Sunday, March 27, 2022

Could the metabolism of cilia and flagella rely on gravitationally dark electrons?

The metabolism of cilia and flagella (see this) is poorly understood. According to the recent measurements (see this) in sea urchin sperm (length ≈ 50 μm , 0.2 μm diameter) show that the energy consumed per flagellar beat corresponds to ≈ 2 × 105 ATP molecules. There is no GTP inside cilium as in the case of axonal MTs (see this). It is difficult to understand how ATP machinery could provide the metabolic energy feed.

This motivates the question about whether local ciliary metabolism could rely on the transformation of valence electrons of some biologically important ions to dark electrons at the gravitational MB and vice versa? The reduction of hgr for electrons would provide the metabolic energy related by a factor me/mp ≈ 2-11 to the ordinary. About 4× 108 gravitationally dark electrons would transform to ordinary ones in a single stroke of cilium.

Electronic metabolic energy quantum would relate like cent to dollar and make possible a more refined metabolism with fine tuning. Electronic metabolism could also be an essential part of ordinary metabolism.

Consider now the idea more quantitatively.

  1. What could be the electronic analog of ATP machinery. All biologically important ions can be considered as effective ions with some valence electrons at gravitational MB. In particular, the bosonic ions Ca++, Mg++ and Fe++ could have Bose-Einstein condensates of gravitationally dark Cooper pairs at the gravitational MB.

    Ca++ waves play a key role in cellular biology, Fe++ is essential for oxygen based metabolism, and Mg++ is important in bio-catalysis: for instance, ATP must bind to Mg ions in order to become active.

  2. Suppose that one replaces h with hgr in the Schrödinger equation for the valence electrons. The binding energies are scaled down by 1/n2, n= ℏgr/ℏ= GMme/v0ℏ= 2π rs, E/Le β0, rs,E≈ .9 cm, Le= h/me ≈ 2.4× 1012 m. For β0=1, this gives n≈ 2.4× 1010. The radii a of Bohr orbits would be scaled up by n2 ≈ 5.8× 1020 from a(Z) = Z2a0, a0≈.5 × 10-10 m giving a≈ 2.9× Z2× 1010 m For Z≥ 3 (Li), a is longer than the astronomical unit AU=15× 1010 m (distance from Earth to Sun). The electromagnetic binding energy would be very near to zero.

    The gravitational interaction would dominate and cannot be neglected. The Schrödinger equation would reduce in an excellent approximation to that for the gravitational potential. Note however that the description of dark gravitational particles in terms of wave functions concentrated at flux tubes is the more realistic option than ordinary Schrödinger equation assuming total delocalization.

  3. What could be the mechanism transforming valence electrons to dark electrons? This should happen for positively charged biologically important ions, in particular for the bosonic ions Ca++, Mg++ and Fe++. The consumption of metabolic energy would correspond to a deionization of dark ion Ca++ and this might make it possible to test the proposal. For instance, Ca++ could accompany ciliary waves.
Where could the energy for ionization come from?
  1. This question is also encountered in the chemistry of electrolytes (see this). It is very difficult to understand how the external electromagnetic potentials, which give rise to extremely weak electric fields in atomic scales, could lead to ionization. The acceleration of electrons in the electric field along dark flux tubes involves very small dissipation and can easily give rise to electron energies making ionization possible.
  2. MTs have a longitudinal electric field, which by the generalization of Maxwell's equations to many-sheeted space-time (in stationary situation potential difference is same for paths along different space-time sheets) gives rise to an electric field along the magnetic flux tubes. These flux tubes need not be gravitational.

    By darkness, the dissipation rate is low. Could the acceleration along flux tubes, in particular MT flux tubes, lead to the ionization? Could the electret property of linear biomolecules quite generally serve for the purpose of generating electronic metabolic energy storages in this manner?

  3. Assuming opposite charges +/- ZMT at the ends of dark magnetic flux tube associated with the MT, one obtains a rough estimate. The length of the cilium is L≤ 10-4 m and its radius is R ≈ 2× 10-7 m. The estimate for the energy gained by a unit charge e as it travels through the ciliary MT is E≈ ZMTe2 L/R2 ≈ ZMT× 2.85 eV. The valence electron energy for atomic number Z with principal quantum number n (giving the row of the Periodic Table) is E≈ (Z/n)2 × 13.6 eV. The ionization condition would be ZMT> (Z2/n2)× 13.6/2.85. For the double ionization in the case of Ca++ with Z=20 and n=3 this would give ZMT> 212.
See the article Hen and egg problems of biology from TGD point of view or the chapter Molecular Signalling from the TGD Point of View.

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

Articles and other material related to TGD.

Saturday, March 26, 2022

Quantum gravitation in TGD inspired quantum biology

The theory of Penrose and Hameroff assigns to microtubules quantum gravity in Planck length scale. In the TGD Universe, one does just the opposite. The hierarchy of effective Planck constants assigns to quantum gravitation quantum coherence scale even in the scales of astrophysical objects.

This inspires the proposal that protons at hydrogen bonds and also the valence electrons of metals can be transferred to the gravitational Bohr orbits. This proposal unifies the previous picture. For electrons the reduction of binding energy would be a fraction me/mp from that for protons. This would give a precise identification for the notion of dark ion as an effective ion due to the delocalization of a proton of hydrogen bond or of valence electron. This leads to the understanding of the role of quantum gravity in the TGD inspired quantum biology.

About the notion of magnetic body (MB)

The proposed picture allows us to reconsider a long-standing question relating to the notion of MB with an onion-like layered structure. What could this sentence mean quantitatively?

  1. The 4-surfaces X4 with 1-D CP2 projection and 3-D M4 projection having 2-D membrane as E3 projection are good candidates for various membrane objects in TGD Universe. The E3 projection is not a 2-D minimal surface although X4 is and this possible if the 1-D CP2 projection is dynamical. The flux tubes of MB should be assignable to kind of membrane-like surface.
  2. The gravitational magnetic body could be a layered structure containing the Bohr orbits with Bohr radii rn ∝ n2 of particles in the gravitational field of Earth. Particles with different masses would concentrate at the same orbits. Earth could be seen as a gravitational analog of atom containing large numbers of particles at the Bohr orbits. Physical intuition suggests that Exclusion Principle applies only inside the Bohr orbits which correspond to flux tubes. The dynamics of bio-sphere would involve an an essential manner quantum gravitation.
  3. Flux sheets with a cylindrical rotational symmetry containing the orbits can be considered. These surfaces should be realized as preferred extremals of the action and should be minimal surfaces in H=M4× CP2. As closed surfaces they cannot define minimal surfaces of the Euclidean 3-space E3. Indeed, soap bubbles are not minimal surfaces but require a constant pressure difference between interior and exterior. The analog of pressure difference would be non-trivial and dynamic 1-D projection of 4-D surface to CP2 (see this). The liberation of metabolic energy quantum would be analogous to a transition of hydrogen atom to a lower energy state.
Cell membrane, nerve pulse and quantum gravitation

This picture makes it also possible to formulate a more precise view about the model of cell membrane as a generalized Josephson junction for which the generalized Josephson energy for charge Ze is the sum EJ = ZeV +Δ Ec of ordinary Josephson energy ZeV and difference Δ Ec of dark cyclotron energies for the flux tubes at the two sides of the cell membrane having in general different strengths of magnetic field.

The model requires large heff in order that Josephson frequencies can correspond to frequencies in the EEG range. This justifies the assumption that dark ions have heff=hgr . The ionization would be effective and caused by the transformation of protons of hydrogen bonds and valence electrons to dark charge carriers at the gravitational flux tubes.

The physical meaning of the criticality against the generation of nerve pulse for a critical membrane potential eVcr ≈ .05 eV has remained open.

  1. Since voltage gives rise to negative potential energy, it seems clear that there must be positive contribution to the energy and this could come from the reduction Δ Egr of the gravitational potential energy due to the positive resp. effective ionization of atoms of metal atoms resp. electronegative atoms with hydrogen bonds.

    The reduction of the gravitational potential energy for electrons is fraction me/mp from that for protons so that protonic contribution should dominate in the reduction of gravitational potential energy if dark electrons and protons correspond to the same shell of gravitational atom. The first guess is that the energy shell and thus the distance from the Earth's surface is the same.

    The parametrization of the reduction of the gravitational energy per atom and for the difference Δ Ec of cyclotron energies should in the standard picture correspond to a thermo-dynamical formulation using chemical potentials to fix the ion concentrations. The water has very special thermodynamic properties in the range between freezing and boiling points and anomalies are largest near physiological temperatures. This would be due to the presence of dark hydrogen bonds, which supports the view that the number of dark protons and electrons depends on temperature.

  2. In the first approximation the negative Coulombic interaction energy for the cell membrane is given by ECoul= -Qtot eV =-∑i Ni(out) Zi eV, where Ni is the number effective ions with charge Zie. The contribution of positive charges is negative since V corresponds to a negative net charge for the cell. The situation is stable for |ECoul| > |ECoul,crit|= Np Δ Egr. The system becomes critical at QtoteVcr= NpΔ Egr. The system becomes critical at QtoteVcr= NpΔ Egr. The value of the critical potential energy is given by eVcr= Np Δ Egr/Qtot and is roughly constant for a given neuron. This suggests that the ratio Np/Qtot characterizes the cell. Neurons and ordinary cells could differ in that ordinary cells are either subcritical or so overcritical that nerve pulses do not occur. Subcriticality looks the more plausible option. The emergence of the nervous system would mean the discovery of quantum criticality as a control tool of MB.
  3. In the generation of the nerve pulse the dark protons and electrons become ordinary ones in the reduction hgr→heff< < hgr for them and the membrane potential changes sign. In ZEO this transition could correspond to BSFR ("big" state function reduction) inducing time reversal and change of membrane potential. The second BSFR would bring back the original situation and membrane potential would return to the over-critical value.
Microtubules and quantum gravitation

In the TGD Universe quantum gravitation would be associated with the cell membrane, in particular neuronal membrane. Quantum gravitation has been speculatively assigned with microtubules (MTs) rather than cellular or neuronal membranes. What is the situation in TGD?

  1. Axonal MTss are highly critical systems, which continually change their lengths. The surface of MTs has one GDP per tubulin dimer and the ends of MT has GTPs so that there is a constant negative charge per unit length. The number of GTPs is larger at the second end so that there is an electric field along MT.
  2. GTP<ftrightarrow GDP process accompanies the variation of the length of the MT. The transformation of the protons assignable to the phosphate hydrogen bonds to gravitationally dark protons could be an essential element of the MT dynamics. The periods of increasing/decreasing MT length could be initiated by BSFR and would correspond to different arrows of time. The effective ionization affects the effective charge of the axonal interior and therefore of membrane potential. This suggests a strong correlation with the variation of axonal MT lengths and nerve pulse propagation.

    The propagation of nerve pulse through the myelinated sections of the axons, where ion transfer with cell exterior is not possible, remains a mystery in the standard model. Without axonal MTs the nerve pulse propagation would not be possible. This could allow us to understand why various neuronal diseases involve a reduced MT stability (this).

See the article Hen and egg problems of biology from TGD point of view or the chapter Molecular Signalling from the TGD Point of View.

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

Articles and other material related to TGD.

Wednesday, March 23, 2022

About prebiotic counterparts of tRNA and metabolic machinery

The question about the prebiotic counterparts of tRNA and tRNA-amino acid pairing stimulates also questions about the prebiotic counterpart of metabolic machinery.

What can one say about pre-tRNA?

What could be the prebiotic counterpart of tRNA?

  1. DtRNA should have a molecular counterpart. The simplest guess is that it corresponds to an RNA type codon appearing in tRNA but somehow differing from it. Pre-tRNA could simply be the (AAC-H)3' end of the acceptor stem with AAC replaced with XYZ, where ZYZ denotes the codon part of tRNA. The addition of a hydrogen atom would relate pre-tRNA codon to ordinary RNA codon.
  2. The bond energy for the pre-tRNA-AA pair as the energy of the ester bond would be about .5 eV, which corresponds to the metabolic energy quantum. Energy is therefore required to "charge" pre-tRNA. This requires metabolic energy and in the absence of ATP machinery, the energy should come from its predecessor. What prebiotic metabolism could be, will be discussed in the next section.
  3. If this step works, the polymerization of tRNAs involving the transformation of the ester bond of pre-tRNA-AA to AA-AA peptide bond can occur spontaneously since the peptide bond has bond energy of order .1 eV. This would give rise to polypeptides. This process would be like a translation process for RNA but without an RNA template and therefore the outcome would be random. Also the RNA polymerization in this manner can be considered, now however the RNA-RNA valence bond has considerably higher bond energy.
  4. If DRNA-RNA sequences are formed, they might be transformed to AA sequences by pre-translation process using pre-tRNA and resonance mechanism pairing DRNAs and dark counterparts of pre-tRNA-AA pairs. This would define the pre-translation process.
What could the prebiotic metabolic machinery be?

Metabolic machinery should have a prebiotic counterpart and have .5 eV as metabolic energy quantum.

  1. Could the splitting of a hydrogen bond with bond energy about .5 eV provide the energy needed in the formation of pre-tRNA-AA ester bond? IR photons are most effective in causing Pollack effect in water: could also they induce pre-tRNA-AA pairing? Both options would require the presence of water. In principle, the proposed mechanism could lead to a generation of water molecules (the energy of O-H bond is 4.81 eV) already at temperatures of few Kelvin.
  2. Could MB somehow provide the metabolic energy quantum? Gravitational flux tubes are in a central role in the TGD inspired quantum biology. Iit was observed (see this) that the gravitational binding energy of a nucleon in the gravitational field of Earth is .67 eV. This is somewhat larger than the metabolic energy quantum. A dark proton at a distance of about .34 RE, RE Earth radius, from the surface of Earth has gravitational binding energy of .5 eV.

    The bond energy of the hydrogen bond is .5 eV. Could it correspond to the reduction of the gravitational binding energy due to the delocalization of a dark proton to a gravitational flux tube? Could the hydrogen bond become dark with heff= hgr or could the proton of the ordinary hydrogen bond be dark?

    The transformation of a dark proton at the gravitational flux tube of MB to an ordinary proton implies a localization having interpretation as falling to the surface of Earth. Could this provide the metabolic energy quantum?

    For a dark variant of hydrogen bond a gravitational flux tube between atoms should form a very long loop at which the gravitationally dark proton would reside. This kind of picture about dark flux tubes associated with gauge interactions has been suggested earlier. For instance, color flux tubes assignable to nuclear protons could extend to distances of order of atomic size.

  3. The observation that gravitational binding energy equals hydrogen bond energy inspires the question whether the ordinary hydrogen bond is dark in a gravitational sense. The delocalization of proton charge to a very long scale would mean that in short scales the hydrogen bonded atom pair has an effective negative charge so that this does not work.

    This observation however suggests that phosphate ionization could be interpreted as a formation of a dark hydrogen bond. Phosphate is electronegative and forms hydrogen bonds. This would explain why phosphate ions have such a central role in metabolism. Effective ionization serves as the signature of the delocalization. Also other electronegative ions could play the role of phosphate and arsenite has done this in some bacterial systems (see this).

    The pre-biotic counterpart of metabolic machinery should have involved phosphate ions or some other electronegative ions forming dark hydrogen bonds.

  4. For electrons the gravitational binding energy at height .34 RE is about .25 meV. This corresponds to the energy of photons in the microwave background. Could this define a second metabolic energy quantum important in scales by a factor mp/me≈ 211 longer than nanoscale about 1 nm assignable to DNA. This is the length scale of the cell nucleus, microtubules and axons. Intriguingly, the minimal fluctuations of membrane potentials correspond to the so-called miniature end plate potentials .4 mV (see this).

    Metal ions could be atoms with gravitational delocalization of the valence electrons and some of them could serve as analogs of metabolic recurrencies. Some metal ions could take the role of metabolic quantum. Fe++, Ca++, and Mg++ are bosonic ions and are of special importance on living matter. They would be neutral in the scale of gravitational flux tubes.

  5. What would be the size scale Lgr of the gravitational flux tubes? The first estimate is as the Bohr radius Lgr=rn= n2 aB,gr= n2 Λgr,m for the orbit particle in 1/r gravitational potential of Earth. Λgr,m= GM/v0 is gravitational Compton length, which for v0=c is one half of Schwartschild radius of Earth and about .45 cm. For dark cyclotron photons, the wavelength is λ= 1/fc= m/ZeBend. The identification rn≈ λ gives an estimate for the value of n. fc=10 Hz for Fe++ would give for v0=c the estimate λ ≈ 2π RE and n≈ 6× 104.
This picture allows us to reconsider a long-standing question relating to the notion of MB with an onion-like layered structure. What could this sentence mean quantitatively?
  1. The gravitational magnetic body could be a layered structure containing the Bohr orbits with Bohr radii rn ∝ n2 of particles in the gravitational field of Earth. Particles with different masses would concentrate at the same orbits. One would have the shell structure of the ordinary atom.
  2. Flux sheets with a cylindrical rotational symmetry containing the orbits can be considered. These surfaces should be realized as preferred extremals of the action and should be minimal surfaces in H=M4× CP2. As closed surfaces they cannot define minimal surfaces of the Euclidean 3-space E3. Indeed, soap bubbles are not minimal surfaces but require a constant pressure difference between interior and exterior. The analog of pressure difference would be non-trivial and dynamic 1-D projection of 4-D surface to CP2 (see this). The liberation of metabolic energy quantum would be analogous to a transition of hydrogen atom to a lower energy state.
See the article Hen and egg problems of biology from TGD point of view or the chapter Molecular Signalling from the TGD Point of View.

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

Articles and other material related to TGD.

Saturday, March 19, 2022

Hen-egg problem: did RNA or proteins come first?

The notions of magnetic body, dark matter as heff=nh0 phases, dark analogs of information molecules, and resonance mechanism could allow a solution to the hen-egg-problem of biology: which came first, DNA, RNA, or AAs.

Hen-egg problem usually means that something is missing from the conceptual picture and TGD based quantum biology suggests what this missing piece could be. The general solution of the problem in TGD would be that dark analogs of information molecules emerged first simultaneously as Galois confined states of dark proton-triplets and dark photon-triplets.

This made possible resonance communications and the basic recognition mechanism by 3-resonance for dark 3-photons. DX-X pairing was based on energy resonance and these composites were able to find each other by resonance. The reduction of heff for connecting flux tubes in their shortening liberated energy making it possible to overcome the potential wall preventing chemical reactions to occur.

The challenge is to develop a more detailed picture around these basic ideas. I have already earlier considered several proposals for the first steps of the evolution of basic bio-molecules (see this, this and this) but without the recent, rather detailed, view about resonance mechanism combined with the notion of dark 3N-photon and 3N-nucleon as a dark analog of basic biomolecule (see this).

Did the DX-X pairing occur simultaneously for all basic biomolecules?

Consider first the pairing of basic information molecules X (DNA, RNA, tRNA codons and AAs). Their polymers are not considered in this section. The simplest vision is that the dark variants of basic biomolecules emerged by Pollack effect in water irradiated by solar light. This is discussed from the TGD point of view here).

  1. Pollack effect generated exclusion zones (EZs) as negatively charged regions. Part of protons were transferred to magnetic monopole flux tubes of MBs assignable to water clusters and created phases of water with a hexagonal lattice-like structure.
  2. An attractive possibility is that the notion of hydrogen bonds generalizes. The monopole flux tubes could be accompanied by hydrogen bonds. This predicts a length scale hierarchy of hydrogen bonds implying long range quantum correlations in arbitrarily long scales and allowing to understand the strange thermodynamic anomalies of water. The length of the dark flux tube is proportional to heff as also the total energy consisting of K\"ahler magnetic and volume contribution.
  3. Galois confinement as a universal bind mechanism would give rise to sequences of dark protons as bound states. The states of dark proton triplet correspond to DDNAs, DRNAs, DtRNAs and DAAs.

    The pairing of the dark analogs of biomolecules with ordinary biomolecules to form pairs DX-X gave rise to the observed basic biomolecules. DX-X pairing requires that the ordinary biomolecules have transition energies, which correspond to the cyclotron transition energies of DX for the value of heff considered. Ordinary cyclotron transitions and vibrational transitions are good candidates in this respect.

  4. Energy resonance condition for the pairs gives powerful conditions and selects the allowed biomolecules. The selection has not been completely unique. In tRNA the third letter of the chemical codon paired with one of the 32 DtRNAs need not be an ordinary nucleotide and in some viruses adenosine (A) is replaced with 2-amino-adenine ("Z") (see this).
Did AA/DNA/RNA polymers emerge first?

It is not at all clear whether the dark variants of the polymers of basic bio-molecules can emerge spontaneously. The problem is that the formation of valence bonds requires energy. This forces us to consider the TGD counterparts of the usual purely chemical proposals in which basic building bricks DNA, RNA and AAs form polymers. Now one considers an analog of polymerization at the level of DDA, DRNA, and DAA.

The findings of Montagnier et al discussed from the TGD view point in here suggests that remote DNA replication occurs in absence of DNA template but that the presence of DNA polymerase is necessary. Dark DNA sequences generated by remote replication would appear as a template. This suggests DDNA-DNA pairing could occur by polymerization and require the presence of enzymes and metabolic energy feed.

Could proteins (Ps) have served in the role of egg in the chemical sense in the TGD framework? Could the resonance mechanism together with the TGD view about bio-catalysis make it possible to generate DP-P pairs by a polymerization-like process using DP as a template?

  1. The large heff between DP and P would be shortened in a given polymerization step. Energy would be liberated as the dark flux tube bond between DP and P is shortened. This energy should make it possible to overcome the potential wall preventing the formation of the peptide bond and also provide the energy of the peptide bond, which is about .08-.16 eV and considerably smaller than metabolic energy quantum about .5 eV.
  2. The thermal energy at room temperature using the definition ET=kT is .025 eV. Second definition of thermal energy is as the energy for which the distribution of black-body radiation as function of energy is maximum: this gives the energy is ET \simeq .12 eV and rather near to the Josephson energy of the cell membrane for charge Z= 2e is about .1 eV.
  3. The energetic requirements for AA polymerization might be satisfied by using irradiation with photon energy around thermal energy at room temperature. An interesting possibility consider in \cite{allb/geesink} is that a cell membrane formed from lipids and acting as a Josephson junction was formed before the polymerization of AAs and the Josephson radiation from the cell membrane with energy of order .1 eV provided the metabolic energy for the polymerization process.
  4. In the case of DNA and RNA the carbon bond energy between two codons is about 3.2 eV and considerably larger so that the polymerization without enzymes looks highly implausible.
There is empirical and experimental support for this vision. There is evidence for amino acid glycine in interstellar space (see this) but the independent confirmation is lacking.

Also the formation of glycine peptides has been observed in laboratory conditions mimicking the interstellar medium (ISM). The following summarizes the results described in the article of Serge Krasnokutski et al published in Nature (see this). The following summarizes Krasnosutski's non-technical description of the results (see this).

  1. The ultra-low temperatures, common in astrophysical environments, have been believed to freeze out any chemistry in the dense areas of the ISM. Already the discovery of a high abundance of small organic molecules in molecular clouds was a great surprise. But also the formation of amino acids, nucleobases, lipids, and sugars in space has been confirmed.
  2. What about the polymers of AAs? It has been conjectured that the condensation of carbon atoms at the surface of dust particles make possible the formation of organic molecules. Serge Krasnokutski et al indeed demonstrated the formation of glycine polymers from amino ketenes (glycine corresponds NH2-CH2-COOH, aminoketene to NH2-CH-CO and polyglycine to NH-CH2-CO) under laboratory conditions simulating the ISM conditions at temperature T=10 K (see this). A spontaneous(!) formation of relatively short peptides (less than 10-11 monomeric units) was found. The polymerization of amino acids under energetic processing (e.g. heat, pressure, or UV irradiation) is known to occur. Therefore, a further increase in chain length can be expected in natural environments.

    Moreover, by adding other species instead of a proton to the \alpha-carbon atom of amino ketene (nearest to the functional group) during the polymerization, a variety of different peptide chains can be formed. Furthermore, chemical and photochemical modifications of glycine residues in peptides into other amino acid residues were also demonstrated in many works. Thus, the glycine peptides observed in our experiments can be converted into different proteins.

  3. These findings fit nicely with the proposed mechanism for the formation of proteins (or at least short peptides). The mechanism is not chemical, and no radiation is needed since the generalized Josephson radiation would provide the energy of the AA-AA bond, and the formation rate does not vanish at ultralow temperatures.
See the article Hen and egg problems of biology from TGD point of view or the chapter Molecular Signalling from the TGD Point of View.

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

Articles and other material related to TGD.

Thursday, March 17, 2022

Molecular Signalling from the TGD Point of View

The findings of Elowitz et al lead to a formal model suggesting that ligands of type BMP (bone morphogenetic protein) have interactions. The interactions would be non-local so that it is difficult to imagine that they could have chemical origin. The TGD based model for these long range interactions is based on dark photon resonance. For the simplest, receptors would correspond to fixed bio-harmonies. In a single ligand system the ligand would have the bio-harmony of its preferred receptor. The interaction between ligand magnetic bodies would be re-tuning and could replace the preferred bio-harmonies assignable to the participating ligands with distributions of bio-harmonies. Therefore the ligands of the multi-ligand system would couple by bio-resonance also to other than preferred receptors.

The model stimulates questions, which lead to a rather detailed model for the re-tuning and tuning processes at the level of codons and amino acids. The model suggests that the tuning to a given bioharmony for the dark counterparts of basic biomolecules and its stabilization involves epigenetic control based on the methylation of some special DNA and RNA nucleotides and amino-acids acting as analogs of tuning forks.

The proposal that bioharmonies are molecular correlates for emotions suggests that this process involves minimal number of methylations, which define the seed of phase transition to a bioharmony in the scale of the basic unit of genome (such as gene), mRNA sub-unit (splicing) and protein sub-unit.

See the article Molecular Signalling from the TGD Point of View 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.

Tuesday, March 08, 2022

The effects of Cambrian Explosion in deep mantle: TGD point of view

There was an interesting popular article titled "Traces of life in the Earth's deep mantle" in Phys-Org (see this). The article told about the work of Giuliani et all about discussed in the article "Perturbation of the deep-Earth carbon cycle in response to the Cambrian Explosion" (see this).

The sudden emergence of advanced multicellular lifeforms in the Cambrian Explosion (CE) about 540 Ma ago is still one of the great mysteries of mainstream biology. The team led by ETH researcher Andrea Giuliani found in rocks from deep mantle what can be regarded as traces of CE. The proposal is that partly organic material would have been subducted to the deep mantle after CE and changed the isotopic compositions of Carbon and other elements. Also other elements, for instance strontium and hafnium showed a pattern similar to carbon.

The group of Giuliani examined rare diamond-containing volcanic rocks known as kimberlites from different epochs of the Earth's history. These special rocks originate from the lowest regions of the Earth's mantle. The isotopic composition of carbon in about 150 samples of these special rocks was determined. The composition of younger kimberlites, which are less than 250 million years old, was found to vary considerably from that of older rocks. In many of the younger samples, the composition of the carbon isotopes is outside the range that would be expected for typical rocks from the mantle.

The isotope ratio R=13C/12C for Carbon in the deep mantle is considerably lower for the kimberlites younger than 250 Ma whereas the value for kimberlites older than 250 Ma is typical mantle value. The values of younger kimberlites are also more variable. More quantitatively, δ(13C)= (Rsample/Rstandard -1)× 103 serves as a parameter. For a typical sample from the mantle, the value is δ ≈ -5+/- 1 per mille whereas for the studied samples δ is in the range [-20.-30] per mille.

The increased subduction caused by plate tectonics of the material from the surface of Earth could explain this. The estimate is that it takes 200 Ma for the material from the surface to reach the lower mantle. In the standard geology, the natural interpretation is that the dramatic increase in the generation of organic matter in CE has reduced the carbon isotope ratio. One must however assume that the partly organic material from the surface should have ended down to the deep mantle along specific routes by subduction.

Is the TGD inspired hypothesis for Cambrian Explosion life consistent with these findings?

  1. The proposal is that life evolved in underground oceans ("womb of Mother Gaia'') and suddenly emerged to the surface in the CE as highly developed multicellular organisms. CE was caused by a rapid increase of Earth radius by factor 2, which generated bursts of the underground water reservoirs to the surface and created the oceans. The expansion broke the Earth's crust to pieces and led to the emergence of plate tectonics, subduction, and oceans. Note that in Mars this tectonics is not present and the radius of Mars is actually roughly 1/2 of the radius of Earth.
  2. The rapid increase of the Earth radius is the TGD counterpart for a smooth increase of Earth radius in cosmic expansion. All astrophysical objects look as if they would not participate in cosmic expansion: this is a mystery in general relativity. In TGD this mystery is resolved by replacing smooth cosmological expansion with a sequence of rapid expansions followed by stationary periods (see this and this.
Is the TGD view consistent with the findings of Giuliani et al?
  1. The conclusion of Giuliani et al seems undeniable: the isotope decomposition in the mantle changed 200 Ma ago and was caused by the transport of the material affected by CE to the lower mantle.
  2. In the TGD framework these findings do not however force the conclusion that life emerged suddenly in CE. Rather, multicellular life was present in the underground oceans before CE but plate tectonics and subduction were absent.

    The increase of the radius of Earth reduced the average density of Earth dramatically, and created the proposed subduction routes to the lower mantle, which dramatically increased the rate of transport of the organic material to the deep mantle.

  3. >Interestingly, the process analogous to CE appears to have occurred episodically throughout most of Earth’s history, with the oldest diamonds that contain eclogitic inclusions forming at roughly 3 billion years (Ga) (see this). In the TGD framework this suggests that the rapid expansions of Earth have occurred episodically and have led to the emergence of life forms from the interior to the surface and the transport of the material containing organic carbon to the mantle.
See the article Updated version of Expanding Earth model or the chapter Expanding Earth Model and Pre-Cambrian Evolution of Continents, Climate, and Life

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

Articles and other material related to TGD.

Monday, March 07, 2022

Objection against generalized OZI rule

In TGD, only quarks are fundamental particles and all elementary particles and actually all physical states in the fermionic sector are composites of them. This implies that quark and antiquark numbers are separately conserved in the scattering diagrams and the particle reaction only means the-arrangement of the quarks to a new set of Galois singlets.

At the level of quarks, the scattering would be completely trivial, which looks strange. One would obtain a product of quark propagators connecting the points at mass shells with opposite energies plus entanglement coefficients arranging them at positive and negative energy light-cones to groups which are Galois singlets.

This is completely analogous to the OZI role. In QCD it is of course violated by generation of gluons decaying to quark pairs. In TGD, gauge bosons are also quark pairs so that there is no problem of principle.

There is an objection against this picture.

  1. If particle reactions are mere recombinations of Galois singlets with Galois singlets, the quark and antiquark numbers Nq and Nqbar of quark and antiquark numbers are separately conserved (as also their difference Nq-Nqbar). This forbids many reactions, for instance those in which a gauge boson is emitted unless one assumes that many quark states are superpositions of states with a varying total quark number N. This would mean that the extremely simple re-combinatorics picture is lost.
  2. Crossing symmetry, which is a symmetry of standard QFTs, suggests a solution to the problem. Crossing symmetry would mean that one can transfer quarks between initial and final states by changing the sign of the quark four-momentum so that momentum conservation is not violated. Crossing means analytic continuation of the scattering amplitude by replacing incoming (outgoing) momentum p with outgoing (incoming) momentum -p. The scattering amplitudes for reactions for which the quark number is conserved can be constructed using mere recombinatorics, and the remaining amplitudes would be obtained by crossing.
  3. Crossing must respect the Galois singlet property. For instance, the crossing of a single quark destroys Galois singlet. Unless one allows destruction and recombination of Galois singlets, the crossing can apply only to Galois singlets. These rules bring to mind the vanishing of twistor amplitudes when one gluon has negative helicity and the remaining gluons have positive helicity.
See the article About TGD counterparts of twistor amplitudes: part II or the chapter About TGD counterparts of twistor amplitudes.

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

Articles and other material related to TGD. 

TGD view about water memory and the notion of morphogenetic field

Besides general problems, which might be regarded as philosophical, the anomalies of the physicalistic world view have served as the source of inspiration. Several poorly understood phenomena have played a central role in the "Poiroting-like" process leading to the development of TGD based views about quantum biology. Mention only the effects of ELF em fields on vertebrate brain, biophotons, water memory, Pollack effect, and Comorosan effect. The notion of syntropy by Fantappie, which challenges the belief that the arrow of time is not always the same in living systems, has been also inspiring.

In this article I will discuss the TGD based vision and the above listed phenomena, which are often forgotten. I will also compare the TGD based view with the proposed interpretation of morphogenetic field as em field generated by DNA and realizing genetic code discussed in the articles of Savelev et al, and compare it with the TGD based models of genetic code realized in terms of dark nucleons and dark photons. The findings described in these articles and in the articles of Yolene Thomas about water memory also provide new tests for the TGD based view. As always, this kind of process led to some new ideas and insights.

See the article TGD view about water memory and the notion of morphogenetic field 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.