Wednesday, March 19, 2008

TGD based model for the evolution of genetic code: I

The notion of many-sheeted space-time could allow to understand many puzzles related to the pre-biotic evolution (the popular article The Origin of Life on Earth, by Leslie Orgel gives a good overall view about the situation). There are many constraints on the models for pre-biotic evolution. The models have also many difficulties.

In TGD framework the situation looks much better.

  1. TGD replaces materialistic view about universe with a continual re-creation in which classical universe in 4-dimensional sense is replaced by a new one in each quantum jump.
  2. p-Adic length scale hypothesis allows to formulate the notion of evolution precisely as a generation of increasingly larger space-time sheets characterized by preferred p-adic primes. A second aspect is the emergence of new levels in dark matter hierarchy making possible macroscopic quantum coherence and inducing great leaps in evolution.
  3. Also a hierarchy of dark weak bosons and gluons becomes an essential part of the physics of living matter.
  4. The notion of field/magnetic body carrying dark matter is a further key element in the model and has become increasingly important during years, and the vision about DNA-cell membrane system as a topological quantum computer utilizing braids defined by magnetic flux tubes connecting nucleotides to lipids meant a breakthrough in the understanding of the real function of DNA in information processing. The magnetic flux tubes connecting biomolecuiles and the phase transitions changing the value of Planck constant associated with them and thus inducing shortening or lengthening of braid strands provide a completely new view about the miracles of bio-catalysis and this hypothesis has begun to show its power.

A good manner to introduce the essentials of the TGD inspired model for the prebiotic evolution is by a sequence of questions and answers.

Q: Is life as we know it result of an accident?


A: Quantum TGD predicts a genuine cosmic evolution occurring by quantum jumps for which dynamics is characterized by Negentropy Maximization Principle. The generalization of the notion of space-time implies dark matter hierarchy with levels characterized by arbitrarily large values of Planck constant so that macroscopic quantum coherence is possible even in astrophysical length scales. Even astrophysical systems are analogous to atomic systems which implies a strong standardization of planetary system so that Earth like planets are abundant. There are also other good reasons for why the evolution of life would not have been accident in TGD Universe and life should appear everywhere in TGD Universe.

Q: What were the most primitive living systems?

A: The notion of magnetic body brings to biology several completely new elements. Magnetic flux quanta containing dark charged matter and quantum controlling ordinary matter in plasma phase is perhaps the simplest system which can develop characteristics of a living system. The braiding of magnetic flux tubes makes possible topological quantum computation and a fundamental representation of memories and its presence could be even taken as a definition for what it is to be living. Tqc programs correspond to asymptotic self organization patterns for liquid flows inducing braidings and are non-trivial in presence of external energy feed.

Q: How metabolic machinery emerged?

A: Many-sheeted space-time concept predicts a hierarchy of universal metabolic energy quanta as differences of zero point kinetic energies for space-time sheets characterized by different p-adic length scales. What remains is to understand how chemical energy storage and utilization mechanisms developed.

Q: What is behind biocatalytic machinery?

A: The magnetic flux tubes connecting bio-molecules imply long range correlations between molecules. The reduction of Planck constant for magnetic flux tubes implying their shortening provides a mechanism making possible for bio-molecules to "find" each other in a very selective manner, and explains also why molecules end up to precisely defined conformations necessary for a selective bio-catalysis. This picture leads to amazingly detailed understanding of existing results about emergence of biomolecules in experimental arrangements modelling "primordial soup".

Q: How symbolic dynamics emerged?

A: The notion of N-atom suggested by the fractionization of electron quantum numbers for dark matter hierarchy brings in a candidate for a symbolic dynamics assigning to molecules "names" which need not correlate very strongly with the chemical properties of the molecule but would dictate to a high degree its biochemical behavior. Molecular "sex" emerges in the sense that molecules labeled with "names" and "co-names" tend to pair. The model of DNA as tqc assumes a 4-coloring of braid strands realized by an assignment of DNA nucleotides to quarks and anti-quarks. Also this means symbolic dynamics since only molecules connected by colored braids have high probability to participate in same biochemical reaction and do it in a very specific manner. Since the quarks involved with braid strands can have fractional charges, molecular sex can be realized also in this manner.

Q: What selected the bio-molecules during chemical evolution?

A: The proposed symbolic dynamics based on the notions of colored braids and N-atom poses very strong constraints on the subsets of bio-molecules that can react with considerable rates. The assignment of quark to nucleotides via the correspondence A,T,G,C→ u,uc,d,dc allows to basic rules about distribution of nucleotides in DNA and genes (differing from each other) and in mRNA in terms of approximate matter antimatter symmetry, isospin symmetry and the breaking of these symmetries. Matter antimatter asymmetry is visible also in the experiments trying to mimic primordial life.

Q: How biochemical pathways emerged?

A: It is now possible to realize in practice sequences of arbitrarily complex self-catalyzing biochemical reactions utilizing DNA hairpins. The mechanism generalizes to more complex molecules. At a given step of the reaction sequence the structure formed during the previous steps acts as a key fitting to a lock represented by some hairpin in the solution, and opens it to a linear molecule and in this manner makes it a key. The braids between reactants make it possible for the key and lock to find each other.

Q: How genetic code evolved?

A: The following gives a summary about what might have happened.

  1. The symmetries of the third codon of the genetic code allow in DNA as tqc model an interpretation as isospin and matter antimatter symmetries for quarks and antiquarks assigned with DNA nucleotides and representing 4-color of braid strands. These symmetries together with the study of the detailed structure of tRNA lead to a model for the evolution of the genetic code as a fusion of a non-deterministic 1-code and one-to-one 2-code corresponding to the conjugation of mRNA molecules.
  2. During RNA era two kinds of RNAs, call them RNA1 and RNA2, were present and played the roles of mRNA and aminoacid sequences. 2-code resp. 1-code mediated the analog of replication resp. translation using hairpin like molecules tRNA1 and tRNA2 to bring in RNA nucleotides and RNA doublets to the growing RNAi sequence. Amino-acids attached to the stem of tRNA2 acted as catalysts.
  3. The transition to RNA-aminoacid(-sequence) era took place via a fusion of the tRNA1 and tRNA2 to the ordinary tRNA and instead of sequences of two kinds of RNAs were replaced by aminoacid sequences were formed. Without primordial RNA variant of ribosomes binding aminoacids together by peptide bonds the transition to RNA-protein dominated era would not have been possible. The active part of recent ribosomes is indeed RNA molecule.
  4. After a period of symbiosis involving all these three tRNAs a transition to DNA-RNA-aminoacid world took place as an aminoacid sequence acting like reverse transcriptase emerged.

Q: Did RNA world precede the life as we know it?

A: The model for the evolution of the genetic code forces to conclude that RNA world preceded the recent biology and allows also to deduce that the nucleotides involved with second form of RNA where A,T,U,I(nositol). The exotic RNA in question could have been 2',5' form of RNA rather than 3',5' RNA but this is not the only possibility.

Genetic code was implicitly present already during RNA era in the sense that aminoacids and RNA di-nucleotides were paired by braid strands (given aminoacid was connected to a dinucleotide defining the first two nucleotides of codons coding aminoacid). Hence the strong form of RNA world hypothesis would be wrong: aminoacids would have played a key role although their sequences would have been absent. Some examples are in order.

  1. For instance, the aminoacids found from meteorites correspond to four dinucleotides GX, X= A,U,G,C. Second example: it has been possible to synthesize only A and G but not T and C in absence of enzymes. The interpretation is in terms of strong matter antimatter asymmetry at quark level. The proposal is that in the presence of aminoacids braided to dinucleotides it should be possible to produce dinucleotides XY for which some codons XYZ code for the aminoacid.
  2. One can also understand the strange finding that it possible to synthesize conjugate polymer from RNA template but the production of conjugate of conjugate is not possible. The braid strands connecting template and its conjugate explain the mysterious finding and the presence of aminoacids could provide a mechanism to overcome the difficulty.
  3. Polymers are formed only if the solution contains right handed nucleotides. Also primordial chirality selection could be understood in terms of braids: right handed nucleotides would be connected to left handed aminoacids and vice versa and these phases separate from each other. The difference in energy of these states is large as compared to that predicted by standard model since TGD predicts scaled up variants of weak interactions for which weak bosons are effectively massless in biologically relevant length scales.

Q: Does the notion of protocell make sense?

A: The model of DNA as tqc involves essentially the magnetic flux tubes connecting DNA nucleotides and cell membrane. Since topological quantum computation should have taken place also during the RNA era, some kind of cell membrane consisting of exotic RNA should have been present. It has been found that DNA indeed forms membrane like structures which are liquid crystals consisting of sequences of DNA nucleotides with length up to 20 nucleotides (See this) and same might be true in the case of exotic RNA.

Q: How life could evolve in the harsh primordial environment? Does the notion of primordial ocean make sense?

A: It seems plausible that primordial life came from interstellar space. Evolving life had however to cope with the grave difficulties due to the irradiation by UV light and meteoric bombardment. A simple solution of these problems is to evolve in the interior of Earth, say in underground lakes. This idea conforms nicely with the observation that continents would have formed a single super continent at time of Cambrian explosion provided the radius of Earth at that time was by a factor 1/2 smaller than now. TGD predicts that cosmic evolution does not occur continuously but by quantum jumps in which the Planck constant of appropriate space-time sheet increases. A phase transition of this kind increasing the radius of Earth during a relatively short time interval would have led to a burst of life from underground lakes to the surface of Earth. This would also explain the sudden emergence of a huge variety of highly developed life forms during Cambrian explosion.

The answers to these questions give only a rough view about TGD based model of prebiotic evolution. A detailed picture (still developing) can be found from the completely rewritten chapter Prebiotic Evolution in Many-Sheeted Space-time of the book "Genes and Memes", which I have re-organized completely to better reflect the progress due to the model of DNA as topological quantum computer.


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