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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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 uc, dc 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.
- How to split the braid strands in a controlled manner? High Tc 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.
- 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.
- 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+Pi 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.