Saturday, December 08, 2007

DNA as a topological quantum computer: III

I have discussed various ideas about topological quantum computation in two previous postings. In DNA as a topological quantum computer I discussed general ideas, and made a general suggestion about how DNA might act as a topological quantum computer. In Some ideas about topological quantum computation in TGD Universe I continued with futher general ideas about braiding and its relation to tqc.

Braids code for topological quantum computation. One can imagine many possible identifications of braids but this is not essential for what I am going to say below.

  1. What is highly non-trivial that the motion of the ends of strands defines both time-like and space-like braidings with latter defining in a well-defined sense a written version of the tqc program, kind of log file. The manipulation of braids is a central element of tqc and if DNA really performs tqc, the biological unit modifying braidings should be easy to identify. An obvious signature is the 2-dimensional character of this unit and the alert and informed reader might be able to guess the rest.

  2. One can also wonder exactly what part of DNA performs tqc and alert and informed reader might have answer also to this question. In the following I propose an improved view about tqc performed by DNA inspired by these guesses.

1. Sharing of labor

The braid strands must begin from DNA double strands. Precisely which part of DNA does perform tqc? Genes? Introns? Or could it be conjugate DNA which performs tqc? The function of conjugate DNA has indeed remain mystery and sharing of labor suggests itself.

Conjugate DNA would do tqc and DNA would "print" the outcome of tqc in terms of RNA yielding aminoacids in 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. This hypothesis will be taken as starting point in the following considerations.

2. Cell membranes as modifiers of braidings defining tqc programs?

What part of the cell or nucleus is specialized to perform braiding operations? The first guess was that nucleotides of the intronic part of DNA are permuted without any change in the sequence: the argument was that if introns do not express themselves chemically this activity does not perturb tqc. At the second thinking this does not look a good idea at all. First of all, introns are transcribed but then spliced out from the transcript. Secondly, they are now known to express themselves by producing RNA having some function as I had myself explained earlier (and forgotten it!). Something much more elegant is required. Two days ago I started to reconsider the problem and ended up with a nice little argument allowing to understand why cell membrane is necessary and why it is liquid crystal.

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.

  1. Consider first the anatomy of membranes. Cell membrane and membranes of nuclear envelope consist of 2 lipid layers whose hydrophobic ends point towards interior. There is no water here nor any direct perturbations from the environment or interior milieu of cell. Nuclear envelope consists of two membranes having between them an empty volume of thickness 20-40 nm. The inner membrane consists of two lipid layers like ordinary cell membrane and outer membrane is connected continuously to endoplasmic reticulum which forms a part of highly folded cell membrane. Many biologists believe that cell nucleus is a prokaryote, which began to live in symbiosis with prokaryote defining the cell membrane.

  2. What makes dancing possible is that the phospholipid layers of the cell membrane are liquid crystals: the lipids can move freely in the horizontal direction but not vertically. "Phospho" could relates closely to the metabolic energy needs of dancers. If these lipids are self-organized around braid strands, their dancing patterns along the membrane surface would be an ideal manner to modify braidings since the lipids would have standard positions in a lattice. This would be like dancing on a chessboard. As a matter fact, living matter is full of self-organizing liquid crystals and one can wonder whether the deeper purpose of their life be running and simultaneous documentation of tqc programs?

  3. Ordinary computers have operating system: a collection of standard programs -the system - and similar situation should prevail now. The "printing" of outputs of tqc would correspond to this kind of standard program. This tqc program should not receive any input from the environment of the nucleus and should therefore correspond to braid strands connecting conjugate strand with strand. Braid strands would go only through the inner nuclear membrane and return back and would not be affected much since the volume between inner and outer nuclear membranes is empty. This assumption looks ad hoc but it will be found that the requirement that these programs are inherited as such in the cell replication necessitates this kind of structure.

  4. The braid strands starting from the conjugate DNA could traverse several time through the highly folded endoplasmic reticulum but without leaving cell interior and return back to nucleus and modify tqc by intracellular input. Braid strands could also traverse the cell membrane and thus receive information about the exterior of cell. Both of these tqc programs could be present also in monocellulars (prokaryotes) but the braid strands would always return back to the nucleus. In multicellulars (eukaryotes) braid strands could continue to another cell and give rise to "social" tqc programs performed by the multicellular organisms. Note that the topological character of braiding does not require isolation of braiding from environment. It might be however advantageous to have some kind of sensory receptors amplifying sensory input to standardized re-braiding patterns. Various receptors in cell membrane would serve this purpose.

  5. If braid strands carry 4-color (A,T,C,G) then also lipid strands should carry this kind of 4-color. The lipids whose hydrophobic ends can be joined to form longer strand should have same color. This color need not be chemical in TGD Universe.

  6. Braid strands can end up at the parquet defined by ends of the inner phospholipid layer: their distance of inner and outer parquet is few nanometers. They could also extend further.

    1. If one is interested in connecting cell nucleus to the membrane of another cells, the simpler option is formation of hole defined by a protein attached to cell membrane. In this case only the environment of second cell affects the braiding assignable to the first cell nucleus.
    2. The bi-layered structure of the cell membrane could be essential for the build-up of more complex tqc programs since the strands arriving at two nearby hydrophobic 2-surfaces could combine to form longer strands. The formation of longer strands could mean the fusion of the two nearby hydrophobic two-surfaces in the region considered. This would allow to connect cell nucleus and cell membrane to a larger tqc unit and cells to multicellular tqc units so that the modification of tqc programs by feeding the information from the exteriors of cells - essential for the survival of multicellulars - would become possible. It would be essential that only braid strands of same color are connected in this process and splitting of strands and their reconnection defines a manner to change braidings.

4. Quantitative test for the proposal

There is a simple quantitative test for the proposal. A hierarchy of tqc programs is predicted, which means that the number of lipids in the nuclear inner membrane should be larger or at least of same order of magnitude that the number of nucleotides. For definiteness take the radius of the lipid molecule to be about 5 Angstroms (probably somewhat too large) and the radius of the nuclear membrane about 2.5 μm.

For our own species the total length of DNA strand is about one meter and there are 30 nucleotides per 10 nm. This gives 6.3×107 nucleotides: the number of intronic nucleotides is only by few per cent smaller. The total number of lipids in the nuclear inner membrane is roughly 108. The number of lipids is roughly twice the number nucleotides. The number of lipids in the membrane of a large neuron of radius of order 10-4 meters is about 1011. The fact that the cell membrane is highly convoluted increases the number of lipids available. Folding would make possible to combine several modules in sequence by the proposed connections between hydrophobic surfaces.

5. Cell replication and tqc

One can look what happens in the cell replication in the hope of developing more concrete ideas about tqc in multicellular system. This process must mean a replication of the braid's strand system and a model for this process gives concrete ideas about how multicellular system performs tqc.

  1. During mitosis chromosomes are replicated. During this process the strands connecting chromosomes become visible: the pattern brings in mind flux tubes of magnetic field. For prokaryotes the replication of chromosomes is followed by the fission of the cell membrane. Also plant nuclei separated by cellulose walls suffer fission after the replication of chromosomes. For animals nuclear membranes break down before the replication suggesting that nuclear tqc programs are reset and newly formed nuclei start tqc from a clean table. For eukaryotes cell division is controlled by centrosomes. The presence of centrosomes is not necessary for the survival of the cell or its replication but is necessary for the survival of multicellular. This conforms with the proposed picture.

  2. If the conjugate strands are specialized in tqc, the formation of new double strands does not involve braids in an essential manner. The formation of conjugate strand should lead to also to a generation of braid strands unless they already exist as strands connecting DNA and its conjugate and are responsible for "printing". These strands need not be short. The braiding associated with printing would be hardware program which could be genetically determined or at least inherited as such so that the strands should be restricted inside the inner cell membrane or at most traverse the inner nuclear membrane and turn back in the volume between inner membrane and endoplasmic reticulum.

    The return would be most naturally from the opposite side of nuclear membrane which suggest a breaking of rotational symmetry to axial symmetry. The presence of centriole implies this kind of symmetry breaking: in neurons this breaking becomes especially obvious. The outgoing braid strands would be analogous to axon and returning braid strands to dendrites. Inner nuclear membrane would decompose the braiding to three parts: one for strand, second for conjugate strand, and a part in the empty space inside nuclear envelope.

  3. The formation of new DNA strands requires recognition relying on "strand color" telling which nucleotide can condense at it. The process would conserve the braidings connecting DNA to the external world. The braidings associated with the daughter nuclei would be generated from the braiding between DNA and its conjugate. As printing software they should be identical so that the braiding connecting DNA double strands should be a product of a braiding and its inverse. This would however mean that the braiding is trivial. The division of the braid to three parts hinders the transformation to a trivial braid if the braids combine to form longer braids only during the "printing" activity.

  4. The new conjugate strands are formed from the old strands associated with printing. In the case of plants the nuclear envelope does not disintegrate and splits only after the replication of chromosomes. This would suggest that plant cells separated by cell walls perform only intracellular tqc. Hermits do not need social skills. In the case of animals nuclear envelope disintegrates. This is as it must be since the process splits the braids connecting strand and conjugate strands so that they can connect to the cell membrane. The printing braids are inherited as such which conforms with the interpretation as a fixed software.

  5. The braids connecting mother and daughter cells to extranuclear world would be different and tqc braidings would give to the cell a memory about its life-cycle. The age ordering of cells would have the architecture of a tree defined by the sequence of cell replications and the life history of the organism. The 4-D body would contain kind of log file about tqc performed during life time: kind of fundamental body memory.

  6. Quite generally, the evolution of tqc programs means giving up the dogma of genetic determinism. The evolution of tqc programs during life cycle and the fact that half of them is inherited means kind of quantum Lamarckism. This inherited wisdom at DNA level might partly explain why we differ so dramatically from our cousins.

6. Sexual reproduction and tqc

  1. Sexual reproduction of eukaryotes relies on haploid cells differing from diploid cells in that chromatids do not possess sister chromatids. Whereas mitosis produces from single diploid cell two diploid cells, meiosis gives rise to 4 haploid cells. The first stage is very much like mitosis. DNA and chromosomes duplicate but cell remains a diploid in the sense that there is only single centrosome: in mitosis also centrosome duplicates. After this the cell membrane divides into two. At the next step the chromosomes in daughter cells split into two sister chromosomes each going into its own cell. The outcome is four haploid cells.

  2. The presence of only single chromatid in haploids means that germ cells would perform only one half of the "social" tqc performed by soma cells who must spend their life cycle as a member of cell community. In some cells the tqc would be performed by chromatids of both father and mother making perhaps possible kind of stereo view about world and a model for couple - the simplest possible social structure.

  3. This brings in mind the sensory rivalry between left and right brain: could it be that the two tqc:s give competing computational views about world and how to act in it? We would have inside us our parents and their experiences as a pair of chromatids representing chemical chimeras of chromatid pairs possessed by the parents: as a hardware - one might say. Our parents would have the same mixture in software via sharing and fusion of chromatid mental images or via quantum computational rivalry. What is in software becomes hardware in the next generation.

  4. The ability of sexual reproduction to generate something new relates to meiosis. During meiosis genetic recombination occurs via chromosomal crossover which in string model picture would mean splitting of chromatids and the recombination of pieces in a new manner (A1+B1)+(A2+B2) → (A1+B2)+(A2+B1) takes place in crossover and (A1+B1+C1)+(A2+B2+C2) → (A1+B2+C1)+(A2+B1+C2) in double crossover. New hardware for tqc would result by combining pieces of existing hardware. What this means in terms of braids should be clarified.

  5. Fertilization is in well-define sense the inverse of meiosis. In fertilization the chromatids of spermatozoa and ova combine to form the chromatids of diploid cell. The recombination of genetic programs during meiosis becomes visible in the resulting tqc programs.

7. What is the role of centrosomes and basal bodies?

Centrosomes and basal bodies form the main part of Microtubule Organizing Center. They are somewhat mysterious objects and at first do not seem to fit to the proposed picture in an obvious manner.

  1. Centrosomes consist two centrioles forming a T shaped antenna like structure in the center of cell. Also basal bodies consist of two centrioles but are associated with the cell membrane. Centrioles and basal bodies have cylindrical geometry consisting of nine triplets of microtubules along the wall of cylinder. Centrosome is associated with nuclear membrane during mitosis.

  2. The function of basal bodies which have evolved from centrosomes seems to be the motor control (both cilia and flagella) and sensory perception (cilia). Cell uses flagella and cilia to move and perceive. Flagella and cilia are cylindrical structures associated with the basal bodies. The core of both structures is axoneme having 9×2+2 microtubular structure. So called primary cilia do not posses the central doublet and the possible interpretation is that the inner doublet is involved with the motor control of cilia. Microtubules of the pairs are partially fused together.

  3. Centrosomes are involved with the control of mitosis. Mitosis can take place also without them but the organism consisting of this kind of cells does not survive. Hence the presence of centrosomes might control the proper formation of tqc programs. The polymerization of microtubules is nucleated at microtubule self-organizing center which can be centriole or basal body. One can say that microtubules which are highly dynamical structures whose length is changing all the time have their second end anchored to the self-organizing center. Since this function is essential during mitosis it is natural that centrosome controls it.

  4. The key to the understanding of the role of centrosomes and basal bodies comes from a paradox. DNA and corresponding tqc programs cannot be active during mitosis. What does then control mitosis?

    1. Perhaps centrosome and corresponding tqc program represents the analog of the minimum seed program in computer allowing to generate an operating system like Windows 2000 (the files from CD containing operating system must be read!). The braid strands going through the microtubuli of centrosome might define the corresponding tqc program. The isolation from environment by the microtubular surface might be essential for keeping the braidings defining these programs strictly unchanged.
    2. The RNA defining the genome of centrosome (yes: centrosome has its own genome defined by RNA rather than DNA!) would define the hardware for this tqc. The basal bodies could be interpreted as a minimal sensory-motor system needed during mitosis.
    3. As a matter fact, centrosome and basal bodies could be seen as very important remnants of RNA era believed by many biologists to have preceded DNA era. This assumption is also made in TGD inspired model of prebiotic evolution.
    4. Also other cellular organelles possessing own DNA and own tqc could remain partly functional during mitosis. In particular, mitochondria are necessary for satisfying energy needs during the period when DNA is unable to control the situation so that they must have some minimum amount of own genome.

  5. Neurons do not possess centrosome which explains why they cannot replicate. The centrioles are replaced with long microtubules associated with axons and dendrites. The system consisting of microtubules corresponds to a sensory-motor system controlled by the tqc programs having as a hardware the RNA of centrosomes and basal bodies. Also this system would have a multicellular part.

  6. Intermediate filaments, actin filaments, and microtubules are the basic building elements of the eukaryotic cytoskeleton. Microtubules, which are hollow cylinders with outer radius of 24 nm, are especially attractive candidates for structures carrying bundles of braid strands inside them. The microtubular outer-surfaces could be involved with signalling besides other well-established functions. It would seem that microtubules cannot be assigned with tqc associated with nuclear DNA but with RNA of centrosomes and could contain corresponding braid strand bundles. It is easy to make a rough estimate for the number of strands and this would give an estimate for the amount of RNA associated with centrosomes. Also intermediate filaments and actin filaments might relate to cellular organelles having their own DNA.

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

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