DNA as topological quantum computer: XII
In previous postings I, II, III, IV, V, VI, VII, VIII, IX, X, XI I have discussed various aspects of the idea that DNA could acts as a topological quantum computer using fundamental braiding operation as a universal 2gate.
One of the challenges is the realization of single particle gates representing U(2) rotation of the qubit. The first thing to come mind was that U(2) corresponds to U(2) rotation induced by magnetic field and electric fields. Yesterday I realized much more elegant realization in terms of SU(3) rotation, where SU(3) is color group associated with strong interactions. Soon I remembered that there is direct evidence for the prediction that color SU(3) is associated with tqc and thus cognition: something that does not come first in mind! I have myself written text about the strange finding of topologist Barbara Shipman suggesting that quarks are in some mysterious manner involved with honeybee dance and proposed an interpretation.
1. The realization of 1gate in terms of ordinary rotations
The realization of single particle gates as U(2) transformations leads naturally to the extension of the braid group by assigning to the strands sequences of group elements satisfying the group multiplication rules. The group elements associated with a n^{th} strand commute with the generators of braid group which do not act on n^{th} strand. G would be naturally subgroup of the covering group of rotation group acting in spin degrees of spin 1/2 object. Since U(1) transformations generate only an overall phase to the state, the presence of this factor might not be necessary. A possible candidate for U(1) factor is as a rotation induced by a timelike parallel translation defined by the electromagnetic scalar potential Φ=A_{t}.
A possible realization for single particle gate characterized by s subset SU(2) would be as SU(2) rotation induced by a magnetic pulse. This transformation is fixed by the rotation axis and rotation angle around this axes. This kind of transformation would result by applying to the strand a magnetic pulse with magnetic field in the direction of rotation axes. The duration of the pulse determines the rotation angle. Pulse could be created by bringing a magnetic flux tube to the system, letting it act for the required time, and moving it away. U(1) phase factor could result from the electromagnetic gauge potential as a nonintegrable phase factor exp(ie∫ A_{t}dt/hbar) coming from the presence of scale potential Φ=A_{t} in the Hamiltonian.
One can criticize this model. The introduction of magnetic pulses does not look an attractive idea and seems to require additional structures besides magnetic flux tubes (MEs?). It would be much nicer to assign the magnetic field with the flux tubes defining the braid strands. The rotation of magnetic field would however require changing the direction of braid strands. This does not look natural. Could one do without this rotation by identifying spin like degree of freedom in some other manner? This is indeed possible.
2. The realization of 1gate in terms of color rotations
TGD predicts a hierarchy of copies of scaled up variants of both weak and color interactions and these play a key role in TGD inspired model of living matter. Both weak isospin and color isospin could be considered as alternatives for the ordinary spin as a realization of qubit in TGD framework. Below color isospin is discussed. Below color isospin is discussed but one could consider also a realization in terms of nuclei and their exotic counterparts differing only by the replacement of neutral color bond between nuclei of nuclear string with a charged one. Charge entanglement between nuclei would guarantee overall charge conservation.
 Each spacetime sheet of braid strands contains quark and antiquark at its ends. Color isospin and hypercharge label their states. Two of the quarks of the color triplet form doublet with respect to color isospin and the third is singlet and has different hyper charge Y. Hence qubit could be realized in terms of color isospin I_{3} instead of ordinary spin but third quark would be inert in the Boolean sense. Qubit could be also replaced with qutrit and isospin singlet could be identified as a statement with illdefined truth value. Trits are used also in ordinary computers. In TGD framework finite measurement resolution implies fuzzy qubits and the third state might relate to this fuzziness.
 Magnetic flux tubes are also color magnetic flux tubes carrying nonvanishing classical color gauge field in the case that they are nonvacuum extremals. The holonomy group of classical color field is an Abelian subgroup of the U(1)× U(1) Cartan subgroup of color group. Classical color magnetic field defines the choice of quantization axes for color quantum numbers. For instance, magnetic moment is replaced with color magnetic moment
and this replacement is in key role in simple model for color magnetic spin spin splittings
between spin 0 and 1 mesons as well as spin 1/2 and 3/2 baryons.
 There is a symmetry breaking of color symmetry to subgroup U(1)_{I3}× U(1)_{Y} and color singletness is in TGD framework replaced by a weaker condition stating that physical states have vanishing net color quantum numbers. This makes possible the measurement of color quantum numbers in the manner similar to that for spin. For instance, color singlet formed by quark and antiquark with opposite color quantum numbers can in the measurement of color quantum numbers of quark reduce to a state in which quark has definite color quantum numbers. This state is a superposition of states with vanishing Y and I_{3} in color singlet and color octet representations. Strong form of color confinement would not allow this kind of measurement.
 Color rotation in general changes the directions of quantization axis of I_{3} and Y and generates a new state basis. Since U(1)× U(1) leaves the state basis invariant, the space defined by the choices of quantization axes is 6dimensional flag manifold F=SU(3)/U(1)×U(1). In contrast to standard model, color rotations in general do not leave classical electromagnetic field invariant since classical em field is a superposition of color invariant induced Kähler from and color noninvariant part proportional classical Z^{0} field. Hence, although the magnetic flux tube retains its direction and shape in M^{4} degrees of freedom, its electromagnetic properties are affected and this is visible at the level of classical electromagnetic interactions.
 If color isospin defines the qubit or qutrit in topological quantum computation, color quantum numbers and the flag manifold F should have direct relevance for cognition. Amazingly, there is a direct experimental support for this! Years ago topologist Barbara Shipman made the intriguing observation that honeybee dance can be understood in terms of a model involving the flag manifold F (see this, this, and this). This led her to propose that quarks are in some mysterious manner involved with the honeybee dance. My proposal was that color rotations of the spacetime sheets associated with neurons represent geometric information: sensory input would be coded to color rotations defining the directions of quantization axes for I_{3} and Y. Subsequent state function reduction would provide conscious representations in terms of trits characterizing for instance sensory input symbolically.
I introduced also the notions of geometric and sensory qualia corresponding to the two choices involved with the quantum measurement: the choice of quantization axes performed by the measurer and the "choice" of final state quantum numbers in state function reduction. In the case of honeybee dance geometric qualia could code information about the position of the food source. The changes of color quantum numbers in quantum jump were identified as visual colors. In state function reduction one cannot speak about change of quantum numbers but about their emergence. Therefore one must distinguish between color qualia and the conscious experience defined by the emergence of color quantum numbers: the latter would have interpretation as qutrit.
To sum up, this picture suggests that 1gates of DNA tqc (understood as "dance of lipids") are defined by color rotations of the ends of spacelike braid strands and at lipids. The color rotations would be induced by sensory and other inputs to the system. Topological quantum computation would be directly related to conscious experience and sensory and other inputs would fix the directions of the color magnetic fields.
For details see the chapter DNA as Topological Quantum Computer.
