Monday, July 30, 2018

TGD approach to the hen-or-egg problems of biology

Standard biology suffers from several hen-or-egg problems. Which came first: genes or metabolism? The problem is that genes require metabolism and metabolism requires genes! Genes-first leads to the vision about RNA world and metabolism-first to lipids world idea.

The emergence of basic biomolecules is the second problem. What selected these relatively few basic molecules from huge multitude of molecules? And again the hen-egg problems emerge. Which came first: proteins or the translation machinery producing them from RNA? Did RNA arrive before proteins or did proteins and RNAs necessary for their transcription and translation machinery emerge first. One can argue that ribozymes served as catalysts for RNA replication but how RNAs managed to emerge without replication machinery involving ribozymes? What about DNA: did it emerge before RNA or could it have emerged from RNA? It seems that something extremely important is missing from the picture.

TGD predicts the existence of dark variants of basic biomolecules DNA, RNA, tRNA, and amino-acids (AAs).
One can ask whether something very simple could be imagined by utilizing the potential provided by dark variants of bio-molecules present already from beginning and providing both genes and metabolism simultaneously.

One can start from a couple of observations which forced myself to clarify myself some aspects of TGD view and also to develop an alternative vision about prebiotic period.

  1. Viruses are probable predecessors of cellular life. So called positive sense single stranded RNA (ssRNA) associated with viruses can form temporarily double strands and in this state replicate just like DNA (see this). The resulting single stranded RNA can in turn be translated to proteins by using ribosomal machinery. RNA replication takes place in so called viral replication complexes associated with internal cell membranes, and is catalyzed by proteins produced by both virus and host cell.

    Could ribozyme molecules have catalyzed RNA replication during RNA era? For this option AA translation would have emerged later and the storage of genetic information to DNA only after that. There is however the question about the emergence of AAs and of course, DNA and RNA. Which selected just them from enormous variety of options.

  2. Lipid membranes are formed by self-organization process from lipids and emerge spontaneously without the help of genetic machinery. It would be surprising if prebiotic life would not have utilized this possibility. This idea leads to the notion of lipid life as a predecessor of RNA life. In this scenario metabolism would have preceded genes (see this and this).

Consider now the situation in TGD.
  1. The dark variants of DNA, RNA, AA, and tRNA would provide the analogs of genes and all basic biomolecules present from the beginning together with lipid membranes whose existence is not a problem. They would also provide a mechanism of metabolism in which energy feed by (say) solar radiation creates so called exclusion zones (EZs) of Pollack in water bounded by a hydrophilic substance. EZs are negatively charged regions of water giving rise to a potential gradient (analog of battery) storing chemically the energy provided by sunlight and the formation of these regions gives rise to dark nuclei at magnetic flux tubes with scaled down binding energy.

    When the p-adic length scale of these dark nuclei is liberated binding energy is liberated as metabolic energy so that metabolic energy feed giving basically rise to states with non-standard value heff/h=n of Planck constant is possible. For instance, processes like protein folding and muscle contraction could correspond to this kind of reduction of heff liberating energy and also a transformation of dark protons to ordinary protons and disappearance of EZs.

    The cell interiors are negatively charged and this is presumably true for the interiors of lipid membranes in general and they would therefore correspond to EZs with part of protons at magnetic flux tubes as dark nuclei representing dark variants of basic biomolecules. Already this could have made possible metabolism, the chemical storage of metabolic energy to a potential gradient over the lipid membrane, and also the storing of the genetic information to dark variants of biomolecules at the magnetic flux tubes formed in Pollack effect.

  2. Biochemistry would have gradually learned to mimic dark variants of basic processes as a kind of shadow dynamics. Lipid membranes could have formed spontaneously in water already during prebiotic phase when only dark variants of DNA, RNA, AAs and tRNA, water, and lipids and some simple bio-molecules could have been present. The dark variants of replication, transcription and translation would have been present from the beginning and would still provide the templates for these processes at the level of biochemistry.

    Dark-dark pairing would rely on resonant frequency pairing by dark photons and dark-ordinary pairing to resonant energy pairing involving transformation of dark photon to ordinary photon. The direct pairing of basic biomolecules with their dark variants by resonance mechanism could have led to their selection explaining the puzzle of why so few biomolecules survived.

    This is in contrast with the usual view in which the emergence of proteins would have required the emergence of translation machinery in turn requiring enzymes as catalyzers so that one ends up with hen-or-egg question: which came first, the translation machinery or proteins. In RNA life option similar problem emerges since RNA replication must be catalyzed by ribozymes.

  3. Gradually DNA, RNA, tRNA, and AA would have emerged by pairing with their dark variants by resonance mechanism. The presence of lipid membranes could have been crucial in catalyzing this pairing. Later ribozymes could have catalyzed RNA replication by the above mentioned mechanism during RNA era: note however that the process could be only a shadow of much simpler replication for dark DNA. One can even imagine membrane RNAs as analogs of membrane proteins serving as receptors giving rise to ionic channels. Note however that in TGD framework membrane proteins could have emerged very early via their pairing with dark AA associated with the membrane. These membrane proteins and their RNA counterparts could have evolved into transcription and translation machineries.

    DNA molecules would have emerged through pairing with dark DNA molecules. The difference between deoxi-ribose and ribose would correspond to the difference between dark RNA and dark DNA manifesting as different cyclotron frequencies and energies making possible the resonant pairing for frequencies and energies. Proteins would have emerged as those proteins able to pair resonantly with dark variants of amino-acid sequences without any pre-existing translational machinery. It is difficult to say in which order the basic biomolecules would have emerged. They could have emerged even simultaneously by resonant pairing with their dark variants.

See either the article New results in the model of bio-harmony or the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology.

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

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