Quantum gravitation as an explanation for the different chemistries of living and inanimate matter

If gravitationally dark hydrogen and valence bonds are relevant to biology, their effects should distinguish between matter in vivo, gel phase and matter in vitro. The difference should be especially clear at physiological temperatures. Is there any empirical evidence for the deviations from what is inspected on the basis of the standard biochemical intuition?

The interactions between DNA metal ions present living matter could serve as a test for the proposal. In the TGD framework, both metal ions and DNA could be gravitationally dark (in vivo or gel phase) or ordinary (in vitro phase).

1. For the DNA and metal ions as they are usually understood, the phosphate ions (PO₄)^- of DNA should have interactions with metal ions and the concentrations should affect the properties of DNA. This should be true both in vivo and in vitro.
2. In the TGD framework, DNA strand in vivo and in gel phase would be accompanied by a dark DNA strand. The phosphate ions (PO₄)^- would be replaced with pseudo-ions (PO₄)^"-", in the sense that the ion O^- would be replaced with agravitationally hydrogen bonded structure O...H-O-H such that the HB carries a gravitationally dark proton delocalized in a very long scale. The effective negative charge would be associated with OH^"-" pseudo ion rather than being a real negative charge assignable to O.

   Outside the physiological temperature range and in vitro, the oxygen ion would be real and the situation would be as in the standard chemistry apart from the possible effects of darkness of metal ions. The simplest assumption is that both metal ions and DNA are dark at the same temperature range only.

3. (Gravitationally) dark metal ions of type X⁺⁺ would also have a dark valence electron at flux tube. One can speak of dark salt since flux tube bonds would connect X with H₂O₂. Same applies to Cooper pairs of dark ions X⁺.

   The phosphate of DDNA-DNA pair has Coulomb interaction with neither ordinary nor dark ions but the metal ion would interact with OH^"-". This suggests that the presence of metal ions does, and ions in general, has no strong effect on the DNA properties in vivo. Besides realizing genetic code, dark DNA would shield the system from the perturbations caused by various ions.

4. Experimentally this seems to be the case. Most interactions between DNA and ions are modelled and studied experimentally in dilute water solutions. According to the following article, under these conditions the DNA interaction with charged ligands, the helix-coil transition temperature, and other DNA properties are strongly dependent on the low-molecular-weight salt concentration, see the same article and references therein. However, for condensed DNA states (fibers, gels) or in vivo, similar characteristics are often independent of or only slightly dependent on the ionic composition of the solvent.

See the article Quantum gravitation and quantum biology in TGD Universe 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.

Could quantum gravitation play a key role in the DNA metabolism and DNA replication and transcription?

TGD inspired quantum biology leads to the proposal that quantum gravitational variants of hydrogen bonds (HBs) and valence bonds assignable to metal atoms play a fundamental role in metabolism and biocatalysis.

DNA base pairs are connected by 2 (A-T) or 3 (G-C) hydrogen bonds (HBs): what could this mean from the point of view of DNA energy metabolism and from the point of view of the splitting of DNA double strand in DNA replication and transcription?

1. If these strands can appear as dark gravitational strands, the maximum of 2 (3) metabolic quanta could be liberated in A-T (G-C) pairs via a transformation to ordinary HBs. Could this serve as a yet-unidentified source of metabolic energy in the replication and transcription?
2. Could the dark/organic mono-phosphates of the double DNA strand serve as a source of metabolic energy for DNA transferred to the HBs connecting base pairs?
3. Suppose that the DDNA parallel to DNA corresponds to a sequence of gravitational HBs B_gr as loops associated with the organic phosphates. Codon would correspond to a bound state of dark protons associated with three dark gravitational HBs.

   Consider an ordinary HB A_ord associated with a base pair and B_gr associated with the corresponding dark/organic phosphate. Can one transform A_ord to A_gr to achieve the transfer of metabolic energy?

   Two reconnections for a HB pair (A_ord,B_gr) can transform the pair to (A_gr,B_ord). The gravitational dark proton and metabolic energy would be transferred to basepair from the organic phosphate, which itself would become an organic phosphate ion P₁^-.

   Note: Also the phospholipids of the cell membrane are accompanied by a monophosphate group. Also microtubules are accompanied by GMPs. Could they serve as metabolic energy sources in the cell membrane using the above described mechanism?

The splitting of HBs between base pairs (see this) plays a fundamental role in DNA opening necessary for DNA replication and transcription. These HBs must split during replication and transcription and many other processes such as selective recognition of DNA by proteins, regulation of RNA cleavage by site-specific mutations, and intermolecular interaction of proteins with their target DNA or RNA. Could the notion of gravitational HB provide insights about the process?

1. As the figures of (see this) illustrate, the base pairs of the double DNA/RNA strand have 2 or 3 HBs. HBs of type N-H...O and H-N...O and N-H...N (called imino HB) are possible. Imino HB appears for both A-T with 2 HBs and G-C with 3 HBs.

   Since the hydrogen of X-H...Y is nearer to Y than X, the splitting is expected to give X+ H-Y, X, Y in {N,O}. This is indeed the case when X and Y are different. However, the imino HB N-H...N actually splits to N-H + N rather than the expected N + H-N. An exchange of a hydrogen atom is said to occur.

2. The temporary formation of a gravitationally dark HB could explain how this is possible. The gravitationally dark proton is at a large distance from the N atoms so that they are in a symmetric position and both outcomes for the splitting are equally probable so that the exchange rate increases.
3. This requires a temporary transformation of N-H...N HB to a gravitationally dark HB. Could double reconnection transform the pair (A_ord,B_gr formed by N-H...N HB and dark HB of phosphate bond to (A_gr,B_ord), which then splits?

See the article Quantum gravitation and quantum biology in TGD Universe 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.

Quantum gravitational metabolism in contrast to the standard view about metabolism

In the TGD framework, the gravitational magnetic body would play a key role in metabolism. In the sequel this notion and also a concrete model for the somewhat mysterious high energy phosphate bond (HEPB), playing a fundamental role in the standard picture, is considered. The facts that DNA base pairs are connected by 2 or 3 hydrogen bonds (HBs) and nucleosides are accompanied by monophosphate ions suggest a possible application to DNA metabolism.

Gravitational magnetic body and metabolism

In the TGD framework magnetic body (MB) would serve as the controlling agent receiving sensory information as a frequency modulated dark Josephson radiation and controlling the cell by using dark cyclotron radiation coming as pulses corresponding to resonant receival of Josephson radiation.

The large value of h_eff=h_gr=GMm/v₀ implies that the dark cyclotron radiation in the EEG range would correspond to visible and UV energies.

The intuitive notion is that MB consists of U-shaped monopole flux tubes extending from the system considered and serving as kinds of tentacles. These flux tubes for two systems can reconnectand form a pair of flux tubes connecting the system if the cyclotron frequencies of the tubes are the same so that cyclotron resonance becomes possible.

The question of what the notion of gravitational MB does mean, was considered in here.

1. The dark flux tube would be gravitational with h_eff=h_gr. Gravitational flux tubes have lengths, which can be of the order of Earth size scale and the radii of gravitational Bohr orbits define a natural scale form them.
2. The elongated gravitational flux tubes could correspond to either hydrogen- or valence bonds. The loop-like bond could connect nearby atoms just like the ordinary bond. The delocalization of the charge to the flux tube leads to an effectively ionized donor atom.
3. All values of h_eff are possible. For electromagnetic flux tubes the values of h_eff/h are not very large. This picture leads to a view about hydrogen and valence bonds as bonds having h_eff/h>1 (see this). Also gravitational variants of hydrogen and valence bonds are possible. In this case, the proton or electron would be vertically delocalized in the Earth scale so that the donor atom would be effectively ionized. For instance, a phosphate ion could be an effective ion having a gravitational hydrogen bond with the hydrogen of a water molecule.
4. A gravitational valence bond, connecting a metal atom with an atom with an opposite valence, would lead to effective ionization of the metal atom. For instance, biologically important bosonic ions such as Ca⁺⁺, Mg⁺⁺, Fe⁺⁺ and Zn⁺⁺ associated with their oxides could correspond to effective ions like this.

   The signature would be a pairing with a neutral oxygen atom by a gravitational valence bond. I have introduced the notion of dark ion to explain the findings of Blackman and others and dark ion could correspond to this kind of pair. Note that the original variant of the model assumed that the entire ion is dark, the later version assumed that the valence electron of free atom is dark, and the model considered here assumes that darkness is a property of bond.

5. The effective ionization requires energy Δ E to compensate the increment of the gravitational potential energy given by Δ E=(< V_gr(R)>-V_gr(R_E)). Here E_gr(R) is gravitational potential energy proton or electron, and R_E denotes the radius of Earth, and R is the distance of the point of flux tube from the center of Earth.

   This estimate neglects the kinetic energy of the dark particle at the flux loop. This assumption is not consistent with the localization near the top of the loop so that the estimate can serve only as a rough order of magnitude estimate.

6. The maximal value for Δ E for electron Cooper pair (dark Cooper pair is at infinite distance) corresponds to V_gr(R_E)= .36 meV to be compared with the energy scale .3 meV defined by the temperature of 3 K microwave background and to the value .4 meV of the miniature potential. This suggests that, in the case of the electron, the reduction of kinetic energy contributes more than 10 per cent to the Δ E.

   For a single dark proton one has V_gr(R_E)≈ .34 eV, which is below the nominal value of the metabolic energy currency about .5 eV. If a single dark proton is involved, the reduction kinetic energy should contribute at least 32 per cent to Δ E.

   For a dark proton Cooper pair, one has the maximal value of Δ E= .68 eV somewhat above the metabolic energy quantum. These findings support the idea that both proton and electron Cooper pairs give rise to metabolic energy quanta. The challenge is to understand the mechanism for the formation of proton Cooper pairs.

7. The transformation of electrons and protons between ordinary and gravitationally dark states would be a key process of metabolism and biocatalysis. This conforms with the fact that proton and electron exchanges play a key role in biology. For instance, phosphorylation means that the receiving molecule gains phosphate, which can form gravitationally a dark hydrogen bond so that the system becomes metabolically active. This would correspond to the activation in bio-catalysis.

   DNA base pairs are connected by 2 (A-T) or 3 (G-C) hydrogen bonds. If these strands can appear as dark gravitational strands, the maximum of 2 (3) metabolic quanta could be liberated in A-T (G-C) pairs via a transformation to ordinary hydrogen bonds. Could this serve as a yet-unidentified source of metabolic energy in the replication and transcription?

8. In the same way, in a redox reaction, the electron donor is oxidized and the electron receiver is reduced. Reduced molecule gains the ability to have a gravitationally dark electron, and therefore becomes metabolically active in the electronic sense. Redox reaction would be the electronic counterpart for phosphorylation.

Dark gravitational bonds, high energy phosphate bond, and DNA

How could the somewhat mysterious high energy phosphate bond (HEPB) associated with di-phospates (DP) and tri-phosphates (TP) relate to the gravitationally dark hydrogen bonds (HBs)?

1. HEPB (see this) is identified as the bond ...--O--... connecting to P atoms in ATP or ADP (see this). Hydrolysis involves also one H₂O molecule. The -O-P bond splits inducing the splitting of ATP to ADP and inorganic phosphate P_i. One cannot assign HEPBs to the monophosphates (MPs) associated with DNA so that the splitting of the O-P bond must play an essential role..
2. It is best to start by listing the facts about ATP\rightarrow ADP +P_i+2H⁺ reaction for which the Wikipedia article (see (see this) gives both graphical representation and the overall formula for the reaction.

   In the initial state 4 O-atoms of ATP have a visible negative charge. The simplest assumption is that all ions O^- actually correspond to gravitationally hydrogen bonded O...H pairs with a delocalized proton charge so one should use the notation O^"-". The same assumption is natural also for ADP and AMP. This would define the meaning of organic phosphates. In the final state both P_i and ADP have visible charge -3 to give a total visible charge -6.

   2H⁺ in the final state guarantees the conservation of the visible charge in the reaction.

3. The P(O^"-")₂ of the third phosphate transforms to an inorganic phosphate P_i. A natural interpretation is that the gravitationally dark protons become ordinary ones. This explains 2H⁺ in the final state. This reaction would liberate part of the metabolic energy.
4. One H₂O molecule is used in the reaction. The natural assumption is that one hydrogen of H₂O has a dark gravitational HB with the oxygen appearing in O-P of (O^"-"₂P=O)-O-P... so that it one has O^"-" visible charge -1. The bond ...P-O-...H becomes the effective oxygen ion of ...P-O^"-" of P_i so that P_i would not be completely inorganic. The remaining OH of the water molecule becomes one O^"-" of P of ADP. Also this reaction can liberate metabolic energy.

DNA base pairs are connected by 2 (A-T) or 3 (G-C) HBs: what could this mean from the point of view of DNA energy metabolism?

1. If these strands can appear as dark gravitational strands, the maximum of 2 (3) metabolic quanta could be liberated in A-T (G-C) pairs via a transformation to ordinary HBs. Could this serve as a yet-unidentified source of metabolic energy in the replication and transcription?
2. Could the dark/organic mono-phosphates of the double DNA strand serve as a source of metabolic energy for DNA transferred to the HBs connecting base pairs?
3. Suppose that the DDNA parallel to DNA corresponds to a sequence of gravitational HBs B_gr as loops associated with the organic phosphates. Codon would correspond to a bound state of dark protons associated with three dark gravitational HBs.

   Consider an ordinary HB A_ord associated with a base pair and B_gr associated with the corresponding dark/organic phosphate. Can one transform A_ord to A_gr to achieve the transfer of metabolic energy?

   Two reconnections for a HB pair (A_ord,B_gr) can transform the pair to (A_gr,B_ord). The gravitational dark proton and metabolic energy would be transferred to basepair from the organic phosphate, which itself would become an organic phosphate ion P₁^-.

   Note: Also the phospholipids of the cell membrane are accompanied by a monophosphate group. Also microtubules are accompanied by GMPs. Could they serve as metabolic energy sources in the cell membrane using the above described mechanism?

See the article Quantum gravitation and quantum biology in TGD Universe 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.

Objection against the quantum gravitational metabolism

TGD based view about quantum gravity, which involves in an essential manner gravitational flux tubes and the notion of gravitational Planck constant h_gr, leads to a very nice picture about metabolism predicting correct order of magnitude for the metabolic energy quantum .5 eV assignable to the proton of the hydrogen bond transformed to a long gravitational loop in Earth scale. This increases the energy of the proton and the increment serves as metabolic energy liberated when the loop reduces to an ordinary hydrogen bond in the transition h_gr→ h.

A new metabolic energy quantum assignable to a dark electron Cooper pair is predicted and is assignable to a dark gravitational valence bond of metal ion X⁺⁺ or two metal ions of type X⁺ forming a dark Cooper pair with hydrogen peroxide H₂O₂, which is reactive oxygen species (ROS). As in the case of the dark proton of the hydrogen bond, only an effective ion is in question since the Cooper pair is at the gravitational flux tube.

Note that the transformation of the proton of hydrogen bond and electrons of valence bonds provides a mechanism, which makes it possible to control for instance membrane potential which is expected to be central in the control of nerve pulse generation. DNA base pairs are connected by hydrogen bonds and the control mechanism might be at use also here.

An estimate for its maximal value is obtained by scaling the ordinary metabolic quantum by the ration m_e/m_p and equal to .36 meV. The miniature membrane potential has value about .4 meV which is 10 per cent larger.

In the first approximation, the estimate for the maximum of the metabolic energy quantum is as the gravitational binding energy at the surface of Earth. The estimate neglects the kinetic energy of the dark particle at the flux tube, which can be reduced as the flux tube reduces to ordinary valence bond or hydrogen bond.

According to the simple model, bio-chemistry would strongly depend on the local gravitational environment. Could this be used to kill the idea?

1. For an object with mass M and radius R, the estimated maximal gravitational metabolic energy quantum E_max is scaled up by factor is scaled up by a factor z= (M/M_E)× (R_E/R). The values of z for Mars, Venus, and Moon are (.02,.86,.05). For Venus, which is called the sister planet of Earth, z is not too far from unity. Note that in the case of the Moon, the Earth's gravitational potential and therefore E_max associated with it would be by a factor z= R_E/R_Moon= .017 smaller than at the surface of Earth.

   Solar gravitational potential cannot come to rescue. At distance of AU (Earth's distance from Sun) the scaling factor of E_max would be z= (M_S/M_E) (R_E/AU) =.014. The values E_max are typically few per cent of the desired value.

   The model in its simplest version would predict that terrestrial life is not possible on Mars and Moon. Humans have however successfully visited the Moon.

2. Rather than giving up the idea, it is better to ask what goes wrong with the simplest model. It is assumed that dark charge at the gravitational bond does not possess any kinetic energy, which would increase the value of the metabolic energy quantum. This is of course an oversimplification and already the predicted slightly too low maximal value of the gravitational electronic metabolic energy quantum suggests that kinetic energy cannot be neglected.

   The simplest model for the particle at gravitational valence bond is as a particle in a box with kinetic energies given by E_n= n²ℏ_eff²/mL², L the length of the loop. If L scales like h_eff, the kinetic energy does not depend on h_eff. Therefore the scale of kinetic contribution can be estimated in a molecular length scale.

   Could the system adapt to a reduction of the maximal gravitational potential at the surface of Moon, Mars, or Venus by increasing the average value of n in the superposition of the standing waves having maximum at the top of the valence loop? The system would adapt by increasing the localization of the dark charge at the top of the loop. The reduction of the bond length would mean reduction of the superposition to n=0 wave so that the kinetic energy would be indeed liberated.

See the article Quantum gravitation and quantum biology in TGD Universe or the chapter with the same title.

To sum up, the model survived the first killer test and led to a more precise formulation of the hypothesis. For a summary of earlier postings see Latest progress in TGD.

Articles and other material related to TGD.

Is Standard Model tumbling down?: W boson mass is .1 per cent higher than predicted!

Particle physicists have found a new anomaly (see this). The  measured mass of the W boson is by .1 per cent higher than predicted by high precision calculation! For a layman .1 per cent does not sound like an earthquake but, in the accuracies achieved, it is. Weak interactions are indeed weak, this kind of accuracy is possible. Physics has become incredibly precise!  

This makes every builder of TOE humble! Of course, a new theory cannot achieve the precision of the predictions of the standard model. What is needed  is understanding at a qualitative level and despite its marvellous accuracy, standard model cannot provide this understanding.

This anomaly  suggests new massive particles. Also the earlier earthquakes,  the CP breaking anomaly of B mesons and   g-2 anomaly  for muon,  suggest new massive  particles.

Using the language of  quantum field theory (QFT),  new particles should appear in self-energy loops of the W boson. Also the QFT limit of TGD uses this language although it is replaced with something much more elegant at the fundamental level (see this and this).

Can one understand these anomalies in the TGD framework.

1. In the TGD framework, the family replication phenomenon for fermions (one has three  quark and lepton generations) is  explained topologically and the  CKM mixing of fermions as induced by their  topological mixing.   This goes outside the standard model which just assumes CKM mixing without any attempt to understand it.

    The new physics prediction is that also the gauge bosons and graviton have the analog of family replication (see this and this).  

2. Fermions would have 3 generations, which correspond to 3  topologies for a  2-D  wormhole throat characterized by the number of handles: sphere, torus as sphere with one handle, and  sphere with two handles.  

    For a higher number of handles, one would have analogs of many-particle states with handles regarded as particles moving around the sphere like free particles: mass spectrum would be continuous - one could talk about ur particles.

   For the 3 lightest genera there is  Z₂ conformal symmetry irrespective of conformal moduli. This symmetry  allows a bound state of 2-handles. One can assign a dynamically generated symmetry group SU(3)_g to these 3 fermion states (electron, muon, tau + plus neutrinos and 3 quark generations). Fermions of these  3 generations  form a triplet.

3. Bosons would correspond to pairs of wormhole throats characterized by handle number and group theoretically  to  a tensor product  3× 3  of fermion  triplets (see this and this).  This would give a singlet and octet. Singlet would correspond to ordinary gauge bosons and gravitons. For singlet, ordinary gauge bosons,  the couplings to fermions would be the same for all genera.  

   Octet would contain 2 states with vanishing SU(3)_g quantum numbers plus 3+3=6  SU(3)_g charged states. Let us refer to  these 2  states as "2 exotics". The 2 exotics  have vanishing SU(3)_g quantum numbers and  are  analogs of  neutral pion π0 and η in good old hadron physics involving strong isospin and strangeness.  

   An intuitive guess is that the 3+3  SU(3)_g "charged" states are heavy (analogous to kaon K and charged pions π^{+/- in the old-fashioned   quark model). Thus 2+6  new states with the same standard model quantum numbers as the existing ones, are predicted, and the 2 exotics are expected to be light.} 

The  exotics appear in  various loop corrections at the QFT limit of TGD.

1. Exotics could explain the anomalous CP violation for neutral B mesons. The couplings to fermions  specified by SU(3)_g charge matrices, which are  orthogonal for the 3 generations and therefore cannot be the same for all generations. One  would have a violation of universality and this is at the core of CP violation anomaly.  
2. The (2) exotics could also explain the anomaly of g-2 anomaly (yes: anomaly of anomaly!) of muon.

 Could the  exotics also explain  the W mass anomaly?  Could a mixing  between ordinary gauge bosons and  (2)  exotics give a positive  contribution to the  self-energy loops of W and increase the mass slightly?  If  the mass changes in this manner, it must increase. This is encouraging.

1. Fermionic generations mix topologically. For instance, a sphere becomes a quantum superposition of several topologies  containing  mostly sphere  and  a little bit of torus and also  a sphere with two handles.  CKM mixing  is essentially the  difference of the topological mixings for U and D type quarks.

   Could also  gauge bosons with the same SU(3)_g quantum numbers belonging to singlet and octet  mix?  A pair of spherical wormhole throats  would get a small contribution from a pair of torus and g=2  wormholes.

2. Could one find some support for the mixing   idea existing hadron physics? Vector boson dominance of the good old hadron physics assumed that photons can mix with rho mesons. ρ mesons correspond to quark pairs completely analogous to the analog of the  first SU(3)_g singlet (analog of pion).

    This  mixing would be caused by the decay of photons to a quark pair in turn forming a ρ meson.

   Exactly the same could happen for SU(3)_g.   An ordinary gauge boson would decay to a virtual quark pair,   which would combine with a small amplitude also  to an exotic gauge boson, which is actually a superposition of fermion pairs in TGD. This would be  induced by  the topological mixing.

3. What about self energy corrections from the  intermediate gauge boson pairs appearing in self-energy loops? They are certainly very small but in the TGD framework, they do not appear at the fundamental level in the lowest order.

   The reason is  that in the   TGD  Universe also gauge bosons are  quark and lepton pairs: there are no fundamental bosons in the TGD Universe since bosons emerge from fermions as fermion-antifermion pairs (two pairs for gravitons).

   Also leptons,  could emerge from quarks but that is another story (see  this). The  fundamental particle physics  reduces to that for quarks (see  thisthis).

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

Articles and other material related to TGD.

The language of fungi

After having written an article related to the pre-neutral system (pre-cns) I learned of a fascinating discovery of Andrew Adamatsky (see this), who has studied sponges and found that they show electrical activity sequences of analogs of action potentials ('spikes').

The abstract of the article gives an overview about the findings.

Fungi exhibit oscillations of extracellular electrical potential recorded via differential electrodes inserted into a substrate colonised by mycelium or directly into sporocarps. We analysed electrical activity of ghost fungi (Omphalotus ni- diformis), Enoki fungi (Flammulina velutipes), split gill fungi (Schizophyllum commune) and caterpillar fungi (Cordyceps militari). The spiking characteristics are species specific: a spike duration varies from one to 21 hours and an amplitude from 0.03 mV to 2.1 mV.

We found that spikes are often clustered into trains. Assuming that spikes of electrical activity are used by fungi to communicate and process information in mycelium networks, we group spikes into words and provide a linguistic and information complexity analysis of the fun- gal spiking activity. We demonstrate that distributions of fungal word lengths match that of human languages. We also construct algorithmic and Liz-Zempel complexity hierarchies of fungal sentences and show that species S. commune generate most complex sentences.

The amplitude of spikes varies in the range .03- 2.1 meV. This range is consistent with the interpretation as analogs of miniature potentials corresponding to the reduction of the gravitational energy and having maximal value .4 meV. The natural question is whether this kind of communication is specific to fungi or occurs also in preunoral and neuronal systems in general.

The language hypothesis conforms with the TGD based view that the dark variants of genetic code realized using as codons dark photon triplets analogous to 3-chords defining what I call bioharmony serving as a correlate for emotional state and fundamental level (see this and this). Dark 3N-photons as representation of for instance genes, define analogs of music pieces. For the TGD based view of the emergence of human language see (see this). Genetic code would have number theoretic and geometric origin and would be universal. It would have several realizations and be realized also in other than biological systems.

Dark 3N-photons are analogous to Bose-Einstein condensate of 3N-photons and correspond to so-called Galois singlets, whose formation would rely on a universal number theoretical mechanism for the formation of bound states.

The sequence of dark codons selects the receiver, which must possess the same sequence of dark nucleon triplets to achieve resonance. If the frequency scale is modulated, the reception generates a sequence of 3N-pulses analogous to nerve pulse sequence and in this way transforms information coded to frequency modulation to a pulse sequence.

See the article Quantum gravitation and quantum biology in TGD Universe 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.

Implications of the model of pre-nervous system to the basic biochemistry and model nerve pulse

In the following I try sharpen the basic notions and the ideas about what happens in nerve pulse conduction. Also the relationship between biochemistry and TGD view about quantum biology will be discussed and lead to highly non-trivial insights about the role of the basic biomolecules.

1. Clarification of some basic concepts

In the following I try to further clarify the basic notions used in order to identify the weaknesses of the scenario.

1.1 About the notion of dark ion

The original view was that dark ion as a whole resides at the flux tube. Later this statement became more precices: dark ion is touches the , say gravitational, dark flux tube with h_eff>h. This applies also to both gravitational, electromagnetic, weak, and color flux tubes and ordinary bonds correspond to electromagnetic flux tubes with h_eff=h_em (see this).

The entire dark ion touching the flux tube would have wave function in the magnetic field of flux tube having the touching point as argument. Cyclotron states are natural.

The more precise view considered already earlier is that one has effective ion: the dark elecron or Cooper pair resides at gravitational flux tube is not bound to the atom as effective ion. The predictions for dark cyclotron states are same as for the older picture and the predictions related to the dark electron or proton are new.

1.2 About the notion of electric flux quantum

What does one mean the flux tube parallel to axon?

1. I have talked assigned to axon a magnetic flux tube parallel to it and accompanied by magnetic flux tubes transversal to it. This would correspond to a 3-D network of flux tubes.

   The problem has been how to describe the membrane structure with electric field and electric flux orthogonal to the flux tube. This situation requires genuine electric flux quanta analogous to magnetic flux quanta and the time dependent deformations of the magnetic flux tube cannot give them. However, magnetic flux tubes allow very simple time dependent deformations allowing longitudinal electric flux along the tube.

2. Could electric flux quanta associated with a pair of lipid layers correspond to a pair of membrane-like objects having 1+2-D rather than 4-D M⁴ projection connected by time-dependent deformations of transversal magnetic flux tubes carrying a longitudinal electric field?
3. Unfortunateluy, I did not have any candidate for an explicit solution of field equations describing 2-D membrane-like object such as cell body or axon. For some time ago I finally understood 2-D membrane-like objects in terms of 3+1-D minimal surfaces in H=M⁴× CP₂.

   M⁴ projection is 3-D and E³ projection 2-D membrane. The basic problem is posed by the fact that 2-D closed minimal surfaces are not possible. For soap bubbles a pressure difference over the soap bubble is required and one loses minimal surface property. The solution of the problem was that the 1-D CP₂ projection of the surface is dynamical and allows 4-D minimal surface. The simplest option is that it represents rotating geodesic circle.

4. Therefore one can ask whether lipid bilayer could have pair of electric bodies (EBs) serving for them as a kind of template and connected by transversal elecric flux tubes carrying a longitudinal rather than transversal electric field.

2. Gravitationally dark effective ions

Besides organic molecules but also metal ions are fundamental for metabolism and bio-catalysis. This led to the TGD inspired proposal that they give rise to dark ions and the recent work gives further support for the view is that gravitationally dark electrons given them their special role

1. Various bosonic effective metal ions and their Cooper pairs can get paired by gravitational flux tube with atoms of opposite total valence. The distance between paired system can become due the relative motion of the atoms considered. Also reconnections of gravitational flux tubes could cause this.

   Correlations are predicted between the members of pairs. The presence of gravitational hydrogen- and valence bonds implying the presence of effectiove ions could distinguish biochemistry from chemistry. Also electrolysis, and therefore organic chemistry in general, involves the ionization of atoms very difficult to understand without the notion of dark gravitational valence- and hydrogen bonds. Also the physics of water is full of thermodynamical anomalies suggesting the presence of these bonds.

2. According to standard chemistry, one has equilibrium X(OH)₂ ↔ X⁺⁺ +2OH^- for X = Ca, Mg, Fe in water environment. Gravitational effective ionization effectively breaks charge conservation and one would obtain quantum correlated pairs formed from X⁺⁺ connected by flux tubes H₂O₂. Gravitationally dark electrons would not be visible. This would mean apparent charge non-conservation, which could be tested as deviation of the concentrations from the prediction n(X⁺⁺) =2n(OH^-).

   This could happen also for water itself. H₃ O)⁺ and OH^- ions are present. OH is not stable but the pairing 2(H₃ O)⁺ + 2H₂O₂ by gravitational hydrogen bonds is possible. Also H₂O + OH^- pairs with one dark gravitational proton are possible. The concentrations of (H₃ O)⁺ and OH^- would be different.

2.1 Signatures of dark effective ions

The ions Ca⁺⁺, Mg⁺⁺, Fe⁺⁺ and Li⁺, Na⁺, K⁺ would be actually effective ions with gravitationally dark valence bonds. Dark effective ions have special signatures, which allow to test the TGD view.

1. These effective ions effectively break charge conservation. Is the transformation of X(OH)₂ \rightarrow X⁺⁺ + H₂ O₂ rather than X(OH)₂ \rightarrow X⁺⁺ + 2OH^- in question as would be if electrons become gravitationally dark. Note that hydrogen peroxide H₂ O₂ is a reactive oxygen species (ROS) (see this) playing a very important role in biology. ROS are produced in biological processes, in particular metabolic process such as respiration and photosynthesis. TGD view would mean that ROS are not a nuisance but an essential element of electron based metabolism.

   For X⁺ , X= Li,Na,K, the electrons of the Cooper pair are paired with two OHs. Two XOHs forms Cooper pair of X⁺:s correlated hydrogen peroxide H₂O₂. This would represent new physics and effective charge non-conservation.

2. Quantum gravitational correlations between H₂O₂ and Ca⁺⁺, Mg⁺⁺, Fe⁺⁺ and between H₂O₂ and between Cooper pars of Li⁺, Na⁺, K⁺ are predicted and this prediction might be testable.

2.2 Some facts about Calcium ions

Basic facts about Ca ions allow to get idea about the implications of new metabolic quantum and the quantum gravitational realization of metabolic energy quanta.

1. Calcium ions (Ca⁺⁺) contribute to the physiology and biochemistry of organisms' cells. They play an important role in signal transduction pathways, where they act as a second messenger, in neurotransmitter release from neurons, in contraction of all muscle cell types, and in fertilization.
2. Calcium phosphate see this appearing in bones combines effecitive ions possibly having gravitationally dark protons and electrons (Calcium phosphate is also considered in (see this). Posner molecule [(PO₄)^-3)]₆Ca⁺²₉ made of 6 phosphate ions and 9 calcium ions would be the key player and has been proposed to play central role in consciousness theory (see this and this). I have considered Posner molecules from the TGD point of view in (see this).
3. Ca⁺⁺ currents initiate action potentials. Voltage gated Ca⁺⁺ channels emerge first in the maturing of neuron and also in evolution of nervous system (already monocellular eukariotes generate action potentials). Na⁺ channels emerge later. The action potentials pulses have a longer dead time for Ca⁺⁺ than for Na⁺.

   For instance, Ca⁺⁺ initiates a contraction of muscle and helps to maintain the potential difference over cell membrane, which conforms with the proposed role in electronic metabolism.

4. Ca⁺⁺ appears as a second messanger molecule. The TGD view about second messanger molecules is discussed in (see this). Cell interior, in particular mitochondria and endoplasmic membranes contain storages of Ca⁺⁺. Mitochondria would thus involve both forms of metabolism.

2.3 Ca⁺⁺ waves

Ca⁺⁺ waves could be effective ions due to gravitationally dark Cooper pairs.

1. Ca⁺⁺ waves very important in biology and appear in cell interior and between cells. A calcium wave is defined as a localized increase in cytosolic Ca⁺⁺ that is followed by a succession of similar events in a wave-like fashion. Ca⁺⁺ waves can be restricted to one cell (intracellular) or transmitted to neighboring cells (intercellular) (see this).
2. Calcium waves are also associated with glial cells. Ca⁺⁺ waves are of special importance in astrocytes and other glial cells (see this). This should relate to electronic metabolism of the primary cilia associated with both neurons and glial cells.

   Calcium waves and miniature potentials would naturally relate to dark electron metabolism. Both glial cells and neurons have primary cilia acting as sensory receptors and since cilia cannot use ATP metabolism, electronic metabolism is natural.

3. About the model for the nerve pulse

Could one construct a simplified TGD based model for the nerve pulse (see this) using this kind of picture utilizing holography meaning that one can take the EBs as basic objects to which one can assign densities of various ions atoms and normal components of electric field as charge densities? Can one decompose these densities to various contribution assignable to ions or effective ions?

The basic physical picture would be as follows. The transformation of the pairs of metal atom with atoms with total valence equal to that of metal would generate gravitational dark metal atoms, which are effective ions which correlate with the paired atoms. The valence charge of the metal atom effectively disappears and implies an effective charge non-conservation. In nerve pulse these effective ions would disappear and would look like charge non-conservation. Also effective ionic currents appear.

1. Josephson currents are assumed to flow along dark flux tubes connecting the two systems and electric field would be along them. Gravitationally dark protons and electrons reside at gravitational flux tubes as very long loops connecting cell interior and exterior. Dark ions are associated with these flux tubes (touch them).
2. What kind of dark Josephson currents could flow along them? If the two atoms are localized at the ends pf the dark gravitational valence- of hydrogen bond at the opposite sites of the membrane, the dark electron and proton Josephson currents can run along gravitational flux tube. For this option dark ion currents cannot flow between interior and exterior.

   Gravitational flux tubes assignable to valence and hydrogen would connect systems such as X⁺⁺, X =Ca, Mg, Fe and hydrogen peroxide H₂O₂, which is a reactive oxygen species (ROS). The currents would flow between systems containing these dark ions and molecules.

3. Hodgkin-Huxley model (see this) assumes ohmic currents. Are they real currents or only an effective description? Ohmic currents signal about the reduction to a shorter length scales than say quantum gravitational scale, the value of h_eff for the flux tube descreases and liberates metabolic energy: in this case elecgtonic metabolic quantum.

   Action potential means that gravitational valence- and hydrogen bonds become ordinary. Corresponding Josephson currents disappear. The corresponding dark em charge becomes visible and the charge densities inside and outside neuronal membrane change and Josephson currents disappear. The change of charge densities in the BSFR inducing action potential implies effective currents and Ohmic currents could be an effective description for this process. This interpretation of Ohmic currents would hold quite generally.

4. More than 100 miniature potentials induced by Ach vesicles are needed to initiate nerve pulse in synaptic contact. The miniature potential corresponds to a liberation gravitational electronic metabolic quantum as a transfromation of gravitationally dark electron to ordinary one. This critical reduction of membrane potential would induce the reduction of menbrane potential below the critical value and induce action potential.

   Also protonic metabolic quanta are involved and would relate to the ordinary metabolism based on ATP machinery.

Membrane potential changes sign during nerve pulse. What could be the interpretation in ZEO?

1. If the generation of action potential corresponds to two subsequent BSFRs as a kind of quantum tunneling even, the arrow of time temporarily changes at MB and changes the effective arrow of time at the level of the ordinary biomatter. Gel-sol phase transition in the neuron interior near neuronal membrane signals about about the reduction of quantum coherence scale.
2. The TGD based description for the change of the sign of the membrane potential is in terms of the model of nerve pulse describing the ground state as a soliton/oscillon sequence and mathematically equivalent to a sequence of gravitational penduli rotating/oscillating in synchrony. Can one choose between these options.

   Critical membrane potential would correspond to a situation in which the rotation changes to oscillation or vice versa. The fact that the membrane potential changes sign and has original magnitude, supports the soliton model. The rotation frequency would transformation to vibration frequency, decrease further, change sign and eventually transform to a negative rotation frequency. The arrow of time would have changed. The reverse of this process would correspond to the second BSFR leading to hyperpolarization.

See the article Quantum gravitation and quantum biology in TGD Universe 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. 


How animals without brain can behave as if they had brain?

The TGD based view about cell and neuronal membrane, nerve pulse and EEG assumes pre-neural level which is quantal. In this view, cell membranes act as Josephson junctions and communicate sensory input to the magnetic body (MB) of the system as dark Josephson radiation. MB in turn controls the cell by dark cyclotron radiation produced as pulses as MB receives frequency modulated Josephson radiation resonantly.

The assumption is that gravitational MB corresponds to gravitational Planck constant and that dark particles are at gravitational Bohr orbits assignable to MB. This correctly predicts metabolic energy quantum as the energy liberated as a dark proton drops from the orbit to an orbit with radius equal to Earth radius. For electron Cooper pairs this predicts electronic metabolic energy quantum which corresponds to the so-called miniature potential. Electronic metabolism would solve the problem due the lack of ATP machinery inside cilium or near it.

Cilium can be interpreted as a predecessor of the axonal membrane and the pre-nerve pulses are predicted to be equal to miniature potentials and the reported 'spikes' as analogs of nerve pulses are assigned with de-adhesion of cilium from its neighbor or the surfaces at which the animal moves. The 'spikes' correspond to at least 100 miniature potentials just as real spikes do.

Cilium is modeled as a 2-D quantum gravitational pendulum with gravitational Planck constant controlled by MB using electronic metabolic energy quanta and the resulting model for the motion is in many respects similar to the model of nerve pulse.

See the article How animals without brain can behave as if they had brain?.

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

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 h_gr for electrons would provide the metabolic energy related by a factor m_e/m_p ≈ 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 h_gr in the Schrödinger equation for the valence electrons. The binding energies are scaled down by 1/n², n= ℏ_gr/ℏ= GMm_e/v₀ℏ= 2π r_{s, E}/L_e β₀, r_s,E≈ .9 cm, L_e= h/m_e ≈ 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 +/- Z_MT 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≈ Z_MTe² L/R² ≈ Z_MT× 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 Z_MT> (Z²/n²)× 13.6/2.85. For the double ionization in the case of Ca⁺⁺ with Z=20 and n=3 this would give Z_MT> 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.

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 m_e/m_p 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 r_n ∝ 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 E_J = ZeV +Δ E_c of ordinary Josephson energy ZeV and difference Δ E_c 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 h_eff in order that Josephson frequencies can correspond to frequencies in the EEG range. This justifies the assumption that dark ions have h_eff=h_gr . 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 eV_cr ≈ .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 E_gr 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 m_e/m_p 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 E_c 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 E_Coul= -Q_tot eV =-∑_i N_i(out) Z_i eV, where N_i is the number effective ions with charge Z_ie. The contribution of positive charges is negative since V corresponds to a negative net charge for the cell. The situation is stable for |E_Coul| > |E_Coul,crit|= N_p Δ E_gr. The system becomes critical at Q_toteV_cr= N_pΔ E_gr. The system becomes critical at Q_toteV_cr= N_pΔ E_gr. The value of the critical potential energy is given by eV_cr= N_p Δ E_gr/Q_tot and is roughly constant for a given neuron. This suggests that the ratio N_p/Q_tot 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 h_gr→h_eff< < h_gr 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.

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 R_E, R_E 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 h_eff= h_gr 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 R_E 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 m_p/m_e≈ 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 L_gr of the gravitational flux tubes? The first estimate is as the Bohr radius L_gr=r_n= n² a_B,gr= n² Λ_gr,m for the orbit particle in 1/r gravitational potential of Earth. Λ_gr,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/f_c= m/ZeB_end. The identification r_n≈ λ gives an estimate for the value of n. f_c=10 Hz for Fe⁺⁺ would give for v₀=c the estimate λ ≈ 2π R_E 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 r_n ∝ 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.

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

The notions of magnetic body, dark matter as h_eff=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 h_eff 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 h_eff 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 h_eff 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 h_eff 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 E_T=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 E_T \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.

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.

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)= (R_sample/R_standard -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.

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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 N_q and N_qbar of quark and antiquark numbers are separately conserved (as also their difference N_q-N_qbar). 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.

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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.