Could TGD provide a vision about evolution at the gene level?

Could TGD provide a concrete view of evolution at the level of genes? How could new genes appear? Genetic engineering produces them artificially. Does Nature also perform genetic engineering? One can try to answer the question using the basic ideas of TGD inspired biology.

1. The predicts the presence of dark variants of DNA, mRNA, and tRNA associated with flux tubes with codons realized as dark proton triplets. Amino-acids do not carry constant negative charges so that dark proton triplets might not be present at the corresponding monopole flux tubes permanently.

   The hypothesis is that the DNA, mRNA, and tRNA and possibly also AA sequences pair with their dark variants. Resonance coupling by dark 3N-photons would make this possible: N corresponds to the number of codons or AAs).

   DNA replication, transcription, translation occur at the level of dark DNA and the counterparts of these processes at the level of chemistry correspond to an induced shadow dynamics, a kind of mimicry.

2. There are good reasons to expect that the dark variants of basic information molecules, such as DNA and RNA, consisting of dark proton triplets, could be dynamical. This makes possible a kind of R&D lab. How could this be realized? The DNA double strand is not dynamical but RNA is. If the dynamics of RNA is induced from that of dark RNA, dark RNA could make possible experimentation producing new kinds of genes. The living system would evolve actively rather than by random mutations. Of course, also dark DNA could be dynamical and communicate with ordinary DNA resonantly only when in corresponding quantum states.
3. Zero energy ontology (ZEO) predicts a fundamental error correction mechanism based on a pair of "big" state function reductions (BSFRs) changing the arrow of time temporarily. When the system finds that something goes wrong, it can make a BSFR and return back in geometric time and restart. After the second BSFR the situation might be better. This would be a fundamental mechanism of learning and problem solving. And perhaps also a fundamental mechanism of evolution.
4. ZEO inspires the question whether the time reversals of transcription, of the splicing process of RNA after transcription, and even translation could be possible.

   Could the time reversal of the entire sequence decomposing to transcription of DNA to RNA followed by the splicing of RNA to mRNA followed by the transformation of tRNA and mRNA to AA sequence and mRNA codons produced from tRNA and from the decay of mRNA look like if possible at all? This would give rise to non-deterministic reverse engineering of DNA making possible a generation of modified more complex genes? What would be nice is that random mutations would be replaced by genetic engineering modifying the existing genome by starting from the protein level would be possible.

Consider now what the reverse of the process leading from DNA to proteins would look like. In the initial state amino acid (AA) sequence and RNA codons are present. The central dogma of biology states that information is transferred in the direction of DNA → RNA → proteins so that the first guess for the answer is "No". Could ZEO help?

1. At the first step mRNA and tRNA would be generated from AA sequence by reverse translation. This step seems to be the most vulnerable part of the process.
   1. AA sequence and RNA codons would transform to mRNA and tRNA codons in a process occurring in reversed time time direction. After the first BSFR mRNA and tRNA would appear at the "past" end of increasing causal diamond (CD). After the second BSFR they would appear at the "future" end of the CD. They would apparently pop out of vacuum. One could say that mRNA is reversed engineered from AA. This process is non-deterministic and 1-to-many since many mRNA codons code for a given amino acid.
   2. The process would generate tRNA. Usually tRNA is generated by transcribing an appropriate gene to pre-tRNA. After splicing and other kinds of processing the tRNA\AA is transferred to cytoplasm and AA is added to give the tRNA.

      Suppose that the AA sequence can be feeded to the ribosome machinery (somewhat like AA to tRNA\AA) operating in the reverse time direction. If so, AA sequence is transformed to mRNA sequence parallel to it by adding mRNA codons from cytoplasm to the increasing mRNA sequence and fusing the counterparts of RNA codons to AAs to give tRNA.

   The basic objections against reverse translation will be considered later.
2. The second step would be time reversal of splicing. I would add to the mRNA obtained in this way pieces of RNA. Non-determinism could be involved and only in special cases the outcome would be the RNA produced in the transcription of the original DNA. This is also so because a given AA corresponds to several RNA codons. Also this step would involve the R&D aspect giving rise to active evolution.

   This would generate new introns, which give rise to higher control levels in transcription. Could the emergence of the control levels in this way correspond to the composition f→ g_º f for g: C²→ C² and f=(f₁,f₂): H→ C² defining a space-time surface decomposing to a union of regions given by the roots f=(f₁,f₂)=(0,0). For g=(g₁,Id) with degree d=2 the number of roots is doubled. The prime degrees d=2 and d=3 are favoured since in these cases the roots of the iterates can be solved analytically and one can wonder whether d=3 could correspond to the number of nucleotides for a codon.

3. The third step would be time reversal of transcription and in general does not produce DNA equivalent with the DNA coding for AA sequence. Time reversed splicing would increase the complexity of the DNA. After this the DNA sequence would replicate to double strand.
4. If the dark variant of the reverse process leading from dark AA sequence to dark DNA can occur, the last step would lead to dark DNA strand, which would pair with ordinary DNA. Dark DNA would replicate and this would induce the replication of ordinary DNA strands leading to double DNA strands.

Consider now the objections against the proposal.

1. There exists no "reverse ribosome enzyme" for the reverse translation from protein to DNA. Could the time reversal occurring in BSFR come to the rescue? Could the ribosome machinery operate in the opposite time direction and in this way make possible reverse translation?

   After the first BSFR, the time reversed process would generate mRNA and tRNA from AA sequence and RNA codons and their counterparts in the cytosome and this looks like a decay of mRNA in standard time direction.

2. The tRNA counterpart of RNA could be called tRNA\A. Is a gene activating its generation needed or does the cytosome contain enough tRNA\A generated in the translation. If not, information transfer to DNA to activate it is needed.

   It deserves to be noticed that for years ago I considered the possibility that originally AA sequences catalyzed the formation of RNA sequences and decayed in the process. Then the roles were changed: RNA sequence started to be generated by AA sequence. This process would have been analogous to the reverse translation.

3. The map RNA → proteins is not invertible: this is however not a problem from R&D point of view since it would make possible generation of new DNAs. Furthermore, ZEO is motivated by the small failure of classical determinism for the dynamics of the space-time surfaces. Non-determinism is necessary if one wants to realize R&D lab.
4. Protein folding could be seen as the problem. The protein should be unfolded first but this process occurs routinely under metabolic energy feed. Proteins also suffer modifications after translations but even this is not a problem if one wants to make living organism R&D lab.
5. Is it really possible that reverse translation would not have been observed? Could a more prosaic and realistic option be the decay of AA sequence to AAs and the fusion of AAs and tRNA-AA codons to tRNA occurring in the standard view about generation of tRNA. Indeed, since AA sequence does not carry a negative constant charge density, h_eff hypothesis suggests that it is not accompanied by a dark variant consisting of dark proton triplets (as I have suggested earlier).

   The optimistic hope is that quantum coherence allows the reverse translation to occur for the entire AA or sequence or part of it, at least with some probability. If so, the RNAs combine in the process to RNA sequence accompanied by dark RNA.

To sum up, the first step of the reverse process is clearly the vulnerable part of the proposal.

See the article Could life have emerged when the universe was at room temperature? or the chapter Quantum gravitation and quantum biology in TGD Universe.

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.