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Magnetospheric Consciousness

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Year 2015

Do neurons have their personal genomes?

Genetics is experiencing a revolution as the information technology has made possible new research methods and old dogmas must be given up. Before continuing, thanks for Ulla for giving links (see this and this) explaining the results of the article discussed in more detail: this led to a correction of some misunderstandings. See also this for a background.

It has been discovered that brain cells have a mosaic like distribution of genomes (see this, this, and this). In standard framework this mosaic should be created by random mutations.

The mechanism of mutation is reported to involve transcription rather than DNA replication. The mutation would take place for DNA when its is copied to RNA after opening of the DNA double strand. The mutations would have occurred during the period when neurons replicate and the mutation history can be read by studying the distributions of changes in the genome.

This brings in mind the finding that "knockout", that is removing a part of gene does not affect transcription (see the earlier blog posting). This suggests that the dark DNA is not changed in these modifications and mRNA is determined by the dark DNA, which would serve as a template for transcription rather than ordinary DNA. If this were the case also for neurons, the mutations of neuronal genes should not affect the gene transcription at all, and there would be no negative (or positive) effects on brain function. This seems too conservative. The mutations should have some rmore active role.

One can consider also different interpretation. The mutations of DNA could be induced by the dark DNA. As dark DNA changes, ordinary DNA associated with it is forced to change too - sooner or later. Especially so when the genome is in a state in which mutations can take place easily. Neurons during to replication stage could have such quantum critical genomes.

Evolution would not be mere selection by a survival of random mutations by external environment in the time scale much longer than lifetime of individual - but a controlled process, which can occur in time scale shorter than lifetime and differently inside parts of say brain. This is what the idea TGD inspired biology suggests. The modified DNA could be dark DNA and and serve as template for transcription and also induce transformation of ordinary DNA associated with it.

Whether this change can be transferred to the germ cells to be transferred to the offspring remains of course an open question. One can imagine that dark DNA strands (magnetic flux tubes) can penetrate germ cells and replace the earlier dark DNA sections and induce change of ordinary DNA. Or is a more delicate mechanism involving dark photons in question. With inspiration coming from the findings reported by Peter Gariaev I have proposed a model of remote DNA replication suggesting that DNA can be replicated remotely if the needed nucleotides are present: the information about DNA could be transferred as dark photons, which can be transformed to ordinary photons identified as bio-photons. Could Lysenko have been at least partially right despite that he was a swindler basing his views on ideology?

In any case, TGD inspired biology allows to imagine a controlled evolution of DNA in analogy to that what occurs in R&D departments of modern technological organizations. The notion of dark DNA suggests that biological systems indeed have a "R&D department" in which new variants of DNA studied as "dark DNA" sequences realised as dark proton sequences - same about dark RNA, and amino-acids and even tRNA. The possibility to transcribe RNA from dark DNA would mean that the testing can be carried in real life situations.

There indeed exists evidence that traumatic - and thus highly emotional - memories may be passed down through generations in genome . Could the modifications of brain DNA represent long term memories as the above described experiment suggests? Could the memories be transferred to the germ cells using the mechanism sketched above?

For background see the new chapter Dark matter, quantum gravity, and prebiotic evolution or the article "Direct Evidence for Dark DNA?!".

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 Quantum Gravity, Dark Matter, and Prebiotic Evolution

Ribosome as the first self-replicator?

In the group Thinking Allowed Original there as a link to a popular article describing a highly interesting work by M. Root-Bernstein and R. Root-Bernstein (daughter and father). The title of the popular article "Forget the selfish gene: Evolution of life is driven by the selfish ribosome, research suggests". As a matter of fact, the article itself is not selling anything of type "selfish X", a dogma which to my opinion is more or less dead: synergy and quantum coherence are much more promising notions relevant to biomatter. "Selfish X" is a paradigm, which suits much better to the description of cancer. The title of the article "The ribosome as a missing link in the evolution of life" would have been much more appropriate also for the popular article.

First a summary of motivations by authors. The basic problem relates to the emergence of life and there are many theories. The models can be divided to "genetics first" and "metabolism first" type models.

  1. RNA world is basic example of "genetics first" models. The problem of the "genetics first models" is that it is difficult to understand how prebiotic life could have coped before the complex molecular machinery of metabolism. The second problem of RNA world is that polynucleotides and proteins almost certainly co-evolved. So called compositional replication models start from this assumption but have difficulties in explain replication schemes. Both approaches fail to explain how complex cells emerged from molecular evolution. It is however known that lipid layers of cell membrane are emergent structures not coded by genes (soap films).
  2. Second class of models try to proceed from complexity to simplicity by assuming the first replicator (pro-cell typically) but are not able to answer the question "What before this?". The natural assumption is that simple bio-molecules gradually evolved to polymers and polymer aggregates and eventually cell membrane emerged.
According to authors, the challenge is to bridge the gap between self-replicating polymers and fully functional cell by identifying intermediate structures able to replicate, restore and replicate information, capture metabolic components and energy, and transform all these into biochemical networks.

Trying to catch the idea

The basic idea of the authors is simple and brilliant. Ribosome is the transcription machinery transforming DNA to proteins. Also the first replicator must have contained the transcription machinery. Perhaps the first replicator was minimal and contained just this machinery! Perhaps ribosome or its predecessor ("pre-ribosome") indeed was the first self-replicator. One would have beautiful self-reference: ribosome would be the recipe for making a copy about the recipe! Brings in mind Gödel-Escher-Bach!

This assumption is highly non-trivial. In the following I try to sketch for myself what this could mean. In the following I drop "pre"or notational convenience with understanding that ribosome, RNA, amino-acid etc. means "pre-ribosome", "pre-RNA", "pre-amino-acid", "pre-tRNA" etc.. In TGD framework pre-ribosome could be of non-biochemical nature and realized at the level of dark matter.

  1. It seems natural to assume that the basic raw material consisted of RNA and amino-acid molecules in the environment. Ribosome could use them to build copies of itself. The question how these were generated will not be considered now.
  2. Ribosome consists of rRNA and proteins and uses tRNA to associated to mRNA sequence amino-acid sequence. If ribosome was the first replicator realizing genetic code as mRNA-amino-acid correspondence it had to use its own rRNA as a template for the translation to a corresponding protein.

    If nothing has changed after the emergence of the recent replication mechanisms, the testable prediction is that ribosome amino-acids are images of rRNA sequences under genetic code. One of course expects that the stricture of ribosome has not conserved in precise sense so that this prediction could be too strong.

  3. tRNA is a molecule of form RNA-X-amino-acid and rRNA should have contained the genetic information allowing to transcribe and translate the RNA and amino-acid polymers appearing in tRNA.
According to the article these predictions are indeed tested in the work considered for Escheria Coli bacterium and it is found that the findings are consistent with the hypothesis.

On basis of these observations one can try to imagine how the ribosome or its predecessor "pre-ribosome" might have replicated.

  1. Both the basic units of RNA sequences and corresponding amino-acid polymers of rRNA had to replicate. The most economic assumption is that this occurred simultaneously.
  2. One can imagine that rRNA "gene" and the protein coded by it arranged themselves so that they were parallel. The amino-acid coded by rRNA codon acted as a catalyzer for the attachment of a conjugate of rRNA codon to the growing rRNA sequence just as in DNA replication promoter catalyzes the replication. rRNA codon in turm acted as a catalyzer for the addition of new amino-acid to the growing protein. tRNA molecules of form RNA-X-amino-acid from the environment provided the needed RNA codon and amino-acid.

    Remark: I have already earlier considered an RNA world scenario in which amino-acids of tRNA catalyzed the replication of RNA sequences. When DNA emerged, the roles would have changed and amino-acid sequence was formed instead of the replication of RNA.

    This replication differs from ordinary transcription. In transcription incoming mRNA sequences produce amino-acid sequences as tRNAs attach to the mRNA codons of mRNA attached to the ribosome. tRNA looses its amino-acid but keeps RNA. Now tRNA loses both amino-acid and RNA codon and only the unit X in tRNA? RNA-X-amino-acid remains.

    At some step of evolution the replication of rRNA would have ceased to occur and tRNA would have kept its RNA in the double translation process. Is this possibly biologically?

  3. Concerning tRNA there are many possibilities. One can imagine that ribosome and Xs could have served as co-replicators. The reaction X→ RNA-X-amino-acid and its inverse could have occurred spontaneously. The resulting complex would have attached to the end of RNA-amino-acid sequence associated with some portion of mRNA just as it does in ordinary translation . In the replication or ribosome RNA-X-amino-acid would have attached to ribosome and X:s would have been produced in the replication of X forming a part of ribosome. In the environment the attachment of RNA and corresponding amino-acid to X would have taken place.

A possible objection is based on ontogenesis-recapitulates-phylogeny vision (ORP). The replicating pre-ribosomes should be still there but they are not. There should be some very simple mechanism preventing the replication but still one can ask whether the ribosomal replication could not occur in special circumstances.

How the pre-ribosome as first replicator relates to TGD approach?

TGD framework predicts that replication as a splitting of 3-surfaces to two copies is a fundamental mechanism of quantum TGD analogous to the 1→ 2 decay of elementary particle and the replication of DNA, cells, etc... should reduce to a hierarchy of replications starting from long length scales and proceeding as replications at shorter length scales with master slave relationship between the subsequent levels of the scale hierarchy.

This identification of replication as a mere splitting of 3-surfaces saying nothing about what happens for the quantum states associated with them is too general to allow to talk about unique primary replicator. If one however restricts the consideration to systems consisting of RNA and amino-acid sequences the idea about ribosome as primary replicator becomes highly non-trivial.

In TGD framework it is possible that pre-biopolymers were not bio-polymers but their dark counterparts formed from dark protons sequences at magnetic flux tubes with states of dark proton in 1-1 corresponds with DNA ,RNA, amino-acids and tRNA. If so pre-ribosome was realized at the level of dark matter as dark ribosome - a complex formed by dark analogs of bio-polymers.

If so, then pre-ribosome consisting of dark matter at flux quanta could be the primary replicator and the formation of its bio-molecular counterpart would be induced from that of dark pre-ribosome like the dynamics of slave in master slave hierarchy.

This raises questions. How does this replication proceed? Does ribosome still replicate as all other biological structures do and induce replication of low ever level structures in the dark matter hierarchy? Does the ordinary biomatter induced at the lowest level of hierarchy would only make visible this replication?

In the following I briefly summarize the basic TGD based notions involved in attempt to answer these questions.

4-D self-organization and magnetic body

One class of questions concerns the roles of self-organization and genetices. Even the definition of the notion of self-organization is poorly defined. In TGD zero energy ontology (ZEO) forms the basic framework of both quantum TGD proper and its applications to consciousness and biology. In zero energy ontology (ZEO) self-organization is replaced with self-organization by quantum jump sequence leading to the emergence of not only 3-D spatial patters but also of 4-D behavioral patterns: one can say that living system is 4-dimensional and also its geometric past changes in quantum jumps (Libet's findings).

  1. Various motor actions of magnetic body appear as basic processes of the quantum self-organization. This includes braiding and knotting, heff changing phase transitions changing the lengths fo flux tubes, reconnections allowing to build connections between different system consisting of flux tube pairs, and also replication. Also signalling by dark photons is an essential part of the picture and the general hypothesis is that dark photons have same universal energy spectrum as bio-photons and thus in the energy range of molecular transition energies.
  2. Replication in TGD framework occurs at the fundamental level as a replications of 3-surface and is completely analogous to 1→ 2 decay for point elementary particle. This replication could take place for the magnetic flux quanta representing various biopolymers and higher level structures and induced the replication at the level of visible matter. As noticed, this replication is not enough in biology and must be accompanied by the replication of the quantum states associated with 3-surfaces.
  3. One key question is how the bio-molecular processes arranged into a functional network. Here the hypothesis that magnetic flux tubes form a 3-D grid analogous to coordinate grid with points of grid at intersections of 3 flux tubes and flux tubes as coordinate lines is very attractive. This Indra's web would be behind the gel like structure of cellular water and make it single coherent unit. Behavioral modes would be time evolutions of this grid: motor actions of the magnetic body - or hierarchy of them.

Does dark matter induced the dynamics of visible biomatter?

The idea that dark matter induces the dynamics of biomatter is extremely attractive since the enormous complexity of biochemistry would be only adaptation to the dynamics of the much simple almost topological dynamics of the master represented as flux tubes carrying dark matter.

  1. In TGD framework there are good reasons to believe that water contained the prebiotic life forms as dark analogs of various biomolecules consisting of dark proton sequences at magnetic flux tubes with the states of dark proton in 1-1 correspondence with various bio-polymers (DNA,RNA, amino-acids, tRNA). These string like objects would be dark nuclei but with a large value of Planck heff=n× h constant and with same size scale as biopolymers. The proposal is that they are present also in living matter and that is interaction between various levels based on dark photons which give bio-photons as decay products.
  2. All the basic processes such as transcription, translation, and replication would be realized already at this level. The analogs of these processes assigning to dark analogs of biopolymers the biopolymers themselves would have evolved later. (ORP) suggests that ordinary biopolymers are accompanied by parallel flux tubes carrying dark protons sequences representing them. Ordinary manner would condense around dark matter.

    The strongest assumption is that dark processes induce their bio-chemical counterparts as biomolecules attach to the magnetic flux tubes for which they form images at the level of visible matter. This might explain why strong dehydration leads to denaturation of biomolecules and why denatured biomolecules are not biologically active. Dark DNA would represent the "soul" of DNA not present in denatured DNA! Same of course would apply to other biopolymers: the loss of dark matter would induce the in vivo → in vitro transformation.

    I have proposed the identification of dark counterparts of RNAs and amino-acids as complex braided and knotted structures with braiding carrying information making possible topological quantum computation like processes and topological realization of memory. DNA would provide a symbolic representation coding also the braiding characteristics of the dark amino-acid sequence. Dark amino-acid sequence would represent the braiding physically ad dark DNA as a sequence of symbols.

    Cyclotron frequencies are crucial for communication and the strength of magnetic field on flux tubes emanating transversally from dark amino-acid sequence would be determined by the state of dark proton. The correspondence between dark RNA and amino-acid would be determined by the condition that cyclotron frequencies are identical for the corresponding dark proton states (DNA and mRNA, RNA and amino-acid) so that resonant interaction is possible.

  3. This picture conforms with the chemical properties of DNA, RNA and proteins.
    1. RNA does not appear as double strands and in unfolded form is much less stable than DNA. This conforms with the fact that DNA serves as an information storage providing symbolic representation of RNA and amino-acids including their folding or at least braiding. RNA in turn would provide the concrete representation for braiding and folding.
    2. DNA double strand is stable against hydrolysis but only inside cell - this could be due to the fact that the phase of water is ordered and ice-like so that it cannot induce hydrolysis by providing water molecules - perhaps the fourth phase of water discovered by Pollack and leading to the formation of dark proton sequences in TGD framework is in question.
    3. The braiding structure of DNA is repetitive and carries no information. This conforms with the idea that DNA and its dark variant provide a purely symbolic representations in terms of genetic code for the corresponding amino-acid - and RNA polymers including also their braiding.
  4. One can invent objections against the hypothesis that the dynamics of biopolymers is induced from that for their dark variants.
    1. RNA is not stable against hydrolysis but it can gain stability by folding. Thus the shape of RNA molecule would not be determined by its dark variant in conflict with induction hypothesis. One can however consider the much weaker possibility that dark sector determines only topological dynamics. Only the braiding of the fold RNA molecules would determined by the braiding of dark variant.
    2. DNA double strand is stable and braided in repetitive and very simple manner. If chemistry determines the stability of the DNA double strand then DNA double strand would induce the braiding of dark DNA strand rather than vice versa. Now one can argue that if dark DNA appears as double strand this forces the repetitive braiding.

To how high level can one continue this parallelism. For instance, does it make sense to talk about dark variants of cell and cell membrane? Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously.

  1. Here the findings of Pollack about the generation of exclusion zones, which are negatively charged regions of water obeying exotic stoichiometry H1.5O, are suggestive. The TGD based model assumes that a phase transition generating dark protons sequences at flux tubes of magnetic body outside the EZ takes place. The self-organization at the level of ordinary matter would generate dark matter at quantum criticality - a basic aspect of self-organization process leading to higher hierarchy levels taking the role of master. Dark matter would be the master or rather - there would be entire hierarchy of masters labelled by the values of heff. I have also considered the possibility that the generation of large heff phases happens at criticality quite universally so that life would be universal phenomenon rather than random thermodynamical fluctuation.
  2. EZs with sizes about 200 microns (size of cell) could have been the prebiotic cells. There is also evidence that EZs consist of structures with size of order micron called coherent regions (CDs to be not confused with Causal Diamonds!). Could they have been the predecessors of the cell nuclei inside which dark DNA would be stable? The TGD model for the formation of EZs assumes that they are formed from CDs under irradiation.

    This picture leads also to a view about metabolism predict that UV radiation with energies about 12.6 eV must play a key role in metabolism. The proposal is that this radiation arrives as dark photons along magnetic flux tubes of the magnetic body and excites water molecules inside CDs so that they are energetically at distance of about .5 eV from the splitting of OH bond. The excitation of water molecules inside CDs by metabolic energy quantum of nominal value .5 eV transforms this phase to EZs of Pollack.

Emergence of life as emergence of dark matter?

Many basic questions of biology seem to be hen-egg questions such as "genetics or metabolism?", "cell membrane or biomolecules?", "DNA or RNA?", "RNA or amino-acids?", etc.. This suggests that there exists a deeper level and emergence at this level induced the emergence at the level of biochemistry and cell biology.

In TGD the emergence of living systems would reduce to the emergence of dark matter as large heff phases of ordinary matter taking place at quantum critical and perhaps even critical systems.

  1. The question whether genetics or metabolism emerged first ceases to be relevant in this framework, where basic physics provides candidates for the fundamental mechanisms of metabolism (for instance liberation of zero point kinetic energy when the p-adic length scale of space-time sheet (magnetic flux tube) increases).

    Also genetic code would have been realized already before biochemistry if dark proton sequences provided the counterparts for the fundamental biomolecules. The dark biology as dark nuclear physics would make itself visible via biochemistry induced by it. We would see directly the dynamics of dark matter just by looking living systems!

  2. If one takes this picture seriously, then also pre-RNA and various other pre-biopolymers could have been realized in terms dark proton sequences associated with dark magnetic flux tubes. The dark replication process could have been the arrangement of RNA and amino-acid flux tube portions in parallel and replication of the dark proton sequences with the help of the analog of tRNA attaching to the corresponding amino-acid. In this framework the notion of dark ribosome makes sense. It would however replicate only in cell replication.
  3. In the biochemical scenarios also the emergence of DNA looks like mystery. In TGD framework dark DNA could have emerged at the same time as dark RNA and dark amino-acids as CDs and EZs emerged and make the stable presence of also ordinary DNA inside CDs and EZs. All basic biomolecules and prebiotic cell and metabolism would have accompanied the emergence of CDs and EZs under the irradiation of water feeding metabolic energy and giving rise to prebiotic photosynthesis (note that the negative net charge of DNAs could be due to the fact that part of protons is at dark flux tubes). Dark DNA could be interpreted as an information storage representing the braiding patterns of dark RNA and dark amino-acids symbolically.
  4. In this framework the basic step of the replication is the generation of flux tube parallel to the flux tube from which one forms copy or map (say in DNA replication and and transcription). How this happens?

    A possible answer to the question relies on the earlier proposal that living system involves kind of coordinate grid formed from magnetic flux tubes serving as coordinate lines and meeting each other at the points of the grid. The replication process would involved translation of nearby flux parallel flux tube of the grid near to a given flux tube assignable to say DNA strand as a first step - maybe by heff reducing phase transition for flux tubes orthogonal the flux tube. After this the building bricks of the new biomolecule would be brought along either of the remaining locally orthogonal flux tubes - perhaps by heff reducing phase transition. The basic structure would be this Indras web containing visible matter at its nodes with dynamics consisting of magnetic motor actions.

This vision involves of course considerable challenges. One should model the dark ribosome counterparts of the replication process for dark DNA, transcription of dark DNA to dark mRNA, translation of dark mRNA to dark amino-acids, and also possible self-replication of dark ribosome.

For background see the chapter Quantum gravity, dark matter, and prebiotic evolution of "Genes and Memes". See also the article Was ribosome the first self-replicator?.

Could Podkletnov effect be understood using heff= heff hypothesis?

Podkletnov discovered his effect around 1982. There are funny co-incidences involved. I got my PhD. Podkletnov was kicked out from Tampere University and I was soon to find that it is impossible to find any funding for my work: situation is still the same! God can forgive but not colleagues. I have considered possible models for Pokletnov effect in TGD framework for years ago assuming that the propagation of gravitons along topological light rays attached to magnetic flux tubes mediate gravitational interaction. A lot of progress has taken since then. Therefore reconsideration is well-motivated.

The effect itself looks rather complex. The experiment involves a levitating disk above a toroidal magnet. Solenoids generating AC fields with frequency in the range 50-106 Hz are used to rotate the disk. Above the disk at height of 15 mm is a sample of silicon with weight of 5.47834 g. The claim is that both the rotating disk and sample lose part of their weight: the estimate varies from .3 per cent to few per cent. The effect was resonance like above frequency 105 Hz: below this the weight fluctuates. The size of the effect increases with rotation frequency.

Some background

It is best to start by introducing some background.

  1. The first thing to notice is that f=6× 105 Hz is cyclotron frequency of electrons in the magnetic field Bend=.2 Gauss introduced to explain the quantal effects of ELF em fields on brain which appear at multiples of cyclotron frequencies of biologically important ions. The recent model for bio-photons as decay products of dark protons predicts that their spectrum correspond to a spectrum of Bend. Could it be that the magnetic fields at the flux tubes involved has spectrum of Bend and resonant transfer of energy in the frequency range containing f=6× 105 Hz takes place?
  2. The hypothesis heff = hgr = GMD m/v0, where MD is the dark mass assignable with large system (Earth now) and v0 is velocity parameter is relatively new piece of TGD inspired quantum biology. One obtains a rough estimate MD/M ≈ 2. × 10-4 for the fraction of dark matter in the case of Earth and assignable to the dark magnetic body of Earth. One implication of hgr=heff hypothesis at gravitation mediating flux tubes is that cyclotron frequencies of particles do not depend on the mass of the particle and cyclotron energy spectrum of dark photons is universal and identifiable as that associated with bio-photons. Second implication is that each charged particle corresponds to particular value of Planck constant so that in many-sheeted space-time they populate different flux tubes: this could be very relevant for biology since cell would not be anymore a random soup of molecules. The model for the Pioneer and Flyby anomalies leads to the estimate MD/M≈ 1.3× 10-4 consistent with the above estimate.
  3. I have considered recently a model for the fountain effect of superfluidity considering the possibility that dark phases of matter in TGD sense might be associated with all critical situations - both ordinary critical and quantum critical phase transitions - in which long range fluctuations correlations explained in terms of generation of dark matter are present.

    The superfluid is able to climb from vessel along its walls apparently defying gravitation. The TGD explanation is in terms of large Planck constant hgr=heff hypothesis. The large value of hgr implies macroscopic quantum gravitational coherence and that the quantum states in gravitational field for dark 4He atoms have macroscopic size. In particular, the flow along walls is effectively free flow.

The anomaly in the measurement of Cooper pair mass in rotating superconductors

One has discovered an anomalous outcome in the mass measurements of Cooper pairs in the case of rotating superconductors. The measured mass of Cooper pair in rotating super conductor is slightly larger than the mass of the pair which must be slightly below the sum of the masses. Tajmar et al try to explain the anomaly is in terms of a gigantic gravimagnetic London effect associated with a rotating superconductor.

  1. Recall that in in the ordinary London effect a magnetic field proportional to the negative of rotation frequency is generated inside super-conductor: usually the magnetic field is expelled. London magnetic field corresponds to a magnetic dipole proportional the negative of the rotation frequency (this follows from the negative sign of the charge carriers). The natural expectation is that this gives rise to a dipole field outside the superconductor. The dipole moment would be generated by electron current at the surface of the superconductor.
  2. The idea is to to introduce gravitational superconductivity for which all kinds of particles participate in the flow which would be analogous to super-fluidity. One can also speak about gravitational Meissner effect and massivation of graviton as analog of massivation of photons in the ordinary Meissner effect. Also the notion of London magnetic field might generalizes and gives rise to a dipole like gravimagnetic field outside the super-conductor. Now however negative charge is replaced by mass, which is positive so that the sign of the effect changes. The predicted effect is however completely negligible using the existing estimates for the mass of the graviton.
  3. The crazy proposal of Tajmar et al is that a gravimagnetic field larger than that predicted by GRT by a factor of order 1024 is associated with the rotating super-conductor and combines and produces the slight deviation of the measured mass of the Cooper pair from real when this since the Cooper pair couples also to gravimagnetic field besides magnetic field. The reason is that the effective magnetic field contains a small contribution of gravimagnetic field so that the measurement gives too large a result for the mass of the Cooper pair.
In standard model plus GRT this kind of effect is impossible. In TGD framework the hierarchy of Planck constants suggests two alternative explanations.
  1. The London magnetic field (also gravimagnetic) is a purely quantal effect and proportional to the square h2 of Planck constant. If h is replaced with say heff = hgr≈ 1012 h the effect is enormous as compared to that predicted by GRT! There is however an objection: one cannot perform this replacement for ordinary London field! Why?
  2. Many-sheeted space-time allows to consider also alternative model in which the change of mass is due to a generation of the analog of dark London magnetic field at dark magnetic flux tubes: electron would couple to the sum of these fields since it would have topological sum contacts to both space-time sheets This magnetic field is proportional to dark matter density and ρD/ρ=MD/M≈ 2× 10-4 would give a correct order of magnitude estimate.
  3. Since gravimagnetic and magnetic fields are expressible in terms of CP2 coordinates and their gradients, one can wonder whether the two explanations are actually equivalent.

What about Podkletnov effect?

Also Pokdletknov effect is associated with a rotating superconductor and one can ask whether the above ideas apply also to it.

  1. The vision that dark variants of elementary particles are associated with all critical phenomena suggest that a critical phenomenon is in question also now and part of the matter - at least part of Cooper pairs - are in dark phase at magnetic flux tubes satisfying heff= hgr. Could large heff=hgr be involved also with Podkletnov's effect? Could the reported loss of the weight of the (not necessarily) rotating disk and and of the sample by .3 per cent be due to the transformation of part of Cooper pairs to large heff=hgr phase de-localized to the magnetic flux tubes along which gravitational force is mediated in a scale considerably larger than that of the sample and disk? Also the air above the rotating superconductor was reported to start to rise. Could this be that also air molecules lost some of their electrons to the dark flux tubes in this manner? Since electron mass is about 2-11 fraction of proton mass, also protons and heavier particles should leak to the dark phase to achieve weight loss of order per cent. This effect would be present already for the non-rotating superconductor and would be much like the fountain effect in superfluidity according to TGD.
  2. As the frequency of AC fields is increased, the weight of the sample fluctuates but above 105 Hz it stabilizes and is resonant like. Levitation is essentially due to the gradient of the magnetic energy associated with AC fields. Could part of AC photons transform to dark photons and could the large energy of dark photons - in visible and UV range - mean much larger excluded magnetic energy in the volume of the gravi-superconducting sample and rotating superconducting disk and in this manner induce stronger levitating effect becoming stronges at cyclotron resonance energies. Resonance absorption would take place when the frequency is in the region of electron cyclotron frequencies for the flux tubes. Also coherence would be achieved thanks to the presence of Bose-Einstein condensates of electronic Cooper pairs.
  3. One should explain also the increase of the reported loss of the weight with the rotation velocity of the superconducting disk. Rotation generating the mass current should generate dipolar gravimagnetic field with strength proportional to the rotation frequency (and accompanied by ordinary magnetic fields). The increasing strength of the gravimagnetic field would mean increase in the number of flux quanta or increase of the field strength at the flux tubes. At least in the first case more particles could end up to the dark phase leading to the reduction of effective weight of the sample and rotating disk. This gravimagnetic dipole field would naturally correspond to the gravimagnetic London field continued outside the superconducting rotating disk acting as a magnetic dipole.

See the chapter Quantum gravity, dark matter, and prebiotic evolution or the article Could Podkletnov effect be understood using heff= heff hypothesis?.

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