Wednesday, December 26, 2007

DNA as a topological quantum computer: VIII

In previous postings I, II, III, IV, V, VI, VII I have discussed various aspects of the idea that DNA could acts as a topological quantum computer using fundamental braiding operation as a universal 2-gate.

In the following I will consider first the realization of the basic braiding operation: this requires some facts about phospholipids which are summarized first. Also the realization of braid color is discussed. This requires the coding of the DNA color A,T,C,G to a property of braid strand which is such that it is conserved meaning that after halting of tqc only strands with same color can reconnect. This requires long range correlation between lipid and DNA nucleotide. It seems that strand color cannot be chemical. Quark color is essential element of TGD based model of high Tc superconductivity and provides a solution to the problem: the four neutral quark-antiquark pairs with quark and antiquark at the ends of color flux tube defining braid strand would provide the needed four colors.

A. Some facts about phospholipids

Phospholipids - which form about 30 per cent of the lipid content of the monolayer - contain phosphate group. The dance of lipids requires metabolic energy and the hydrophilic ends of the phospholipid could provide it. They could also couple the lipids to the flow of water in the vicinity of the lipid monolayer possibly inducing the braiding. Of course, the causal arrow could be also opposite.

The hydrophilic part of the phospholipid is a nitrogen containing alcohol such as serine, inositol or ethanolamine, or an organic compound such as choline. Phospholipids are classified into 3 kinds of phosphoglycerides and sphingomyelin.

A.1 Phosphoglycerides

In cell membranes, phosphoglycerides are the more common of the two phospholipids, which suggest that they are involved with tqc. One speaks of phosphotidyl X, where X= serine, inositol, ethanolamine is the nitrogen containing alcohol and X=Ch the organic compound. The shorthand notion OS, PI, PE, PCh is used.

The structure of the phospholipid is most easily explained using the dancer metaphor. The two fatty chains define the hydrophobic feet of the dancer, glycerol and phosphate group define the body providing the energy to the dance, and serine, inositol, ethanolamine or choline define the hydrophilic head of the dancer (perhaps "deciding" the dancing pattern).

There is a lipid asymmetry in the cell membrane. PS, PE, PI in cytoplasmic monolayer (alcohols). PC (organic) and sphingomyelin in outer monolayer. Also glycolipids are found only in the outer monolayer. The asymmetry is due to the manner that the phospholipids are manufactured.

PS in the inner monolayer is negatively charged and its presence is necessary for the normal functioning of the cell membrane. It activates protein kinase C which is associated with memory function. PS slows down cognitive decline in animals models. This encourages to think that the hydrophilic polar end of at least PS is involved with tqc, perhaps to the generation of braiding via the coupling to the hydrodynamic flow of cytoplasm in the vicinity of the inner monolayer.

A. 2. Fatty acids

The fatty acid chains in phospholipids and glycolipids usually contain an even number of carbon atoms, typically between 14 and 24 making 5 possibilities altogether. The 16- and 18-carbon fatty acids are the most common. Fatty acids may be saturated or unsaturated, with the configuration of the double bonds nearly always cis. The length and the degree of unsaturation of fatty acids chains have a profound effect on membranes fluidity as unsaturated lipids create a kink, preventing the fatty acids from packing together as tightly, thus decreasing the melting point (increasing the fluidity) of the membrane. The number of unsaturaded cis bonds and their positions besides the number of Carbon atoms characterizes the lipid. Quite generally, there are 3n Carbons after each bond. The creation of unsatured bond by removing H atom from the fatty acid could be an initiating step in the basic braiding operation creating room for the dancers. The bond should be created on both neighboring lipids simultaneously.

B. How the braiding operation could be induced?

One can imagine several models for what might happen during the braiding operation in the lipid bilayer. One such view is following.

  1. The creation of unsaturated bond and involving elimination of H atom from fatty acid would lead to cis configuration and create the room needed by dancers. This operation should be performed for both lipids participating in the braiding operation. After the braiding it might be necessary to add H atom back to stabilize the situation. The energy needed to perform either or both of these operations could be provided by the phosphate group.

  2. The hydrophilic ends of lipids couple the lipids to the surrounding hydrodynamic flow in the case that the lipids are able to move. This coupling could induce the braiding. The primary control of tqc would thus be by using the hydrodynamic flow by generating localized vortices. There is considerable evidence for water memory but its mechanism remains to be poorly understood. If also water memory is realized in terms of the braid strands connecting fluid particles, DNA tqc could have evolved from water memory.

  3. Sol-gel phase transition is conjectured to be important for the quantum information processing of cell (see this). In the transition which can occur cyclically actin filaments (also at EEG frequencies) are assembled and lead to a gel phase resembling solid. Sol phase could correspond to tqc and gel to the phase following the halting of tqc. Actin filaments might be assignable with braid strands or bundles of them and shield the braiding. Also microtubules might shield bundles of braid strands.

  4. Only inner braid strands are directly connected to DNA which also supports the view that only the inner monolayer suffers a braiding operation during tqc and that the outer monolayer should be in a "freezed" state during it. There is a net negative charge associated with the inner mono-layer possibly relating to its participation to the braiding. The vigorous hydrodynamical flows known to take place below the cell membrane could induce the braiding.

C. How braid color could be realized?

The conserved braid color is not necessary for the model but would imply genetic coding of the tqc hardware so that sexual reproduction would induce an evolution of tqc hardware. Braid color would also make the coupling of foreign DNA to the tqc performed by the organism difficult and realize an immune system at the level of quantum information processing.

The conservation of braid color poses however considerable problems. The concentration of braid strands of same color to patches would guarantee the conservation but would restrict the possible braiding dramatically. A more attractive option is that the strands of same color find each other automatically by energy minimization after the halting of tqc. Electromagnetic Coulomb interaction would be the most natural candidate for the interaction in question. Braid color would define a faithful genetic code at the level of nucleotides. It would induce long range correlation between properties of DNA strand and the dynamics of cell immediately after the halting of tqc.

C.1 Chemical realization of color is not plausible

The idea that color could be a chemical property of phospholipids does not seem plausible. The lipid asymmetry of the inner and outer monolayers excludes the assignment of color to the hyrdrophilic group PS, PI, PE, PCh. Fatty acids have N=14,...,24 carbon atoms and N=16 and 18 are the most common cases so that one could consider the possibility that the 4 most common feet pairs could correspond to the resulting combinations. It is however extremely difficult to understand how long range correlation between DNA nucleotide and fatty acid pair could be created.

C.2 Could quark pairs code for braid color?

It seems that the color should be a property of the braid strand. In TGD inspired model of high Tc super-conductivity (see this) wormhole contacts having u and dc and d and uc quarks at the two wormhole throats feed electron's gauge flux to larger space-time sheet. The long range correlation between electrons of Cooper pairs is created by color confinement for an appropriate scaled up variant of chromo-dynamics which are allowed by TGD. Hence the neutral pairs of colored quarks whose members are located the ends of braid strand acting like color flux tube connecting nucleotide to the lipid could code DNA color to QCD color.

For the pairs udc with net em charge the quark and anti-quark have same sign of em charge and tend to repel each other. Hence the minimization of electro-magnetic Coulomb energy favors the neutral configurations uuc, ddc and uuc, and ddc coding for A, G (say) and their conjugates T and C. After the halting of tqc only these pairs would form with a high probability. The reconnection of the strands would mean a formation of a short color flux tube between the strands and the annihilation of quark pair to gluon. Note that single braid strand would connect DNA color and its conjugate rather than identical colors so that braid strands connecting two DNA strands (conjugate strands) should always traverse through an even (odd) number of cell membranes.

For details see the chapter DNA as Topological Quantum Computer of "Genes and Memes".

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