Thursday, January 10, 2008

DNA as a topological quantum computer: XI

In previous postings I, II, III, IV, V, VI, VII, VIII, IX, X 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.

Since the representation in the book and in previous postings is bottom-up and not well-organized, it is perhaps worth of providing a summary about the model in both bottom-up (very briefly) and top-to-bottom manner.

1. Bottom-up approach

I ended up with the third model in bottom-up manner and this representation is followed also in the text. The model which looks the most plausible one relies on two specific ideas.

  1. Sharing of labor means conjugate DNA would do tqc and DNA would "print" the outcome of tqc in terms of RNA yielding aminoacids in the case of exons. RNA could result in the case of introns. The experience about computers and the general vision provided by TGD suggests that introns could express the outcome of tqc also electromagnetically in terms of standardized field patterns. Also speech would be a form of gene expression. The quantum states braid would entangle with characteristic gene expressions.

  2. The manipulation of braid strands transversal to DNA must take place at 2-D surface. The ends of the space-like braid are dancers whose dancing pattern defines the time-like braid, the running of classical tqc program. Space-like braid represents memory storage and tqc program is automatically written to memory during the tqc. The inner membrane of the nuclear envelope and cell membrane with entire endoplasmic reticulum included are good candidates for dancing halls. The 2-surfaces containing the ends of the hydrophobic ends of lipids could be the parquets and lipids the dancers. This picture seems to make sense.

2. Top-down approach

One ends up to the model also in top-down manner.

  1. Darwinian selection for which 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.

  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.

  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 not 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.

  6. There are several problems related to the details of the realization. How nucleotides A,T,C,G are coded to strand color and what this color corresponds to? The prediction that wormhole contacts carrying quark and anti-quark at their ends appear in all length scales in TGD Universe resolves the problem. How to split the braid strands in a controlled manner? High Tc super conductivity provides the 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 saves the situation now: after the splitting the flux returns back along the second space-time sheet of wormhole magnetic field.

To sum up, it seems that essentially all new physics involved with TGD based view about quantum biology enter to the model in crucial manner.

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

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