but propagate in reverse time direction and have negative energies. There is a considerable evidence for this notion. Phase conjugate laser beams known to obey second law in reverse time direction would be one example. There are also old observations of Akimov and Kozyrev claiming that the instrument of Akimov gives three images of distant astrophysical objects: one would be from past, one from recent, and one from future. I do not know about the construction of Kozyrev's instrument but one can ask whether it involved concave lenses. Also the notion of syntropy introduced by the Italian physicists Fantappie conforms with this picture. In biology syntropy is in central role since in biology time reversed radiation would play a key role.
  3. Since the sign of the energy is negative for phase conjugate photons, their refractive index is negative. n2 for concave lense and n1 for the medium behind lense must have opposite signs to explain the claims of Santilli and colleagues. This happens if the incoming negative energy photons from the geometric future are transformed to positive energy photons photons at the surface of the lense. This process would represent time reflection of the incoming negative energy photons to ordinary positive energy photons propagating inside lense.
The claimed results could be an outcome of a bad experimentation. What however remains is a test of ZEO - or more precisely, the notion of time reversed photons - using telescopes with convex lenses. The implication would be possibility to see to the geometric future using telescopes with concave lenses! An entire geometric future of the Universe would be open to us! This possibility is a good enough reason for seeing the trouble of proving experimentally that Santilli is (and I am) wrong! Negative index of refraction as a function of frequency is a real phenomenon in condensed matter physics (see this), and one can of course ask whether also it involves the transformation of positive energy photons to negative energy photons.

For background see the chapter TGD About Concrete Realization of Remote Metabolism.

TGD and Teslaphoresis

The title of the popular article is "Reconfigured Tesla coil aligns, electrifies materials from a distance" tells about the effects involved. The research group is led by Paul Churukuri and there is also an abstract about the work in ADS Nano journal. This article contains also an excellent illustration allowing to understand both the Tesla coil and the magnetic and electric fields involved. The abstract of the paper provides a summary about the results.

This paper introduces Teslaphoresis, the directed motion and self-assembly of matter by a Tesla coil, and studies this electrokinetic phenomenon using single-walled carbon nanotubes (CNTs). Conventional directed self-assembly of matter using electric fields has been restricted to small scale structures, but with Teslaphoresis, we exceed this limitation by using the Tesla coil’s antenna to create a gradient high-voltage force field that projects into free space. CNTs placed within the Teslaphoretic (TEP) field polarize and self-assemble into wires that span from the nanoscale to the macroscale, the longest thus far being 15 cm. We show that the TEP field not only directs the self-assembly of long nanotube wires at remote distances (≥ 30 cm) but can also wirelessly power nanotube-based LED circuits. Furthermore, individualized CNTs self-organize to form long parallel arrays with high fidelity alignment to the TEP field. Thus, Teslaphoresis is effective for directed self-assembly from the bottom-up to the macroscale.

Concisely: what is found that single-walled carbon nanotubes (CNTs) polarise and self-assemble along the electric fields created by capacitor in much longer length scales than expected. Biological applications (involving linear molecules like microtubules) come in mind. CNTs tend to also move towards the capacitance of the secondary coil of the Tesla coil (TC).

It is interesting to understand the TGD counterparts for the Maxwellian em fields involved with Tesla coils and it is found that many-sheetedness of space-time is necessary to understand the standing waves also involved. The fact that massless extremals (MEs) can carry light-like currents is essential for modelling currents classically using many-sheeted space-time. The presence of magnetic monopole flux tubes distinguishing TGD from Maxwellian theory is suggestive and could explain why Teslaphoresis occurs in so long length scales and why it induces self-organization phenomena for CNTs. The situation can be seen as a special case of more general situation encountered in TGD based model of living matter.

For background see the chapter About Concrete Realization of Remote Metabolism or the article Teslaphoresis and TGD.

Qualia in Zero Energy Ontology

The TGD inspired theory of (qualia has evolved gradually to its recent form.

  1. The original vision was that qualia and and other aspects of consciousness experience are determined by the change of quantum state in the reduction: the increments of quantum numbers would determine qualia. I had not yet realized that repeated state function reduction (Zeno effect) realized in ZEO is central for consciousness. The objection was that qualia change randomly from reduction to reduction.
  2. Later I ended up with the vision that the rates for the changes of quantum numbers would determine qualia: this idea was realized in terms of sensory capacitor model in which qualia would correspond to kind of generalized di-electric breakdown feeding to subsystem responsible for quale quantum numbers characterizing the quale. The Occamistic objection is that the model brings in an additional element not present in quantum measurement theory.
  3. The view that emerged while writing the critics of IIT was that qualia correspond to the quantum numbers measured in the state function reduction. That in ZEO the qualia remain the same for the entire sequence of repeated state function reductions is not a problem since qualia are associated with sub-self (sub-CD), which can have lifetime of say about .1 seconds! Only the generalization of standard quantum measurement theory is needed to reduce the qualia to fundamental physics. This for instance supports the conjecture that visual colors correspond to QCD color quantum numbers. This makes sense in TGD framework predicting a scaled variants of QCD type physics even in cellular length scales.

    This view implies that the model of sensory receptor based on the generalization of di-electric breakdown is wrong as such since the rate for the transfer of the quantum numbers would not define the quale. A possible modification is that the analog of di-electric breakdown generates Bose-Einstein condensate and that the the quantum numbers for the BE condensate give rise to qualia assignable to sub-self.

For background see the chapter General Theory of Qualia or the article TGD Inspired Comments about Integrated Information Theory of Consciousness.

Direct evidence for dark DNA?!

This morning I learned in Sciencedaily about extremely interesting finding related to DNA. The finding is just what breakthrough discovery should be: it must be something impossible in the existing world view.

What has been found is that knock-out (removing parts of gene to prevent transcription to mRNA) and knock-down of gene (prevent protein translation) seem to have different consequences. Removing parts of gene need not have the expected effect at the level of proteins! Does this mean that somehow DNA as a whole can compensate the effects caused by knock-out but not those by knock-down?

Could this be explained by assuming that genome is a hologram as Gariaev et al have first suggested? Also TGD leads to a vision about living system as a conscious hologram. Small local changes of genes could be compensated. Somehow the entire genome would react like brain to a local brain damage: other regions of brain take the duties of the damaged region.

Could the idea about DNA double strand as nano-brain having left and right strands instead of hemispheres help here. Does DNA indeed act as a macroscopic quantum unit? The problem is that transcription is local rather than holistic process. Something very simple should lurk behind the compensation mechanism.

Could transcription transform dark DNA to dark mRNA?

Also the TGD based notion of dark DNA comes in mind (see this and this). Dark DNA consists of dark proton sequences for which states of single DNA proton correspond to those of DNA, mRNA, aminoacids, and tRNA. Dark DNA is one of the speculative ideas of TGD inspired quantum biology getting support from Pollack's findings . Ordinary biomolecules would only make their dark counterparts visible: dark biomolecules would serve as a template around which ordinary biomolecules such as DNA strands are formed in TGD Universe.

Although ordinary DNA is knocked out of ordinary gene, dark gene would still exist! If dark DNA actually serves as template for the transcription to mRNA, everything is still ok after knockout! Could it be that we do not understand even transcription correctly? Could it actually occur at the level of dark DNA and mRNA?! Dark mRNA would attach to dark DNA after which ordinary mRNA would attach to the dark mRNA. One step more!

Damaged DNA could still do its job! DNA transcription would would have very little to do with bio-chemistry! If this view about DNA transcription is correct, it would suggest a totally new manner to fix DNA damages. These damages could be actually at the level of dark DNA, and the challenge of dark genetic engineering would be to modify dark DNA to achieve a proper functioning.

Could dark genetics help to understand the non-uniqueness of the genetic code?

Also translation could be based on pairing of dark mRNA and dark tRNA. This suggests a fresh perspective to some strange and even ugly looking features of the genetic code. Are DNA and mRNA always paired with their dark variants? Do also amino-acids and anticodons of tRNA pair in this manner with their dark variants? Could the pairings at dark matter level be universal and determined by the pairing of dark amino-acids with the anticodons of dark RNA? Could the anomalies of the code be reduced to the non-uniqueness of the pairing of dark and ordinary variants of basic bio-molecules (pairings RNA--dark RNA, amino-acid-- dark amino-acid, and amino-acid--ordinary amino-acid in tRNA).

  1. There are several variants of the genetic code differing slightly from each other: correspondence between DNA/mRNA codons and amino-acids is not always the same. Could dark-dark pairings be universal? Could the variations in dark anticodon - anticodon pairing and dark amino-acid-amino-acid pairing in tRNA molecules explain the variations of the genetic code?
  2. For some variants of the genetic code a stop codon can code for amino-acid. The explanation at the level of tRNA seems to be the same as in standard framework. For the standard code the stop codons do not have tRNA representatives. If stop codon codes for amino-acids, the stop codon has tRNA representation. But how the mRNA knows that the stop codon is indeed stop codon if the tRNA associated with it is present in the same cell?

    Could it be that stop codon property is determined already at the level of DNA and mRNA? If the dark variant of genuine stop codon is missing in DNA and therefore also in mRNA the translation stops if it is induced from that at the level of dark mRNA. Could also the splicing of mRNA be due to the splitting of dark DNA and dark mRNA? If so genes would be separated from intronic portions of DNA in that they would pair with dark DNA. Could it be that the intronic regions do not pair with their dark counterparts. They would be specialized to topological quantum computations in the TGD inspired proposal.

    Start codon (usually AUG coding met) serves as a start codon defining the reading frame (there are 3 possible reading frames). Dark DNA would naturally begin from this codon.

  3. Also two additional amino-acids Pyl and Sec appear in Nature. Gariaev et al have proposed that the genetic code is context dependent so that the meaning of DNA codon is not always the same. This non-universality could be reduced to the non-uniqueness of dark amino-acid--amino-acid pairing in tRNA if genetic code is universal.

Could dark genetics help to understand wobble base pairing?

Wobble base pairing is second not-so-well understood phenomenon. In the standard variant of the code there are 61 mRNAs translated to amino-acids. The number of tRNA anticodons (formed by the pairs of amino-acid and RNA molecules) should be also 61 in order to have 1-1 pairing between tRNA and mRNA. The number of ordinary tRNAs is however smaller than 61 in the sense that the number of RNAs associated with them is smaller than 45. tRNA anticodons must be able to pair with several mRNA codons coding for given amino-acid. This is possible since tRNA anticodons can be chosen to be representative for the mRNA codons coding a given amino-acid in such that all mRNA codons coding for the same amino-acid pair with at least one tRNA anticodon.

  1. This looks somewhat confusing but is actually very simple: genetic code can be seen as a composite of two codes: first 64 DNAs/mRNAs to are coded to N<45 anticodons in tRNA, and then these N anticodons are coded to 20 amino-acids. One must select N anticodon representatives for the mRNAs in the 20 sets of mRNA codons coding for a given amino-acid such that each amino-acid has at least one anticodon representative. A large number of choices is possible and the wobble hypothesis of Crick pose reduce the number of options.
  2. The wobble hypothesis of Crick states that the nucleotide in the third codon position of RNA codon of tRNA has the needed non-unique base pairing: this is clear from the high symmetries of the third basis. There is exact U-C symmetry and approximate A-G symmetry with respect to the third basis of RNA codon (note that the conjugates of RNA codons are obtained by A↔U and C↔G permutations).
  3. The first two basis in the codon pair in 1-1 manner to the second and third basis of anticodon. The third basis of anticodon corresponds to the third letter of mRNA codon. If it is A or C the correspondence is assumed to be 1-to-1: this gives 32 tRNAs. If the first basis of anticodon is G or U the 2 mRNA basis can pair with it: they would be naturally A for G and C for U by symmetry. One would select A from A-G doublet and C from U-C double. This would give 16 anticodons: 48 anticodons altogether, which is however larger than 45. Furthermore, this would not give quite the correct code since A-G symmetry is not exact.

    Smaller number of tRNAs is however enough since the code has almost symmetry also with respect to A and C exchange not yet utilized. The trick is to replace in some cases the first basis of anticodon with Inosine I, which pairs with 3 mRNA basis. This replacement is possible only for those amino-acids for which the number of RNAs coding the amino-acid is 3 or larger (the amino-acids coded by 4 or 6 codons).

  4. It can be shown at least 32 different tRNAs are needed to realize genetic code by using wobble base pairing. Full A-C and G-U symmetry for the third basis of codon would give 16+16=32 codons. Could one think that tRNA somehow realizes this full symmetry?
How dark variants of could help to understand wobble base pairing? Suppose for a moment that the visible genetics be a shadow of the dark one and fails to represent it completely. Suppose the pairing of ordinary and dark variants of tRNA anticodons resp. amino-acids and that translation proceeds at the level of dark mRNA, dark anticodons, and dark amino-acids, and is made visible by its bio-chemical shadow. Could this allow to gain insights about wobble base pairing? Could the peculiarities of tRNA serve for some other - essentially bio-chemical - purposes?

The basic idea would be simple: chemistry does not determine the pairing but it occurs at the level of the dark mRNA codons and dark tRNA anticodons. There would be no need to reduce wobble phenomenon to biochemistry and the only assumption needed would be that chemistry does not prevent the natural dark pairing producing standard genetic code apart from the modifications implied by non-standard dark amino-acid--amino-acid pairing explaining for different codes and the possibility that stop codon can in some situation pair with dark mRNA.

One can consider two options.

  1. The number of dark tRNAs is 64 and the pairings between dark mRNA and dark anticodons and dark anticodons and dark amino-acids are 1-to-1 and only the pairing between dark RNA codons and anticodons in tRNA is many-to-1.
  2. The model of dark genetic code) suggests that there are 40 dark proton states, which could serve as dark analogs of tRNA. This number is larger than 32 needed to realize the genetic code as a composite code. I have cautiously suggested that the proposed universal code could map dark mRNA states of the same total spin (there is breaking of rotational symmetry to that around the axis of dark proton sequences) to dark tRNA/dark amino-acid states with the same total spin. The geometric realization would in terms of color flux tubes connecting the dark protons of corresponding dark proton sequences. Also in ordinary nuclei nucleons are proposed to be connected by color flux tubes so that they form nuclear strings and dark proton sequences would be essentially dark variants of nuclei.
One should understand the details of the dark mRNA--tRNA anticodon correspondence. One can also ask whether the dark genetic code and the code deduced from the geometric model for music harmony in terms of Platonic solids are mutually consistent. This model implies the decomposition of 60+4 DNA codons to 20+20+20+4 codons, where each "20" corresponds to one particular icosahedral Hamilton's cycle with characteristic icosahedral symmetries. "4" can be assigned to tetrahedron regarded either disjoint from icosahedron or glued to it along one of its faces. This allows to understand both the standard code and the code with two stop codons in which exotic amino-acids Pyl and Sec appear. One should understand the compositeness 64→ 40\→20 of the dark genetic code and and whether it relates to the icosatetrahedral realization of the code.

I have proposed that dark variants of transcription, translation, etc.. can occur and make possible kind of R&D laboratory so that organisms can test the consequences of variations of DNA. If ordinary translation and transcription are induced from their dark variants and if dark biomolecules could also appear as unpaired variants, these processes could occur as purely dark variants. Organisms could indeed do experimentation in the virtual world model of biology and pairing with ordinary bio-molecules would make things real.

For background see the chapter Homeopathy in Many-Sheeted Space-time

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