Friday, April 27, 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 charge before the state function reduction. This requires that there are flux tubes connecting the receptor unit to a unit representing "external world and having vanishing color charge. 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 correspond 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. Living matter as conscious hologram metaphor suggests a fractal hierarchy of qualia.

    After state function reduction reducing the entanglement the flux tubes split and the receptor becomes un-entangled with external world and has vanishing color charges. At the level of conscious experience this means that there can be only memory about the quale experience. The sensation of quale lasts with respect to subjective time as long as the negentropic entanglement prevails. There is an obvious analogy with Orch OR proposal of Hamerofr and Penrose in which also period of conscious experience ends with state function reduction.

  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. The analog of di-electric breakdown however still applies in the sense that its analog induces large polarization. Several mechanisms generating larger polarization are of course possible. One can ask how essential the electromagnetic polarization of cell membrane is for the generation of qualia at cell level. Note also that biomolecules are quite generally polar molecules.

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 symmetric 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.

This model is not 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!;-)


At 9:08 AM, Blogger ThePeSla said...

I see this theory is close to the unique quasic vision which does have many unique forms of which so many have tried to organize the gene code.

Many have played this glass bead game (and that is perhaps the only cultural predicent to find in the literature, that book) but it seems to me we share one converging vision- as did Gammow for example (which shows the superstring and Majorana ideas of particles more than four things needed as bases. In fact there are now echos of several bases like 8 of possible physical systems and structures.)

This epiphany came for me in the summer of 1974 (I have somewhere the exact moment, I wrote it down) in summer. That was a long time ago for an idea for an advancement in science to slowly awaken in the experimental world.

By qualia I assume you are asking or relating this to something to ground consciousness?

Your development is much needed in what I imagine a more hyperbolic space as a matter of clarity.

Now as we jump thru the blog pages in such space reading each others work, perhaps a closed cell system, what do you make of Lubos recent insightful question- where are the spinors?

Also advanced theory looks deeper between the atoms and count in the bases themselves.


At 9:29 AM, Anonymous said...

Dear ThePesla,

by qualia I mean possibly existing fundamental attributes of sensory experience: colors, attributes of hearing, smells, tastes, attributes of touch, etc.. Just like quantum numbers characterize quantum states, I assume the qualia correspond to quantum number increments in quantum jump which is basic building brick of consciousness.

Lubos asks Why spinor rather that where are the spinors. My answer is that elementary bosons can be constructed from fermions (described by spinors): this is implied by WCW geometry if WCW spinor fields are interpreted in terms of fermionic Fock states. This bosonic emergence simplifies enormously the theory.

One of the amazing discoveries of Dirac was entanglement orientation relation allowing to see how 2pi rotation is topologically non-trivial whereas 4pi rotation is trivial for a cube connected by threads to the corners of a bigger cube. This space-time correlate for fundamental character of spinors emerges from the braiding.

Permutations of particles associated with say linear structure induces braiding as space-time correlate and statistics (Fermi or BE) leads to correlation between qualia assignable to spin and color quantum numbers and braidings. More than I could ever dream.

At 6:00 PM, Blogger ThePeSla said...

Yes, Matti I read it wrong, rather in the back of my mind one should ask where are the spinnors much like it seems they should ask where are the Higgs? I thought Lubos would be open to this idea but on rereading it carefully (my eyes are deep in to a lot of art and learning to use lap tops and the old coffee shop computers and how to post on blogspot and so on) I really only see group theory or string theory 101 which I guess is a service of sorts, but he only talks about groups in terms of continuous groups, infinitesimal change even the Clifford kind.

What are we doing with four things, that included Kea, who tries to realte some 4 color theorem of which some say is evidence of a pseudo science.

You and I know well the twilight zone, and even Lubos mentions higher things on spinors not known, thinking we will find out not seeing we have already, the problems between describing three or four, or four and five dimensions. Where we do not understand clearly we qualify our assertions.

So, with the closed quantum view I do not see how we can answer what in my eyes is already answers- the question of how gravity might be quantized. Yes the orthogons have a special place, a dualism of sorts when we think of them as absolutely finite. This must be a known thing in the algebra but I worked it out intuitively long ago.
1963 and 1968 the dualism first for three space then icoshedral on the DNA. Of course it was just a private hobbly far from the consensus there was a unified geometry.

My point is that gravity as such and I do not mean just SO(32) is quantized if they could see it- between our views this shows how it is if we better understand the finite- there is no mystery on this low level.

So, from a global view from where do the spinors emerge to become in real space trivial and sting space beyond the scope of its discussion?

What is outside your connected paths of wormholes? Is it there we can go no further analyzing qualia?
The corners of cube is not the deepest way to count them and that alone is the origin of "restrictions" not the reality.

But I meant to tell you, after all these decades, and you an example, I doubt that anyone will hear such truths however they are presented. That must harder for someone who counts on it for work or career (I have other hobbies to fall back on like poetry and music but no one read my two thousand poem here last decade as I dont exist unless part of a university.

But I must tell you, I just dont care anymore. You know all that half and double stuff is shades of Riemann and Poincare - that is not quite enough.

Thank you for the reply, you are closer than so many others to my isolated view. You remind me constantly of the really important issues in physics and not the fads of the day.


At 7:40 PM, Anonymous said...

Dear Orwin, I got the comment below to blog by email but it is not visible in blog. The new version of blogger works rather badly. There are continual problems of all kinds. It could be also a virus attack: not for the first time during these years!

Genes are transferable from chloroplasts to nucleus without loss of function:

This implies context-free grammar, so think automorophisms/Kolmogorov

On the stats/theory front, is this perhaps the generalization you need:

A Geometric Action for the Courant Bracket

Xiaolong Liu, Leopoldo A. Pando Zayas, VGJ Rodgers, Leo Rodriguez

An important operation in generalized complex geometry is the Courant
bracket which extends the Lie bracket that acts only on vectors to a pair
given by a vector and a p-form. We explore the possibility of promoting the
elements of the Courant bracket to physical fields by constructing a
geometric action based on the Kirillov-Kostant symplectic form. For the
$p=0$ forms, the action generalizes Polyakov's two-dimensional quantum
gravity when viewed as the geometric action for the Virasoro algebra. We
show that the geometric action arising from the centrally extended Courant
bracket for the vector and zero form pair is similar to the geometric
action obtained from the semi-direct product of the Virasoro algebra with a
U(1) affine Kac-Moody algebra. For arbitrary $p$ restricted to a Dirac
structure, we derived the geometric action and exhibit generalizations for
almost complex structures built on the Kirillov-Kostant symplectic form. In
the case of p+1 dimensional submanifolds, we also discuss a generalization
of a Kahler structure on the orbits.


How to relate this back to number theory is a larger question, but this
shows you path shadowed by the awkwardly large presence of Andre Weil:

Calabi-Yau Manifolds Over Finite Fields, II

Philip Candelas, Xenia de la Ossa, Fernando Rodriguez-Villegas

We study zeta-functions for a one parameter family of quintic threefolds
defined over finite fields and for their mirror manifolds and comment on
their structure. The zeta-function for the quintic family involves factors
that correspond to a certain pair of genus 4 Riemann curves. The appearance
of these factors is intriguing since we have been unable to `see' these
curves in the geometry of the quintic. Having these zeta-functions to hand
we are led to comment on their form in the light of mirror symmetry. That
some residue of mirror symmetry survives into the zeta-functions is
suggested by an application of the Weil conjectures to Calabi-Yau
threefolds: the zeta-functions are rational functions and the degrees of
the numerators and denominators are exchanged between the zeta-functions
for the manifold and its mirror. It is clear nevertheless that the
zeta-function, as classically defined, makes an essential distinction
between Kahler parameters and the coefficients of the defining polynomial.
It is an interesting question whether there is a `quantum modification' of
the zeta-function that restores the symmetry between the Kahler and complex
structure parameters. We note that the zeta-function seems to manifest an
arithmetic analogue of the large complex structure limit which involves
5-adic expansion.


Posted by Orwin to TGD diary at 3:36 PM

At 7:55 PM, Anonymous said...

Dear Orwin,

a comment to your mysteriously missing comment returned back. The transfer of genes from chlorolasts to nucleus without loss of function is highly interesting. Could this kind of transfer occur for gene of any kind and make genetic engineering much easier than thought?

The two key problems were thought to be following.

*The promoter regions located in upstream from gene: the proteins of nucleus were not expected to recognize them so that transcription would not start.

*Introns are present in genome and the splicing of mRNA produced in transcription involves removal of intron regions: this was thought not to be possible in nucleus for genes of chloroplasts.

Surprisingly, everything however worked fine! Introns behaved politely and helped in the splicing!

To me this is support for the view that DNA is only the hardware of topological quantum computation like processes to which introns directly participate by their braidings. The software defined by magnetic body of DNA giving rise to braiding is also there. Not only genes but also the software is moved to the nucleus in the process!

Maybe it is high time for biologists to take the quantum computer metaphor seriously and make the conclusions! And maybe neuroscientists should give up the attempts to force brain a classical computer!

At 8:05 PM, Anonymous said...

Dear Orwin:

concerning the link to geometric action for the Courant Bracket. The choice of action principle is not a problem in TGD. Kahler action is the correct choice. The open problems/conjectures relate to the preferred extremals of Kahler acrion. Are they quaternionic 4-surfaces in some sense (two alternatives)?

As a matter fact, the value of Kahler action for preferred extremal reduces to Chern-Simons terms associated with the ends of space-time surface at light-like boundaries of CD by holography and its strong form suggests even reduction to a 2-D area for preferred string world sheet.

Concerning second link, Calabi-Yau manifolds have very little to do with TGD. TGD is something very different from superstring models. Zeta function for manifold is of course interesting notion and Zeta function defined by the generalized eigenvalues of the modified Dirac operator might be highly relevant in TGD context.

At 10:33 AM, Blogger ThePeSla said...


To make things clearer I am now posting on these ideas (see Pseudovectors... etc) Drawing a picture which may inspire new thoughts in the interpretation of the observer.

What is trhe four color theorem for example but the Dirac operators with the assumption it is proved in these exotic kinds of higher spaces? Biological codes and cosmic codes have this in common as analogs on many levels.

In this respect it is those who cling to restricted ideas on general numbers and space that are the psuedoscientist at worse or at best children not fully aware of the big adult world actions and words they use.

If my use of this program is likewise too simple, perhaps you can be a bridge to show my error- yes your last line on eigenvalues is a great key diagonally in the quasic plane with structured information that indeed is highly relevant in TGD context as it is in the information physics of the quasifinite quasic view.

Of course you and I have gotten a little further than mere restricted and complete proof of Riemann and zetas and so on- that is somewhere beyond the proving in the next level of space. I am not sure just how close this has to relate to say microtubil code concepts in order to ground the phenomeon of consciousness.


At 10:49 AM, Blogger Ulla said...

Time patterns? The stochastic model also formed a ZEO in LTP, that is polarization and depolarisation,

Epigenome as external world, fixed into small molecules inside the cell. So the external world lies tight against the Self? The same is seen in perineural sheet and neuron. Cancers too? Here they say that glioblastomas use the inner of the neuron, the cytosceleton, for the transmission. Not the membrane.

I have looked at this a bit, but have it not yet ready. This is interesting. What does the stochastic resonance REALLY mean? Note that Rakovic also use it in his model of neural networks? Is this the Higgs mechanism principle?

Today it seems probable that cognition is some superposition of fields, but I still don't understand your comment on effects only, not waves. Can the effects form a continuous and almost linear field alone? That means they travel without position, and free themselves from the bondings to mass? Is that what virtual 'particles' (not quantized) do?

At 12:00 PM, Blogger Ulla said...

Transactions on Computational Systems Biology XIII, Volym 13

...but at a deeper level than the standard stochastic chemical reaction model and in a dynamic rather than static manner; the objects of this system are equivalence classes of information sources and their crosstalk, rather than simple final states of a chemical system. A groupoid based on equivalence-classes of information sources dual to cognitive processes. The groupoid charachters the available dynamical manifolds, and breaking of the groupoid symmetry by epigenetic crosstalk, creates more complex objects of considerable interest. This leads to the possibility, indeed, the necessity of epigenetic Deus ex Machina mechanisms - analogous to programming, stochastic resonance etc. to force transitions between the different possible modes within and across dynamic manifolds. In one model the external 'programmer' creates the manifold structure, and the system hunts within that structure for the solution to the problem according to equivalence classes of 'paths' on the manifold.

Equivalence classes of states give dual information sources. Equivalence classes of information sources give different charachteristic dynamic manifolds. Equivalence classes of one-way developmental paths produces different directed homotopy topologies charachterizing those dynamical manifolds. This introduces the possibility of having different quasi-stable modes within individual manifolds, and leads to ideas of holonomy... p 150.


A manifold is like a membrane? Earlier I told about the 5/2 and 2/3 division of the 'membrane'.


At 4:30 AM, Blogger Matti Pitkanen said...

To Ulla:

In the above text manifold is taken to be sub-manifold of some space characterizing the dynamics of model. It has nothing to do with space-time or its sub-manifolds such as magnetic bodies and is not primary in this sense.

At 8:15 AM, Blogger Ulla said...

Seems they have found a new particle, made of 3 quarks :D


At 9:04 PM, Anonymous said...

To Ulla:

This particle is so called xi_b. It is prediction of standard quark model so that nothing anomalous is involved.

At 12:08 AM, Anonymous ◘Fractality◘ said...


The unexpected prediction of the model is that braiding would correlate directly with qualia.

Could this prediction also apply to the qualia generated by certain molecules? Braiding of flux tubes for the molecule and the associated sensory receptor?

At 9:57 AM, Blogger ThePeSla said...


But this would not be the complete picture of all such higher spaces even if it appears so. Such a result would merely confirm the expectations of the model and is blind to the higher connections or ambiguities between such tubes or paths. In that sense qualia are invisible beyond a certain level of theory.

The question you ask of course is a view of scale values in the TGD space- but is is OK to tie these down to physical processes if you want- but even in quantum theory there is more to it when we ask what is sensing things and on what scale.


At 10:34 AM, Blogger Ulla said...

Qualia as a superposition or the quantum phenomenon of measuring both wave and particle at the same time? This would be quantum measurement? Earlier we talked of only classic measurement was possible. IF I understood right?

At 11:19 AM, Blogger Ulla said...

Cooperative Lamb Shift in an Atomic Vapor Layer of Nanometer Thickness

J. Keaveney, A. Sargsyan, U. Krohn, I. G. Hughes, D. Sarkisyan, and C. S. Adams
Phys. Rev. Lett. 108, 173601 (2012)
Published April 23, 2012 | PDF (free)

Sarfatti also has some links about non-local time,

At 2:27 AM, Anonymous said...

To Fractality:

Yes. The prediction is that qualia are possible also at molecular level. Fractal hierarchy of qualia or living matter as conscious hologram.

At 10:17 PM, Blogger Ulla said...

Under certain conditions, the plasma—which is where fusion reactions take place—disappears in under a millisecond. there is a practical limit to how dense the plasma in a reactor can be. Beyond a certain density, the plasma becomes unstable, dissipates its energy, and disappears. Because researchers don't understand exactly what causes this, it's difficult to predict exactly when the collapse will happen, so researchers avoid getting close to that limit in experimental reactors.

Susy islands or wormholes to another spacetime sheet? :D


Post a Comment

<< Home