Tuesday, June 26, 2018

About dark variants of DNA, RNA, and amino-acids

To make progress one must construct a concrete model for the dark nuclei. The recent picture relies strongly on various anomalies to which TGD provides a solution. The TGD inspired model for "cold fusion leads to the notion of dark nuclear physics - actually hierarchy of them labelle by the values of heff/h=n and corresponding p-adic length scales. Second basic idea is that cylindrical variants of EZs discovered by Pollack (see this) give rise to the dark counterparts of DNA, RNA, and amino-acids as dark proton sequences. tRNAs would be analogs of tritium and 3He. Pollack effect serves as a strong constraint for the model. Also the effects of ELF em fields on vertebrate brain combined with the rather recent finding about clustering of RNA II polymerase molecules exhibiting Comorosan effect provide valuable constraints on the model (see this) . The outcome of the arguments is that single strand of DNA, mRNA, tRNA and amino-acids most naturally correspond to k=149 and double stranded DNA to k=151.

Remark: The following argumentation is kind of Sherlock-Holmes-ing using all possible hints as constraints to select between imagined options rather than glorious march from axioms to theorems and thus not science in the usual sense.

1. Why one must have k=151 for dark DNA

Concerning the identification of the size scale of dark DNA one can consider several options. It however turns out that the p-adic length scale assignable to dark DNA is most naturally k=151 corresponding to the thickness 10 nm of DNA coil. The hypothesis that the integer k labelling p-adic length scale is prime is attractive working hypothesis leaving very few options under consideration. The options k=137 and k=149 are excluded since the pairing of dark DNA and ordinary DNA would not be possible without the coiling of ordinary RNA around dark DNA. This leaves only options for which k≥ 149 for prime values of k.

For prime values of k the options k<149 are not possible for dark DNA since ordinary DNA should coil around dark DNA. There is also second objection against k<149 from energetics inspiring the hypothesis DNA corresponds to k=151.

  1. The scaling of the dark nuclear binding energy Eb∼ 7 MeV per nucleon as L(107)/L(k) predicts very high binding energies for primes k<149. For instance, k=139 would correspond to the scaled binding energy Eb(139)=Eb L(107)/L(139), Ebsim 7 MeV, which is typical nuclear binding energy. This gives Eb(139)=Eb/2(139-107)/2=.14 keV.

  2. The TGD based explanation of Pollack effect provides a consistency test for the idea. In Pollack effect IR light (besides either kinds of energy feeds) induces the formation of negative charged exclusion zones (EZs) in water bounded by gel phase. In TGD based model this would correspond to the formation of dark proton sequences at magnetic flux tubes. The scale of dark nuclear binding energy would be most naturally in eV scale. The binding energy scale of hydrogen atoms in water molecules is about 5 eV which suggests that the binding energy scale for dark protons sequences is smaller since otherwise energy would be liberated. This would suggest k=149 as will be found.

  3. One can imagine that an external perturbation induces

    1. a transition in which the proton bound to water molecule transforms to its dark variant in higher energy state or

    2. that the proton goes over a potential wall, whose height is measured in eV:s.

    If the dark nuclear binding energy is higher than the binding energy of proton in water molecule, the process should liberate energy and could occur spontaneously unless high potential wall prevents it. Hence the first option seems the only realistic one. Note that one could consider the cancellation of dark nuclear binding energy and repulsive Coulomb energy which scale in the same manner as function of p-adic length scale so that still the net energy would scale increase in shorter p-adic length scales.

Pollack effect suggests that if k is prime, one must have k=149 for dark proton sequences formed in Pollack effect.

  1. For k=149 one has Eb(151)∼ Eb/2(149-107)/2=3.5 eV for Eb= 7 MeV, which is in UV range slightly above the visible range. The binding energy of hydrogen atom in water is about 5 eV which would require the incoming radiation to have energy 1.5 eV which is indeed in IR range. This option looks therefore realistic.

  2. For k=151 one would have Eb(151)∼ 7 MeV/2(151-107)/2=1.75 eV, which just above the IR energy range. Now the energy needed to transform ordinary protons to dark protons in Pollack effect would be in UV range so that this options seems to be excluded.

This argument suggests that dark proton sequences generated in Pollack effect are analogs of single DNA strand, which would naturally correspond to L(149)= L(151)/2. Also RNA would naturally correspond to this scale.
  1. L(151)≈ 10 nm is the thickness of coiled DNA double strand. The size scale of dark nucleons would be L(151) and the dark DNA strand should be horizontally scaled variant of ordinary DNA strand by a scaling factor λ ∼ L(151)/.33 nm = 30. DNA double strand would be obtained by a transversal scaling from the ordinary DNA double strand.

  2. The higher coilings of DNA could correspond to higher horizontally scaled variants of DNA corresponding to k=157,163, 167. k=167 would correspond to nuclear membrane length scale of 2.5 μm. The emergence of nuclear membrane in k=151 length scale would have been accompanied by the emergence of dark DNA in this scale. Cell membrane could correspond to k=173 and p-adic length scale 17.6 μm. Neurons have size varying from 4-100 micrometers (the definition of size depends on whether one includes axons) and might correspond to k=179,181 and length scales of .16 mm and perhaps even .32 mm.

The only justification for this speculative picture is that it is consistent with the other basic ideas about TGD inspired quantum biology.
  1. Cisse et al (see this found that RNA II polymerase molecules cluster during transcription and their dynamics involves multiples of the time scale τ=5 seconds. Comorosan reported long time ago that just these time scales are universal bio-catalysis The TGD inspired model (see this) for the findings of Cisse et al allows to sharpen the TGD based view about quantum biology considerably.

  2. The basic parameter of the model is the value of gravitational Planck constant hbargr= GMDm/v0 assigned to magnetic flux tubes mediating gravitational interactions. Already earlier work gives estimates for the value MD of dark mass and velocity parameter v0 and the model leads to the same estimates. The identification of the values of τ as Josephson periods assuming the potential difference V along flux tubes connecting reacting molecules is universal and same as over neuronal membrane fixed the value of hgr. The value of V along flux tube serving as Josephson junction would be universal
    and equal to membrane potential. Josephson radiation would have energies coming as multiples ot ZeV just above the thermal energy at physiological temperatures fixed by the membrane potential.

  3. The model forces the conclusion that the endogenous magnetic field Bend has at its upper bound Bend=.2 Gauss deduced from the findings of Blackman about effects of ELF em fields on vertebrate brain. The earlier ad hoc hypothesis was that Bend=.2 Gauss is minimum value of Bend. Furthermore, for the required value of hgr Bend=.2 Gauss corresponds to dark cyclotron energy of .12 keV, which is surprisingly large energy at the upper end of UV band: the earlier intuitive guess was that energy scale is in visible range.

    Also harmonics of cyclotron frequencies were found to have effects so that really large energy scales are involved with the interaction of ELF radiation and one can ask whether this picture really makes sense. This raises a question about the mechanism of the interaction of ELF em radiation with living matter. One also wonder why the ELF radiation has effects on both behavior and physiology.


    1. that dark photons with energies coming as multiples of .12 keV are in question,

    2. that these dark photons excite dark cyclotron states in the cellular length scale deduced from flux quantization and

    3. that the dark cyclotron photons radiated as the excited cyclotron states return to the ground states perform some control action on ordinary DNA coil - this is in accordance with the basic vision about the role of magnetic body.

    X rays have energy range varying from 100 eV to 100 keV and wavelengths varying from 10 nm to .01 nm. The wavelength of an ordinary photon resulting from dark photon with energy of .12 keV would be of order 10 nm, the radius of DNA coil for k=151!

    Could this energy induce an analog of standing em wave in transversal degrees of freedom of DNA perhaps transformable to many phonon state with very large number of photos and thus classical acoustic wave? This would allow to understand how cyclotron harmonics can have non-trivial effects. The effects of ELF radiation on behavior and physiology could be understood as gene expression induced by the irradiation.

Both dark cyclotron radiation and radiation generated in dark nuclear transitions could have biological effects

  1. Can one relate energy scale of .12 keV associated with dark cyclotron radiation to atomic physics? The ionization energies behave as Z2eff/n2, where Zeff is nuclear charge minus the charge of the closed shells. Zeff is also reduced by electronic screening by other valence electrons. The binding energies of valence electrons decrease with the principal quantum number n so that only n=2 row of the periodic table might allow so high ionization energies for valence electrons.

    Oxygen is certainly the first candidate to consider. The ionization energy for oxygen is .12 eV from an estimate assuming that the effective nuclear charge is 6 (with the contribution of 2 valence electrons subtracted). The actual value is 68.9 eV: the reduction is due to electron screening. This value is smaller than the estimate estimate for Eb=.12 keV and since harmonics of this energy are involved, the interpretation in terms of ionization does not make sense.

  2. Not only oxygen but also heavier elements are ionized in living matter and at least to me this has remained more or less a mystery. Could dark photons emitted by dark nuclei of MB perform control by inducing the transitions and even ionization of oxygen and other biologically important atoms. The process could proceed also in opposite direction. The energy scale would correspond to that of nuclear excitations scaled down by the above ratio of p-adic length scales. If the energy scale of ordinary nuclear excitations is taken to be about 1 MeV, the dark energy scale for k=127 assignable to the dark nuclei created in "cold fusion" is keV. For k=131 the scale would be 250 eV and above the ionization energy scales for valence electrons. For k=137 the scale would be 17 keV. These dark nuclear transitions could generate dark photons inducing transitions of atoms and even ionizations.

2. What about dark variants of RNA, tRNA, and amino-acids?

Also RNA and amino-acids should have dark variants and one should understand their role. Suppose that the integer k characterizing the p-adic length scale is prime. The vision about RNA era preceding DNA era suggests that RNA accompanying dark RNA is at lower level in the evolution, and hence the value of heff is smaller for dark RNA than for dark DNA. Also the p-adic length scale for RNA would be shorter.

  1. The most natural option is that RNA corresponds to k=149 as also single DNA strand. This would conform with the above suggestion that the Pollack effect generates k=149 dark proton sequence (dark RNA?). DNA double strand would correspond to k=151.

    The emergence of k=151 level would mean the emergence of structures with scale characterized by L(151). This includes DNA double strand forming a coil with thickness L(151) and nuclear and cell membranes. During RNA era these structures would have been absent.Both DNA double strand and cell membrane have binary structures. Therefore single DNA strand and lipid layer could correspond to k=149. In transcription DNA opens and double strand becomes pair of strands having naturally k=149. Therefore mRNA should have also k=149.

  2. If amino-acids correspond to k=149 then also tRNA should correspond to k=149. On the other hand, tRNA does not form strands and should be more elementary structure than RNA. Could tRNA corresponds to k=139 or k=137? This would require that also the attached amino-acid would correspond to k=139 or k=137, which does not look plausible.

    Remark: TGD vision assumes tRNA was present already at RNA era and the role of amino-acid in tRNA was to catalyze RNA replication. In fact, RNA could have been just tRNA at very early stages.

What about amino-acids? The following arguments suggest that one has k=149 for both amino-acids and RNA.
  1. For dark amino-acids one can imagine p-adic evolutionary hierarchy analogous to that for DNA. In TGD inspired vision amino-acid sequences emerged together with DNA. Proteins can appear also as coils. Since mRNA pairs with single DNA strand and amino-acids with mRNA, it seems that amino-acids should correspond to k≥ 149?

  2. One could however argue that amino-acids are building bricks rather than information molecules and k could be rather small for dark amino-acids. Dark amino-acids should pair with proteins. Pairing without coiling is possible only if the length per letter is same as the length per amino-acid and thus same as for DNA letter, which is longer than the length taken by k=139 dark proton. Also this suggests k=149 for dark amino-acids and their coiling around the ordinary amino-acids.

See the article About dark variants of DNA, RNA, and amino-acids, the longer article About the Correspondence of Dark Nuclear Genetic Code and Ordinary Genetic Code, or the chapter with the same title.

For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

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