DNA as topological quantum computer: XIV

I have worked hardly in refining the chapters about quantum biology in TGD Universe. DNA as topological quantum computer was the original idea that has generalized considerably and led to a beautiful unification of various basic ideas. I attach below the abstract of the chapter DNA as topological quantum computer contained in the book "Genes and Memes".

This chapter represents a vision about how DNA might act as a topological quantum computer (tqc). Tqc means that the braidings of braid strands define tqc programs and M-matrix (generalization of S-matrix in zero energy ontology) defining the entanglement between states assignable to the end points of strands define the tqc usually coded as unitary time evolution for Schrödinger equation. One can ends up to the model in the following manner.

1. Darwinian selection for which the standard theory of self-organization provides a model, should apply also to tqc programs. Tqc programs should correspond to asymptotic self-organization patterns selected by dissipation in the presence of metabolic energy feed. The spatial and temporal pattern of the metabolic energy feed characterizes the tqc program - or equivalently - sub-program call.
2. Since braiding characterizes the tqc program, the self-organization pattern should correspond to a hydrodynamical flow or a pattern of magnetic field inducing the braiding. Braid strands must correspond to magnetic flux tubes of the magnetic body of DNA. If each nucleotide is transversal magnetic dipole it gives rise to transversal flux tubes, which can also connect to the genome of another cell. As a matter fact, the flux tubes would correspond to what I call wormhole magnetic fields having pairs of space-time sheets carrying opposite magnetic fluxes.
3. The output of tqc sub-program is probability distribution for the outcomes of state function reduction so that the sub-program must be repeated very many times. It is represented as four-dimensional patterns for various rates (chemical rates, nerve pulse patterns, EEG power distributions,...) having also identification as temporal densities of zero energy states in various scales. By the fractality of TGD Universe there is a hierarchy of tqcs corresponding to p-adic and dark matter hierarchies. Programs (space-time sheets defining coherence regions) call programs in shorter scale. If the self-organizing system has a periodic behavior each tqc module defines a large number of almost copies of itself asymptotically. Generalized EEG could naturally define this periodic pattern and each period of EEG would correspond to an initiation and halting of tqc. This brings in mind the periodically occurring sol-gel phase transition inside cell near the cell membrane. There is also a connection with hologram idea: EEG rhythm corresponds to reference wave and nerve pulse patters to the wave carrying the information and interfering with the reference wave.
4. Fluid flow must induce the braiding which requires that the ends of braid strands must be anchored to the fluid flow. Recalling that lipid mono-layers of the cell membrane are liquid crystals and lipids of interior mono-layer have hydrophilic ends pointing towards cell interior, it is easy to guess that DNA nucleotides are connected to lipids by magnetic flux tubes and hydrophilic lipid ends are stuck to the flow.
5. The topology of the braid traversing cell membrane cannot be affected by the hydrodynamical flow. Hence braid strands must be split during tqc. This also induces the desired magnetic isolation from the environment. Halting of tqc reconnects them and make possible the communication of the outcome of tqc.

There are several problems related to the details of the realization.

1. How nucleotides A,T,C,G are coded to the strand color and what this color corresponds to physically? There are two options which could be characterized as fermionic and bosonic.
   i) Magnetic flux tubes having quark and anti-quark at their ends with u,d and u_c, d_c coding for A,G and T,C. CP conjugation would correspond to conjugation for DNA nucleotides.
   ii) Wormhole magnetic flux tubes having wormhole contact and its CP conjugate at its ends with wormhole contact carrying quark and anti-quark at its throats. The latter are predicted to appear in all length scales in TGD Universe.
2. How to split the braid strands in a controlled manner? High T_c super conductivity provides a possible mechanism: braid strand can be split only if the supra current flowing through it vanishes. A suitable voltage pulse induces the supra-current and its negative cancels it. The conformation of the lipid controls whether it it can follow the flow or not.
3. How magnetic flux tubes can be cut without breaking the conservation of the magnetic flux? The notion of wormhole magnetic field could save the situation now: after the splitting the flux returns back along the second space-time sheet of wormhole magnetic field. An alternative solution is based on reconnection of flux tubes. Since only flux tubes of same color can reconnect this process can induce transfer of strand color: "color inheritance": when applied at the level of amino-acids this leads to a successful model of protein folding. Reconnection makes possible breaking of flux tube connection for both the ordinary magnetic flux tubes and wormhole magnetic flux tubes.
4. How magnetic flux tubes are realized? The interpretation of flux tubes as correlates of directed attention at molecular level leads to concrete picture. Hydrogen bonds are by their asymmetry natural correlates for a directed attention at molecular level. Also flux tubes between acceptors of hydrogen bonds must be allowed and acceptors can be seen as the subjects of directed attention and donors as objects. Examples of acceptors are aromatic rings of nucleotides, O= atoms of phosphates, etc.. A connection with metabolism is obtained if it is assumed that various phosphates XMP,XDP,XTP, X=A,T,G,C act as fundamental acceptors and plugs in the connection lines. The basic metabolic process ATP® ADP+P_i allows an interpretation as a reconnection splitting flux tube connection, and the basic function of phosphorylating enzymes would be to build flux tube connections as also of breathing and photosynthesis.

The model makes several testable predictions about DNA itself. In particular, matter-antimatter asymmetry and slightly broken isospin symmetry have counterparts at DNA level induced from the breaking of these symmetries for quarks and antiquarks associated with the flux tubes. DNA cell membrane system is not the only possible system that could perform tqc like activities and store memories in braidings: flux tubes could connect biomolecules and the braiding could provide an almost definition for what it is to be living. Even water memory might reduce to braidings.

The model leads also to an improved understanding of other roles of the magnetic flux tubes containing dark matter. Phase transitions changing the value of Planck constant for the magnetic flux tubes could be key element of bio-catalysis and electromagnetic long distance communications in living matter. For instance, one ends up to what might be called code for protein folding and bio-catalysis. There is also a fascinating connection with Peter Gariaev's work suggesting that the phase transitions changing Planck constant have been observed and wormhole magnetic flux tubes containing dark matter have been photographed in his experiments.

A code for protein folding and bio-catalysis

The TGD inspired model for the evolution of genetic code leads to the idea that the folding of proteins obeys a folding code inherited from the genetic code. After some trials one ends up with a general conceptualization of the situation with the identification of wormhole magnetic flux tubes as correlates of 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. By their asymmetric character hydrogen bonds are excellent candidates for magnetic flux tubes serving as correlates of attention at molecular level.

The constant part of free amino-acid containing O-H, O=, and NH₂ would correspond to the codon XYZ in the sense that the flux tubes would carry the "color" representing the four nucleotides in terms of quark pairs. Color inheritance by flux tube reconnection makes this possible. For the amino-adics inside protein O= and N-H would correspond to YZ. Also flux tubes connecting the acceptor atoms of hydrogen bonds are required by the model of DNA as topological quantum computer. The long flux tubes between O= atoms and their length reduction in a phase transition reducing Planck constant could be essential in protein-ligand interaction.

The model predicts a code for protein folding: depending on whether also =O-O= flux tubes are allowed or not, Y=Z or Y=Z_c condition is satisfied by the amino-acids having N-H-O= hydrogen bond. For =O-O= bonds Y-Y_c pairing holds true. Y=Z_c option predicts the average length of alpha bonds correctly. Y=Z rule is favored by the study of alpha helices for four enzymes: the possible average length of alpha helix is considerably longer than the average length of alpha helix if gene is the unique gene allowing to satisfy Y=Z rule. The explicit study of alpha helices for four enzymes demonstrates that the failure to satisfy the condition for the existence of hydrogen bond fails rarely and at most for two amino-acids (for 2 amino-acids in single case only). For beta sheets there ar no failures for Y=Z option.

The information apparently lost in the many-to-one character of the codon-amino-acid correspondence would code for the folding of the protein and similar amino-acid sequences could give rise to different foldings. Also catalyst action would reduce to effective base pairing and one can speak about catalyst code. The DNA sequences associated with alpha helices and beta sheets are completely predictable unless one assumes a quantum counterpart of wobble base pairing meaning that N-H flux tubes are before hydrogen bonding in quantum superpositions of braid colors associated with the third nucleotides Z of codons XYZ coding for amino-acid. Only the latter option works. The outcome is very simple quantitative model for folding and catalyst action based on minimization of energy and predicting as its solutions alpha helices and beta sheets.

I want to express my gratitude for Dale Trenary for interesting discussions, for suggesting proteins which could allow to test the model, as well as providing concrete help in loading data help from protein data bank. Also I want to thank Timo Immonen for loaning the excellent book "Proteins: Structures and Molecular Properties" of Creighton. Also Pekka Rapinoja for writing the program transforming protein data file to a form readable by MATLAB.

For details see the new chapter A Model for Protein Folding and Bio-catalysis of "Genes and Memes".