Wednesday, February 27, 2008

DNA as topological quantum computer and ageing

The notion of anomalous em charge is one of the basic implications of the many-sheeted space-time concept. It can be assigned to wormhole contacts carrying fermion and antifermion quantum numbers at their throats. If the classical electromagnetic fields at the two space-time sheets are different, the wormhole contact couples to the difference of vector potentials and behaves like a particle with anomalous charge although the net charge is vanishing.

In the model of DNA as topological quantum computer the braid strands (whose braiding defines tqc program) emanate from DNA nucleotides and end up to the lipids of the nuclear and cellular membranes. They are colored in the sense that one can tell whether the strand arrives from A,T,C or G. This is achieved by representing the braid strand as a wormhole magnetic flux tube with CP conjugate wormhole throats at its ends. To A,T,C,G one assigns a wormhole contact with quark u,d or its antiquark at the "upper" throat and its CP conjugate at the "lower" throat.

There are also symmetries: A and T resp. G and C are mapped to quark and its antiquark so that DNA conjugation corresponds to CP conjugation. Chargaff's rules A≈ T and G≈ A for single DNA strand state that DNA as a whole is matter-antimatter symmetric. A and G are mapped to u,d or their antiquarks and correspond therefore to isospin doublet. This allows to interpret the almost exact A-G and T-C symmetries of the third nucleotide of codon in terms of strong isospin symmetry. Both symmetries can break down for short portions of DNA.

The anomalous em charge of DNA is due to the fact that DNA is negatively charged (2 units of charge per nucleotide due to phosphate) and generates classical em field at the "upper" sheet of wormhole magnetic flux tube. The nearly vanishing Qa for DNA is interpreted as a stability condition for DNA. For long DNA strands Chargaff's rules A≈ T and G≈ A indeed guarantee the vanishing of Qa since A and T resp. C and G correspond to quark and its antiquark. There are four options concerning nucleotide quark correspondence and therefore also the identification of Qa: for one of them one has Qa= [2(A-T)-(G-C)]/3. Integer valuedness allows color singletness for the many quark-antiquark state assignable to DNA strand via the mapping of A,T,C,G to quarks and antiquarks.

Telomeres are of special interests as far as anomalous em charge is considered. Chromosomes are not copied completely in cell replication, and one function of telomeres is to guarantee that the translated part of genome replicates completely for sufficiently many cell divisions. Telomeres consists of 3-20 kilobases long repetitions of TTAGGG, and there is a 100-300 kilobases long repeating sequence between telomere and the rest of the chromosome. Telomeres can form can also 4-stranded structures. Telemere end contains a hair-pin loop as a single stranded part, which prevents the action of DNA repair enzymes on the chromosome end.

Telomerase is a reverse transcriptase enzyme involved with the synthesis of telomeres using RNA strand as a template but since its expression is repressed in many types of human cells, telomere length shortens in each cell replication. In the case of germ cells, stem cells and white blood cells telomerase is expressed and telomere length preserved. Telomere shortening is known to relate to ageing related diseases. On the other hand, overactive telomere expression seems to correlate with cancer.

If telomeres possess braid strands, the compensation of Qa might provide an additional reason for their presence. If this the case and if telomeres are strict multiples of TTAGGG, the shortening of telomeres generates a non-vanishing Qa unless something happens for the active part of DNA too. Color singletness condition should however remain true: the disappearance of 3n multiples of TTAGGG in each replication is the simplest guess for what might happen. In any case, DNA strands would become unstable in cell replication. Qa could be reduced by a partial death of DNA in the sense that some portions of braiding disappear. Also this would induce ill functioning of tqc harware perhaps related to ageing related diseases. Perhaps evolution has purposefully developed this ageing mechanism since eternal life would stop evolution.

For a more detailed exposition and background see the chapter DNA as Topological Quantum Computer of "Genes and Memes".

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