How did metabolism emerge?: breathing soil as a guideline

This finding relates in an interesting way to the TGD inspired view that life and even genetic code are universal. Even quartz crystals (see this) could be living in a primitive sense and the basic quantum mechanism would be the same as for ordinary life. Pollack effect (see this, this this, this, this, this) in which protons are kicked to the magnetic body and generate in this way negatively charged exclusion zone (EZ) would be fundamental for metabolism. The dropping of dark protons from the magnetic body in the reverse Pollack effect would liberate the metabolic energy.

The findings of Fontaine's Lab suggest that in soil a hugely simplified variant of Krebs cycle and electron transport chain (ETC) make possible breathing producing CO₂ originates basically from the COOH groups of proteins. Consider first how the process occurs in biology.

1. The function of the Krebs cycle is to strip high energy electrons of the fuel and feed them to the electron transport chain (ETC) liberating the energy of electrons. According to the standard view, this creates electrochemical gradient pumping hydrogen ions across the mitochondrial membrane.
2. Krebs cycle strips electrons from the 2-carbon compounds obtained from the pyruvates combining with vitamin A to form Co-A involving citrate with 6 C atoms. Krebs cycle has as wastes CO₂ and water as the end product of ETC. The electrons striped from the counterpart provide the needed energy to kick the H⁺ ions to the magnetic body.
3. Krebs cycle is preceded by the splitting of glucose C₆H₁₂ O₆ with 6 carbon atoms to two pyruvate molecules C₃H₃O₃^- with 3 C atoms plus 2 net ATP molecules and NADH moleculefeeding high energy electrons into electron transport chain (ETC). Before entering the Krebs cycle, the 3-carbon molecule pyruvate is transferred into the mitochondrial matrix. Here, the enzyme complex pyruvate dehydrogenase removes a carbon atom from pyruvate to release the first molecule of CO₂. The outcome is H₂C=(CH)-O^- with two C atoms, which is attached to Coenzyme A to form Acetyl-CoA.  
4. First glucose molecule with 6 C atoms and serving as a fuel is decomposed to two pyruvate molecules. Before entering the Krebs cycle, the 3-carbon molecule pyruvate is transported into the mitochondrial matrix. Here, the enzyme complex pyruvate dehydrogenase removes a carbon atom from pyruvate to release the first molecule of CO₂.
5. The remaining 2-carbon fragment -(C=O)-CH₃, acetyl group, is fused to Coenzyme-A to form Acetyl-Co-A (Co-A is a complex molecule derived from vitamin B₅). Acetyl-Co-A is transported to the mitochondrial matrix and meets oxaloacetate with 4 C atoms to form citric acid with 6 C atoms. Citric acid flows through the cycle and comes back as C0-A ready to take to the process a new -(C=O)-CH₃ molecule.

Could TGD explain what happens in breathing without enzymes? The findings of Fontaine's Lab suggest that in soil a hugely simplified analogs of the process leading from glucose to two pyruvates, Krebs cycle and ETC make possible breathing producing CO₂ originates basically from the COOH groups of proteins.

In the case of the soil there are no enzymes, so that the splitting of glucose to pyruvates, the Krebs cycle and ETC should be replaced with something dramatically simpler.

1. Already in the splitting of glucose to pyruvate generates ATP and therefore also dark protons. What comes to mind is that the Pollack effect for some 6 -OH groups of glucose C₆H₁₂O₆ could transform them to O^- plus dark protons at the magnetic body. 2 pyruvate molecules would be obtained if only a single H⁺ per pyruvate ion is transformed to a dark proton.
2. In the TGD framework, the transfer of H⁺ ions from the interior of the mitochondria to their exteriors during ETC is replaced by their transfer to the magnetic body of the system. The transfer makes the system negatively charged and this provides the interior of EZ with additional negative charge. In fact, cells are always negatively charged: this can be explained by the charges of DNA and RNA strands carrying constant charge density which is 3 unit charges per codon. In this case, the units of 3 dark protons representing dark codons are stable against the reverse Pollack effect.
3. The energy liberated by the stripped electrons in ETC would be used to transfer ordinary H⁺ ions to dark protons at the magnetic body of mitochondria rather than to the exterior of the mitochondria. The dark protons would be attached to ADP to form ATP acting as a shuttle carrying dark protons to the user molecule. The metabolic energy would be used as the dark proton becomes an ordinary proton in the reverse Pollack effect.

One can also imagine a more effective option for metabolism.

1. All 6 -OH groups of the glucose transformed to O^- plus a dark proton. This would lead to 2 C₃H₃(O^-)₃ molecules with 3 dark protons at their magnetic bodies, which could liberate metabolic energy in the reverse Pollack effect.

   Remarkably, each molecule has 3 dark protons and in the TGD view of genetic code they would define dark codons. Large values of h_eff mean algebraic complexity and intelligence. Could these dark codons give for the system the IQ needed to drive the process further on?

2. The splitting of C₃ H₃(O^-)₃ to CO₂ and acetyl molecule (C-O^-)-CH₃, involving the dropping of 2 further dark protons back to oxygen ions to form -OH groups, would generate CO₂ and the acetyl group. This process could be an ultra simplified version of the steps preceding ETC. The further dropping of the third dark proton to acetyl ion would be the counterpart of ETC and would also liberate metabolic energy.

See the article A possible TGD based narrative for how life might have evolved or the chapter with the same title.

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

For the lists of articles (most of them published in journals founded by Huping Hu) and books about TGD see this.