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The model for the evolution of genetic code leads to the idea that the folding of proteins obeys a code inherited from genetic code in the sense that aminoacid behaves like the conjugate Yc of the middle nucleotide of the codon XYZ coding for it and that flux tubes connecting aminoacids to each other connect conjugate aminoacids behaving like Y and Yc. Also catalyst action would reduce to effective base pairing in this picture. After some trials one ends up with a general conceptualization of the situation with the identification of wormhole magnetic flux tubes as correlates for attention at molecular level so that a direct connection with TGD inspired theory of consciousness emerges at quantitative level. This allows a far reaching generalization of the DNA as topological quantum computer paradigm and makes it much more detailed. Also earlier vision about function of neurotransmitters and other information molecules as carriers of links in the web formed by living body becomes very concrete. The final outcome is very simple quantitative model for folding and catalyst action based on minimization of energy and consistent with basic experimental facts as well as general ideas.
Because the model represents a quantitative breakthrough in the evolution of the TGD based view about quantum biology and to save the time required by the painstaking manual tex-html translation, I decided to represent the material also as article entitled From Genetic Code to Code for Folding and Catalysis. The background making it easier to understand can be found in the chapter Evolution in Many-Sheeted Space-time containing also the article as a section.
Biochemistry represents extremely complex and refined choreography. It is hard to believe that this reduces to a mere an unconscious and actually apparent fight for chemical survival. In TGD Universe consciousness would be involved even at the molecular level and magnetic body would be the choreographer whose dance would induce the molecular activities. This picture combined with the idea of standard plugs through and terminals at which flux tubes end, leads to a third trial to understand catalytic code.
The third trial differs from the second trial in that the letters X,Y,Z of the codon XYZ coding for the aminoacid do not correspond to COOH, residy R, and NH2 group. Rather, free aminoacid behaves like XY as in the first trial and X and Y correspond to flux tubes ending at OH and =O in COOH group. For the new option all - not only alpha helical and beta sheeted - aminoacids in the interior of the aminoacid sequence behave like the conjugate of letter Y for the codon XYZ coding for the aminoacid. The new model predicts that DNA, mRNA, tRNA, and aminoacids are in general connected by braid strands and provides a detailed picture about the role of braidings in transcription and translation. The topological dynamics of the magnetic body, its motor activities, would induce catalytic dynamics. Also a far reaching generalization of DNA as tqc paradigm emerges (see the postings I, II, III, IV, V, VI, VII, VIII, IX, X, XI, XII,XIII).
1. Flux tubes as a correlate for directed attention
Molecular survival is the standard candidate for the fundamental variational principle motivating the molecular intentional actions. There is entire hierarchy of selves and the survival at the higher level of hierarchy would force co-operation and altruistic behavior at the lower levels. One might hope that this hypothesis reduces to Negentropy Maximization Principle, which states the information contents of conscious experience is maximized. If this picture is accepted, the evolution of molecular system is analogous to the evolution of a society.
Directed attention is the basic aspect of consciousness and the natural guess would be that directed attention corresponds to the formation of magnetic flux tubes between subject and target. The directedness property requires some manner to order the subject and target.
Attention can be also redirected. For this process there is a very nice topological description as a reconnection of flux tubes. What happens is that flux tubes A→ B and C → D fuse for a moment and become flux tubes A→ D and C→ B. This process is possible only if the strands have same color so that the values of the quark charges associated with A and B are same.
This kind of process can modify tqc programs. For instance, in the case of the flux tubes coming from nucleotides X and Xc and ending to the lipid layer this process means that X and Xc and corresponding lipids become connected and genome builds memory representation about this process via similar link. If proteins are connected with mRNA connected to DNA in this manner, this process would allow the formation of flux tubes between aminoacids of two proteins in such a manner that protein would inherit from DNA codon the color of the middle nucleotide and its interactions effectively reduce to base pairing.
DNA would have memory representation about molecular processes via these changing braiding topologies, and one could say that these molecular processes reflect the bodily motions of the magnetic body. Entire molecular dynamics of the organism could represent an enormous tqc induced by the motor activities of the magnetic body. At the level of sensory experience similar idea has been discussed earlier: Out of Body Experiences and illusions such as train illusion could be understood in terms of motor action of magnetic body inducing virtual sensory percepts.
Attention can be also switched on and off. Here the structure of the lipid ends containing two nearby situated =O:s suggest the mechanism: the short flux tube connecting =O:s disappears. The minimization of Coulomb interaction energy at each end implies that re-appearance of the flux tubes creates a short flux tube with the original strand color.
2. Where do flux tubes begin from?
The view about magnetic body as a controller of biological body using genome as a control tool suggests that DNA is to a high degree responsible for directed attention and other molecules as targets so that flux tubes emanate from DNA nucleotides. The reason would be that the aromatic cycles of DNA correspond to larger value of Planck constant.
Some chemical or geometric property of DNA nucleotides or of DNA nucleotides of DNA strand could raise them to the role of subject. Aromatic cycle property correlates with the symmetries associated with large value of Planck constant and is the best candidate for this property. If this is accepted then also some aminoacid residues might act as subjects. Phe, His, Trp, Tyr contain aromatic cycle. The derivatives of Trp and Tyr act as neurotransmitters and His is extremely effective nucleophilic catalyst. This would make possible more specific catalytic mechanisms through the pairing of Phe, His, Trp, and Tyr with residues having flux tube terminals.
This raises the question about the physical interaction determining the color of the strand emerging from the aromatic cycle. The interaction energy of quark at the end of flux tube with the classical electromagnetic fields of nuclei and electrons of the ring should determine this. The wormhole contact containing quark/antiquark at the throat at space-time sheet containing nuclei and electrons could also delocalize inside the ring. One of the earliest hypothesis of TGD inspired model for living matter was that wormhole Bose-Einstein condensates could be crucial for understanding of the behavior of biomolecules. Wormhole throats with quark and antiquark at their throats appear also in the model of high Tc superconductivity. The only manner for the electronic space-time sheet to feed its electromagnetic gauge flux to larger space-time sheets using exactly two wormhole contacts is to use wormhole contacts with uc and d at their "upper" throat (T,G). For proton one would have dc and u at their "upper" throat (A,C). The presence of electron or proton at nucleotide space-time sheet near the end of flux tube might allow to understand the correlation. The transfer of electrons and protons between space-time sheets with different p-adic length scale is basic element of TGD based model of metabolism so that there might be some relation.
3. What aminoacids can act as plugs and terminals of flux tubes?
Standardization constraint suggests that flux tubes are attached to standard plugs and terminals. The explicit study of various biological molecules and the role of water in biology suggests that =O serves as a plug to which flux arrives and from which it continues. The intuitive reason for the proposal is that =O allows two hydrogen bonds. OH would in turn correspond to a terminal at which flux tube ends. One might be very naive and say that conscious biomolecules have learned the fundamental role of oxygen and water in the metabolism and become very attentive to the presence of =O and OH. =O appears in the residues of Asp, Glu, Asn, Gln. OH groups appear inside the residues of Asp,Glu and Ser, Thr.
It might not be very wise to restrict the molecular attention to only =O and OH and it is probably better to speak about probabilities for the flux tubes to attach to various kinds of terminals. Both SH and NH2 are chemically like OH both these them could act as terminals of flux tubes: NH2 (Asp,Gly,Glu,Arg) contain NH2 and Cys contains SH.
4. Directed attention generates memory representations and tqc like processes
Directed attention induces braiding if the target is moving and changing its shape. This gives rise to a memory representation of the behavior of the object of attention and also to a tqc like process. A considerable generalization of tqc paradigm suggests itself. Tqc could be induced by the braiding between DNA and lipids, DNA and proteins via folding processes, DNA RNA braiding and braiding between DNA and its conjugate, DNA and protein braiding. The outcome of tqc would be represented as the temporal patterns of biochemical concentrations and rates and there would be hierarchy of p-adic time scales and those associated with the dark matter hierarchy.
For instance, the protein content of lipid membranes is about 50 per cent and varies between 25 and 75 per cent so that protein folding and lipid flow could define tqc programs as self-organization patterns. The folding of protein is dynamical process: alpha helices are created and disappear in time scale of 10-7 seconds and the side chains of protein can rotate.
The details of the tqc like process depend on what one assumes. The minimal scenario is deduced from the transcription and translation processes and from the condition that magnetic body keeps control or at least keeps book about what happens using genome as a tool. The picture would be essentially what one might obtain by applying a rough model for web in terms of nodes and links.
4. Introns and DNA-protein attachment
An example is the situation in which protein acts as an enzyme attaching on DNA. Suppose that this process effectively reduces to a base pairing between aminoacid and DNA nucleotide. Protein can attach to any portion of DNA. Since nucleotide triplets and aminoacids in the first approximation correspond to same length in the respective chains, amino-acid is expected to correspond to nucleotide triplet. The simplest interaction is the attachment to the gene coding for the aminoacid itself but much more general enzymatic interactions are possible. This works if the gene does not contain introns or if the attachment is along single exon.
It is known that DNA can change its conformation from strand during enzyme-DNA action and the contraction of DNA strand might make possible to have enzyme-DNA interaction also in the case that attachment region corresponds to several exons. One can of course ask whether genes containing introns tend to code for proteins which are used for topological quantum computations. Introns, perhaps the repeating sequences with no obvious function, would have at least this useful function but very probably much more useful ones too (they are now known to be transcribed to RNA and TGD suggest that language corresponds to intronic gene expression). The emergence of introns might be somewhat like the emergence of information society.
The foldings of proteins tend to be conserved in the evolution whereas primary structure can change quite a lot apart from some aminoacids critical for enzymatic action. This confirms with the effective base pairing interaction between aminoacids and DNA and would mean that DNA-aminoacid tqc programs are rather robust against mutations.
5. Evolution and braidings
The evolution at the molecular level corresponds to the emergence of increasingly complex molecules using as basic building blocks aminoacid chains and non-translated residues attached to them in the post-translational processing of the aminoacid chains. Also increasingly complex reaction paths emerge. Molecular survival and the competition for the metabolic resources at molecular level could be seen as the basic driving force of this evolution.
Typically, in the original situation the enzymes would have received the substrate molecules from the environment but sooner or later this would have become difficult. The solution would have been a synthesis of the substrate from simpler ingredients by starting from some precursor.
If molecules (with magnetic bodies included) are conscious entities able to direct attention, one can imagine that magnetic body controlling them with the mediation of genome and able to actively modify it, could help through modifications of the genome to create to the catalyst a binding site able to bind the precursor. Immune system is doing this very intensively. If the enzyme binding the precursor already exists, a combination of genes coding for the enzyme and the enzyme having the metabolites as ligands could allow to achieve this. All this would reduce to the motor activities of magnetic body, in particular reconnection of flux tubes, kind of Shivas dance. Genome would not be anymore a sequence of DNA developing through random mutations under selection pressures.
Can one make any clear cut predictions about preferred mutations?
In this framework aminoacids would have appeared before their precursors and possessed some function in RNA world, say the catalysis of join of RNA2 dinucleotides to the increasing chain as I have proposed. Competition might have led to the situation in which RNA2 learned to catalyze selectively generation of aminoacids from much simpler precursors (three of the proposed precursors contain only C,=O, and O-). The reduced genetic code would have been present at two levels: reader can decide whether this is a shortcoming of the model or a fundamental biochemical duality implying an exponential amplification of RNA and aminoacid populations.
For details see the chapter Evolution in Many-Sheeted Space-time.
I have discussed the model for the evolution of genetic code in previous postings (I,II,III). Thanks to the Ulla Mattfolk I learned about the idea of protein folding code - something which is expected to exist but is not understood. This led to a trial for the folding code discussed in posting III) and based on the assumption that aminoacid behaves like dinucleotide. This trial did not work but the learning of some basic facts about proteins and their interactions inspired second trial according to which aminoacid in the interior of aminoacid sequences behave like the conjugate of the nucleotide Y of the codon XYZ coding for it. This trial seems to work.
There exists a wonderful book "Proteins: Structures and Molecular Properties" by Thomas E. Creighton and published 1993 by W. H Freeman Company. In the following I freely refer to the general facts discussed in this book rather than referring separately to every detail. While reading this book I learned that the first guess for the code of catalysis was wrong but is also became clear what was wrong. It became clear that free aminoacid should behave like the conjugate of the DNA codon XYZ -rather than only XY- but that an aminoacid inside aminoacid sequence effectively reduces to Y since the formation of the peptide bonds by the elimination of water molecule and formation of NH---O= hydrogen bonds effectively eliminates X and Z. The ends of aminoacid behave like dicodons which conforms with their special role in biocatalysis. Only aminoacids for which Y corresponds to quarks (not antiquarks) can form hydrogen bonds so that hydrophilic-hydrophobic dichotomy corresponds to a strong matter antimatter asymmetry at quark level.
1. Matter antimatter asymmetry at the level of interactions of aminoacids
The first thing that I learned was that second nucleotide Y in the codon XYZ coding for aminoacid is what matters. Only Y=A,G aminoacid residue can form hydrogen bonds and is hydrophilic and thus interacts strongly with water and DNA and RNA. In T,C case the formation of hydrogen bonds is impossible or rare (ser,thr). In their interactions with water these aminoacids are passive, or rather-avoid water- and tend to interact with each other. This division is fundamental for the understanding of the interactions of aminoacids. The division of aminoacids to hydrophobic resp. non-hydrophobic ones corresponds to the assignment of quarks to A and G and antiquarks to T and C so that strong matter antimatter asymmetry is in question. Similar asymmetry appears in cosmology: in TGD Universe antimatter resides inside cosmic strings in the interior of big voids containing matter as galaxies at their boundaries so that one can understand why antimatter is not visible.
2. Flux tubes can connect with all electronegative atoms
Also a plausible answer to the question which atoms can be connected by flux tubes emerges.
3. What can one learn from the formation of alpha helices and beta sheets?
The formation of peptide bonds by the elimination of H2O= molecules and generation of hydrogen bonds between NH and O= is an essential step in the formation of alpha helices and beta sheets. Second observation is that aminoacids decompose naturally into three parts corresponding to O=COH, R, and NH2. This suggests that aminoacid actually corresponds to the entire DNA codon XYZ coding for it. OH could correspond to Z , R to Y, and NH2 to Z. In the formation of peptide bond the flux tube connecting to COH and thus to Z would be taken by the water molecule created in the formation of peptide bond leaving only XY. The first flux tube would connect HN and O= so that X would pair with Xc assignable to O. There are no problems with the formation of bond if O= can correspond to any code letter as in the case of water. Water would correspond to matter antimatter symmetric phase and an interesting question is what counterpart this phase could have in cosmology (bosonic matter?).
The aminoacid inside protein would effectively behave like Yc in the effective base pairing. Depending on whether it corresponds to quark or antiquark, aminoacid would be hydrophilic or hydrophobic- or rather - able to form hydrogen bonds or not. Since hydrophobic aminoacids cannot form hydrogen bonds, the formation of these residue pairs would be inhibited. The hydrophilic and hydrophobic residues could tend to avoid each other and the phase transitions increasing Planck constant would make this possible. It must be emphasized that this brings in strong long range correlation between the dynamics of the aminoacid residues belonging to the first and third (second and fourth) column of the code table.
Hydrophilic aminoacids would form hydrogen bonds which each other and with DNA and RNA. In catalytic biding sites this kind of hydrogen bonds are formed between polar groups: also hydrogen bonds with water are formed and they tend to neutralize possible static charges. Ser (UCZ) and thr (ACZ) are the only effectively hydrophobic aminoacids containing OH group (and thus strictly speaking amphiphilic). Perhaps it is not an accident thr the codon ACC coding for thr appears in the stem of tRNA containing aminoacid. Ser and thr are indeed able to form hydrogen bonds with hydrophilic aminoacids and the prediction is that these aminoacids have form XGZ belonging to the last column of the code table. There are however very few biochemical reactions of this kind useful for proteins. Ser is exceptional in that it is predicted to be able to form flux tubes connecting ser_1 coded by TCZ with ser2 coded by AGZ, Z=T,C. The OH group of ser can be seen as a correlate for this property.
The aminoacids at the ends of the polymer behave effectively like dinucleotides. The aminoacid coded by XYZ would base pair like XcYc if in the beginning of polymer and to YcZc if at the end of polymer. These nucleotides should have very special selective role in DNA-aminoacid and RNA-aminoacid interactions. Remarkably, it is known that the cutting of COOH and NH2 away from the end of polymer in general makes protein folding impossible (also mutations can affect dramatically folding). The first nucleotide of protein is usually met containing sulphur and the conjugation associates met with stop and tyr codons. The association of met with stop is indeed natural for the free NH2 of met having no hydrogen bond in the beginning of the sequence.
According to Creighton, the binding sites of catalyst and ligand in the reaction complex are conjugates both geometrically and physically. It would be nice to have a concrete representation of this conjugacy in terms of the genetic code. Geometric conjugacy is easy to understand in terms of the lock and key picture but I am not quite sure what physical conjugacy could mean. Standard physics intuition would suggests that hydrophilic aminoacids that behave as acids resp. bases attract each other. This option does not possess any obvious formulation in the proposed picture. Matter antimatter conjugation for the second nucleotide Y of XYZ looks however very natural so that the aminoacids in the first and third (second and fourth) row of the code table would tend to pair with each other. This mechanism might be flexible enough to allow to find a conjugate of a given binding site by trial and error. The interpretation would be that hydrophobia tends to create concave and hydrophily convex structures. The attraction between Y and Yc in the braided conjugate regions would due to the Coulomb interaction between quark and antiquark at the ends of the wormhole flux tube.
The strong correlation between RNA dinucleotide and aminoacid in the case of tRNA conforms with this picture. The third flux tube associated with the aminoacid could connect with the third codon after the transition to RNA-aminoacid era. During RNA era tRNA2 would have connected the O=C-OH part of the aminoacid to water molecule.
4. Interactions with DNA
Also in the interactions with DNA and RNA the aminoacid in the interior of the sequence would base-pair" like Yc. The original idea about molecular sex would transform in the sense that the companion of the hydrophilic aminoacid would DNA nucleotide in general. Hydrophobic aminoacids would behave like hermits. The generic contacts with DNA would be contacts with single nucleotide and there would be 4 different basic contacts. Aminoacids are indeed known to form contacts with single nucleotide. Hydrophilic contacts would be favored and hydrophobic contacts avoided so that again Y=A,G aminoacids would play at the outer boundary of DNA would play the active role. The aminoacids inside a given column of the code table would interact in very much the same manner with DNA nucleotides as far as formation of hydrogen bonds is considered. The terminals of the protein polymer are predicted to behave like XcYc resp. YcZc if the corresponding codon is XYZ. Again only hydrophilic codons are expected to be able to form hydrogen bonds. N-terminal is usually met and met and should avoid DNA.
5. Interactions of proteins with ions and electrons
Proteins interact also with electrons and ions. Typical process are the addition or removal of proton, electron, ion such Ca++, or molecule such as O2. These interactions are not well understood. For instance, the interactions involve the transfer of electrons between ligand protein and protein inducing oxidation (electron is given), reduction (electron is received) or redox reaction (both reduction and oxidation take place). In metabolism redox process is central. These reactions are reversible and it is difficult to understand how electrons are able make their long journey from the interior of the ligand so fast and avoiding dissipative effects. The formation of cyclotron Bose-Einstein condensates and electronic Cooper pair condensates at the magnetic flux tubes connecting ligand and protein could be the solution of the mystery.
6. How DNA nucleotides are connected with the hydrophilic ends of lipids?
It was assumed that braid strands defined by "wormhole magnetic" flux tubes join nucleotides to lipids and can continue through the nuclear or cell membrane but are split during tqc. The hydrophilic ends of lipids attach to water molecules and self-organization patterns for the water flow in gel phase induce a 2-D flow in the lipid layer which is liquid crystal defining tqc programs at the classical level as braidings. The flow indeed induces braiding if one assumes that during topological computation the connection through the cell membrane is split and reconnected after the halting of tqc.
The challenge is to understand microscopically how the flux tube joins DNA nucleotide to the phospholipid. What is clear that the points at which the flux tubes attach should be completely standard plugs and the mechanism giving rise to polypeptids is an excellent guide line here. Recall that phospholipid, the dancer, has two hydrophobic legs and head. Each leg has at the hydrophilic end O=C-O-C part joining it to glyceride connected to monophosphate group in turn connected to the hydrophilic residue R. The most often appearing residues are serine, inositol, ethanolamine, and choline. Only three of these appear in large quantities and there is asymmetry between cell exterior and interior.
Let us denote by =O1 and =O2 the two oxygens in question (analogs of right and left hemispheres!). The proposal is that DNA nucleotide and =O1 are connected by a flux tube: the asymmetry between right and left lipid legs should determine which of the legs is "left leg" and which O= is the "left brain hemisphere". =O2, the holistic "right brain hemisphere", connects in turn to the flux tube coming from the other symmetrically situated =O2 at the outer surface of the second lipid layer. Besides this =O1 and =O2 are connected by a flux tube serving as switch on both sides of the membrane. The assumption that two flux tubes enter to =O is consistent with the fact that two hydrogen bonds to =O are possible. During tqc this short flux tube is split or disappears. The lipid residue R couples with the flow of the liquid in gel phase. Since =O is in question the quark or antiquark at the end can correspond to the DNA nucleotide in question. Also the necessary complete correlation between quarks and antiquark charges at the ends of flux tubes associated with =O1 and =O2 can be understood as being due to the minimization of Coulomb interaction energy.
The phosphate groups associated with nucleotides of DNA strand contain also =O, which could act as a plug to which the flux tube from the nucleotide is attached. =O appears in biomolecules involved with varying functions such as signalling, control, and metabolism. =O might act as a universal plug to which flux tubes from electronegative atoms of information molecules can attach their flux tubes. This would also provide a concrete realization of the idea that information molecules (neurotransmitters, hormones) are analogous to links in Internet (see this): they would not represent the information but establish a communication channel. The magnetic flux tube associated with the information molecule would connect it to another cell and by the join to =O plug having flux tube to another cell, say to its nucleus, would create a communication or control channel.
To repeat the earlier statement, this proposal for the folding code - or rather, the code of entire biocatalysis - is so beautiful that it deserves to be killed: this should be easy for a professional biochemist. If the hypothesis survives, it would provide a royal road to the understanding of the catalytic bio-chemistry.
For details see the chapter Evolution in Many-Sheeted Space-time.
Ulla Mattfolk sent me again an interesting link, which happened to relate directly to what I have been doing during the last week, that is application of DNA as topological quantum computer hypothesis to the understanding of the evolution of the genetic code. The link was to an article about the idea of protein folding code - something which is expected to exist but is not understood. See also this. I realized that the prebiotic 2-code assigning to RNA dinucleotides aminoacids might define the folding code. This code would specify also what kind of catalytic reactions can occur between proteins and would dictate the catalytic stereo chemistry - or rather its changes - to a high degree.
Consider now objections against the proposal.
To sum up, this proposal for the folding code - or rather, the code of entire biocatalysis - is so beautiful that it deserves to be killed: this should be easy for a professional biochemist. If the hypothesis survives, it would provide a royal road to the understanding of the catalytic bio-chemistry.
The net is wonderful. Yesterday evening I decided to search for "../articles/ about the possible role of dinucleotides in prebiotic evolution. "Dinucleotide" as a search word gave something about NADH and the only thing I understood that this is not relevant. Then I decided to be very optimistic and use as search words "dinucleotide" "prebiotic" simultaneously. To my surprise I found two gems which guaranteed that I did not sleep too much during the last night!
The first gem did not relate to dinucleotides in a direct manner but I learned that the attempts to synthesize RNA sequences from nucleotides lead to 2',5' form of RNA: recall that the production of 3',5' RNA sequences has not been successful, only single nucleotides have been produced (see the article Experimental Testing of Theories of an Early RNA World by A. D. Ellington). This fits completely with the cautious hypothesis that RNA1 indeed corresponds to 2',5' form of RNA consisting of A,G,U,I and that ordinary 3',5' RNA, which I call RNA2, emerged as dinucleotides, which can polymerize to longer sequences and that this process was catalyzed by aminoacids.
Second gem was directly related to dinucleotides, prebiotics, and genetic code. Somewhat disappointingly, I am not the only person who has considered the idea of 2-code. The title of the paper by S.D. Copley. E. Smith and H. J. Morowitz was A mechanism for the association of aminoacids with their codons and the origin of the genetic code. To very briefly summarize the content of the paper (I am of course not chemist and I see the paper from by "biomolecules connected by magnetic flux tubes" perspective so that it is easy to ridicule me).
Consider now the interpretation of the results in TGD framework.
The coding of the reaction pathway would be in terms of braid strands. The two ("wormhole") magnetic flux tubes beginning from the X and Y would end up to the precursor. The quark u,d or antiquark uc, dc labeling X would tell which precursor the magnetic flux tube ends at. What is the rule involved? What property of nucleotide X and precursor fixes the correspondence characterizing reaction pathway? It certainly seems that the flux tube connects X to a catalytic "hot spot" since X and this hot spot must end up near to each other in the phase transition reducing Planck constant and thus length of the magnetic flux tube. The charges possibly assignable with the hot spots - what ever they are - is a good guess but there is more involved.
It seems that the nucleotides of codon are like 4-digits with first digits having the highest significance. The division of dinucleotide XY to two nucleotides should correspond to a similar division UV of the precursor to two parts. U would change in the reaction in the same manner for all aminoacids resulting from a given precursor but the change should depend on X. One can identify at U as a portion at the right end of the precursor (see the article). The left end of precursor would in turn connect with Y.
An ideal experimentalist with infinite brilliance and funding resources and enjoying endless trust of decision makers might be interested in carrying out the following experiments.
For details see the chapter Evolution in Many-Sheeted Space-time.
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.
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.
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.
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 Evolution in Many-Sheeted Space-time.