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.