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Genes and Memes

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Year 2012

Constraints on the fermionic realization of genetic code from the model for color qualia

The original model for DNA as topological quantum computer assigns to DNA nucleotides quarks at ends of flux tubes or quark pairs at the ends of wormhole flux tubes. This is only the realization that came first to my mind in TGD Universe where dark variants of quarks can define QCD like physics even in cellular length scales. One can actually imagine several realizations of the genetic code and the first realization is far from being the simplest one. It is enough to have four different particles or many-particle quantum states to build at least formally a map from A,T,C, G to four states. It is obvious that the number of possible formal realizations is limited only by the imagination of the theoretician. Additional conditions are required to fix the model.

Fermionic representation

Consider first the fermionic representations in the general case without specifying what fermions are.

  1. The original proposal was that DNA nucleotides correspond to flux tubes with quark q and antiquark qbar at the ends of the parallel flux sheets extremely near to each other. Second options relies on wormhole magnetic flux tubes in which case quark pair qqbar is at both ends. Quarks u, d and their antiquarks would code for A,T,C,G. The spin of quarks is not taken into account at all in this coding: why not restrict the consideration to single quark. The total quark charge at given end of flux tube pair vanishes and flux tube ends carry opposite quark charges.

    The nice feature of this option is that one could understand the generation of color qualia in the model of sensory receptor in simple manner to be discussed below. Even if one accepts the arguments supporting the view that dark quarks in cell scale are natural outcome of the hierarchy of Planck constants, one could argue that the presence of both quarks and antiquarks does not conform with matter antimatter asymmetry (not that one can however identify the analog of matter antimatter asymmetry at DNA level).

  2. Spin states for fermion pairs assigned with two parallel magnetic flux tubes with the magnetic field generated by spin provide much simpler representation for nucleotides. Similar fermion pair would reside at the second end of flux tube pair.
    1. It is is essential that rotational symmetry is broken and reduces to rotational symmetry around the direction of flux tubes so that spin singlet and spin 0 state of triplet mix to form states for which each fermion is in spin eigenstate. The states must be antisymmetric under exchange of the protons and spin 1/0 states are antisymmetric/symmetric in spatial degrees of freedom (wave functions located to the ends of flux tubes). The states with definite spin for given flux tube are mixtures of s=1 states with vanishing spin projection and s=0 state.
    2. It is not quite clear whether one should treat fermion pairs as identical bosons with 3+1 spin states since in TGD framework one considers disjoint partonic 2-surfaces and the situation is not that of QFT in M4. This interpretation would require totally symmetry of the states under permutations of bosonic states defined by the 3+1 spin states. Coding by spin requires that each nucleotide corresponds to a state with a well defined spin. In field theory language the state would be obtained by applying bosonic oscillator operators generating states of given spin localized to a given nucleotide position.
    3. The classical correlate for the permutations of coordinates of fermions has interpretation as braiding for the flux tubes of the flux tube pair. In the similar manner the permutation of the flux tube pairs associated with nucleotides has interpretation as braiding of the 3-braids formed form from flux tube pairs. Braiding therefore gives a representation of spin analogous to the well-known orientation entanglement relation invented by Dirac and providing geometric representation of spin 1/2 property.
Various options for the fermionic representation of A,T,C,G

Fermionic representations allows several options since fermion can be electron, u or d quark, or proton. Wormhole magnetic fields would not be needed in this case.

  1. The problem of electron and proton options is that it does not allow realization of color qualia. There is also the well-known problem related to the stability of DNA caused by the phosphate charge of -2 units per nucleotide. Somehow this charge should be screened. In any case, the charge -2 should correspond to the electron pair at the DNA end of the flux tube for electron option. For proton option the charge would be screened completely. One could of course consider also the large hbar color excitations of ordinary protons instead of quark at its nucleotide ends. This option would however require the modification of quark wave functions inside proton and this option will not be discussed here.
  2. Quark option would give rise to both color and allow also to reduce the electronic charge of -2 units by 4/3 units to -2/3 units in the case of u quark pair. This would help to stabilize DNA. In the case of d quarks the charge would increase to -10/3 units and is not favored by stability argument. Flux tube pairs assigned to single nucleotide define diquarks with spin 1 or spin 0.
    1. Diquarks behave ass identical bosons with 3+1 spin states and 3× 3 color states. The states with well defined symmetry properties in spin degrees of freedom have such properties in spatial degrees of freedon. This means that one obtains a superposition of flux tube pairs with are either braided or unbraided. Triplet/singlet state is symmetric/antisymmetric and total asymmetry could be guaranteed by assuming symmetry/antisymmetry in spatial degrees of freedom and antisymmetry/symmetry in color degrees of freedom. This would give anti-triplet/6-plet in color degrees of freedom. Spatial symmetry would favor antitriplet and diquark would behave like antiquark with respect to color. Let us assume antitriplet state for definiteness.
    2. DNA codon corresponds to three-di-quark state. This state must be totally symmetric under the exchange of bosons. One can have total symmetry in both spatial and color degrees of freedom or total antisymmetry/symmetry in spatial and total antisymmetry/symmetry in color degrees of freedom.The first option gives 10-dimensional color multiplet and the second one color singlet. Braiding is maximal and symmetric/antisymmetric in these case. One can consider also mixed symmetries. In this case one has color octet which is antisymmetric with respect to the first nucleotide pair and symmetric with respect to first nucleotide pair and third nucleotide. The braiding of the first two nucleotides must be antisymmetric and the braiding of this pair with third nucleotide. The conclusion would be that color multiplets correspond to well defined braidings and one would therefore have directed connection with topological quantum computation. Color octet is especially interesting concerning the representation of color qualia.
The challenge of all these options (note that the representability of color selects quark option) is to find a good justification for why the assignment of A,T,C,G to quark states or spin states is unique dynamically. Stability argument is expected to help here.

Realization of color qualia for quark option

Consider now how one could understand the generation of qualia for quark option.

  1. The generation of qualia involves interaction with external world giving rise to a sensory percept. In the case of visual colors it should correspond to a measurement of quark color and should give rise to eigenstages of color at the ends of flux tubes at DNA nucleotides for a nucleus or cell of photoreceptor. A modification of capacitor model is needed. Color polarization is still essential but now polarization in nucleus or cell scale is transformed in the generation of color quale to a polarization in longer length scale by the reconnection of flux tubes so that their ends attach to "external world". The nucleus/cell becomes color and state function reduction selects well defined quantum numbers. It is natural to assume that the entanglement in other degrees of freedom after color measurement is negentropic.
  2. Does the "external world" corresponds to another cell or to the inner lipid layers of the cell membrane containing the nucleus. In the first case flux tubes would end to another cell. If the nuclei of receptor cells are integrate to a larger structure by magnetic flux sheets traversing through them one can also consider the possibility that the polarization in the scale of cell nucleus (recall that the nucleus has also double lipid layer) is transformed to a polarization in cell scale so that similar process in cell scale gives rise to qualia.
  3. The entire receptor unit must have net color after the state function reduction. This requires that there are flux tubes connecting the receptor unit to a unit representing "external world". If second cell is the "external world" these flux tubes must go through the pair of lipid layers of both cell membrane and end up to the nucleus of cell in the environment. If external world corespond to the complement of nucleus inside cell the inner layers of cell membrane represents external world. Cell membrane indeed serves as sensory receptor in cell length scale. One can of course have sensory qualia in various length scales so that both options are probably correct and a kind of fractal hierarchy is very natural giving rise also to our qualia at some higher level.
  4. Consider now how the color qualia are generated.
    1. There must be two flux tube states. In the first state there are two flux tube beginning from cell nucleus A and ending to the inner lipid layer a1 and flux tube beginning from the outer lipid layer a2 and ending cell nucleus B. Both flux tubes have vanishing net color so that cells have vanishing net colors. This could be regarded as the resting state of the receptor. The lipids in layers a1 and a2 are connected by another short flux tube. Same for b1 and b2.
    2. The second flux tube state corresponds to long flux tubes connecting the nuclei of cells A and B. The ends carry opposite color charges. In this case the net color of both A and B is non-vanishing. This state would be an outcome of a reconnection process in which the flux tubes from A to a1 and B to a2 re-connect with the short flux tube connecting lipid layers a1 and a2.
    3. When these flux tubes carry opposite colors numbers at their ends, the cell possess net color charge and can represent color quale. Or rather, creation of this kind of flux tube connections would give rise to the color charging of the receptor cell with external world carrying opposite color charge.
One can argue that this mechanism is not quite in spirit with color capacitor model. Polarization is still essential but now polarization in receptor scale is transformed to polarization in longer length scale by the reconnection of flux tubes. This model is neither consistent with the naive expectation that the quale is generated after state function reduction. Rather, the beginning of sensation of quale means beginning of negentropic entanglement and fusion with external world and state function usually associated with the quantum measurement would mean the end of the sensation and separation from the external world! Maybe one can say that state function reduction means that experience is replaced with a memory "I had the sensation of quale"! Krishnamurti would certainly agree!;-)

The unexpected prediction of the model is that braiding would correlate directly with qualia. This would mean also a connection between quantum computation and qualia. This condition emerges from Fermi/Bose-Einstein statistics correlating braiding with symmetry properties of color states and spin states. Quite generally, the correlation of braiding with the symmetries of wave functions as functions of points of braid end points would allow to have direct geometric correlate between induced entanglement and braiding as naive intuitive expectations have suggested.

For background see the chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems.

How to build a quantum computer from magnetic flux tubes?

Magnetic flux tubes play a key role in TGD inspired model of quantum biology. Could the networks of magnetic flux tubes containing dark particles with large hbar in macroscopic quantum states and carrying beams of dark photons define analogs of electric circuits? This would be rather cheap technology since no metal would be needed for wires. Dark photon beams would propagate along the flux tubes representing the analogs of optical cables and make possible communications with maximal signal velocity.

I have actually made much more radical proposal in TGD inspired quantum biology. According to this proposal, flux tube connections are dynamical and can be changed by reconnection of two magnetic flux tubes. The signal pathways A→ C and B→ D would be transformed to signal pathways to A→ D and B→ C by reconnection. Reconnection actually represents a basic stringy vertex. The contraction of magnetic flux tubes by a phase transition changing Planck constant could be fundamental in bio-catalysis since it would allow distant molecules connected by flux tubes to find each other in the molecular crowd.

DNA as a topological quantum computer is the idea that I have been developing for 5 years or so. I have concentrated on the new physics realization of braids and devoted not much thought to how the quantum computer problems might run in this framework. I was surprised to realize how little I know about what happens in even ordinary computation. Instead of going immediately to Wikipedia I take the risk of publicly making myself fool and try to use my own brain.

1. What can one learn from ordinary computer programs

One could begin with the question what happens in classical computation. How the program is realized and how it runs? The notion of Turing machine represents an extreme abstraction mentioning nothing about the technical side and does not help much in attempts to answer these questions. Turing paradigm also assumes that program is a temporal sequence of operations. These operations could however correspond to a linear spatial sequences and inputs and outputs in this case would correspond to boundary values at the ends of the linear structure. This requires that the dynamics is such that evolution in spatial direction is analogous to a deterministic time evolution. In this case it is much easier to imagine biological realizations of quantum computer programs in TGD inspired bio-world.

To develop concrete ideas, one can start from the picture provided by ordinary computer program.

  1. Programs consist of temporal/spatial sequences of commands and commands represent basic functions from which one can build more complex functions by the composition of functions having some numbers of input and output arguments. The eventual output variable can be expressed by printing of a piece of text or as an image in the computer screen. Each step in the program corresponds to a composition of functions: fn+1= gn+1 o fn. There is some minimal set of primitive/prime functions from which one builds up more complex functions by composition.

  2. How this is realized at the level of hardware? One can assume that the basic functions are at some fixed places in the computer memory having addresses given by integers represented as bit sequences. This address represents the command - a name of the function. The names for input variables and output variables are bit sequences giving the addresses of the places containing the values of these variables. Program is a sequence of commands represented as bit sequences giving the address of the function to be computed at a given step and the addresses of inputs and outputs. As the processing unit reads the command, it generates/activates connections from the addresses of inputs to the address representing the function and from this address to the addresses of outputs.

    Essentially the challenge is to reconnect, build/activate connections. An interesting question is whether learning as strengthening of synaptic connections is one particular example of this process.

  3. How the sequence of bits representing command address is realized? As the processing unit reads the address of command it should automatically create/activate a connection from this address to the command address. The connections from the processing unit to the addresses could exist physically as wirings.

  4. It is not necessary that program is dynamical so that the inputs and outputs would be initial and final values of variables. Inputs and outputs could also correspond to values of variables at the ends of a linear structure. In topological quantum computation space-like entanglement would represent superposition of input-output pairs characterizing a function as a rule with instances represented as instances appearing in the superposition.

If this picture is roughly correct, re-connection would be the basic process. Reconnection is the basic process for magnetic flux tubes and ADP↔ ATP has been assigned to this process with ATP molecule serving as a relay activating the flux tube connection. Maybe ADP-ATP process, which is usually seen as a basic step of metabolism, could be seen as the core step for quantum computation performed by living matter. One expects that the presence ATP makes the rule represented by negentropic quantum entanglement conscious.

2. Quantum computation magnetic flux tubes as connections

Consider now quantum computation could take place in a circuitry having magnetic flux tubes as wires and some bio-molecules of groups of them as units defining prime functions. DNA as topological quantum computer could be taken as a starting point. The outcome of quantum computation is determined statistically as ensemble average so that a large number of copies of the program should be present and realized in terms of groups of cells or molecules connected by braidings if the quantum computation is space-like. This option seems more natural than time-like quantum computation realized as a 2-D liquid flow of lipids in the lipid layers of the cell membrane.

2.1 The hardware

Consider first the hardware of topological quantum computation using space-like braids.

  1. Magnetic flux tubes would represent the wires along which inputs and outputs travel in the case of classical computation or dynamical quantum computation. In the case of space-like topological quantum computation entanglement is between the ends of the flux tubes.

  2. Variables could be represented in many manners. For space-like quantum computations they could correspond to spin states of dark electrons at flux tubes or to polarization states of dark electrons at the flux tubes. In the original model of DNA as topological quantum computer quarks and antiquarks where proposed as a representation of genetic codons: also this quite science fictive option could make sense in TGD Universe since TGD predicts scaled versions of QCD like dynamics and presence of elementary particles in several p-adic scales and in scales dictated by value of Planck constant for given p-adic length scale.

    The spin states of electron pair has been proposed as one possible representation of the 4 genetic codons. Quantum variables would be represented by qubit sequences and the measurement of qubit would give a bit sequence characterizing the classical value of the variable. Bio-molecules would be natural places for storing the values of the variables. For dynamical computations the values of variables could be transmitted using dark photons.

  3. There would exist basic processing units calculating the prime functions from which more complex functions would be obtained as composites. Basic units could correspond to bio-molecules. In the case of classical computation the inputs to molecules and outputs from them would travel along the flux tubes. In quantum computation these signals could be used to control the initial values of the variables. Molecules could also serve as gates for quantum computation.

2.2 Representation of programs

The basic program units in the case of quantum computation would be represented by braidings.

  1. If the ends of braid strands are able to move freely when needed, it becomes possible to re-write programs. Lipid layers of cell membrane can be in liquid crystal state so that these are ideal for this purpose. The time-like braiding resulting from lipid flow and representing running topological quantum computation program would induce space-like braiding representing space-like topological quantum computation or a rule. A particular quantum computer program represented as space-like braiding of the flux tubes would result as liquid crystal melts for a moment and freezes again.

    The process in which proteins covered by ordered water analogous to ice temporarily melt and form aggregates is basic process induced by the feed of energy to the cellular system and could be compared to cellular summer. This process could mean quite generally molecular re-programming induced by the flow of cellular water inducing molecular flows inducing re-braidings. The braiding would also store the highlights of the cellular summer to cellular memory! This could be also seen learning by a modification of various quantum computer programs.

  2. Negentropic entanglement is highly suggestive and would conform with the idea that the rule represented by entanglement represents conscious information or information which can become conscious. The process of becoming conscious information could involve ATP→ ADP and de-activating the flux tube and destroy the information. Time-like braiding represented by liquid flow would modify space-like braiding.

    It is not quite clear whether the information is conscious when negentropic entanglement (and ATP) is present - as Bohm's notion of active information would suggest - or when ATP is transformed to ADP and connection becomes passive. Negentropic entanglement can be stable with respect to NMP so that the presence of ATP could mean period of conscious experience - negentropic entanglement could be analogous to active information.

    TGD based model for the memory recall by sending negative energy signals to geometric past suggests that the absorption of negative energy photon transforms ATP to ADP. Conscious experience is regenerated in the geometric now where the negative energy signal came from - perhaps by transforming ADP to ATP by using the negative resulting by sending of negative energy signal! Conscious reading would be actually memory recall and analogous to teleportation? The destruction of the representation of memory in the geometric past would have interpretation in terms of no-cloning theorem.

  3. Static realizations of the programs are easier to imagine since no temporal codes are needed for the transfer of bits. An attractive idea is that the computations are represented by static entanglements for linear structures and that time-like braiding allows to modify the programs.

2.3 The realization of program

The program would be basically a sequence of address lists. Address list would contain the address of the function to be performed and the addresses of the input molecules and output molecules. How to represent the address physically?

  1. The simplest manner to realize this would use existing flux tubes connecting the processing unit to all possible input and output addresses as well as command addresses, and activate those flux tubes to which input and output data are assigned and reconnect them to the flux tubes connecting processing unit to the unit representing the function. The processing unit would have flux tubes coming from all possible inputs, going to all possible outputs, flux tubes going to places representing functions and coming from these places. Processing unit would be like a relay station or old fashioned telephone center whose sole purpose would be to create connections by reconnecting flux tubes. ATP molecule would be probably involved with the activation and - allowing a sloppy language - one could say that communication line becomes conscious when ATP is attached to it.

    1. Addressing would be just selection of activated molecules and analogous to that used in telephone network or computer network connected by cables. This would require static flux tube network and flux tubes could be either active or passive. In passive state flux tubes could be short-cut by a reconnection with hydrogen bond so that the ends of cut flux tube would end up to water molecules. This is however not necessary. Activation in absence of the short cut would involve reconnection of a flux tube with a flux tube connecting two parts of ATP - possibly hydrogen bond again- so that ATP becomes part of the flux tubes. If also short cut is involved, the strands coming to the two water molecules reconnect and generate hydrogen bond and flux tube to which ATP would attach in the proposed manner. As ATP is used it transforms to ADP and de-attaches from the flux tube.

    2. One can imagine also a dynamical addressing based on the generation of magnetic flux tubes between inputs and submodules. The computational process could be still space-like. The first manner to realize dynamical addressing would be by attaching to the ends of dynamical flux tubes biomolecules, which bind to specific receptors. Receptor mechanism would allow to connect distant cells to each other and build a magnetic flux tube connection between them. Computational unit specialized to run a specific program could excrete biomolecules binding to the input and output receptors: this program would realized function in terms of space-like entanglement. Glands emit hormones binding to receptors and various glands could in principle serve as computational units. Various information molecules bind very selectively and this might also relate to quantum space-like computations.

    3. Second mechanism of dynamical addressing would use dark photons. In this case resonant interaction selecting the target would replace the receptor mechanism. In this kind of situation one can claim that flux tubes are un-necessary, one can use just resonance to build connection to a desired place just as one does in radio communications. Of course, topological light rays could be accompanied by flux tubes. For instance, DNA nucleotide could attach by flux tube to its conjugate in distant DNA molecule and if the connection is based on resonance only similar nucleotide sequences could connect with each other. I have discussed this kind of mechanism in a model for remote replication of DNA based on the experimental work by Peter Gariaev and his group. The resonance mechanism could also make possible to establish flux tube connections and the quantum computation could be a static operation.

  2. DNA as topological quantum computer vision gives some idea about how the computer program could be realized as a spatial linear structure.

    1. Program would be a sequence of topological quantum computations. Given topological quantum computation would be represented by a braiding of flux tubes connecting DNA nucleotides with the lipid molecules of the inner lipid layer. Program would correspond to a linear sequence of cells with the outer lipid layer connected to the DNA of the second cell.

    2. Lipid flows at given lipid layer could be used to rewrite programs and the programs could respond to the changes in environment in this manner: this would require that the lipid layer is in liquid crystal state during the period when program is changed. Also nerve pulse patterns would induce these flows. Programs would also represent memories as rules realized as quantum abstractions or as quantum functions.

    3. The program would "run" in the spatial direction. The selection of active input and output variables would be by acting the connection from molecule in question by attaching ATP as a relay through which the reconnected flux tube would traverse. This would be also part of the writing of the program. The superposition of entangled inputs and outputs could be seen as a quantum superposition of classical programs assigning outputs to inputs. Also microtubule-lipid layer braiding suggested also to play a key role in the realization of memories could give rise to similar space-like quantum computation representing rules.

    4. The effective 2-dimensionality implied by strong form of holography implied in turn by strong form of general coordinate invariance means that the physics depends on partonic 2-surfaces and 4-D tangent space data at them. This suggests that the dynamics on space-like 3-surfaces and light-like orbits of partonic 2-surfaces is fixed by a process analogous to gauge selection. Does just this effective gauge symmetry make possible to write quantum computer programs? Already ordinary deterministic computer program means selection of one particular dynamics from several alternative options suggesting that strict determinism is broken.

  3. What could be the role of bio-catalysis in the computation? Bio-catalysis is a central part of the biological information processing and it would not be surprising if the catalysts connected by flux tubes to substrate molecules were involved with the computations. An attractive idea is that various information molecules binding to receptors involved with bio-control (neurotransmitters, hormones, etc...) are involved with building the flux tube connections between cells. These bio-molecules could carry the ends of flux tubes to special places for which receptors serve as addresses and in this manner build hardware for topological quantum computation involving inputs and outputs in distant parts of the body. The final output could be transformed to controlled gene expression. Quite generally, catalysts bind very selectively and could play a role similar that played by information molecules in building up the quantum computer programs.

  4. One can imagine also purely classical computation based on catalytic mechanism probably allowing generalization to quantum case. The idea is that computer program - understood now as dynamical structure - is analogous to what happens in fairy tale in which hero finds a key which fits to a lock of a room containing a key which... There exists a beautiful realization of classical computation in terms of chemical concentrations using DNA. The output of given reaction representing computational step appears in the next reaction provide the system contains additional participating molecules, which could be both substrate molecules and catalysts. The program could be represented as concentrations of molecules needed at intermediate steps and lock-to-key mechanism guarantees that they are performed in the correct temporal order. Inputs and output molecules could be connected by flux tubes to bio-molecules which bind to specific receptors associated with the molecule representing the particular subprogram. This would automatically create a large number of classical computations proceeding in fixed order, maybe even quantum computations.

For a pdf version of this article see How to build a quantum computer from magnetic flux tubes? or the chapter DNA as Topological Quantum Computer.

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