Thursday, February 02, 2017

Why metabolism and what happens in bio-catalysis?

TGD view about dark matter gives also a strong grasp to metabolism and bio-catalysis - the key elements of biology.

Why metabolic energy is needed?

The simplest and at the same time most difficult question that innocent student can make about biology class is simple: "Why we must eat?". Or using more physics oriented language: "Why we must get metabolic energy?". The answer of the teacher might be that we do not eat to get energy but to get order. The stuff that we eat contains ordered energy: we eat order. But order in standard physics is lack of entropy, lack of disorder. Student could get nosy and argue that excretion produces the same outcome as eating but is not enough to survive.

We could go to a deeper level and ask why metabolic energy is needed in biochemistry. Suppose we do this in TGD Universe with dark matter identified as phases characterized by heff/h=n.

  1. Why metabolic energy would be needed? Intuitive answer is that evolution requires it and that evolution corresponds to the increase of n=heff/h. To see the answer to the question, notice that the energy scale for the bound states of an atom is proportional to 1/h2 and for dark atom to 1/heff2 ∝ n2 (do not confuse this n with the integer n labelling the states of hydrogen atom!).

  2. Dark atoms have smaller binding energies and their creation by a phase transition increasing the value of n demands a feed of energy - metabolic energy! If the metabolic energy feed stops, n is gradually reduced. System gets tired, loses consciousness, and eventually dies. Also in case of cyclotron energies the positive cyclotron energy is proportional to heff so that metabolic energy is needed to generate larger heff and prerequisites for negentropy. In this case one would have very long range negentropic entanglement (NE) whereas dark atoms would correspond to short range NE corresponding to a lower evolutionary level. These entanglements would correspond to gravitational and electromagnetic quantum criticality.

    What is remarkable that the scale of atomic binding energies decreases with n only in dimension D=3. In other dimensions it increases and in D=4 one cannot even speak of bound states! This can be easily found by a study of Schrödinger equation for the analog of hydrogen atom in various dimensions. Life based on metabolism seems to make sense only in spatial dimension D=3. Note however that there are also other quantum states than atomic states with different dependence of energy on heff.

  3. The analogy of weak form of NMP following from mere adelic physics makes it analogous to second law. Could one consider the purely formal generalization of dE=TdS-.. to dE= -TdN-... where E refers to metabolic energy and N refers to entanglement negentropy? No!: the situation is different. The system is not closed system; N is not the negative of thermodynamical entropy S; and E is the metabolic energy feeded to the system, not the system's internal energy. dE= TdN - ... might however make sense for a system to which metabolic energy is feeded.

    Note that the identification of N is still open: N could be identified as N= ∑pNp -S where one has sum of p-adic entanglement negentropies and real entanglement entropy S or as N = ∑pNp. For the first option one would have N=0 for rational entanglement and N>0. for extensions of rationals. Could rational entanglement be interpreted as that associated with dead matter?

  4. Bio-catalysis and ATP→ ADP$ process need not require metabolic energy. A transfer of negentropy from nutrients to ATP to acceptor molecule would be in question. Metabolic energy would be needed to reload ADP with negentropy to give ATP by using ATP synthase as a mitochondrial power plant. Metabolites could be carriers of dark atoms of this kind possibly carrying also NE. They could also carry NE associated with the dark cyclotron states as suggested earlier and in this case the value of heff=hgr would be much larger than in the case of dark atoms.

Conditions on bio-catalysis

Bio-catalysis is key mechanism of biology and its extreme efficacy remains to be understood. Enzymes are proteins and ribozymes RNA sequences acting as biocatalysts.

What does catalysis demand?

  1. Catalyst and reactants must find each other. How this could happen is very difficult to understand in standard biochemistry in which living matter is seen as soup of biomolecules. I have already already considered the mechanisms making it possible for the reactants to find each other. For instance, in the translation of mRNA to protein tRNA molecules must find their way to mRNA at ribosome. The proposal is that reconnection allowing U-shaped magnetic flux tubes to reconnect to a pair of flux tube connecting mRNA and tRNA molecule and reduction of the value of heff=n× h inducing reduction of the length of magnetic flux tube takes care of this step. This applies also to DNA transcription and DNA replication and bio-chemical reactions in general.

  2. Catalyst must provide energy for the reactants (their number is typically two) to overcome the potential wall making the reaction rate very slow for energies around thermal energy. The TGD based model for the hydrino atom having larger binding energy than hydrogen atom claimed by Randell Mills suggests a solution. Some hydrogen atom in catalyst goes from (dark) hydrogen atom state to hydrino state (state with smaller heff/h and liberates the excess binding energy kicking the either reactant over the potential wall so that reaction can process. After the reaction the catalyst returns to the normal state and absorbs the binding energy.

  3. In the reaction volume catalyst and reactants must be guided to correct places. The simplest model of catalysis relies on lock-and-key mechanism. The generalized Chladni mechanism forcing the reactants to a two-dimensional closed nodal surface is a natural candidate to consider. There are also additional conditions. For instance, the reactants must have correct orientation. For instance, the reactants must have correct orientation and this could be forced by the interaction with the em field of ME involved with Chladni mechanism.

  4. One must have also a coherence of chemical reactions meaning that the reaction can occur in a large volume - say in different cell interiors - simultaneously. Here MB would induce the coherence by using MEs. Chladni mechanism might explain this if there is there is interference of forces caused by periodic standing waves themselves represented as pairs of MEs.

Phase transition reducing the value of heff/h=n as a basic step in bio-catalysis

Hydrogen atom allows also large heff/h=n variants with n>6 with the scale of energy spectrum behaving as (6/n)2 if the n=4 holds true for visible matter. The reduction of n as the flux tube contracts would reduce n and liberate binding energy, which could be used to promote the catalysis.

The notion of high energy phosphate bond is somewhat mysterious concept. There are claims that there is no such bond. I have spent considerable amount of time to ponder this problem. Could phosphate contain (dark) hydrogen atom able to go to the a state with a smaller value of heff/h and liberate the excess binding energy? Could the phosphorylation of acceptor molecule transfer this dark atom associated with the phosphate of ATP to the acceptor molecule? Could the mysterious high energy phosphate bond correspond to the dark atom state. Metabolic energy would be needed to transform ADP to ATP and would generate dark atom.

Could solar light kick atoms into dark states and in this manner store metabolic energy? Could nutrients carry these dark atoms? Could this energy be liberated as the dark atoms return to ordinary states and be used to drive protons against potential gradient through ATP synthase analogous to a turbine of a power plant transforming ADP to ATP and reproducing the dark atom and thus the "high energy phosphate bond" in ATP? Can one see metabolism as transfer of dark atoms? Could possible negentropic entanglement disappear and emerge again after ADP→ATP.

Here it is essential that the energies of the hydrogen atom depend on hbareff=n× h in as hbareffm, m=-2<0. Hydrogen atoms in dimension D have Coulomb potential behaving as 1/rD-2 from Gauss law and the Schrödinger equation predicts for D≠ 4 that the energies satisfy En∝ (heff/h)m, m=2+4/(D-4). For D=4 the formula breaks since in this case the dependence on hbar is not given by power law. m is negative only for D=3 and one has m=-2. There D=3 would be unique dimension in allowing the hydrino-like states making possible bio-catalysis and life in the proposed scenario.

It is also essential that the flux tubes are radial flux tubes in the Coulomb field of charged particle. This makes sense in many-sheeted space-time: electrons would be associated with a pair formed by flux tube and 3-D atom so that only part of electric flux would interact with the electron touching both space-time sheets. This would give the analog of Schrödinger equation in Coulomb potential restricted to the interior of the flux tube. The dimensional analysis for the 1-D Schrödinger equation with Coulomb potential would give also in this case 1/n2 dependence. Same applies to states localized to 2-D sheets with charged ion in the center. This kind of states bring in mind Rydberg states of ordinary atom with large value of n.

The condition that the dark binding energy is above the thermal energy gives a condition on the value of heff/h=n as n≤ 32. The size scale of the dark largest allowed dark atom would be about 100 nm, 10 times the thickness of the cell membrane.

For details see the chapter Quantum criticality and dark matter.

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

Articles and other material related to TGD.

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