Tuesday, July 31, 2018

How life began?

The central question of biology is "How life began?" and dark variants of biomolecules suggest not only a solution to various paradoxes but also a concrete answer to this question.

The transcription machinery for rRNA including ribozymes and mRNA coding for the proteins associated with ribosomes is central for the translation. The DNA coding for rRNA is associated with nucleolus (see this) in the center of the nucleus.

  1. After the emergence of the first ribosome the ribosomes of the already existing nucleus can take care of the translation of the ribosomal proteins. But how could the first ribosome emerge? This question leads to a paradox bringing in mind self-reference - the basic theme of Gödel-Escher-Bach of Douglas Hofstadter, perhaps the most fascinating and inspiring book I have ever read. The ribosomal proteins associated with the first ribosomes should have been translated using ribosome, which did not yet exist!

  2. Could the translation of the first ribosomal proteins directly from the dark variants of these proteins solve the paradox? The idea of shadow dynamics induced by the pairing of basic biomolecules with their dark variants even allows to ask whether the replication, transcription, and translation could occur at dark level so that dark genes for ribosomes would be transcribed to dark ribosomal RNA and dark mRNA translated to dark AA associated with the ribosomes. These in turn would pair with ordinary ribosomal RNA and AA.

  3. But what about dark variants of ribosomes? One can encounter the same paradox with them if they are needed for the translation. Could it be that dark variants of the ribosomes are not needed at all for the translation but would only give rise to ordinary ribosomes by the pairings basic biomolecules and their dark variants. Dark DNA would pair with dark mRNA, which pairs spontaneously with dark tRNA. Once the ordinary ribosomes are generated from the dark ribosomes by pairing, they could make the translation much faster.

  4. There is however a problem. Both dark RNA and AA correspond to dark nuclear strings. Dark tRNA realized as nuclear string in the proposed manner does not have a decomposition to dark AA and dark RNA as ordinary tRNA has. The pairing of dark tRNA and dark mRNA should rise to dark AA and dark nuclear string - call it X - serving as the analog for the pairing of mRNA sequence with "RNAs" of tRNAs in the ordinary translation.

  5. How to identify X? Could the translation be analogous to a reaction vertex in which dark mRNA and dark tRNA meet and give rise to dark AA and X? X cannot be completely trivial. Could X correspond to the dark DNA?! If so, the process would transcribe from dark DNA dark RNA and translate from dark RNA and dark tRNA AA and dark DNA. This would lead to an exponential growth of dark DNA and other dark variants of bio-molecules. This exponential growth would induce exponential growth of the basic bio-molecules by pairing. Life would emerge! No RNA era or lipid era might be needed. All basic biomolecules or their precursors could emerge even simultaneously - presumably in presence of lipids - but this is not the only possibility.

One can take a more precise look at the situation and try to understand the emergence of bio-molecules and their basic reactions as shadows of the dark variants of bio-molecules appearing in dark particle reactions. The basic idea is that same dark reaction can give rise to several reactions of biomolecules if varying number of the external dark particles are paired with corresponding bio-molecules. Under what conditions this pairing could occur, is left an open question. Consider now the dark 2→ 2 reactions and possible reactions obtained by pairing of some particles.
  1. The reaction

    DmRNA+DtRNA→ DAA + DDNA

    gives rise to translation mRNA+tRNA → AA if DDNA-DNA pairing does not occur in the final state but other dark particles are paired with the their ordinary variants. If only DmRNA-mRNA and DDNA-DNA pairings occur, the reaction gives the reversal mRNA → DNA of transription.

    It should be easy to check whether this is allowed by the tensor product decomposition for the group representations associated with dark proton triplets. Same applies to other reactions considered below.

    If this reaction is possible then also the reversal

    DAA + DDNA → DmRNA+DtRNA.

    can occur. If only DDNA-DNA and DmRNA-mRNA pairings occur this gives rise to transcription of DNA→ mRNA.
    Also reverse translation AA → mRNA is possible.

  2. One can consider also the reaction

    DmRNA+DtRNA → DAA + DmRNA

    If all pairings except DAA-AA pairing are present, the outcome is instead of translation the replication of mRNA such that the amino-acid in tRNA serves the role of catalyzer. I have considered the possibility that this process preceded the ordinary translation: in a phase transition increasing heff the roles of AA and RNA in tRNA would have changed.

    If this reaction is possible then also its reversal

    DAA + DmRNA → DmRNA+DtRNA

    is allowed. If all pairing except DmRNA-mRNA occur, this gives rise to AA +RNA → tRNA allowing to generate tRNA from AA and RNA (not quite RNA).

  3. The replication of DNA strand would correspond at dark level to a formation of bound states by the reaction

    DDNA+DDNA→ DDNA +bound DDNA

    in which all particles are paired. The opening of DNA double strand would correspond to the reverse of this bound state formation.

These dark particle reactions behind the shadow dynamics of life should be describable by S-matrices, which one might call the S-matrix of life.
  1. For instance for

    DmRNA+DtRNA→ X,

    where X can be DmRNA+DtRNA (nothing happens - forward scattering) or DAA + DDNA and perhaps even DAA+DmRNA, one would have unitary S-matrix satisfying SSdagger=Id giving probability conservation as ∑n pm,n= |Smn|2 =1 as a special case. Writing S=1+iT unitarity gives i(T-T)+TT=0 giving additional constraints besides probability conservation.

    For

    DmRNA+DtRNA→ DAA + DDNA

    the non-vanishing elements of T are only between pairs [(DmRNA,DtRNA), (DAA,DDNA)] for which mRNA pairs with tRNA and DNA codes for AA. Unitary matrix would be coded by amplitudes t(AA,DNAi(A)) satisfying ∑ipi(DAA)=p(DDNA+DAA), pi(AA)=|t(DAA,DDNAi(A)|2. p(DDNA+DAA) equals to p(DDNA+DAA)= (1-p) Br(DDNA+DAA), where p is the probability that nothing happens (forward scattering) and Br(DDNA+DAA) is the branching ratio to DDNA+DAA channel smaller than 1 if Br(DDNA+DmRNA) is non-vanishing. The natural interpretation for pi(AA) would be as probability that DNAi codes for it.

  2. For the reverse reaction

    DAA + DDNA rightarrow DmRNA+DtRNA

    it is natural to assume that DtRNA corresponds to any tRNA, which pairs with RNA. The AA associated with this tRNA is always the same but the counterpart of RNA can vary (wobbling). One can speak of the decomposition of dark genetic code to DmRNA→ DtRNA → DAA to a pair of codes mapping DmRNA to DtNRA and DtRNA to DAA. There is a set tRNAi(mRNA) of tRNAs coding for given mRNA, and the probabilities pi(DmRNA) sum up to p= ∑i pi(DmRNA)= (1-p) Br(DmRNA+DtRNA) , where p is the probability for forward scattering and Br(DmRNA+DtRNA) is the branching fraction. The natural identification of pi(DmRNA) is as the probability that mRNA pairs with tRNAi.

A possible weak point of the proposal is pairing: what are the conditions under which it occurs and are different pairing patterns possible. Possible second weak point is purely group theoretic: one should check whether which reactions are allowed by the tensor product decompositions for the states of dark proton triplets.

See the article Getting philosophical: some comments about the problems of physics, neuroscience, and biology or the chapter Quantum Mind, Magnetic Body, and Biological Body of of "TGD based view about living matter and remote mental interactions".

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

Articles and other material related to TGD.

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